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Correction of bug related to the covariates
1: /* $Id: imach.c,v 1.65 2002/12/11 16:58:19 lievre 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 stable prevalence. 43: 44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). 45: Institut national d'études démographiques, Paris. 46: This software have been partly granted by Euro-REVES, a concerted action 47: from the European Union. 48: It is copyrighted identically to a GNU software product, ie programme and 49: software can be distributed freely for non commercial use. Latest version 50: can be accessed at http://euroreves.ined.fr/imach . 51: **********************************************************************/ 52: 53: #include <math.h> 54: #include <stdio.h> 55: #include <stdlib.h> 56: #include <unistd.h> 57: 58: #define MAXLINE 256 59: #define GNUPLOTPROGRAM "gnuplot" 60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ 61: #define FILENAMELENGTH 80 62: /*#define DEBUG*/ 63: #define windows 64: #define GLOCK_ERROR_NOPATH -1 /* empty path */ 65: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ 66: 67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */ 68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ 69: 70: #define NINTERVMAX 8 71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */ 72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */ 73: #define NCOVMAX 8 /* Maximum number of covariates */ 74: #define MAXN 20000 75: #define YEARM 12. /* Number of months per year */ 76: #define AGESUP 130 77: #define AGEBASE 40 78: #ifdef windows 79: #define DIRSEPARATOR '\\' 80: #define ODIRSEPARATOR '/' 81: #else 82: #define DIRSEPARATOR '/' 83: #define ODIRSEPARATOR '\\' 84: #endif 85: 86: char version[80]="Imach version 0.9, November 2002, INED-EUROREVES "; 87: int erreur; /* Error number */ 88: int nvar; 89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; 90: int npar=NPARMAX; 91: int nlstate=2; /* Number of live states */ 92: int ndeath=1; /* Number of dead states */ 93: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ 94: int popbased=0; 95: 96: int *wav; /* Number of waves for this individuual 0 is possible */ 97: int maxwav; /* Maxim number of waves */ 98: int jmin, jmax; /* min, max spacing between 2 waves */ 99: int mle, weightopt; 100: int **mw; /* mw[mi][i] is number of the mi wave for this individual */ 101: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 102: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between 103: * wave mi and wave mi+1 is not an exact multiple of stepm. */ 104: double jmean; /* Mean space between 2 waves */ 105: double **oldm, **newm, **savm; /* Working pointers to matrices */ 106: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ 107: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; 108: FILE *ficlog; 109: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; 110: FILE *ficresprobmorprev; 111: FILE *fichtm; /* Html File */ 112: FILE *ficreseij; 113: char filerese[FILENAMELENGTH]; 114: FILE *ficresvij; 115: char fileresv[FILENAMELENGTH]; 116: FILE *ficresvpl; 117: char fileresvpl[FILENAMELENGTH]; 118: char title[MAXLINE]; 119: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; 120: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; 121: 122: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; 123: char filelog[FILENAMELENGTH]; /* Log file */ 124: char filerest[FILENAMELENGTH]; 125: char fileregp[FILENAMELENGTH]; 126: char popfile[FILENAMELENGTH]; 127: 128: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH]; 129: 130: #define NR_END 1 131: #define FREE_ARG char* 132: #define FTOL 1.0e-10 133: 134: #define NRANSI 135: #define ITMAX 200 136: 137: #define TOL 2.0e-4 138: 139: #define CGOLD 0.3819660 140: #define ZEPS 1.0e-10 141: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 142: 143: #define GOLD 1.618034 144: #define GLIMIT 100.0 145: #define TINY 1.0e-20 146: 147: static double maxarg1,maxarg2; 148: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2)) 149: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2)) 150: 151: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) 152: #define rint(a) floor(a+0.5) 153: 154: static double sqrarg; 155: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg) 156: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 157: 158: int imx; 159: int stepm; 160: /* Stepm, step in month: minimum step interpolation*/ 161: 162: int estepm; 163: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ 164: 165: int m,nb; 166: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; 167: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; 168: double **pmmij, ***probs; 169: double dateintmean=0; 170: 171: double *weight; 172: int **s; /* Status */ 173: double *agedc, **covar, idx; 174: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; 175: 176: double ftol=FTOL; /* Tolerance for computing Max Likelihood */ 177: double ftolhess; /* Tolerance for computing hessian */ 178: 179: /**************** split *************************/ 180: static int split( char *path, char *dirc, char *name, char *ext, char *finame ) 181: { 182: char *ss; /* pointer */ 183: int l1, l2; /* length counters */ 184: 185: l1 = strlen(path ); /* length of path */ 186: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); 187: ss= strrchr( path, DIRSEPARATOR ); /* find last / */ 188: if ( ss == NULL ) { /* no directory, so use current */ 189: /*if(strrchr(path, ODIRSEPARATOR )==NULL) 190: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ 191: #if defined(__bsd__) /* get current working directory */ 192: extern char *getwd( ); 193: 194: if ( getwd( dirc ) == NULL ) { 195: #else 196: extern char *getcwd( ); 197: 198: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { 199: #endif 200: return( GLOCK_ERROR_GETCWD ); 201: } 202: strcpy( name, path ); /* we've got it */ 203: } else { /* strip direcotry from path */ 204: ss++; /* after this, the filename */ 205: l2 = strlen( ss ); /* length of filename */ 206: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); 207: strcpy( name, ss ); /* save file name */ 208: strncpy( dirc, path, l1 - l2 ); /* now the directory */ 209: dirc[l1-l2] = 0; /* add zero */ 210: } 211: l1 = strlen( dirc ); /* length of directory */ 212: #ifdef windows 213: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } 214: #else 215: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } 216: #endif 217: ss = strrchr( name, '.' ); /* find last / */ 218: ss++; 219: strcpy(ext,ss); /* save extension */ 220: l1= strlen( name); 221: l2= strlen(ss)+1; 222: strncpy( finame, name, l1-l2); 223: finame[l1-l2]= 0; 224: return( 0 ); /* we're done */ 225: } 226: 227: 228: /******************************************/ 229: 230: void replace(char *s, char*t) 231: { 232: int i; 233: int lg=20; 234: i=0; 235: lg=strlen(t); 236: for(i=0; i<= lg; i++) { 237: (s[i] = t[i]); 238: if (t[i]== '\\') s[i]='/'; 239: } 240: } 241: 242: int nbocc(char *s, char occ) 243: { 244: int i,j=0; 245: int lg=20; 246: i=0; 247: lg=strlen(s); 248: for(i=0; i<= lg; i++) { 249: if (s[i] == occ ) j++; 250: } 251: return j; 252: } 253: 254: void cutv(char *u,char *v, char*t, char occ) 255: { 256: /* cuts string t into u and v where u is ended by char occ excluding it 257: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) 258: gives u="abcedf" and v="ghi2j" */ 259: int i,lg,j,p=0; 260: i=0; 261: for(j=0; j<=strlen(t)-1; j++) { 262: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; 263: } 264: 265: lg=strlen(t); 266: for(j=0; j<p; j++) { 267: (u[j] = t[j]); 268: } 269: u[p]='\0'; 270: 271: for(j=0; j<= lg; j++) { 272: if (j>=(p+1))(v[j-p-1] = t[j]); 273: } 274: } 275: 276: /********************** nrerror ********************/ 277: 278: void nrerror(char error_text[]) 279: { 280: fprintf(stderr,"ERREUR ...\n"); 281: fprintf(stderr,"%s\n",error_text); 282: exit(EXIT_FAILURE); 283: } 284: /*********************** vector *******************/ 285: double *vector(int nl, int nh) 286: { 287: double *v; 288: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double))); 289: if (!v) nrerror("allocation failure in vector"); 290: return v-nl+NR_END; 291: } 292: 293: /************************ free vector ******************/ 294: void free_vector(double*v, int nl, int nh) 295: { 296: free((FREE_ARG)(v+nl-NR_END)); 297: } 298: 299: /************************ivector *******************************/ 300: int *ivector(long nl,long nh) 301: { 302: int *v; 303: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); 304: if (!v) nrerror("allocation failure in ivector"); 305: return v-nl+NR_END; 306: } 307: 308: /******************free ivector **************************/ 309: void free_ivector(int *v, long nl, long nh) 310: { 311: free((FREE_ARG)(v+nl-NR_END)); 312: } 313: 314: /******************* imatrix *******************************/ 315: int **imatrix(long nrl, long nrh, long ncl, long nch) 316: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 317: { 318: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 319: int **m; 320: 321: /* allocate pointers to rows */ 322: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 323: if (!m) nrerror("allocation failure 1 in matrix()"); 324: m += NR_END; 325: m -= nrl; 326: 327: 328: /* allocate rows and set pointers to them */ 329: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 330: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 331: m[nrl] += NR_END; 332: m[nrl] -= ncl; 333: 334: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 335: 336: /* return pointer to array of pointers to rows */ 337: return m; 338: } 339: 340: /****************** free_imatrix *************************/ 341: void free_imatrix(m,nrl,nrh,ncl,nch) 342: int **m; 343: long nch,ncl,nrh,nrl; 344: /* free an int matrix allocated by imatrix() */ 345: { 346: free((FREE_ARG) (m[nrl]+ncl-NR_END)); 347: free((FREE_ARG) (m+nrl-NR_END)); 348: } 349: 350: /******************* matrix *******************************/ 351: double **matrix(long nrl, long nrh, long ncl, long nch) 352: { 353: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1; 354: double **m; 355: 356: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 357: if (!m) nrerror("allocation failure 1 in matrix()"); 358: m += NR_END; 359: m -= nrl; 360: 361: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 362: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 363: m[nrl] += NR_END; 364: m[nrl] -= ncl; 365: 366: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 367: return m; 368: } 369: 370: /*************************free matrix ************************/ 371: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch) 372: { 373: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 374: free((FREE_ARG)(m+nrl-NR_END)); 375: } 376: 377: /******************* ma3x *******************************/ 378: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh) 379: { 380: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1; 381: double ***m; 382: 383: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*))); 384: if (!m) nrerror("allocation failure 1 in matrix()"); 385: m += NR_END; 386: m -= nrl; 387: 388: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double))); 389: if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 390: m[nrl] += NR_END; 391: m[nrl] -= ncl; 392: 393: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; 394: 395: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double))); 396: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()"); 397: m[nrl][ncl] += NR_END; 398: m[nrl][ncl] -= nll; 399: for (j=ncl+1; j<=nch; j++) 400: m[nrl][j]=m[nrl][j-1]+nlay; 401: 402: for (i=nrl+1; i<=nrh; i++) { 403: m[i][ncl]=m[i-1l][ncl]+ncol*nlay; 404: for (j=ncl+1; j<=nch; j++) 405: m[i][j]=m[i][j-1]+nlay; 406: } 407: return m; 408: } 409: 410: /*************************free ma3x ************************/ 411: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh) 412: { 413: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END)); 414: free((FREE_ARG)(m[nrl]+ncl-NR_END)); 415: free((FREE_ARG)(m+nrl-NR_END)); 416: } 417: 418: /***************** f1dim *************************/ 419: extern int ncom; 420: extern double *pcom,*xicom; 421: extern double (*nrfunc)(double []); 422: 423: double f1dim(double x) 424: { 425: int j; 426: double f; 427: double *xt; 428: 429: xt=vector(1,ncom); 430: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 431: f=(*nrfunc)(xt); 432: free_vector(xt,1,ncom); 433: return f; 434: } 435: 436: /*****************brent *************************/ 437: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) 438: { 439: int iter; 440: double a,b,d,etemp; 441: double fu,fv,fw,fx; 442: double ftemp; 443: double p,q,r,tol1,tol2,u,v,w,x,xm; 444: double e=0.0; 445: 446: a=(ax < cx ? ax : cx); 447: b=(ax > cx ? ax : cx); 448: x=w=v=bx; 449: fw=fv=fx=(*f)(x); 450: for (iter=1;iter<=ITMAX;iter++) { 451: xm=0.5*(a+b); 452: tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 453: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ 454: printf(".");fflush(stdout); 455: fprintf(ficlog,".");fflush(ficlog); 456: #ifdef DEBUG 457: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); 458: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); 459: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ 460: #endif 461: if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 462: *xmin=x; 463: return fx; 464: } 465: ftemp=fu; 466: if (fabs(e) > tol1) { 467: r=(x-w)*(fx-fv); 468: q=(x-v)*(fx-fw); 469: p=(x-v)*q-(x-w)*r; 470: q=2.0*(q-r); 471: if (q > 0.0) p = -p; 472: q=fabs(q); 473: etemp=e; 474: e=d; 475: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 476: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 477: else { 478: d=p/q; 479: u=x+d; 480: if (u-a < tol2 || b-u < tol2) 481: d=SIGN(tol1,xm-x); 482: } 483: } else { 484: d=CGOLD*(e=(x >= xm ? a-x : b-x)); 485: } 486: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 487: fu=(*f)(u); 488: if (fu <= fx) { 489: if (u >= x) a=x; else b=x; 490: SHFT(v,w,x,u) 491: SHFT(fv,fw,fx,fu) 492: } else { 493: if (u < x) a=u; else b=u; 494: if (fu <= fw || w == x) { 495: v=w; 496: w=u; 497: fv=fw; 498: fw=fu; 499: } else if (fu <= fv || v == x || v == w) { 500: v=u; 501: fv=fu; 502: } 503: } 504: } 505: nrerror("Too many iterations in brent"); 506: *xmin=x; 507: return fx; 508: } 509: 510: /****************** mnbrak ***********************/ 511: 512: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 513: double (*func)(double)) 514: { 515: double ulim,u,r,q, dum; 516: double fu; 517: 518: *fa=(*func)(*ax); 519: *fb=(*func)(*bx); 520: if (*fb > *fa) { 521: SHFT(dum,*ax,*bx,dum) 522: SHFT(dum,*fb,*fa,dum) 523: } 524: *cx=(*bx)+GOLD*(*bx-*ax); 525: *fc=(*func)(*cx); 526: while (*fb > *fc) { 527: r=(*bx-*ax)*(*fb-*fc); 528: q=(*bx-*cx)*(*fb-*fa); 529: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 530: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 531: ulim=(*bx)+GLIMIT*(*cx-*bx); 532: if ((*bx-u)*(u-*cx) > 0.0) { 533: fu=(*func)(u); 534: } else if ((*cx-u)*(u-ulim) > 0.0) { 535: fu=(*func)(u); 536: if (fu < *fc) { 537: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 538: SHFT(*fb,*fc,fu,(*func)(u)) 539: } 540: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 541: u=ulim; 542: fu=(*func)(u); 543: } else { 544: u=(*cx)+GOLD*(*cx-*bx); 545: fu=(*func)(u); 546: } 547: SHFT(*ax,*bx,*cx,u) 548: SHFT(*fa,*fb,*fc,fu) 549: } 550: } 551: 552: /*************** linmin ************************/ 553: 554: int ncom; 555: double *pcom,*xicom; 556: double (*nrfunc)(double []); 557: 558: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 559: { 560: double brent(double ax, double bx, double cx, 561: double (*f)(double), double tol, double *xmin); 562: double f1dim(double x); 563: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 564: double *fc, double (*func)(double)); 565: int j; 566: double xx,xmin,bx,ax; 567: double fx,fb,fa; 568: 569: ncom=n; 570: pcom=vector(1,n); 571: xicom=vector(1,n); 572: nrfunc=func; 573: for (j=1;j<=n;j++) { 574: pcom[j]=p[j]; 575: xicom[j]=xi[j]; 576: } 577: ax=0.0; 578: xx=1.0; 579: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 580: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 581: #ifdef DEBUG 582: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 583: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); 584: #endif 585: for (j=1;j<=n;j++) { 586: xi[j] *= xmin; 587: p[j] += xi[j]; 588: } 589: free_vector(xicom,1,n); 590: free_vector(pcom,1,n); 591: } 592: 593: /*************** powell ************************/ 594: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 595: double (*func)(double [])) 596: { 597: void linmin(double p[], double xi[], int n, double *fret, 598: double (*func)(double [])); 599: int i,ibig,j; 600: double del,t,*pt,*ptt,*xit; 601: double fp,fptt; 602: double *xits; 603: pt=vector(1,n); 604: ptt=vector(1,n); 605: xit=vector(1,n); 606: xits=vector(1,n); 607: *fret=(*func)(p); 608: for (j=1;j<=n;j++) pt[j]=p[j]; 609: for (*iter=1;;++(*iter)) { 610: fp=(*fret); 611: ibig=0; 612: del=0.0; 613: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); 614: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret); 615: for (i=1;i<=n;i++) 616: printf(" %d %.12f",i, p[i]); 617: fprintf(ficlog," %d %.12f",i, p[i]); 618: printf("\n"); 619: fprintf(ficlog,"\n"); 620: for (i=1;i<=n;i++) { 621: for (j=1;j<=n;j++) xit[j]=xi[j][i]; 622: fptt=(*fret); 623: #ifdef DEBUG 624: printf("fret=%lf \n",*fret); 625: fprintf(ficlog,"fret=%lf \n",*fret); 626: #endif 627: printf("%d",i);fflush(stdout); 628: fprintf(ficlog,"%d",i);fflush(ficlog); 629: linmin(p,xit,n,fret,func); 630: if (fabs(fptt-(*fret)) > del) { 631: del=fabs(fptt-(*fret)); 632: ibig=i; 633: } 634: #ifdef DEBUG 635: printf("%d %.12e",i,(*fret)); 636: fprintf(ficlog,"%d %.12e",i,(*fret)); 637: for (j=1;j<=n;j++) { 638: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); 639: printf(" x(%d)=%.12e",j,xit[j]); 640: fprintf(ficlog," x(%d)=%.12e",j,xit[j]); 641: } 642: for(j=1;j<=n;j++) { 643: printf(" p=%.12e",p[j]); 644: fprintf(ficlog," p=%.12e",p[j]); 645: } 646: printf("\n"); 647: fprintf(ficlog,"\n"); 648: #endif 649: } 650: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { 651: #ifdef DEBUG 652: int k[2],l; 653: k[0]=1; 654: k[1]=-1; 655: printf("Max: %.12e",(*func)(p)); 656: fprintf(ficlog,"Max: %.12e",(*func)(p)); 657: for (j=1;j<=n;j++) { 658: printf(" %.12e",p[j]); 659: fprintf(ficlog," %.12e",p[j]); 660: } 661: printf("\n"); 662: fprintf(ficlog,"\n"); 663: for(l=0;l<=1;l++) { 664: for (j=1;j<=n;j++) { 665: ptt[j]=p[j]+(p[j]-pt[j])*k[l]; 666: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 667: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]); 668: } 669: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 670: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p))); 671: } 672: #endif 673: 674: 675: free_vector(xit,1,n); 676: free_vector(xits,1,n); 677: free_vector(ptt,1,n); 678: free_vector(pt,1,n); 679: return; 680: } 681: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 682: for (j=1;j<=n;j++) { 683: ptt[j]=2.0*p[j]-pt[j]; 684: xit[j]=p[j]-pt[j]; 685: pt[j]=p[j]; 686: } 687: fptt=(*func)(ptt); 688: if (fptt < fp) { 689: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 690: if (t < 0.0) { 691: linmin(p,xit,n,fret,func); 692: for (j=1;j<=n;j++) { 693: xi[j][ibig]=xi[j][n]; 694: xi[j][n]=xit[j]; 695: } 696: #ifdef DEBUG 697: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 698: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); 699: for(j=1;j<=n;j++){ 700: printf(" %.12e",xit[j]); 701: fprintf(ficlog," %.12e",xit[j]); 702: } 703: printf("\n"); 704: fprintf(ficlog,"\n"); 705: #endif 706: } 707: } 708: } 709: } 710: 711: /**** Prevalence limit (stable prevalence) ****************/ 712: 713: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) 714: { 715: /* Computes the prevalence limit in each live state at age x by left multiplying the unit 716: matrix by transitions matrix until convergence is reached */ 717: 718: int i, ii,j,k; 719: double min, max, maxmin, maxmax,sumnew=0.; 720: double **matprod2(); 721: double **out, cov[NCOVMAX], **pmij(); 722: double **newm; 723: double agefin, delaymax=50 ; /* Max number of years to converge */ 724: 725: for (ii=1;ii<=nlstate+ndeath;ii++) 726: for (j=1;j<=nlstate+ndeath;j++){ 727: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 728: } 729: 730: cov[1]=1.; 731: 732: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 733: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ 734: newm=savm; 735: /* Covariates have to be included here again */ 736: cov[2]=agefin; 737: 738: for (k=1; k<=cptcovn;k++) { 739: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 740: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/ 741: } 742: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 743: for (k=1; k<=cptcovprod;k++) 744: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 745: 746: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ 747: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ 748: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ 749: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); 750: 751: savm=oldm; 752: oldm=newm; 753: maxmax=0.; 754: for(j=1;j<=nlstate;j++){ 755: min=1.; 756: max=0.; 757: for(i=1; i<=nlstate; i++) { 758: sumnew=0; 759: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; 760: prlim[i][j]= newm[i][j]/(1-sumnew); 761: max=FMAX(max,prlim[i][j]); 762: min=FMIN(min,prlim[i][j]); 763: } 764: maxmin=max-min; 765: maxmax=FMAX(maxmax,maxmin); 766: } 767: if(maxmax < ftolpl){ 768: return prlim; 769: } 770: } 771: } 772: 773: /*************** transition probabilities ***************/ 774: 775: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) 776: { 777: double s1, s2; 778: /*double t34;*/ 779: int i,j,j1, nc, ii, jj; 780: 781: for(i=1; i<= nlstate; i++){ 782: for(j=1; j<i;j++){ 783: for (nc=1, s2=0.;nc <=ncovmodel; nc++){ 784: /*s2 += param[i][j][nc]*cov[nc];*/ 785: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; 786: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/ 787: } 788: ps[i][j]=s2; 789: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/ 790: } 791: for(j=i+1; j<=nlstate+ndeath;j++){ 792: for (nc=1, s2=0.;nc <=ncovmodel; nc++){ 793: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; 794: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/ 795: } 796: ps[i][j]=s2; 797: } 798: } 799: /*ps[3][2]=1;*/ 800: 801: for(i=1; i<= nlstate; i++){ 802: s1=0; 803: for(j=1; j<i; j++) 804: s1+=exp(ps[i][j]); 805: for(j=i+1; j<=nlstate+ndeath; j++) 806: s1+=exp(ps[i][j]); 807: ps[i][i]=1./(s1+1.); 808: for(j=1; j<i; j++) 809: ps[i][j]= exp(ps[i][j])*ps[i][i]; 810: for(j=i+1; j<=nlstate+ndeath; j++) 811: ps[i][j]= exp(ps[i][j])*ps[i][i]; 812: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ 813: } /* end i */ 814: 815: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ 816: for(jj=1; jj<= nlstate+ndeath; jj++){ 817: ps[ii][jj]=0; 818: ps[ii][ii]=1; 819: } 820: } 821: 822: 823: /* for(ii=1; ii<= nlstate+ndeath; ii++){ 824: for(jj=1; jj<= nlstate+ndeath; jj++){ 825: printf("%lf ",ps[ii][jj]); 826: } 827: printf("\n "); 828: } 829: printf("\n ");printf("%lf ",cov[2]);*/ 830: /* 831: for(i=1; i<= npar; i++) printf("%f ",x[i]); 832: goto end;*/ 833: return ps; 834: } 835: 836: /**************** Product of 2 matrices ******************/ 837: 838: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b) 839: { 840: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times 841: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */ 842: /* in, b, out are matrice of pointers which should have been initialized 843: before: only the contents of out is modified. The function returns 844: a pointer to pointers identical to out */ 845: long i, j, k; 846: for(i=nrl; i<= nrh; i++) 847: for(k=ncolol; k<=ncoloh; k++) 848: for(j=ncl,out[i][k]=0.; j<=nch; j++) 849: out[i][k] +=in[i][j]*b[j][k]; 850: 851: return out; 852: } 853: 854: 855: /************* Higher Matrix Product ***************/ 856: 857: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) 858: { 859: /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 860: duration (i.e. until 861: age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 862: Output is stored in matrix po[i][j][h] for h every 'hstepm' step 863: (typically every 2 years instead of every month which is too big). 864: Model is determined by parameters x and covariates have to be 865: included manually here. 866: 867: */ 868: 869: int i, j, d, h, k; 870: double **out, cov[NCOVMAX]; 871: double **newm; 872: 873: /* Hstepm could be zero and should return the unit matrix */ 874: for (i=1;i<=nlstate+ndeath;i++) 875: for (j=1;j<=nlstate+ndeath;j++){ 876: oldm[i][j]=(i==j ? 1.0 : 0.0); 877: po[i][j][0]=(i==j ? 1.0 : 0.0); 878: } 879: /* Even if hstepm = 1, at least one multiplication by the unit matrix */ 880: for(h=1; h <=nhstepm; h++){ 881: for(d=1; d <=hstepm; d++){ 882: newm=savm; 883: /* Covariates have to be included here again */ 884: cov[1]=1.; 885: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM; 886: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; 887: for (k=1; k<=cptcovage;k++) 888: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 889: for (k=1; k<=cptcovprod;k++) 890: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 891: 892: 893: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ 894: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ 895: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 896: pmij(pmmij,cov,ncovmodel,x,nlstate)); 897: savm=oldm; 898: oldm=newm; 899: } 900: for(i=1; i<=nlstate+ndeath; i++) 901: for(j=1;j<=nlstate+ndeath;j++) { 902: po[i][j][h]=newm[i][j]; 903: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]); 904: */ 905: } 906: } /* end h */ 907: return po; 908: } 909: 910: 911: /*************** log-likelihood *************/ 912: double func( double *x) 913: { 914: int i, ii, j, k, mi, d, kk; 915: double l, ll[NLSTATEMAX], cov[NCOVMAX]; 916: double **out; 917: double sw; /* Sum of weights */ 918: double lli; /* Individual log likelihood */ 919: int s1, s2; 920: double bbh; 921: long ipmx; 922: /*extern weight */ 923: /* We are differentiating ll according to initial status */ 924: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ 925: /*for(i=1;i<imx;i++) 926: printf(" %d\n",s[4][i]); 927: */ 928: cov[1]=1.; 929: 930: for(k=1; k<=nlstate; k++) ll[k]=0.; 931: 932: if(mle==1){ 933: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 934: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 935: for(mi=1; mi<= wav[i]-1; mi++){ 936: for (ii=1;ii<=nlstate+ndeath;ii++) 937: for (j=1;j<=nlstate+ndeath;j++){ 938: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 939: savm[ii][j]=(ii==j ? 1.0 : 0.0); 940: } 941: for(d=0; d<dh[mi][i]; d++){ 942: newm=savm; 943: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 944: for (kk=1; kk<=cptcovage;kk++) { 945: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 946: } 947: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 948: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 949: savm=oldm; 950: oldm=newm; 951: } /* end mult */ 952: 953: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 954: /* But now since version 0.9 we anticipate for bias and large stepm. 955: * If stepm is larger than one month (smallest stepm) and if the exact delay 956: * (in months) between two waves is not a multiple of stepm, we rounded to 957: * the nearest (and in case of equal distance, to the lowest) interval but now 958: * we keep into memory the bias bh[mi][i] and also the previous matrix product 959: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the 960: * probability in order to take into account the bias as a fraction of the way 961: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies 962: * -stepm/2 to stepm/2 . 963: * For stepm=1 the results are the same as for previous versions of Imach. 964: * For stepm > 1 the results are less biased than in previous versions. 965: */ 966: s1=s[mw[mi][i]][i]; 967: s2=s[mw[mi+1][i]][i]; 968: bbh=(double)bh[mi][i]/(double)stepm; 969: /* bias is positive if real duration 970: * is higher than the multiple of stepm and negative otherwise. 971: */ 972: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 973: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ 974: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 975: /*if(lli ==000.0)*/ 976: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ 977: ipmx +=1; 978: sw += weight[i]; 979: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 980: } /* end of wave */ 981: } /* end of individual */ 982: } else if(mle==2){ 983: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 984: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 985: for(mi=1; mi<= wav[i]-1; mi++){ 986: for (ii=1;ii<=nlstate+ndeath;ii++) 987: for (j=1;j<=nlstate+ndeath;j++){ 988: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 989: savm[ii][j]=(ii==j ? 1.0 : 0.0); 990: } 991: for(d=0; d<=dh[mi][i]; d++){ 992: newm=savm; 993: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 994: for (kk=1; kk<=cptcovage;kk++) { 995: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 996: } 997: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 998: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 999: savm=oldm; 1000: oldm=newm; 1001: } /* end mult */ 1002: 1003: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 1004: /* But now since version 0.9 we anticipate for bias and large stepm. 1005: * If stepm is larger than one month (smallest stepm) and if the exact delay 1006: * (in months) between two waves is not a multiple of stepm, we rounded to 1007: * the nearest (and in case of equal distance, to the lowest) interval but now 1008: * we keep into memory the bias bh[mi][i] and also the previous matrix product 1009: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the 1010: * probability in order to take into account the bias as a fraction of the way 1011: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies 1012: * -stepm/2 to stepm/2 . 1013: * For stepm=1 the results are the same as for previous versions of Imach. 1014: * For stepm > 1 the results are less biased than in previous versions. 1015: */ 1016: s1=s[mw[mi][i]][i]; 1017: s2=s[mw[mi+1][i]][i]; 1018: bbh=(double)bh[mi][i]/(double)stepm; 1019: /* bias is positive if real duration 1020: * is higher than the multiple of stepm and negative otherwise. 1021: */ 1022: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ 1023: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ 1024: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */ 1025: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 1026: /*if(lli ==000.0)*/ 1027: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ 1028: ipmx +=1; 1029: sw += weight[i]; 1030: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1031: } /* end of wave */ 1032: } /* end of individual */ 1033: } else if(mle==3){ /* exponential inter-extrapolation */ 1034: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1035: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1036: for(mi=1; mi<= wav[i]-1; mi++){ 1037: for (ii=1;ii<=nlstate+ndeath;ii++) 1038: for (j=1;j<=nlstate+ndeath;j++){ 1039: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1040: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1041: } 1042: for(d=0; d<dh[mi][i]; d++){ 1043: newm=savm; 1044: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1045: for (kk=1; kk<=cptcovage;kk++) { 1046: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1047: } 1048: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1049: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1050: savm=oldm; 1051: oldm=newm; 1052: } /* end mult */ 1053: 1054: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ 1055: /* But now since version 0.9 we anticipate for bias and large stepm. 1056: * If stepm is larger than one month (smallest stepm) and if the exact delay 1057: * (in months) between two waves is not a multiple of stepm, we rounded to 1058: * the nearest (and in case of equal distance, to the lowest) interval but now 1059: * we keep into memory the bias bh[mi][i] and also the previous matrix product 1060: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the 1061: * probability in order to take into account the bias as a fraction of the way 1062: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies 1063: * -stepm/2 to stepm/2 . 1064: * For stepm=1 the results are the same as for previous versions of Imach. 1065: * For stepm > 1 the results are less biased than in previous versions. 1066: */ 1067: s1=s[mw[mi][i]][i]; 1068: s2=s[mw[mi+1][i]][i]; 1069: bbh=(double)bh[mi][i]/(double)stepm; 1070: /* bias is positive if real duration 1071: * is higher than the multiple of stepm and negative otherwise. 1072: */ 1073: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */ 1074: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ 1075: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ 1076: /*if(lli ==000.0)*/ 1077: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ 1078: ipmx +=1; 1079: sw += weight[i]; 1080: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1081: } /* end of wave */ 1082: } /* end of individual */ 1083: }else{ /* ml=4 no inter-extrapolation */ 1084: for (i=1,ipmx=0, sw=0.; i<=imx; i++){ 1085: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; 1086: for(mi=1; mi<= wav[i]-1; mi++){ 1087: for (ii=1;ii<=nlstate+ndeath;ii++) 1088: for (j=1;j<=nlstate+ndeath;j++){ 1089: oldm[ii][j]=(ii==j ? 1.0 : 0.0); 1090: savm[ii][j]=(ii==j ? 1.0 : 0.0); 1091: } 1092: for(d=0; d<dh[mi][i]; d++){ 1093: newm=savm; 1094: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; 1095: for (kk=1; kk<=cptcovage;kk++) { 1096: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; 1097: } 1098: 1099: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1100: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); 1101: savm=oldm; 1102: oldm=newm; 1103: } /* end mult */ 1104: 1105: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ 1106: ipmx +=1; 1107: sw += weight[i]; 1108: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; 1109: } /* end of wave */ 1110: } /* end of individual */ 1111: } /* End of if */ 1112: for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; 1113: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ 1114: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ 1115: return -l; 1116: } 1117: 1118: 1119: /*********** Maximum Likelihood Estimation ***************/ 1120: 1121: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) 1122: { 1123: int i,j, iter; 1124: double **xi,*delti; 1125: double fret; 1126: xi=matrix(1,npar,1,npar); 1127: for (i=1;i<=npar;i++) 1128: for (j=1;j<=npar;j++) 1129: xi[i][j]=(i==j ? 1.0 : 0.0); 1130: printf("Powell\n"); fprintf(ficlog,"Powell\n"); 1131: powell(p,xi,npar,ftol,&iter,&fret,func); 1132: 1133: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); 1134: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); 1135: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); 1136: 1137: } 1138: 1139: /**** Computes Hessian and covariance matrix ***/ 1140: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double [])) 1141: { 1142: double **a,**y,*x,pd; 1143: double **hess; 1144: int i, j,jk; 1145: int *indx; 1146: 1147: double hessii(double p[], double delta, int theta, double delti[]); 1148: double hessij(double p[], double delti[], int i, int j); 1149: void lubksb(double **a, int npar, int *indx, double b[]) ; 1150: void ludcmp(double **a, int npar, int *indx, double *d) ; 1151: 1152: hess=matrix(1,npar,1,npar); 1153: 1154: printf("\nCalculation of the hessian matrix. Wait...\n"); 1155: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n"); 1156: for (i=1;i<=npar;i++){ 1157: printf("%d",i);fflush(stdout); 1158: fprintf(ficlog,"%d",i);fflush(ficlog); 1159: hess[i][i]=hessii(p,ftolhess,i,delti); 1160: /*printf(" %f ",p[i]);*/ 1161: /*printf(" %lf ",hess[i][i]);*/ 1162: } 1163: 1164: for (i=1;i<=npar;i++) { 1165: for (j=1;j<=npar;j++) { 1166: if (j>i) { 1167: printf(".%d%d",i,j);fflush(stdout); 1168: fprintf(ficlog,".%d%d",i,j);fflush(ficlog); 1169: hess[i][j]=hessij(p,delti,i,j); 1170: hess[j][i]=hess[i][j]; 1171: /*printf(" %lf ",hess[i][j]);*/ 1172: } 1173: } 1174: } 1175: printf("\n"); 1176: fprintf(ficlog,"\n"); 1177: 1178: printf("\nInverting the hessian to get the covariance matrix. Wait...\n"); 1179: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n"); 1180: 1181: a=matrix(1,npar,1,npar); 1182: y=matrix(1,npar,1,npar); 1183: x=vector(1,npar); 1184: indx=ivector(1,npar); 1185: for (i=1;i<=npar;i++) 1186: for (j=1;j<=npar;j++) a[i][j]=hess[i][j]; 1187: ludcmp(a,npar,indx,&pd); 1188: 1189: for (j=1;j<=npar;j++) { 1190: for (i=1;i<=npar;i++) x[i]=0; 1191: x[j]=1; 1192: lubksb(a,npar,indx,x); 1193: for (i=1;i<=npar;i++){ 1194: matcov[i][j]=x[i]; 1195: } 1196: } 1197: 1198: printf("\n#Hessian matrix#\n"); 1199: fprintf(ficlog,"\n#Hessian matrix#\n"); 1200: for (i=1;i<=npar;i++) { 1201: for (j=1;j<=npar;j++) { 1202: printf("%.3e ",hess[i][j]); 1203: fprintf(ficlog,"%.3e ",hess[i][j]); 1204: } 1205: printf("\n"); 1206: fprintf(ficlog,"\n"); 1207: } 1208: 1209: /* Recompute Inverse */ 1210: for (i=1;i<=npar;i++) 1211: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; 1212: ludcmp(a,npar,indx,&pd); 1213: 1214: /* printf("\n#Hessian matrix recomputed#\n"); 1215: 1216: for (j=1;j<=npar;j++) { 1217: for (i=1;i<=npar;i++) x[i]=0; 1218: x[j]=1; 1219: lubksb(a,npar,indx,x); 1220: for (i=1;i<=npar;i++){ 1221: y[i][j]=x[i]; 1222: printf("%.3e ",y[i][j]); 1223: fprintf(ficlog,"%.3e ",y[i][j]); 1224: } 1225: printf("\n"); 1226: fprintf(ficlog,"\n"); 1227: } 1228: */ 1229: 1230: free_matrix(a,1,npar,1,npar); 1231: free_matrix(y,1,npar,1,npar); 1232: free_vector(x,1,npar); 1233: free_ivector(indx,1,npar); 1234: free_matrix(hess,1,npar,1,npar); 1235: 1236: 1237: } 1238: 1239: /*************** hessian matrix ****************/ 1240: double hessii( double x[], double delta, int theta, double delti[]) 1241: { 1242: int i; 1243: int l=1, lmax=20; 1244: double k1,k2; 1245: double p2[NPARMAX+1]; 1246: double res; 1247: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4; 1248: double fx; 1249: int k=0,kmax=10; 1250: double l1; 1251: 1252: fx=func(x); 1253: for (i=1;i<=npar;i++) p2[i]=x[i]; 1254: for(l=0 ; l <=lmax; l++){ 1255: l1=pow(10,l); 1256: delts=delt; 1257: for(k=1 ; k <kmax; k=k+1){ 1258: delt = delta*(l1*k); 1259: p2[theta]=x[theta] +delt; 1260: k1=func(p2)-fx; 1261: p2[theta]=x[theta]-delt; 1262: k2=func(p2)-fx; 1263: /*res= (k1-2.0*fx+k2)/delt/delt; */ 1264: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ 1265: 1266: #ifdef DEBUG 1267: 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); 1268: 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); 1269: #endif 1270: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */ 1271: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){ 1272: k=kmax; 1273: } 1274: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ 1275: k=kmax; l=lmax*10.; 1276: } 1277: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 1278: delts=delt; 1279: } 1280: } 1281: } 1282: delti[theta]=delts; 1283: return res; 1284: 1285: } 1286: 1287: double hessij( double x[], double delti[], int thetai,int thetaj) 1288: { 1289: int i; 1290: int l=1, l1, lmax=20; 1291: double k1,k2,k3,k4,res,fx; 1292: double p2[NPARMAX+1]; 1293: int k; 1294: 1295: fx=func(x); 1296: for (k=1; k<=2; k++) { 1297: for (i=1;i<=npar;i++) p2[i]=x[i]; 1298: p2[thetai]=x[thetai]+delti[thetai]/k; 1299: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 1300: k1=func(p2)-fx; 1301: 1302: p2[thetai]=x[thetai]+delti[thetai]/k; 1303: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 1304: k2=func(p2)-fx; 1305: 1306: p2[thetai]=x[thetai]-delti[thetai]/k; 1307: p2[thetaj]=x[thetaj]+delti[thetaj]/k; 1308: k3=func(p2)-fx; 1309: 1310: p2[thetai]=x[thetai]-delti[thetai]/k; 1311: p2[thetaj]=x[thetaj]-delti[thetaj]/k; 1312: k4=func(p2)-fx; 1313: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */ 1314: #ifdef DEBUG 1315: 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); 1316: 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); 1317: #endif 1318: } 1319: return res; 1320: } 1321: 1322: /************** Inverse of matrix **************/ 1323: void ludcmp(double **a, int n, int *indx, double *d) 1324: { 1325: int i,imax,j,k; 1326: double big,dum,sum,temp; 1327: double *vv; 1328: 1329: vv=vector(1,n); 1330: *d=1.0; 1331: for (i=1;i<=n;i++) { 1332: big=0.0; 1333: for (j=1;j<=n;j++) 1334: if ((temp=fabs(a[i][j])) > big) big=temp; 1335: if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 1336: vv[i]=1.0/big; 1337: } 1338: for (j=1;j<=n;j++) { 1339: for (i=1;i<j;i++) { 1340: sum=a[i][j]; 1341: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 1342: a[i][j]=sum; 1343: } 1344: big=0.0; 1345: for (i=j;i<=n;i++) { 1346: sum=a[i][j]; 1347: for (k=1;k<j;k++) 1348: sum -= a[i][k]*a[k][j]; 1349: a[i][j]=sum; 1350: if ( (dum=vv[i]*fabs(sum)) >= big) { 1351: big=dum; 1352: imax=i; 1353: } 1354: } 1355: if (j != imax) { 1356: for (k=1;k<=n;k++) { 1357: dum=a[imax][k]; 1358: a[imax][k]=a[j][k]; 1359: a[j][k]=dum; 1360: } 1361: *d = -(*d); 1362: vv[imax]=vv[j]; 1363: } 1364: indx[j]=imax; 1365: if (a[j][j] == 0.0) a[j][j]=TINY; 1366: if (j != n) { 1367: dum=1.0/(a[j][j]); 1368: for (i=j+1;i<=n;i++) a[i][j] *= dum; 1369: } 1370: } 1371: free_vector(vv,1,n); /* Doesn't work */ 1372: ; 1373: } 1374: 1375: void lubksb(double **a, int n, int *indx, double b[]) 1376: { 1377: int i,ii=0,ip,j; 1378: double sum; 1379: 1380: for (i=1;i<=n;i++) { 1381: ip=indx[i]; 1382: sum=b[ip]; 1383: b[ip]=b[i]; 1384: if (ii) 1385: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 1386: else if (sum) ii=i; 1387: b[i]=sum; 1388: } 1389: for (i=n;i>=1;i--) { 1390: sum=b[i]; 1391: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 1392: b[i]=sum/a[i][i]; 1393: } 1394: } 1395: 1396: /************ Frequencies ********************/ 1397: void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) 1398: { /* Some frequencies */ 1399: 1400: int i, m, jk, k1,i1, j1, bool, z1,z2,j; 1401: int first; 1402: double ***freq; /* Frequencies */ 1403: double *pp; 1404: double pos, k2, dateintsum=0,k2cpt=0; 1405: FILE *ficresp; 1406: char fileresp[FILENAMELENGTH]; 1407: 1408: pp=vector(1,nlstate); 1409: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); 1410: strcpy(fileresp,"p"); 1411: strcat(fileresp,fileres); 1412: if((ficresp=fopen(fileresp,"w"))==NULL) { 1413: printf("Problem with prevalence resultfile: %s\n", fileresp); 1414: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); 1415: exit(0); 1416: } 1417: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); 1418: j1=0; 1419: 1420: j=cptcoveff; 1421: if (cptcovn<1) {j=1;ncodemax[1]=1;} 1422: 1423: first=1; 1424: 1425: for(k1=1; k1<=j;k1++){ 1426: for(i1=1; i1<=ncodemax[k1];i1++){ 1427: j1++; 1428: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); 1429: scanf("%d", i);*/ 1430: for (i=-1; i<=nlstate+ndeath; i++) 1431: for (jk=-1; jk<=nlstate+ndeath; jk++) 1432: for(m=agemin; m <= agemax+3; m++) 1433: freq[i][jk][m]=0; 1434: 1435: dateintsum=0; 1436: k2cpt=0; 1437: for (i=1; i<=imx; i++) { 1438: bool=1; 1439: if (cptcovn>0) { 1440: for (z1=1; z1<=cptcoveff; z1++) 1441: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 1442: bool=0; 1443: } 1444: if (bool==1){ 1445: for(m=firstpass; m<=lastpass; m++){ 1446: k2=anint[m][i]+(mint[m][i]/12.); 1447: if ((k2>=dateprev1) && (k2<=dateprev2)) { 1448: if(agev[m][i]==0) agev[m][i]=agemax+1; 1449: if(agev[m][i]==1) agev[m][i]=agemax+2; 1450: if (m<lastpass) { 1451: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 1452: freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i]; 1453: } 1454: 1455: if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) { 1456: dateintsum=dateintsum+k2; 1457: k2cpt++; 1458: } 1459: } 1460: } 1461: } 1462: } 1463: 1464: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); 1465: 1466: if (cptcovn>0) { 1467: fprintf(ficresp, "\n#********** Variable "); 1468: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 1469: fprintf(ficresp, "**********\n#"); 1470: } 1471: for(i=1; i<=nlstate;i++) 1472: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); 1473: fprintf(ficresp, "\n"); 1474: 1475: for(i=(int)agemin; i <= (int)agemax+3; i++){ 1476: if(i==(int)agemax+3){ 1477: fprintf(ficlog,"Total"); 1478: }else{ 1479: if(first==1){ 1480: first=0; 1481: printf("See log file for details...\n"); 1482: } 1483: fprintf(ficlog,"Age %d", i); 1484: } 1485: for(jk=1; jk <=nlstate ; jk++){ 1486: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 1487: pp[jk] += freq[jk][m][i]; 1488: } 1489: for(jk=1; jk <=nlstate ; jk++){ 1490: for(m=-1, pos=0; m <=0 ; m++) 1491: pos += freq[jk][m][i]; 1492: if(pp[jk]>=1.e-10){ 1493: if(first==1){ 1494: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 1495: } 1496: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); 1497: }else{ 1498: if(first==1) 1499: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 1500: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); 1501: } 1502: } 1503: 1504: for(jk=1; jk <=nlstate ; jk++){ 1505: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 1506: pp[jk] += freq[jk][m][i]; 1507: } 1508: 1509: for(jk=1,pos=0; jk <=nlstate ; jk++) 1510: pos += pp[jk]; 1511: for(jk=1; jk <=nlstate ; jk++){ 1512: if(pos>=1.e-5){ 1513: if(first==1) 1514: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 1515: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); 1516: }else{ 1517: if(first==1) 1518: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 1519: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); 1520: } 1521: if( i <= (int) agemax){ 1522: if(pos>=1.e-5){ 1523: fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); 1524: probs[i][jk][j1]= pp[jk]/pos; 1525: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ 1526: } 1527: else 1528: fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); 1529: } 1530: } 1531: 1532: for(jk=-1; jk <=nlstate+ndeath; jk++) 1533: for(m=-1; m <=nlstate+ndeath; m++) 1534: if(freq[jk][m][i] !=0 ) { 1535: if(first==1) 1536: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); 1537: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); 1538: } 1539: if(i <= (int) agemax) 1540: fprintf(ficresp,"\n"); 1541: if(first==1) 1542: printf("Others in log...\n"); 1543: fprintf(ficlog,"\n"); 1544: } 1545: } 1546: } 1547: dateintmean=dateintsum/k2cpt; 1548: 1549: fclose(ficresp); 1550: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); 1551: free_vector(pp,1,nlstate); 1552: 1553: /* End of Freq */ 1554: } 1555: 1556: /************ Prevalence ********************/ 1557: 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) 1558: { /* Some frequencies */ 1559: 1560: int i, m, jk, k1, i1, j1, bool, z1,z2,j; 1561: double ***freq; /* Frequencies */ 1562: double *pp; 1563: double pos, k2; 1564: 1565: pp=vector(1,nlstate); 1566: 1567: freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); 1568: j1=0; 1569: 1570: j=cptcoveff; 1571: if (cptcovn<1) {j=1;ncodemax[1]=1;} 1572: 1573: for(k1=1; k1<=j;k1++){ 1574: for(i1=1; i1<=ncodemax[k1];i1++){ 1575: j1++; 1576: 1577: for (i=-1; i<=nlstate+ndeath; i++) 1578: for (jk=-1; jk<=nlstate+ndeath; jk++) 1579: for(m=agemin; m <= agemax+3; m++) 1580: freq[i][jk][m]=0; 1581: 1582: for (i=1; i<=imx; i++) { 1583: bool=1; 1584: if (cptcovn>0) { 1585: for (z1=1; z1<=cptcoveff; z1++) 1586: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 1587: bool=0; 1588: } 1589: if (bool==1) { 1590: for(m=firstpass; m<=lastpass; m++){ 1591: k2=anint[m][i]+(mint[m][i]/12.); 1592: if ((k2>=dateprev1) && (k2<=dateprev2)) { 1593: if(agev[m][i]==0) agev[m][i]=agemax+1; 1594: if(agev[m][i]==1) agev[m][i]=agemax+2; 1595: if (m<lastpass) { 1596: if (calagedate>0) 1597: freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; 1598: else 1599: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; 1600: freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 1601: } 1602: } 1603: } 1604: } 1605: } 1606: for(i=(int)agemin; i <= (int)agemax+3; i++){ 1607: for(jk=1; jk <=nlstate ; jk++){ 1608: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) 1609: pp[jk] += freq[jk][m][i]; 1610: } 1611: for(jk=1; jk <=nlstate ; jk++){ 1612: for(m=-1, pos=0; m <=0 ; m++) 1613: pos += freq[jk][m][i]; 1614: } 1615: 1616: for(jk=1; jk <=nlstate ; jk++){ 1617: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) 1618: pp[jk] += freq[jk][m][i]; 1619: } 1620: 1621: for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; 1622: 1623: for(jk=1; jk <=nlstate ; jk++){ 1624: if( i <= (int) agemax){ 1625: if(pos>=1.e-5){ 1626: probs[i][jk][j1]= pp[jk]/pos; 1627: } 1628: } 1629: }/* end jk */ 1630: }/* end i */ 1631: } /* end i1 */ 1632: } /* end k1 */ 1633: 1634: 1635: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); 1636: free_vector(pp,1,nlstate); 1637: 1638: } /* End of Freq */ 1639: 1640: /************* Waves Concatenation ***************/ 1641: 1642: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) 1643: { 1644: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. 1645: Death is a valid wave (if date is known). 1646: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i 1647: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] 1648: and mw[mi+1][i]. dh depends on stepm. 1649: */ 1650: 1651: int i, mi, m; 1652: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; 1653: double sum=0., jmean=0.;*/ 1654: int first; 1655: int j, k=0,jk, ju, jl; 1656: double sum=0.; 1657: first=0; 1658: jmin=1e+5; 1659: jmax=-1; 1660: jmean=0.; 1661: for(i=1; i<=imx; i++){ 1662: mi=0; 1663: m=firstpass; 1664: while(s[m][i] <= nlstate){ 1665: if(s[m][i]>=1) 1666: mw[++mi][i]=m; 1667: if(m >=lastpass) 1668: break; 1669: else 1670: m++; 1671: }/* end while */ 1672: if (s[m][i] > nlstate){ 1673: mi++; /* Death is another wave */ 1674: /* if(mi==0) never been interviewed correctly before death */ 1675: /* Only death is a correct wave */ 1676: mw[mi][i]=m; 1677: } 1678: 1679: wav[i]=mi; 1680: if(mi==0){ 1681: if(first==0){ 1682: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i); 1683: first=1; 1684: } 1685: if(first==1){ 1686: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i); 1687: } 1688: } /* end mi==0 */ 1689: } 1690: 1691: for(i=1; i<=imx; i++){ 1692: for(mi=1; mi<wav[i];mi++){ 1693: if (stepm <=0) 1694: dh[mi][i]=1; 1695: else{ 1696: if (s[mw[mi+1][i]][i] > nlstate) { 1697: if (agedc[i] < 2*AGESUP) { 1698: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 1699: if(j==0) j=1; /* Survives at least one month after exam */ 1700: k=k+1; 1701: if (j >= jmax) jmax=j; 1702: if (j <= jmin) jmin=j; 1703: sum=sum+j; 1704: /*if (j<0) printf("j=%d num=%d \n",j,i); */ 1705: } 1706: } 1707: else{ 1708: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); 1709: k=k+1; 1710: if (j >= jmax) jmax=j; 1711: else if (j <= jmin)jmin=j; 1712: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ 1713: sum=sum+j; 1714: } 1715: jk= j/stepm; 1716: jl= j -jk*stepm; 1717: ju= j -(jk+1)*stepm; 1718: if(mle <=1){ 1719: if(jl==0){ 1720: dh[mi][i]=jk; 1721: bh[mi][i]=0; 1722: }else{ /* We want a negative bias in order to only have interpolation ie 1723: * at the price of an extra matrix product in likelihood */ 1724: dh[mi][i]=jk+1; 1725: bh[mi][i]=ju; 1726: } 1727: }else{ 1728: if(jl <= -ju){ 1729: dh[mi][i]=jk; 1730: bh[mi][i]=jl; /* bias is positive if real duration 1731: * is higher than the multiple of stepm and negative otherwise. 1732: */ 1733: } 1734: else{ 1735: dh[mi][i]=jk+1; 1736: bh[mi][i]=ju; 1737: } 1738: if(dh[mi][i]==0){ 1739: dh[mi][i]=1; /* At least one step */ 1740: bh[mi][i]=ju; /* At least one step */ 1741: printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i); 1742: } 1743: if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm); 1744: } 1745: } /* end if mle */ 1746: } /* end wave */ 1747: } 1748: jmean=sum/k; 1749: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); 1750: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); 1751: } 1752: 1753: /*********** Tricode ****************************/ 1754: void tricode(int *Tvar, int **nbcode, int imx) 1755: { 1756: 1757: int Ndum[20],ij=1, k, j, i, maxncov=19; 1758: int cptcode=0; 1759: cptcoveff=0; 1760: 1761: for (k=0; k<maxncov; k++) Ndum[k]=0; 1762: for (k=1; k<=7; k++) ncodemax[k]=0; 1763: 1764: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { 1765: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 1766: modality*/ 1767: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/ 1768: Ndum[ij]++; /*store the modality */ 1769: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ 1770: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 1771: Tvar[j]. If V=sex and male is 0 and 1772: female is 1, then cptcode=1.*/ 1773: } 1774: 1775: for (i=0; i<=cptcode; i++) { 1776: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */ 1777: } 1778: 1779: ij=1; 1780: for (i=1; i<=ncodemax[j]; i++) { 1781: for (k=0; k<= maxncov; k++) { 1782: if (Ndum[k] != 0) { 1783: nbcode[Tvar[j]][ij]=k; 1784: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ 1785: 1786: ij++; 1787: } 1788: if (ij > ncodemax[j]) break; 1789: } 1790: } 1791: } 1792: 1793: for (k=0; k< maxncov; k++) Ndum[k]=0; 1794: 1795: for (i=1; i<=ncovmodel-2; i++) { 1796: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 1797: ij=Tvar[i]; 1798: Ndum[ij]++; 1799: } 1800: 1801: ij=1; 1802: for (i=1; i<= maxncov; i++) { 1803: if((Ndum[i]!=0) && (i<=ncovcol)){ 1804: Tvaraff[ij]=i; /*For printing */ 1805: ij++; 1806: } 1807: } 1808: 1809: cptcoveff=ij-1; /*Number of simple covariates*/ 1810: } 1811: 1812: /*********** Health Expectancies ****************/ 1813: 1814: 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 ) 1815: 1816: { 1817: /* Health expectancies */ 1818: int i, j, nhstepm, hstepm, h, nstepm, k, cptj; 1819: double age, agelim, hf; 1820: double ***p3mat,***varhe; 1821: double **dnewm,**doldm; 1822: double *xp; 1823: double **gp, **gm; 1824: double ***gradg, ***trgradg; 1825: int theta; 1826: 1827: varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); 1828: xp=vector(1,npar); 1829: dnewm=matrix(1,nlstate*2,1,npar); 1830: doldm=matrix(1,nlstate*2,1,nlstate*2); 1831: 1832: fprintf(ficreseij,"# Health expectancies\n"); 1833: fprintf(ficreseij,"# Age"); 1834: for(i=1; i<=nlstate;i++) 1835: for(j=1; j<=nlstate;j++) 1836: fprintf(ficreseij," %1d-%1d (SE)",i,j); 1837: fprintf(ficreseij,"\n"); 1838: 1839: if(estepm < stepm){ 1840: printf ("Problem %d lower than %d\n",estepm, stepm); 1841: } 1842: else hstepm=estepm; 1843: /* We compute the life expectancy from trapezoids spaced every estepm months 1844: * This is mainly to measure the difference between two models: for example 1845: * if stepm=24 months pijx are given only every 2 years and by summing them 1846: * we are calculating an estimate of the Life Expectancy assuming a linear 1847: * progression inbetween and thus overestimating or underestimating according 1848: * to the curvature of the survival function. If, for the same date, we 1849: * estimate the model with stepm=1 month, we can keep estepm to 24 months 1850: * to compare the new estimate of Life expectancy with the same linear 1851: * hypothesis. A more precise result, taking into account a more precise 1852: * curvature will be obtained if estepm is as small as stepm. */ 1853: 1854: /* For example we decided to compute the life expectancy with the smallest unit */ 1855: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 1856: nhstepm is the number of hstepm from age to agelim 1857: nstepm is the number of stepm from age to agelin. 1858: Look at hpijx to understand the reason of that which relies in memory size 1859: and note for a fixed period like estepm months */ 1860: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 1861: survival function given by stepm (the optimization length). Unfortunately it 1862: means that if the survival funtion is printed only each two years of age and if 1863: you sum them up and add 1 year (area under the trapezoids) you won't get the same 1864: results. So we changed our mind and took the option of the best precision. 1865: */ 1866: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 1867: 1868: agelim=AGESUP; 1869: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 1870: /* nhstepm age range expressed in number of stepm */ 1871: nstepm=(int) rint((agelim-age)*YEARM/stepm); 1872: /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 1873: /* if (stepm >= YEARM) hstepm=1;*/ 1874: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 1875: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 1876: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); 1877: gp=matrix(0,nhstepm,1,nlstate*2); 1878: gm=matrix(0,nhstepm,1,nlstate*2); 1879: 1880: /* Computed by stepm unit matrices, product of hstepm matrices, stored 1881: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ 1882: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); 1883: 1884: 1885: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 1886: 1887: /* Computing Variances of health expectancies */ 1888: 1889: for(theta=1; theta <=npar; theta++){ 1890: for(i=1; i<=npar; i++){ 1891: xp[i] = x[i] + (i==theta ?delti[theta]:0); 1892: } 1893: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 1894: 1895: cptj=0; 1896: for(j=1; j<= nlstate; j++){ 1897: for(i=1; i<=nlstate; i++){ 1898: cptj=cptj+1; 1899: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){ 1900: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; 1901: } 1902: } 1903: } 1904: 1905: 1906: for(i=1; i<=npar; i++) 1907: xp[i] = x[i] - (i==theta ?delti[theta]:0); 1908: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 1909: 1910: cptj=0; 1911: for(j=1; j<= nlstate; j++){ 1912: for(i=1;i<=nlstate;i++){ 1913: cptj=cptj+1; 1914: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ 1915: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; 1916: } 1917: } 1918: } 1919: for(j=1; j<= nlstate*2; j++) 1920: for(h=0; h<=nhstepm-1; h++){ 1921: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 1922: } 1923: } 1924: 1925: /* End theta */ 1926: 1927: trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); 1928: 1929: for(h=0; h<=nhstepm-1; h++) 1930: for(j=1; j<=nlstate*2;j++) 1931: for(theta=1; theta <=npar; theta++) 1932: trgradg[h][j][theta]=gradg[h][theta][j]; 1933: 1934: 1935: for(i=1;i<=nlstate*2;i++) 1936: for(j=1;j<=nlstate*2;j++) 1937: varhe[i][j][(int)age] =0.; 1938: 1939: printf("%d|",(int)age);fflush(stdout); 1940: fprintf(ficlog,"%d|",(int)age);fflush(ficlog); 1941: for(h=0;h<=nhstepm-1;h++){ 1942: for(k=0;k<=nhstepm-1;k++){ 1943: matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); 1944: matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); 1945: for(i=1;i<=nlstate*2;i++) 1946: for(j=1;j<=nlstate*2;j++) 1947: varhe[i][j][(int)age] += doldm[i][j]*hf*hf; 1948: } 1949: } 1950: /* Computing expectancies */ 1951: for(i=1; i<=nlstate;i++) 1952: for(j=1; j<=nlstate;j++) 1953: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ 1954: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; 1955: 1956: /* 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]);*/ 1957: 1958: } 1959: 1960: fprintf(ficreseij,"%3.0f",age ); 1961: cptj=0; 1962: for(i=1; i<=nlstate;i++) 1963: for(j=1; j<=nlstate;j++){ 1964: cptj++; 1965: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) ); 1966: } 1967: fprintf(ficreseij,"\n"); 1968: 1969: free_matrix(gm,0,nhstepm,1,nlstate*2); 1970: free_matrix(gp,0,nhstepm,1,nlstate*2); 1971: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); 1972: free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); 1973: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 1974: } 1975: printf("\n"); 1976: fprintf(ficlog,"\n"); 1977: 1978: free_vector(xp,1,npar); 1979: free_matrix(dnewm,1,nlstate*2,1,npar); 1980: free_matrix(doldm,1,nlstate*2,1,nlstate*2); 1981: free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); 1982: } 1983: 1984: /************ Variance ******************/ 1985: 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) 1986: { 1987: /* Variance of health expectancies */ 1988: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ 1989: /* double **newm;*/ 1990: double **dnewm,**doldm; 1991: double **dnewmp,**doldmp; 1992: int i, j, nhstepm, hstepm, h, nstepm ; 1993: int k, cptcode; 1994: double *xp; 1995: double **gp, **gm; /* for var eij */ 1996: double ***gradg, ***trgradg; /*for var eij */ 1997: double **gradgp, **trgradgp; /* for var p point j */ 1998: double *gpp, *gmp; /* for var p point j */ 1999: double **varppt; /* for var p point j nlstate to nlstate+ndeath */ 2000: double ***p3mat; 2001: double age,agelim, hf; 2002: double ***mobaverage; 2003: int theta; 2004: char digit[4]; 2005: char digitp[25]; 2006: 2007: char fileresprobmorprev[FILENAMELENGTH]; 2008: 2009: if(popbased==1){ 2010: if(mobilav!=0) 2011: strcpy(digitp,"-populbased-mobilav-"); 2012: else strcpy(digitp,"-populbased-nomobil-"); 2013: } 2014: else 2015: strcpy(digitp,"-stablbased-"); 2016: 2017: if (mobilav!=0) { 2018: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 2019: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 2020: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 2021: printf(" Error in movingaverage mobilav=%d\n",mobilav); 2022: } 2023: } 2024: 2025: strcpy(fileresprobmorprev,"prmorprev"); 2026: sprintf(digit,"%-d",ij); 2027: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ 2028: strcat(fileresprobmorprev,digit); /* Tvar to be done */ 2029: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ 2030: strcat(fileresprobmorprev,fileres); 2031: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { 2032: printf("Problem with resultfile: %s\n", fileresprobmorprev); 2033: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); 2034: } 2035: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 2036: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); 2037: fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); 2038: fprintf(ficresprobmorprev,"# Age cov=%-d",ij); 2039: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 2040: fprintf(ficresprobmorprev," p.%-d SE",j); 2041: for(i=1; i<=nlstate;i++) 2042: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); 2043: } 2044: fprintf(ficresprobmorprev,"\n"); 2045: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { 2046: printf("Problem with gnuplot file: %s\n", optionfilegnuplot); 2047: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); 2048: exit(0); 2049: } 2050: else{ 2051: fprintf(ficgp,"\n# Routine varevsij"); 2052: } 2053: if((fichtm=fopen(optionfilehtm,"a"))==NULL) { 2054: printf("Problem with html file: %s\n", optionfilehtm); 2055: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); 2056: exit(0); 2057: } 2058: else{ 2059: 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"); 2060: fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp); 2061: } 2062: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 2063: 2064: 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"); 2065: fprintf(ficresvij,"# Age"); 2066: for(i=1; i<=nlstate;i++) 2067: for(j=1; j<=nlstate;j++) 2068: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); 2069: fprintf(ficresvij,"\n"); 2070: 2071: xp=vector(1,npar); 2072: dnewm=matrix(1,nlstate,1,npar); 2073: doldm=matrix(1,nlstate,1,nlstate); 2074: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); 2075: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 2076: 2077: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); 2078: gpp=vector(nlstate+1,nlstate+ndeath); 2079: gmp=vector(nlstate+1,nlstate+ndeath); 2080: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 2081: 2082: if(estepm < stepm){ 2083: printf ("Problem %d lower than %d\n",estepm, stepm); 2084: } 2085: else hstepm=estepm; 2086: /* For example we decided to compute the life expectancy with the smallest unit */ 2087: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 2088: nhstepm is the number of hstepm from age to agelim 2089: nstepm is the number of stepm from age to agelin. 2090: Look at hpijx to understand the reason of that which relies in memory size 2091: and note for a fixed period like k years */ 2092: /* We decided (b) to get a life expectancy respecting the most precise curvature of the 2093: survival function given by stepm (the optimization length). Unfortunately it 2094: means that if the survival funtion is printed only each two years of age and if 2095: you sum them up and add 1 year (area under the trapezoids) you won't get the same 2096: results. So we changed our mind and took the option of the best precision. 2097: */ 2098: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 2099: agelim = AGESUP; 2100: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 2101: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 2102: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ 2103: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 2104: gradg=ma3x(0,nhstepm,1,npar,1,nlstate); 2105: gp=matrix(0,nhstepm,1,nlstate); 2106: gm=matrix(0,nhstepm,1,nlstate); 2107: 2108: 2109: for(theta=1; theta <=npar; theta++){ 2110: for(i=1; i<=npar; i++){ /* Computes gradient */ 2111: xp[i] = x[i] + (i==theta ?delti[theta]:0); 2112: } 2113: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 2114: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 2115: 2116: if (popbased==1) { 2117: if(mobilav ==0){ 2118: for(i=1; i<=nlstate;i++) 2119: prlim[i][i]=probs[(int)age][i][ij]; 2120: }else{ /* mobilav */ 2121: for(i=1; i<=nlstate;i++) 2122: prlim[i][i]=mobaverage[(int)age][i][ij]; 2123: } 2124: } 2125: 2126: for(j=1; j<= nlstate; j++){ 2127: for(h=0; h<=nhstepm; h++){ 2128: for(i=1, gp[h][j]=0.;i<=nlstate;i++) 2129: gp[h][j] += prlim[i][i]*p3mat[i][j][h]; 2130: } 2131: } 2132: /* This for computing forces of mortality (h=1)as a weighted average */ 2133: for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ 2134: for(i=1; i<= nlstate; i++) 2135: gpp[j] += prlim[i][i]*p3mat[i][j][1]; 2136: } 2137: /* end force of mortality */ 2138: 2139: for(i=1; i<=npar; i++) /* Computes gradient */ 2140: xp[i] = x[i] - (i==theta ?delti[theta]:0); 2141: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); 2142: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 2143: 2144: if (popbased==1) { 2145: if(mobilav ==0){ 2146: for(i=1; i<=nlstate;i++) 2147: prlim[i][i]=probs[(int)age][i][ij]; 2148: }else{ /* mobilav */ 2149: for(i=1; i<=nlstate;i++) 2150: prlim[i][i]=mobaverage[(int)age][i][ij]; 2151: } 2152: } 2153: 2154: for(j=1; j<= nlstate; j++){ 2155: for(h=0; h<=nhstepm; h++){ 2156: for(i=1, gm[h][j]=0.;i<=nlstate;i++) 2157: gm[h][j] += prlim[i][i]*p3mat[i][j][h]; 2158: } 2159: } 2160: /* This for computing force of mortality (h=1)as a weighted average */ 2161: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ 2162: for(i=1; i<= nlstate; i++) 2163: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 2164: } 2165: /* end force of mortality */ 2166: 2167: for(j=1; j<= nlstate; j++) /* vareij */ 2168: for(h=0; h<=nhstepm; h++){ 2169: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; 2170: } 2171: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ 2172: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; 2173: } 2174: 2175: } /* End theta */ 2176: 2177: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ 2178: 2179: for(h=0; h<=nhstepm; h++) /* veij */ 2180: for(j=1; j<=nlstate;j++) 2181: for(theta=1; theta <=npar; theta++) 2182: trgradg[h][j][theta]=gradg[h][theta][j]; 2183: 2184: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ 2185: for(theta=1; theta <=npar; theta++) 2186: trgradgp[j][theta]=gradgp[theta][j]; 2187: 2188: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ 2189: for(i=1;i<=nlstate;i++) 2190: for(j=1;j<=nlstate;j++) 2191: vareij[i][j][(int)age] =0.; 2192: 2193: for(h=0;h<=nhstepm;h++){ 2194: for(k=0;k<=nhstepm;k++){ 2195: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); 2196: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); 2197: for(i=1;i<=nlstate;i++) 2198: for(j=1;j<=nlstate;j++) 2199: vareij[i][j][(int)age] += doldm[i][j]*hf*hf; 2200: } 2201: } 2202: 2203: /* pptj */ 2204: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); 2205: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); 2206: for(j=nlstate+1;j<=nlstate+ndeath;j++) 2207: for(i=nlstate+1;i<=nlstate+ndeath;i++) 2208: varppt[j][i]=doldmp[j][i]; 2209: /* end ppptj */ 2210: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); 2211: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); 2212: 2213: if (popbased==1) { 2214: if(mobilav ==0){ 2215: for(i=1; i<=nlstate;i++) 2216: prlim[i][i]=probs[(int)age][i][ij]; 2217: }else{ /* mobilav */ 2218: for(i=1; i<=nlstate;i++) 2219: prlim[i][i]=mobaverage[(int)age][i][ij]; 2220: } 2221: } 2222: 2223: /* This for computing force of mortality (h=1)as a weighted average */ 2224: for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ 2225: for(i=1; i<= nlstate; i++) 2226: gmp[j] += prlim[i][i]*p3mat[i][j][1]; 2227: } 2228: /* end force of mortality */ 2229: 2230: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); 2231: for(j=nlstate+1; j<=(nlstate+ndeath);j++){ 2232: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); 2233: for(i=1; i<=nlstate;i++){ 2234: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); 2235: } 2236: } 2237: fprintf(ficresprobmorprev,"\n"); 2238: 2239: fprintf(ficresvij,"%.0f ",age ); 2240: for(i=1; i<=nlstate;i++) 2241: for(j=1; j<=nlstate;j++){ 2242: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); 2243: } 2244: fprintf(ficresvij,"\n"); 2245: free_matrix(gp,0,nhstepm,1,nlstate); 2246: free_matrix(gm,0,nhstepm,1,nlstate); 2247: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); 2248: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); 2249: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 2250: } /* End age */ 2251: free_vector(gpp,nlstate+1,nlstate+ndeath); 2252: free_vector(gmp,nlstate+1,nlstate+ndeath); 2253: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); 2254: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ 2255: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); 2256: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ 2257: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); 2258: fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); 2259: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); 2260: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); 2261: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev); 2262: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit); 2263: /* 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); 2264: */ 2265: fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); 2266: 2267: free_vector(xp,1,npar); 2268: free_matrix(doldm,1,nlstate,1,nlstate); 2269: free_matrix(dnewm,1,nlstate,1,npar); 2270: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 2271: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); 2272: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); 2273: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 2274: fclose(ficresprobmorprev); 2275: fclose(ficgp); 2276: fclose(fichtm); 2277: } 2278: 2279: /************ Variance of prevlim ******************/ 2280: 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) 2281: { 2282: /* Variance of prevalence limit */ 2283: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ 2284: double **newm; 2285: double **dnewm,**doldm; 2286: int i, j, nhstepm, hstepm; 2287: int k, cptcode; 2288: double *xp; 2289: double *gp, *gm; 2290: double **gradg, **trgradg; 2291: double age,agelim; 2292: int theta; 2293: 2294: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n"); 2295: fprintf(ficresvpl,"# Age"); 2296: for(i=1; i<=nlstate;i++) 2297: fprintf(ficresvpl," %1d-%1d",i,i); 2298: fprintf(ficresvpl,"\n"); 2299: 2300: xp=vector(1,npar); 2301: dnewm=matrix(1,nlstate,1,npar); 2302: doldm=matrix(1,nlstate,1,nlstate); 2303: 2304: hstepm=1*YEARM; /* Every year of age */ 2305: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 2306: agelim = AGESUP; 2307: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ 2308: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 2309: if (stepm >= YEARM) hstepm=1; 2310: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 2311: gradg=matrix(1,npar,1,nlstate); 2312: gp=vector(1,nlstate); 2313: gm=vector(1,nlstate); 2314: 2315: for(theta=1; theta <=npar; theta++){ 2316: for(i=1; i<=npar; i++){ /* Computes gradient */ 2317: xp[i] = x[i] + (i==theta ?delti[theta]:0); 2318: } 2319: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 2320: for(i=1;i<=nlstate;i++) 2321: gp[i] = prlim[i][i]; 2322: 2323: for(i=1; i<=npar; i++) /* Computes gradient */ 2324: xp[i] = x[i] - (i==theta ?delti[theta]:0); 2325: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); 2326: for(i=1;i<=nlstate;i++) 2327: gm[i] = prlim[i][i]; 2328: 2329: for(i=1;i<=nlstate;i++) 2330: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; 2331: } /* End theta */ 2332: 2333: trgradg =matrix(1,nlstate,1,npar); 2334: 2335: for(j=1; j<=nlstate;j++) 2336: for(theta=1; theta <=npar; theta++) 2337: trgradg[j][theta]=gradg[theta][j]; 2338: 2339: for(i=1;i<=nlstate;i++) 2340: varpl[i][(int)age] =0.; 2341: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); 2342: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); 2343: for(i=1;i<=nlstate;i++) 2344: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ 2345: 2346: fprintf(ficresvpl,"%.0f ",age ); 2347: for(i=1; i<=nlstate;i++) 2348: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 2349: fprintf(ficresvpl,"\n"); 2350: free_vector(gp,1,nlstate); 2351: free_vector(gm,1,nlstate); 2352: free_matrix(gradg,1,npar,1,nlstate); 2353: free_matrix(trgradg,1,nlstate,1,npar); 2354: } /* End age */ 2355: 2356: free_vector(xp,1,npar); 2357: free_matrix(doldm,1,nlstate,1,npar); 2358: free_matrix(dnewm,1,nlstate,1,nlstate); 2359: 2360: } 2361: 2362: /************ Variance of one-step probabilities ******************/ 2363: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) 2364: { 2365: int i, j=0, i1, k1, l1, t, tj; 2366: int k2, l2, j1, z1; 2367: int k=0,l, cptcode; 2368: int first=1, first1; 2369: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; 2370: double **dnewm,**doldm; 2371: double *xp; 2372: double *gp, *gm; 2373: double **gradg, **trgradg; 2374: double **mu; 2375: double age,agelim, cov[NCOVMAX]; 2376: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ 2377: int theta; 2378: char fileresprob[FILENAMELENGTH]; 2379: char fileresprobcov[FILENAMELENGTH]; 2380: char fileresprobcor[FILENAMELENGTH]; 2381: 2382: double ***varpij; 2383: 2384: strcpy(fileresprob,"prob"); 2385: strcat(fileresprob,fileres); 2386: if((ficresprob=fopen(fileresprob,"w"))==NULL) { 2387: printf("Problem with resultfile: %s\n", fileresprob); 2388: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); 2389: } 2390: strcpy(fileresprobcov,"probcov"); 2391: strcat(fileresprobcov,fileres); 2392: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { 2393: printf("Problem with resultfile: %s\n", fileresprobcov); 2394: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); 2395: } 2396: strcpy(fileresprobcor,"probcor"); 2397: strcat(fileresprobcor,fileres); 2398: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { 2399: printf("Problem with resultfile: %s\n", fileresprobcor); 2400: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); 2401: } 2402: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 2403: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); 2404: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 2405: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); 2406: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 2407: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); 2408: 2409: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); 2410: fprintf(ficresprob,"# Age"); 2411: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); 2412: fprintf(ficresprobcov,"# Age"); 2413: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); 2414: fprintf(ficresprobcov,"# Age"); 2415: 2416: 2417: for(i=1; i<=nlstate;i++) 2418: for(j=1; j<=(nlstate+ndeath);j++){ 2419: fprintf(ficresprob," p%1d-%1d (SE)",i,j); 2420: fprintf(ficresprobcov," p%1d-%1d ",i,j); 2421: fprintf(ficresprobcor," p%1d-%1d ",i,j); 2422: } 2423: fprintf(ficresprob,"\n"); 2424: fprintf(ficresprobcov,"\n"); 2425: fprintf(ficresprobcor,"\n"); 2426: xp=vector(1,npar); 2427: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 2428: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); 2429: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); 2430: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); 2431: first=1; 2432: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { 2433: printf("Problem with gnuplot file: %s\n", optionfilegnuplot); 2434: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); 2435: exit(0); 2436: } 2437: else{ 2438: fprintf(ficgp,"\n# Routine varprob"); 2439: } 2440: if((fichtm=fopen(optionfilehtm,"a"))==NULL) { 2441: printf("Problem with html file: %s\n", optionfilehtm); 2442: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); 2443: exit(0); 2444: } 2445: else{ 2446: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); 2447: fprintf(fichtm,"\n"); 2448: 2449: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n"); 2450: 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"); 2451: 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"); 2452: 2453: } 2454: 2455: cov[1]=1; 2456: tj=cptcoveff; 2457: if (cptcovn<1) {tj=1;ncodemax[1]=1;} 2458: j1=0; 2459: for(t=1; t<=tj;t++){ 2460: for(i1=1; i1<=ncodemax[t];i1++){ 2461: j1++; 2462: if (cptcovn>0) { 2463: fprintf(ficresprob, "\n#********** Variable "); 2464: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2465: fprintf(ficresprob, "**********\n#"); 2466: fprintf(ficresprobcov, "\n#********** Variable "); 2467: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2468: fprintf(ficresprobcov, "**********\n#"); 2469: 2470: fprintf(ficgp, "\n#********** Variable "); 2471: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2472: fprintf(ficgp, "**********\n#"); 2473: 2474: 2475: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); 2476: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2477: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">"); 2478: 2479: fprintf(ficresprobcor, "\n#********** Variable "); 2480: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); 2481: fprintf(ficgp, "**********\n#"); 2482: } 2483: 2484: for (age=bage; age<=fage; age ++){ 2485: cov[2]=age; 2486: for (k=1; k<=cptcovn;k++) { 2487: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; 2488: } 2489: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; 2490: for (k=1; k<=cptcovprod;k++) 2491: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; 2492: 2493: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); 2494: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); 2495: gp=vector(1,(nlstate)*(nlstate+ndeath)); 2496: gm=vector(1,(nlstate)*(nlstate+ndeath)); 2497: 2498: for(theta=1; theta <=npar; theta++){ 2499: for(i=1; i<=npar; i++) 2500: xp[i] = x[i] + (i==theta ?delti[theta]:0); 2501: 2502: pmij(pmmij,cov,ncovmodel,xp,nlstate); 2503: 2504: k=0; 2505: for(i=1; i<= (nlstate); i++){ 2506: for(j=1; j<=(nlstate+ndeath);j++){ 2507: k=k+1; 2508: gp[k]=pmmij[i][j]; 2509: } 2510: } 2511: 2512: for(i=1; i<=npar; i++) 2513: xp[i] = x[i] - (i==theta ?delti[theta]:0); 2514: 2515: pmij(pmmij,cov,ncovmodel,xp,nlstate); 2516: k=0; 2517: for(i=1; i<=(nlstate); i++){ 2518: for(j=1; j<=(nlstate+ndeath);j++){ 2519: k=k+1; 2520: gm[k]=pmmij[i][j]; 2521: } 2522: } 2523: 2524: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 2525: gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; 2526: } 2527: 2528: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) 2529: for(theta=1; theta <=npar; theta++) 2530: trgradg[j][theta]=gradg[theta][j]; 2531: 2532: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 2533: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); 2534: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); 2535: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); 2536: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 2537: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); 2538: 2539: pmij(pmmij,cov,ncovmodel,x,nlstate); 2540: 2541: k=0; 2542: for(i=1; i<=(nlstate); i++){ 2543: for(j=1; j<=(nlstate+ndeath);j++){ 2544: k=k+1; 2545: mu[k][(int) age]=pmmij[i][j]; 2546: } 2547: } 2548: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) 2549: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) 2550: varpij[i][j][(int)age] = doldm[i][j]; 2551: 2552: /*printf("\n%d ",(int)age); 2553: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 2554: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 2555: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); 2556: }*/ 2557: 2558: fprintf(ficresprob,"\n%d ",(int)age); 2559: fprintf(ficresprobcov,"\n%d ",(int)age); 2560: fprintf(ficresprobcor,"\n%d ",(int)age); 2561: 2562: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) 2563: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); 2564: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ 2565: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); 2566: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); 2567: } 2568: i=0; 2569: for (k=1; k<=(nlstate);k++){ 2570: for (l=1; l<=(nlstate+ndeath);l++){ 2571: i=i++; 2572: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); 2573: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); 2574: for (j=1; j<=i;j++){ 2575: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); 2576: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); 2577: } 2578: } 2579: }/* end of loop for state */ 2580: } /* end of loop for age */ 2581: 2582: /* Confidence intervalle of pij */ 2583: /* 2584: fprintf(ficgp,"\nset noparametric;unset label"); 2585: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); 2586: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 2587: 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); 2588: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname); 2589: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); 2590: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); 2591: */ 2592: 2593: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ 2594: first1=1; 2595: for (k2=1; k2<=(nlstate);k2++){ 2596: for (l2=1; l2<=(nlstate+ndeath);l2++){ 2597: if(l2==k2) continue; 2598: j=(k2-1)*(nlstate+ndeath)+l2; 2599: for (k1=1; k1<=(nlstate);k1++){ 2600: for (l1=1; l1<=(nlstate+ndeath);l1++){ 2601: if(l1==k1) continue; 2602: i=(k1-1)*(nlstate+ndeath)+l1; 2603: if(i<=j) continue; 2604: for (age=bage; age<=fage; age ++){ 2605: if ((int)age %5==0){ 2606: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM; 2607: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM; 2608: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM; 2609: mu1=mu[i][(int) age]/stepm*YEARM ; 2610: mu2=mu[j][(int) age]/stepm*YEARM; 2611: c12=cv12/sqrt(v1*v2); 2612: /* Computing eigen value of matrix of covariance */ 2613: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 2614: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; 2615: /* Eigen vectors */ 2616: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); 2617: /*v21=sqrt(1.-v11*v11); *//* error */ 2618: v21=(lc1-v1)/cv12*v11; 2619: v12=-v21; 2620: v22=v11; 2621: tnalp=v21/v11; 2622: if(first1==1){ 2623: first1=0; 2624: 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); 2625: } 2626: 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); 2627: /*printf(fignu*/ 2628: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */ 2629: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ 2630: if(first==1){ 2631: first=0; 2632: fprintf(ficgp,"\nset parametric;unset label"); 2633: 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); 2634: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); 2635: 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); 2636: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2); 2637: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12); 2638: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2); 2639: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 2640: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 2641: 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",\ 2642: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 2643: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 2644: }else{ 2645: first=0; 2646: fprintf(fichtm," %d (%.3f),",(int) age, c12); 2647: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); 2648: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); 2649: 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",\ 2650: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ 2651: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); 2652: }/* if first */ 2653: } /* age mod 5 */ 2654: } /* end loop age */ 2655: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2); 2656: first=1; 2657: } /*l12 */ 2658: } /* k12 */ 2659: } /*l1 */ 2660: }/* k1 */ 2661: } /* loop covariates */ 2662: } 2663: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); 2664: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); 2665: free_vector(xp,1,npar); 2666: fclose(ficresprob); 2667: fclose(ficresprobcov); 2668: fclose(ficresprobcor); 2669: fclose(ficgp); 2670: fclose(fichtm); 2671: } 2672: 2673: 2674: /******************* Printing html file ***********/ 2675: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ 2676: int lastpass, int stepm, int weightopt, char model[],\ 2677: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ 2678: int popforecast, int estepm ,\ 2679: double jprev1, double mprev1,double anprev1, \ 2680: double jprev2, double mprev2,double anprev2){ 2681: int jj1, k1, i1, cpt; 2682: /*char optionfilehtm[FILENAMELENGTH];*/ 2683: if((fichtm=fopen(optionfilehtm,"a"))==NULL) { 2684: printf("Problem with %s \n",optionfilehtm), exit(0); 2685: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); 2686: } 2687: 2688: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n 2689: - 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 2690: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n 2691: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n 2692: - Life expectancies by age and initial health status (estepm=%2d months): 2693: <a href=\"e%s\">e%s</a> <br>\n</li>", \ 2694: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres); 2695: 2696: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); 2697: 2698: m=cptcoveff; 2699: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 2700: 2701: jj1=0; 2702: for(k1=1; k1<=m;k1++){ 2703: for(i1=1; i1<=ncodemax[k1];i1++){ 2704: jj1++; 2705: if (cptcovn > 0) { 2706: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 2707: for (cpt=1; cpt<=cptcoveff;cpt++) 2708: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 2709: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 2710: } 2711: /* Pij */ 2712: 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> 2713: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 2714: /* Quasi-incidences */ 2715: 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> 2716: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 2717: /* Stable prevalence in each health state */ 2718: for(cpt=1; cpt<nlstate;cpt++){ 2719: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> 2720: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); 2721: } 2722: for(cpt=1; cpt<=nlstate;cpt++) { 2723: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> 2724: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); 2725: } 2726: fprintf(fichtm,"\n<br>- Total life expectancy by age and 2727: health expectancies in states (1) and (2): e%s%d.png<br> 2728: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 2729: } /* end i1 */ 2730: }/* End k1 */ 2731: fprintf(fichtm,"</ul>"); 2732: 2733: 2734: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n 2735: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n 2736: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n 2737: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n 2738: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n 2739: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 2740: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n 2741: - 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); 2742: 2743: if(popforecast==1) fprintf(fichtm,"\n 2744: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n 2745: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n 2746: <br>",fileres,fileres,fileres,fileres); 2747: else 2748: 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); 2749: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>"); 2750: 2751: m=cptcoveff; 2752: if (cptcovn < 1) {m=1;ncodemax[1]=1;} 2753: 2754: jj1=0; 2755: for(k1=1; k1<=m;k1++){ 2756: for(i1=1; i1<=ncodemax[k1];i1++){ 2757: jj1++; 2758: if (cptcovn > 0) { 2759: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates"); 2760: for (cpt=1; cpt<=cptcoveff;cpt++) 2761: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); 2762: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); 2763: } 2764: for(cpt=1; cpt<=nlstate;cpt++) { 2765: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident 2766: interval) in state (%d): v%s%d%d.png <br> 2767: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); 2768: } 2769: } /* end i1 */ 2770: }/* End k1 */ 2771: fprintf(fichtm,"</ul>"); 2772: fclose(fichtm); 2773: } 2774: 2775: /******************* Gnuplot file **************/ 2776: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ 2777: 2778: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; 2779: int ng; 2780: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { 2781: printf("Problem with file %s",optionfilegnuplot); 2782: fprintf(ficlog,"Problem with file %s",optionfilegnuplot); 2783: } 2784: 2785: /*#ifdef windows */ 2786: fprintf(ficgp,"cd \"%s\" \n",pathc); 2787: /*#endif */ 2788: m=pow(2,cptcoveff); 2789: 2790: /* 1eme*/ 2791: for (cpt=1; cpt<= nlstate ; cpt ++) { 2792: for (k1=1; k1<= m ; k1 ++) { 2793: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); 2794: 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); 2795: 2796: for (i=1; i<= nlstate ; i ++) { 2797: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 2798: else fprintf(ficgp," \%%*lf (\%%*lf)"); 2799: } 2800: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1); 2801: for (i=1; i<= nlstate ; i ++) { 2802: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 2803: else fprintf(ficgp," \%%*lf (\%%*lf)"); 2804: } 2805: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 2806: for (i=1; i<= nlstate ; i ++) { 2807: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); 2808: else fprintf(ficgp," \%%*lf (\%%*lf)"); 2809: } 2810: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1)); 2811: } 2812: } 2813: /*2 eme*/ 2814: 2815: for (k1=1; k1<= m ; k1 ++) { 2816: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1); 2817: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); 2818: 2819: for (i=1; i<= nlstate+1 ; i ++) { 2820: k=2*i; 2821: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1); 2822: for (j=1; j<= nlstate+1 ; j ++) { 2823: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 2824: else fprintf(ficgp," \%%*lf (\%%*lf)"); 2825: } 2826: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); 2827: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); 2828: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1); 2829: for (j=1; j<= nlstate+1 ; j ++) { 2830: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 2831: else fprintf(ficgp," \%%*lf (\%%*lf)"); 2832: } 2833: fprintf(ficgp,"\" t\"\" w l 0,"); 2834: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1); 2835: for (j=1; j<= nlstate+1 ; j ++) { 2836: if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); 2837: else fprintf(ficgp," \%%*lf (\%%*lf)"); 2838: } 2839: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); 2840: else fprintf(ficgp,"\" t\"\" w l 0,"); 2841: } 2842: } 2843: 2844: /*3eme*/ 2845: 2846: for (k1=1; k1<= m ; k1 ++) { 2847: for (cpt=1; cpt<= nlstate ; cpt ++) { 2848: k=2+nlstate*(2*cpt-2); 2849: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); 2850: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); 2851: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 2852: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 2853: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 2854: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); 2855: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); 2856: fprintf(ficgp,"\" t \"e%d1\" w l",cpt); 2857: 2858: */ 2859: for (i=1; i< nlstate ; i ++) { 2860: 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); 2861: 2862: } 2863: } 2864: } 2865: 2866: /* CV preval stat */ 2867: for (k1=1; k1<= m ; k1 ++) { 2868: for (cpt=1; cpt<nlstate ; cpt ++) { 2869: k=3; 2870: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); 2871: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1); 2872: 2873: for (i=1; i< nlstate ; i ++) 2874: fprintf(ficgp,"+$%d",k+i+1); 2875: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); 2876: 2877: l=3+(nlstate+ndeath)*cpt; 2878: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1); 2879: for (i=1; i< nlstate ; i ++) { 2880: l=3+(nlstate+ndeath)*cpt; 2881: fprintf(ficgp,"+$%d",l+i+1); 2882: } 2883: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); 2884: } 2885: } 2886: 2887: /* proba elementaires */ 2888: for(i=1,jk=1; i <=nlstate; i++){ 2889: for(k=1; k <=(nlstate+ndeath); k++){ 2890: if (k != i) { 2891: for(j=1; j <=ncovmodel; j++){ 2892: fprintf(ficgp,"p%d=%f ",jk,p[jk]); 2893: jk++; 2894: fprintf(ficgp,"\n"); 2895: } 2896: } 2897: } 2898: } 2899: 2900: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ 2901: for(jk=1; jk <=m; jk++) { 2902: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 2903: if (ng==2) 2904: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); 2905: else 2906: fprintf(ficgp,"\nset title \"Probability\"\n"); 2907: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); 2908: i=1; 2909: for(k2=1; k2<=nlstate; k2++) { 2910: k3=i; 2911: for(k=1; k<=(nlstate+ndeath); k++) { 2912: if (k != k2){ 2913: if(ng==2) 2914: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); 2915: else 2916: fprintf(ficgp," exp(p%d+p%d*x",i,i+1); 2917: ij=1; 2918: for(j=3; j <=ncovmodel; j++) { 2919: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { 2920: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 2921: ij++; 2922: } 2923: else 2924: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 2925: } 2926: fprintf(ficgp,")/(1"); 2927: 2928: for(k1=1; k1 <=nlstate; k1++){ 2929: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); 2930: ij=1; 2931: for(j=3; j <=ncovmodel; j++){ 2932: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { 2933: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); 2934: ij++; 2935: } 2936: else 2937: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); 2938: } 2939: fprintf(ficgp,")"); 2940: } 2941: fprintf(ficgp,") t \"p%d%d\" ", k2,k); 2942: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,","); 2943: i=i+ncovmodel; 2944: } 2945: } /* end k */ 2946: } /* end k2 */ 2947: } /* end jk */ 2948: } /* end ng */ 2949: fclose(ficgp); 2950: } /* end gnuplot */ 2951: 2952: 2953: /*************** Moving average **************/ 2954: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ 2955: 2956: int i, cpt, cptcod; 2957: int modcovmax =1; 2958: int mobilavrange, mob; 2959: double age; 2960: 2961: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 2962: a covariate has 2 modalities */ 2963: if (cptcovn<1) modcovmax=1; /* At least 1 pass */ 2964: 2965: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ 2966: if(mobilav==1) mobilavrange=5; /* default */ 2967: else mobilavrange=mobilav; 2968: for (age=bage; age<=fage; age++) 2969: for (i=1; i<=nlstate;i++) 2970: for (cptcod=1;cptcod<=modcovmax;cptcod++) 2971: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; 2972: /* We keep the original values on the extreme ages bage, fage and for 2973: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 2974: we use a 5 terms etc. until the borders are no more concerned. 2975: */ 2976: for (mob=3;mob <=mobilavrange;mob=mob+2){ 2977: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ 2978: for (i=1; i<=nlstate;i++){ 2979: for (cptcod=1;cptcod<=modcovmax;cptcod++){ 2980: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; 2981: for (cpt=1;cpt<=(mob-1)/2;cpt++){ 2982: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; 2983: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; 2984: } 2985: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; 2986: } 2987: } 2988: }/* end age */ 2989: }/* end mob */ 2990: }else return -1; 2991: return 0; 2992: }/* End movingaverage */ 2993: 2994: 2995: /************** Forecasting ******************/ 2996: 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){ 2997: 2998: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 2999: int *popage; 3000: double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; 3001: double *popeffectif,*popcount; 3002: double ***p3mat; 3003: double ***mobaverage; 3004: char fileresf[FILENAMELENGTH]; 3005: 3006: agelim=AGESUP; 3007: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; 3008: 3009: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); 3010: 3011: 3012: strcpy(fileresf,"f"); 3013: strcat(fileresf,fileres); 3014: if((ficresf=fopen(fileresf,"w"))==NULL) { 3015: printf("Problem with forecast resultfile: %s\n", fileresf); 3016: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); 3017: } 3018: printf("Computing forecasting: result on file '%s' \n", fileresf); 3019: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); 3020: 3021: if (cptcoveff==0) ncodemax[cptcoveff]=1; 3022: 3023: if (mobilav!=0) { 3024: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3025: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 3026: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3027: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3028: } 3029: } 3030: 3031: stepsize=(int) (stepm+YEARM-1)/YEARM; 3032: if (stepm<=12) stepsize=1; 3033: 3034: agelim=AGESUP; 3035: 3036: hstepm=1; 3037: hstepm=hstepm/stepm; 3038: yp1=modf(dateintmean,&yp); 3039: anprojmean=yp; 3040: yp2=modf((yp1*12),&yp); 3041: mprojmean=yp; 3042: yp1=modf((yp2*30.5),&yp); 3043: jprojmean=yp; 3044: if(jprojmean==0) jprojmean=1; 3045: if(mprojmean==0) jprojmean=1; 3046: 3047: fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 3048: 3049: for(cptcov=1;cptcov<=i2;cptcov++){ 3050: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 3051: k=k+1; 3052: fprintf(ficresf,"\n#******"); 3053: for(j=1;j<=cptcoveff;j++) { 3054: fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 3055: } 3056: fprintf(ficresf,"******\n"); 3057: fprintf(ficresf,"# StartingAge FinalAge"); 3058: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j); 3059: 3060: 3061: for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 3062: fprintf(ficresf,"\n"); 3063: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt); 3064: 3065: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 3066: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 3067: nhstepm = nhstepm/hstepm; 3068: 3069: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3070: oldm=oldms;savm=savms; 3071: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 3072: 3073: for (h=0; h<=nhstepm; h++){ 3074: if (h==(int) (calagedate+YEARM*cpt)) { 3075: fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); 3076: } 3077: for(j=1; j<=nlstate+ndeath;j++) { 3078: kk1=0.;kk2=0; 3079: for(i=1; i<=nlstate;i++) { 3080: if (mobilav==1) 3081: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 3082: else { 3083: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 3084: } 3085: 3086: } 3087: if (h==(int)(calagedate+12*cpt)){ 3088: fprintf(ficresf," %.3f", kk1); 3089: 3090: } 3091: } 3092: } 3093: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3094: } 3095: } 3096: } 3097: } 3098: 3099: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3100: 3101: fclose(ficresf); 3102: } 3103: /************** Forecasting ******************/ 3104: 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){ 3105: 3106: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; 3107: int *popage; 3108: double calagedate, agelim, kk1, kk2; 3109: double *popeffectif,*popcount; 3110: double ***p3mat,***tabpop,***tabpopprev; 3111: double ***mobaverage; 3112: char filerespop[FILENAMELENGTH]; 3113: 3114: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3115: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3116: agelim=AGESUP; 3117: calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; 3118: 3119: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); 3120: 3121: 3122: strcpy(filerespop,"pop"); 3123: strcat(filerespop,fileres); 3124: if((ficrespop=fopen(filerespop,"w"))==NULL) { 3125: printf("Problem with forecast resultfile: %s\n", filerespop); 3126: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); 3127: } 3128: printf("Computing forecasting: result on file '%s' \n", filerespop); 3129: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); 3130: 3131: if (cptcoveff==0) ncodemax[cptcoveff]=1; 3132: 3133: if (mobilav!=0) { 3134: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3135: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ 3136: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 3137: printf(" Error in movingaverage mobilav=%d\n",mobilav); 3138: } 3139: } 3140: 3141: stepsize=(int) (stepm+YEARM-1)/YEARM; 3142: if (stepm<=12) stepsize=1; 3143: 3144: agelim=AGESUP; 3145: 3146: hstepm=1; 3147: hstepm=hstepm/stepm; 3148: 3149: if (popforecast==1) { 3150: if((ficpop=fopen(popfile,"r"))==NULL) { 3151: printf("Problem with population file : %s\n",popfile);exit(0); 3152: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); 3153: } 3154: popage=ivector(0,AGESUP); 3155: popeffectif=vector(0,AGESUP); 3156: popcount=vector(0,AGESUP); 3157: 3158: i=1; 3159: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; 3160: 3161: imx=i; 3162: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; 3163: } 3164: 3165: for(cptcov=1;cptcov<=i2;cptcov++){ 3166: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ 3167: k=k+1; 3168: fprintf(ficrespop,"\n#******"); 3169: for(j=1;j<=cptcoveff;j++) { 3170: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 3171: } 3172: fprintf(ficrespop,"******\n"); 3173: fprintf(ficrespop,"# Age"); 3174: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); 3175: if (popforecast==1) fprintf(ficrespop," [Population]"); 3176: 3177: for (cpt=0; cpt<=0;cpt++) { 3178: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 3179: 3180: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 3181: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 3182: nhstepm = nhstepm/hstepm; 3183: 3184: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3185: oldm=oldms;savm=savms; 3186: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 3187: 3188: for (h=0; h<=nhstepm; h++){ 3189: if (h==(int) (calagedate+YEARM*cpt)) { 3190: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 3191: } 3192: for(j=1; j<=nlstate+ndeath;j++) { 3193: kk1=0.;kk2=0; 3194: for(i=1; i<=nlstate;i++) { 3195: if (mobilav==1) 3196: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; 3197: else { 3198: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; 3199: } 3200: } 3201: if (h==(int)(calagedate+12*cpt)){ 3202: tabpop[(int)(agedeb)][j][cptcod]=kk1; 3203: /*fprintf(ficrespop," %.3f", kk1); 3204: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ 3205: } 3206: } 3207: for(i=1; i<=nlstate;i++){ 3208: kk1=0.; 3209: for(j=1; j<=nlstate;j++){ 3210: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 3211: } 3212: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; 3213: } 3214: 3215: if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 3216: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); 3217: } 3218: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3219: } 3220: } 3221: 3222: /******/ 3223: 3224: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 3225: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); 3226: for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 3227: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 3228: nhstepm = nhstepm/hstepm; 3229: 3230: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3231: oldm=oldms;savm=savms; 3232: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 3233: for (h=0; h<=nhstepm; h++){ 3234: if (h==(int) (calagedate+YEARM*cpt)) { 3235: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); 3236: } 3237: for(j=1; j<=nlstate+ndeath;j++) { 3238: kk1=0.;kk2=0; 3239: for(i=1; i<=nlstate;i++) { 3240: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; 3241: } 3242: if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 3243: } 3244: } 3245: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 3246: } 3247: } 3248: } 3249: } 3250: 3251: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3252: 3253: if (popforecast==1) { 3254: free_ivector(popage,0,AGESUP); 3255: free_vector(popeffectif,0,AGESUP); 3256: free_vector(popcount,0,AGESUP); 3257: } 3258: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3259: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 3260: fclose(ficrespop); 3261: } 3262: 3263: /***********************************************/ 3264: /**************** Main Program *****************/ 3265: /***********************************************/ 3266: 3267: int main(int argc, char *argv[]) 3268: { 3269: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); 3270: int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod; 3271: double agedeb, agefin,hf; 3272: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; 3273: 3274: double fret; 3275: double **xi,tmp,delta; 3276: 3277: double dum; /* Dummy variable */ 3278: double ***p3mat; 3279: double ***mobaverage; 3280: int *indx; 3281: char line[MAXLINE], linepar[MAXLINE]; 3282: char path[80],pathc[80],pathcd[80],pathtot[80],model[80]; 3283: int firstobs=1, lastobs=10; 3284: int sdeb, sfin; /* Status at beginning and end */ 3285: int c, h , cpt,l; 3286: int ju,jl, mi; 3287: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; 3288: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 3289: int mobilav=0,popforecast=0; 3290: int hstepm, nhstepm; 3291: double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; 3292: 3293: double bage, fage, age, agelim, agebase; 3294: double ftolpl=FTOL; 3295: double **prlim; 3296: double *severity; 3297: double ***param; /* Matrix of parameters */ 3298: double *p; 3299: double **matcov; /* Matrix of covariance */ 3300: double ***delti3; /* Scale */ 3301: double *delti; /* Scale */ 3302: double ***eij, ***vareij; 3303: double **varpl; /* Variances of prevalence limits by age */ 3304: double *epj, vepp; 3305: double kk1, kk2; 3306: double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; 3307: 3308: char *alph[]={"a","a","b","c","d","e"}, str[4]; 3309: 3310: 3311: char z[1]="c", occ; 3312: #include <sys/time.h> 3313: #include <time.h> 3314: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; 3315: 3316: /* long total_usecs; 3317: struct timeval start_time, end_time; 3318: 3319: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ 3320: getcwd(pathcd, size); 3321: 3322: printf("\n%s",version); 3323: if(argc <=1){ 3324: printf("\nEnter the parameter file name: "); 3325: scanf("%s",pathtot); 3326: } 3327: else{ 3328: strcpy(pathtot,argv[1]); 3329: } 3330: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/ 3331: /*cygwin_split_path(pathtot,path,optionfile); 3332: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ 3333: /* cutv(path,optionfile,pathtot,'\\');*/ 3334: 3335: split(pathtot,path,optionfile,optionfilext,optionfilefiname); 3336: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 3337: chdir(path); 3338: replace(pathc,path); 3339: 3340: /*-------- arguments in the command line --------*/ 3341: 3342: /* Log file */ 3343: strcat(filelog, optionfilefiname); 3344: strcat(filelog,".log"); /* */ 3345: if((ficlog=fopen(filelog,"w"))==NULL) { 3346: printf("Problem with logfile %s\n",filelog); 3347: goto end; 3348: } 3349: fprintf(ficlog,"Log filename:%s\n",filelog); 3350: fprintf(ficlog,"\n%s",version); 3351: fprintf(ficlog,"\nEnter the parameter file name: "); 3352: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); 3353: fflush(ficlog); 3354: 3355: /* */ 3356: strcpy(fileres,"r"); 3357: strcat(fileres, optionfilefiname); 3358: strcat(fileres,".txt"); /* Other files have txt extension */ 3359: 3360: /*---------arguments file --------*/ 3361: 3362: if((ficpar=fopen(optionfile,"r"))==NULL) { 3363: printf("Problem with optionfile %s\n",optionfile); 3364: fprintf(ficlog,"Problem with optionfile %s\n",optionfile); 3365: goto end; 3366: } 3367: 3368: strcpy(filereso,"o"); 3369: strcat(filereso,fileres); 3370: if((ficparo=fopen(filereso,"w"))==NULL) { 3371: printf("Problem with Output resultfile: %s\n", filereso); 3372: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); 3373: goto end; 3374: } 3375: 3376: /* Reads comments: lines beginning with '#' */ 3377: while((c=getc(ficpar))=='#' && c!= EOF){ 3378: ungetc(c,ficpar); 3379: fgets(line, MAXLINE, ficpar); 3380: puts(line); 3381: fputs(line,ficparo); 3382: } 3383: ungetc(c,ficpar); 3384: 3385: 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); 3386: 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); 3387: 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); 3388: while((c=getc(ficpar))=='#' && c!= EOF){ 3389: ungetc(c,ficpar); 3390: fgets(line, MAXLINE, ficpar); 3391: puts(line); 3392: fputs(line,ficparo); 3393: } 3394: ungetc(c,ficpar); 3395: 3396: 3397: covar=matrix(0,NCOVMAX,1,n); 3398: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ 3399: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; 3400: 3401: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */ 3402: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ 3403: 3404: /* Read guess parameters */ 3405: /* Reads comments: lines beginning with '#' */ 3406: while((c=getc(ficpar))=='#' && c!= EOF){ 3407: ungetc(c,ficpar); 3408: fgets(line, MAXLINE, ficpar); 3409: puts(line); 3410: fputs(line,ficparo); 3411: } 3412: ungetc(c,ficpar); 3413: 3414: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 3415: for(i=1; i <=nlstate; i++) 3416: for(j=1; j <=nlstate+ndeath-1; j++){ 3417: fscanf(ficpar,"%1d%1d",&i1,&j1); 3418: fprintf(ficparo,"%1d%1d",i1,j1); 3419: if(mle==1) 3420: printf("%1d%1d",i,j); 3421: fprintf(ficlog,"%1d%1d",i,j); 3422: for(k=1; k<=ncovmodel;k++){ 3423: fscanf(ficpar," %lf",¶m[i][j][k]); 3424: if(mle==1){ 3425: printf(" %lf",param[i][j][k]); 3426: fprintf(ficlog," %lf",param[i][j][k]); 3427: } 3428: else 3429: fprintf(ficlog," %lf",param[i][j][k]); 3430: fprintf(ficparo," %lf",param[i][j][k]); 3431: } 3432: fscanf(ficpar,"\n"); 3433: if(mle==1) 3434: printf("\n"); 3435: fprintf(ficlog,"\n"); 3436: fprintf(ficparo,"\n"); 3437: } 3438: 3439: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 3440: 3441: p=param[1][1]; 3442: 3443: /* Reads comments: lines beginning with '#' */ 3444: while((c=getc(ficpar))=='#' && c!= EOF){ 3445: ungetc(c,ficpar); 3446: fgets(line, MAXLINE, ficpar); 3447: puts(line); 3448: fputs(line,ficparo); 3449: } 3450: ungetc(c,ficpar); 3451: 3452: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); 3453: delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ 3454: for(i=1; i <=nlstate; i++){ 3455: for(j=1; j <=nlstate+ndeath-1; j++){ 3456: fscanf(ficpar,"%1d%1d",&i1,&j1); 3457: printf("%1d%1d",i,j); 3458: fprintf(ficparo,"%1d%1d",i1,j1); 3459: for(k=1; k<=ncovmodel;k++){ 3460: fscanf(ficpar,"%le",&delti3[i][j][k]); 3461: printf(" %le",delti3[i][j][k]); 3462: fprintf(ficparo," %le",delti3[i][j][k]); 3463: } 3464: fscanf(ficpar,"\n"); 3465: printf("\n"); 3466: fprintf(ficparo,"\n"); 3467: } 3468: } 3469: delti=delti3[1][1]; 3470: 3471: /* Reads comments: lines beginning with '#' */ 3472: while((c=getc(ficpar))=='#' && c!= EOF){ 3473: ungetc(c,ficpar); 3474: fgets(line, MAXLINE, ficpar); 3475: puts(line); 3476: fputs(line,ficparo); 3477: } 3478: ungetc(c,ficpar); 3479: 3480: matcov=matrix(1,npar,1,npar); 3481: for(i=1; i <=npar; i++){ 3482: fscanf(ficpar,"%s",&str); 3483: if(mle==1) 3484: printf("%s",str); 3485: fprintf(ficlog,"%s",str); 3486: fprintf(ficparo,"%s",str); 3487: for(j=1; j <=i; j++){ 3488: fscanf(ficpar," %le",&matcov[i][j]); 3489: if(mle==1){ 3490: printf(" %.5le",matcov[i][j]); 3491: fprintf(ficlog," %.5le",matcov[i][j]); 3492: } 3493: else 3494: fprintf(ficlog," %.5le",matcov[i][j]); 3495: fprintf(ficparo," %.5le",matcov[i][j]); 3496: } 3497: fscanf(ficpar,"\n"); 3498: if(mle==1) 3499: printf("\n"); 3500: fprintf(ficlog,"\n"); 3501: fprintf(ficparo,"\n"); 3502: } 3503: for(i=1; i <=npar; i++) 3504: for(j=i+1;j<=npar;j++) 3505: matcov[i][j]=matcov[j][i]; 3506: 3507: if(mle==1) 3508: printf("\n"); 3509: fprintf(ficlog,"\n"); 3510: 3511: 3512: /*-------- Rewriting paramater file ----------*/ 3513: strcpy(rfileres,"r"); /* "Rparameterfile */ 3514: strcat(rfileres,optionfilefiname); /* Parameter file first name*/ 3515: strcat(rfileres,"."); /* */ 3516: strcat(rfileres,optionfilext); /* Other files have txt extension */ 3517: if((ficres =fopen(rfileres,"w"))==NULL) { 3518: printf("Problem writing new parameter file: %s\n", fileres);goto end; 3519: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; 3520: } 3521: fprintf(ficres,"#%s\n",version); 3522: 3523: /*-------- data file ----------*/ 3524: if((fic=fopen(datafile,"r"))==NULL) { 3525: printf("Problem with datafile: %s\n", datafile);goto end; 3526: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; 3527: } 3528: 3529: n= lastobs; 3530: severity = vector(1,maxwav); 3531: outcome=imatrix(1,maxwav+1,1,n); 3532: num=ivector(1,n); 3533: moisnais=vector(1,n); 3534: annais=vector(1,n); 3535: moisdc=vector(1,n); 3536: andc=vector(1,n); 3537: agedc=vector(1,n); 3538: cod=ivector(1,n); 3539: weight=vector(1,n); 3540: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ 3541: mint=matrix(1,maxwav,1,n); 3542: anint=matrix(1,maxwav,1,n); 3543: s=imatrix(1,maxwav+1,1,n); 3544: tab=ivector(1,NCOVMAX); 3545: ncodemax=ivector(1,8); 3546: 3547: i=1; 3548: while (fgets(line, MAXLINE, fic) != NULL) { 3549: if ((i >= firstobs) && (i <=lastobs)) { 3550: 3551: for (j=maxwav;j>=1;j--){ 3552: cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 3553: strcpy(line,stra); 3554: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); 3555: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); 3556: } 3557: 3558: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); 3559: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); 3560: 3561: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); 3562: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); 3563: 3564: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); 3565: for (j=ncovcol;j>=1;j--){ 3566: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); 3567: } 3568: num[i]=atol(stra); 3569: 3570: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ 3571: 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;}*/ 3572: 3573: i=i+1; 3574: } 3575: } 3576: /* printf("ii=%d", ij); 3577: scanf("%d",i);*/ 3578: imx=i-1; /* Number of individuals */ 3579: 3580: /* for (i=1; i<=imx; i++){ 3581: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3; 3582: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3; 3583: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3; 3584: }*/ 3585: /* for (i=1; i<=imx; i++){ 3586: if (s[4][i]==9) s[4][i]=-1; 3587: 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]));}*/ 3588: 3589: 3590: /* Calculation of the number of parameter from char model*/ 3591: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ 3592: Tprod=ivector(1,15); 3593: Tvaraff=ivector(1,15); 3594: Tvard=imatrix(1,15,1,2); 3595: Tage=ivector(1,15); 3596: 3597: if (strlen(model) >1){ /* If there is at least 1 covariate */ 3598: j=0, j1=0, k1=1, k2=1; 3599: j=nbocc(model,'+'); /* j=Number of '+' */ 3600: j1=nbocc(model,'*'); /* j1=Number of '*' */ 3601: cptcovn=j+1; 3602: cptcovprod=j1; /*Number of products */ 3603: 3604: strcpy(modelsav,model); 3605: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ 3606: printf("Error. Non available option model=%s ",model); 3607: fprintf(ficlog,"Error. Non available option model=%s ",model); 3608: goto end; 3609: } 3610: 3611: /* This loop fills the array Tvar from the string 'model'.*/ 3612: 3613: for(i=(j+1); i>=1;i--){ 3614: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 3615: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ 3616: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ 3617: /*scanf("%d",i);*/ 3618: if (strchr(strb,'*')) { /* Model includes a product */ 3619: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ 3620: if (strcmp(strc,"age")==0) { /* Vn*age */ 3621: cptcovprod--; 3622: cutv(strb,stre,strd,'V'); 3623: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ 3624: cptcovage++; 3625: Tage[cptcovage]=i; 3626: /*printf("stre=%s ", stre);*/ 3627: } 3628: else if (strcmp(strd,"age")==0) { /* or age*Vn */ 3629: cptcovprod--; 3630: cutv(strb,stre,strc,'V'); 3631: Tvar[i]=atoi(stre); 3632: cptcovage++; 3633: Tage[cptcovage]=i; 3634: } 3635: else { /* Age is not in the model */ 3636: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/ 3637: Tvar[i]=ncovcol+k1; 3638: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ 3639: Tprod[k1]=i; 3640: Tvard[k1][1]=atoi(strc); /* m*/ 3641: Tvard[k1][2]=atoi(stre); /* n */ 3642: Tvar[cptcovn+k2]=Tvard[k1][1]; 3643: Tvar[cptcovn+k2+1]=Tvard[k1][2]; 3644: for (k=1; k<=lastobs;k++) 3645: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; 3646: k1++; 3647: k2=k2+2; 3648: } 3649: } 3650: else { /* no more sum */ 3651: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ 3652: /* scanf("%d",i);*/ 3653: cutv(strd,strc,strb,'V'); 3654: Tvar[i]=atoi(strc); 3655: } 3656: strcpy(modelsav,stra); 3657: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); 3658: scanf("%d",i);*/ 3659: } /* end of loop + */ 3660: } /* end model */ 3661: 3662: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. 3663: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ 3664: 3665: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); 3666: printf("cptcovprod=%d ", cptcovprod); 3667: fprintf(ficlog,"cptcovprod=%d ", cptcovprod); 3668: 3669: scanf("%d ",i); 3670: fclose(fic);*/ 3671: 3672: /* if(mle==1){*/ 3673: if (weightopt != 1) { /* Maximisation without weights*/ 3674: for(i=1;i<=n;i++) weight[i]=1.0; 3675: } 3676: /*-calculation of age at interview from date of interview and age at death -*/ 3677: agev=matrix(1,maxwav,1,imx); 3678: 3679: for (i=1; i<=imx; i++) { 3680: for(m=2; (m<= maxwav); m++) { 3681: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ 3682: anint[m][i]=9999; 3683: s[m][i]=-1; 3684: } 3685: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; 3686: } 3687: } 3688: 3689: for (i=1; i<=imx; i++) { 3690: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); 3691: for(m=1; (m<= maxwav); m++){ 3692: if(s[m][i] >0){ 3693: if (s[m][i] >= nlstate+1) { 3694: if(agedc[i]>0) 3695: if(moisdc[i]!=99 && andc[i]!=9999) 3696: agev[m][i]=agedc[i]; 3697: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ 3698: else { 3699: if (andc[i]!=9999){ 3700: printf("Warning negative age at death: %d line:%d\n",num[i],i); 3701: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); 3702: agev[m][i]=-1; 3703: } 3704: } 3705: } 3706: else if(s[m][i] !=9){ /* Should no more exist */ 3707: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); 3708: if(mint[m][i]==99 || anint[m][i]==9999) 3709: agev[m][i]=1; 3710: else if(agev[m][i] <agemin){ 3711: agemin=agev[m][i]; 3712: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/ 3713: } 3714: else if(agev[m][i] >agemax){ 3715: agemax=agev[m][i]; 3716: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ 3717: } 3718: /*agev[m][i]=anint[m][i]-annais[i];*/ 3719: /* agev[m][i] = age[i]+2*m;*/ 3720: } 3721: else { /* =9 */ 3722: agev[m][i]=1; 3723: s[m][i]=-1; 3724: } 3725: } 3726: else /*= 0 Unknown */ 3727: agev[m][i]=1; 3728: } 3729: 3730: } 3731: for (i=1; i<=imx; i++) { 3732: for(m=1; (m<= maxwav); m++){ 3733: if (s[m][i] > (nlstate+ndeath)) { 3734: 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); 3735: 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); 3736: goto end; 3737: } 3738: } 3739: } 3740: 3741: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 3742: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 3743: 3744: free_vector(severity,1,maxwav); 3745: free_imatrix(outcome,1,maxwav+1,1,n); 3746: free_vector(moisnais,1,n); 3747: free_vector(annais,1,n); 3748: /* free_matrix(mint,1,maxwav,1,n); 3749: free_matrix(anint,1,maxwav,1,n);*/ 3750: free_vector(moisdc,1,n); 3751: free_vector(andc,1,n); 3752: 3753: 3754: wav=ivector(1,imx); 3755: dh=imatrix(1,lastpass-firstpass+1,1,imx); 3756: bh=imatrix(1,lastpass-firstpass+1,1,imx); 3757: mw=imatrix(1,lastpass-firstpass+1,1,imx); 3758: 3759: /* Concatenates waves */ 3760: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); 3761: 3762: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ 3763: 3764: Tcode=ivector(1,100); 3765: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 3766: ncodemax[1]=1; 3767: if (cptcovn > 0) tricode(Tvar,nbcode,imx); 3768: 3769: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 3770: the estimations*/ 3771: h=0; 3772: m=pow(2,cptcoveff); 3773: 3774: for(k=1;k<=cptcoveff; k++){ 3775: for(i=1; i <=(m/pow(2,k));i++){ 3776: for(j=1; j <= ncodemax[k]; j++){ 3777: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ 3778: h++; 3779: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; 3780: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ 3781: } 3782: } 3783: } 3784: } 3785: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 3786: codtab[1][2]=1;codtab[2][2]=2; */ 3787: /* for(i=1; i <=m ;i++){ 3788: for(k=1; k <=cptcovn; k++){ 3789: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); 3790: } 3791: printf("\n"); 3792: } 3793: scanf("%d",i);*/ 3794: 3795: /* Calculates basic frequencies. Computes observed prevalence at single age 3796: and prints on file fileres'p'. */ 3797: 3798: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 3799: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 3800: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 3801: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ 3802: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ 3803: 3804: 3805: /* For Powell, parameters are in a vector p[] starting at p[1] 3806: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ 3807: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ 3808: 3809: if(mle>=1){ /* Could be 1 or 2 */ 3810: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); 3811: } 3812: 3813: /*--------- results files --------------*/ 3814: 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); 3815: 3816: 3817: jk=1; 3818: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 3819: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 3820: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); 3821: for(i=1,jk=1; i <=nlstate; i++){ 3822: for(k=1; k <=(nlstate+ndeath); k++){ 3823: if (k != i) 3824: { 3825: printf("%d%d ",i,k); 3826: fprintf(ficlog,"%d%d ",i,k); 3827: fprintf(ficres,"%1d%1d ",i,k); 3828: for(j=1; j <=ncovmodel; j++){ 3829: printf("%f ",p[jk]); 3830: fprintf(ficlog,"%f ",p[jk]); 3831: fprintf(ficres,"%f ",p[jk]); 3832: jk++; 3833: } 3834: printf("\n"); 3835: fprintf(ficlog,"\n"); 3836: fprintf(ficres,"\n"); 3837: } 3838: } 3839: } 3840: if(mle==1){ 3841: /* Computing hessian and covariance matrix */ 3842: ftolhess=ftol; /* Usually correct */ 3843: hesscov(matcov, p, npar, delti, ftolhess, func); 3844: } 3845: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); 3846: printf("# Scales (for hessian or gradient estimation)\n"); 3847: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); 3848: for(i=1,jk=1; i <=nlstate; i++){ 3849: for(j=1; j <=nlstate+ndeath; j++){ 3850: if (j!=i) { 3851: fprintf(ficres,"%1d%1d",i,j); 3852: printf("%1d%1d",i,j); 3853: fprintf(ficlog,"%1d%1d",i,j); 3854: for(k=1; k<=ncovmodel;k++){ 3855: printf(" %.5e",delti[jk]); 3856: fprintf(ficlog," %.5e",delti[jk]); 3857: fprintf(ficres," %.5e",delti[jk]); 3858: jk++; 3859: } 3860: printf("\n"); 3861: fprintf(ficlog,"\n"); 3862: fprintf(ficres,"\n"); 3863: } 3864: } 3865: } 3866: 3867: 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"); 3868: if(mle==1) 3869: 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"); 3870: 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"); 3871: for(i=1,k=1;i<=npar;i++){ 3872: /* if (k>nlstate) k=1; 3873: i1=(i-1)/(ncovmodel*nlstate)+1; 3874: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); 3875: printf("%s%d%d",alph[k],i1,tab[i]); 3876: */ 3877: fprintf(ficres,"%3d",i); 3878: if(mle==1) 3879: printf("%3d",i); 3880: fprintf(ficlog,"%3d",i); 3881: for(j=1; j<=i;j++){ 3882: fprintf(ficres," %.5e",matcov[i][j]); 3883: if(mle==1) 3884: printf(" %.5e",matcov[i][j]); 3885: fprintf(ficlog," %.5e",matcov[i][j]); 3886: } 3887: fprintf(ficres,"\n"); 3888: if(mle==1) 3889: printf("\n"); 3890: fprintf(ficlog,"\n"); 3891: k++; 3892: } 3893: 3894: while((c=getc(ficpar))=='#' && c!= EOF){ 3895: ungetc(c,ficpar); 3896: fgets(line, MAXLINE, ficpar); 3897: puts(line); 3898: fputs(line,ficparo); 3899: } 3900: ungetc(c,ficpar); 3901: 3902: estepm=0; 3903: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); 3904: if (estepm==0 || estepm < stepm) estepm=stepm; 3905: if (fage <= 2) { 3906: bage = ageminpar; 3907: fage = agemaxpar; 3908: } 3909: 3910: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); 3911: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 3912: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); 3913: 3914: while((c=getc(ficpar))=='#' && c!= EOF){ 3915: ungetc(c,ficpar); 3916: fgets(line, MAXLINE, ficpar); 3917: puts(line); 3918: fputs(line,ficparo); 3919: } 3920: ungetc(c,ficpar); 3921: 3922: 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); 3923: 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); 3924: 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); 3925: 3926: while((c=getc(ficpar))=='#' && c!= EOF){ 3927: ungetc(c,ficpar); 3928: fgets(line, MAXLINE, ficpar); 3929: puts(line); 3930: fputs(line,ficparo); 3931: } 3932: ungetc(c,ficpar); 3933: 3934: 3935: dateprev1=anprev1+mprev1/12.+jprev1/365.; 3936: dateprev2=anprev2+mprev2/12.+jprev2/365.; 3937: 3938: fscanf(ficpar,"pop_based=%d\n",&popbased); 3939: fprintf(ficparo,"pop_based=%d\n",popbased); 3940: fprintf(ficres,"pop_based=%d\n",popbased); 3941: 3942: while((c=getc(ficpar))=='#' && c!= EOF){ 3943: ungetc(c,ficpar); 3944: fgets(line, MAXLINE, ficpar); 3945: puts(line); 3946: fputs(line,ficparo); 3947: } 3948: ungetc(c,ficpar); 3949: 3950: fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2); 3951: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); 3952: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); 3953: 3954: 3955: while((c=getc(ficpar))=='#' && c!= EOF){ 3956: ungetc(c,ficpar); 3957: fgets(line, MAXLINE, ficpar); 3958: puts(line); 3959: fputs(line,ficparo); 3960: } 3961: ungetc(c,ficpar); 3962: 3963: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1); 3964: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); 3965: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); 3966: 3967: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); 3968: 3969: /*------------ gnuplot -------------*/ 3970: strcpy(optionfilegnuplot,optionfilefiname); 3971: strcat(optionfilegnuplot,".gp"); 3972: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { 3973: printf("Problem with file %s",optionfilegnuplot); 3974: } 3975: else{ 3976: fprintf(ficgp,"\n# %s\n", version); 3977: fprintf(ficgp,"# %s\n", optionfilegnuplot); 3978: fprintf(ficgp,"set missing 'NaNq'\n"); 3979: } 3980: fclose(ficgp); 3981: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); 3982: /*--------- index.htm --------*/ 3983: 3984: strcpy(optionfilehtm,optionfile); 3985: strcat(optionfilehtm,".htm"); 3986: if((fichtm=fopen(optionfilehtm,"w"))==NULL) { 3987: printf("Problem with %s \n",optionfilehtm), exit(0); 3988: } 3989: 3990: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n 3991: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n 3992: \n 3993: Total number of observations=%d <br>\n 3994: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n 3995: <hr size=\"2\" color=\"#EC5E5E\"> 3996: <ul><li><h4>Parameter files</h4>\n 3997: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n 3998: - Log file of the run: <a href=\"%s\">%s</a><br>\n 3999: - 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); 4000: fclose(fichtm); 4001: 4002: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); 4003: 4004: /*------------ free_vector -------------*/ 4005: chdir(path); 4006: 4007: free_ivector(wav,1,imx); 4008: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); 4009: free_imatrix(bh,1,lastpass-firstpass+1,1,imx); 4010: free_imatrix(mw,1,lastpass-firstpass+1,1,imx); 4011: free_ivector(num,1,n); 4012: free_vector(agedc,1,n); 4013: /*free_matrix(covar,0,NCOVMAX,1,n);*/ 4014: /*free_matrix(covar,1,NCOVMAX,1,n);*/ 4015: fclose(ficparo); 4016: fclose(ficres); 4017: 4018: 4019: /*--------------- Prevalence limit (stable prevalence) --------------*/ 4020: 4021: strcpy(filerespl,"pl"); 4022: strcat(filerespl,fileres); 4023: if((ficrespl=fopen(filerespl,"w"))==NULL) { 4024: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end; 4025: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end; 4026: } 4027: printf("Computing stable prevalence: result on file '%s' \n", filerespl); 4028: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl); 4029: fprintf(ficrespl,"#Stable prevalence \n"); 4030: fprintf(ficrespl,"#Age "); 4031: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); 4032: fprintf(ficrespl,"\n"); 4033: 4034: prlim=matrix(1,nlstate,1,nlstate); 4035: 4036: agebase=ageminpar; 4037: agelim=agemaxpar; 4038: ftolpl=1.e-10; 4039: i1=cptcoveff; 4040: if (cptcovn < 1){i1=1;} 4041: 4042: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 4043: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 4044: k=k+1; 4045: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ 4046: fprintf(ficrespl,"\n#******"); 4047: printf("\n#******"); 4048: fprintf(ficlog,"\n#******"); 4049: for(j=1;j<=cptcoveff;j++) { 4050: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4051: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4052: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4053: } 4054: fprintf(ficrespl,"******\n"); 4055: printf("******\n"); 4056: fprintf(ficlog,"******\n"); 4057: 4058: for (age=agebase; age<=agelim; age++){ 4059: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 4060: fprintf(ficrespl,"%.0f",age ); 4061: for(i=1; i<=nlstate;i++) 4062: fprintf(ficrespl," %.5f", prlim[i][i]); 4063: fprintf(ficrespl,"\n"); 4064: } 4065: } 4066: } 4067: fclose(ficrespl); 4068: 4069: /*------------- h Pij x at various ages ------------*/ 4070: 4071: strcpy(filerespij,"pij"); strcat(filerespij,fileres); 4072: if((ficrespij=fopen(filerespij,"w"))==NULL) { 4073: printf("Problem with Pij resultfile: %s\n", filerespij);goto end; 4074: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end; 4075: } 4076: printf("Computing pij: result on file '%s' \n", filerespij); 4077: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); 4078: 4079: stepsize=(int) (stepm+YEARM-1)/YEARM; 4080: /*if (stepm<=24) stepsize=2;*/ 4081: 4082: agelim=AGESUP; 4083: hstepm=stepsize*YEARM; /* Every year of age */ 4084: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 4085: 4086: /* hstepm=1; aff par mois*/ 4087: 4088: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 4089: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 4090: k=k+1; 4091: fprintf(ficrespij,"\n#****** "); 4092: for(j=1;j<=cptcoveff;j++) 4093: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4094: fprintf(ficrespij,"******\n"); 4095: 4096: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ 4097: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 4098: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ 4099: 4100: /* nhstepm=nhstepm*YEARM; aff par mois*/ 4101: 4102: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4103: oldm=oldms;savm=savms; 4104: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); 4105: fprintf(ficrespij,"# Age"); 4106: for(i=1; i<=nlstate;i++) 4107: for(j=1; j<=nlstate+ndeath;j++) 4108: fprintf(ficrespij," %1d-%1d",i,j); 4109: fprintf(ficrespij,"\n"); 4110: for (h=0; h<=nhstepm; h++){ 4111: fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); 4112: for(i=1; i<=nlstate;i++) 4113: for(j=1; j<=nlstate+ndeath;j++) 4114: fprintf(ficrespij," %.5f", p3mat[i][j][h]); 4115: fprintf(ficrespij,"\n"); 4116: } 4117: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); 4118: fprintf(ficrespij,"\n"); 4119: } 4120: } 4121: } 4122: 4123: varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); 4124: 4125: fclose(ficrespij); 4126: 4127: 4128: /*---------- Forecasting ------------------*/ 4129: if((stepm == 1) && (strcmp(model,".")==0)){ 4130: prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); 4131: if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); 4132: } 4133: else{ 4134: erreur=108; 4135: 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); 4136: 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); 4137: } 4138: 4139: 4140: /*---------- Health expectancies and variances ------------*/ 4141: 4142: strcpy(filerest,"t"); 4143: strcat(filerest,fileres); 4144: if((ficrest=fopen(filerest,"w"))==NULL) { 4145: printf("Problem with total LE resultfile: %s\n", filerest);goto end; 4146: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; 4147: } 4148: printf("Computing Total LEs with variances: file '%s' \n", filerest); 4149: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 4150: 4151: 4152: strcpy(filerese,"e"); 4153: strcat(filerese,fileres); 4154: if((ficreseij=fopen(filerese,"w"))==NULL) { 4155: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 4156: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); 4157: } 4158: printf("Computing Health Expectancies: result on file '%s' \n", filerese); 4159: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); 4160: 4161: strcpy(fileresv,"v"); 4162: strcat(fileresv,fileres); 4163: if((ficresvij=fopen(fileresv,"w"))==NULL) { 4164: printf("Problem with variance resultfile: %s\n", fileresv);exit(0); 4165: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); 4166: } 4167: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 4168: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); 4169: 4170: calagedate=-1; 4171: 4172: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); 4173: 4174: if (mobilav!=0) { 4175: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4176: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ 4177: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); 4178: printf(" Error in movingaverage mobilav=%d\n",mobilav); 4179: } 4180: } 4181: 4182: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 4183: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 4184: k=k+1; 4185: fprintf(ficrest,"\n#****** "); 4186: for(j=1;j<=cptcoveff;j++) 4187: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4188: fprintf(ficrest,"******\n"); 4189: 4190: fprintf(ficreseij,"\n#****** "); 4191: for(j=1;j<=cptcoveff;j++) 4192: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4193: fprintf(ficreseij,"******\n"); 4194: 4195: fprintf(ficresvij,"\n#****** "); 4196: for(j=1;j<=cptcoveff;j++) 4197: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4198: fprintf(ficresvij,"******\n"); 4199: 4200: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 4201: oldm=oldms;savm=savms; 4202: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); 4203: 4204: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); 4205: oldm=oldms;savm=savms; 4206: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav); 4207: if(popbased==1){ 4208: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav); 4209: } 4210: 4211: 4212: fprintf(ficrest,"#Total LEs with variances: e.. (std) "); 4213: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); 4214: fprintf(ficrest,"\n"); 4215: 4216: epj=vector(1,nlstate+1); 4217: for(age=bage; age <=fage ;age++){ 4218: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); 4219: if (popbased==1) { 4220: if(mobilav ==0){ 4221: for(i=1; i<=nlstate;i++) 4222: prlim[i][i]=probs[(int)age][i][k]; 4223: }else{ /* mobilav */ 4224: for(i=1; i<=nlstate;i++) 4225: prlim[i][i]=mobaverage[(int)age][i][k]; 4226: } 4227: } 4228: 4229: fprintf(ficrest," %4.0f",age); 4230: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ 4231: for(i=1, epj[j]=0.;i <=nlstate;i++) { 4232: epj[j] += prlim[i][i]*eij[i][j][(int)age]; 4233: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ 4234: } 4235: epj[nlstate+1] +=epj[j]; 4236: } 4237: 4238: for(i=1, vepp=0.;i <=nlstate;i++) 4239: for(j=1;j <=nlstate;j++) 4240: vepp += vareij[i][j][(int)age]; 4241: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); 4242: for(j=1;j <=nlstate;j++){ 4243: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); 4244: } 4245: fprintf(ficrest,"\n"); 4246: } 4247: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); 4248: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); 4249: free_vector(epj,1,nlstate+1); 4250: } 4251: } 4252: free_vector(weight,1,n); 4253: free_imatrix(Tvard,1,15,1,2); 4254: free_imatrix(s,1,maxwav+1,1,n); 4255: free_matrix(anint,1,maxwav,1,n); 4256: free_matrix(mint,1,maxwav,1,n); 4257: free_ivector(cod,1,n); 4258: free_ivector(tab,1,NCOVMAX); 4259: fclose(ficreseij); 4260: fclose(ficresvij); 4261: fclose(ficrest); 4262: fclose(ficpar); 4263: 4264: /*------- Variance of stable prevalence------*/ 4265: 4266: strcpy(fileresvpl,"vpl"); 4267: strcat(fileresvpl,fileres); 4268: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { 4269: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl); 4270: exit(0); 4271: } 4272: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl); 4273: 4274: for(cptcov=1,k=0;cptcov<=i1;cptcov++){ 4275: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ 4276: k=k+1; 4277: fprintf(ficresvpl,"\n#****** "); 4278: for(j=1;j<=cptcoveff;j++) 4279: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); 4280: fprintf(ficresvpl,"******\n"); 4281: 4282: varpl=matrix(1,nlstate,(int) bage, (int) fage); 4283: oldm=oldms;savm=savms; 4284: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); 4285: free_matrix(varpl,1,nlstate,(int) bage, (int)fage); 4286: } 4287: } 4288: 4289: fclose(ficresvpl); 4290: 4291: /*---------- End : free ----------------*/ 4292: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); 4293: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); 4294: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); 4295: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); 4296: 4297: free_matrix(covar,0,NCOVMAX,1,n); 4298: free_matrix(matcov,1,npar,1,npar); 4299: free_vector(delti,1,npar); 4300: free_matrix(agev,1,maxwav,1,imx); 4301: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 4302: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); 4303: free_ivector(ncodemax,1,8); 4304: free_ivector(Tvar,1,15); 4305: free_ivector(Tprod,1,15); 4306: free_ivector(Tvaraff,1,15); 4307: free_ivector(Tage,1,15); 4308: free_ivector(Tcode,1,100); 4309: 4310: fprintf(fichtm,"\n</body>"); 4311: fclose(fichtm); 4312: fclose(ficgp); 4313: 4314: 4315: if(erreur >0){ 4316: printf("End of Imach with error or warning %d\n",erreur); 4317: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur); 4318: }else{ 4319: printf("End of Imach\n"); 4320: fprintf(ficlog,"End of Imach\n"); 4321: } 4322: printf("See log file on %s\n",filelog); 4323: fclose(ficlog); 4324: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ 4325: 4326: /* 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);*/ 4327: /*printf("Total time was %d uSec.\n", total_usecs);*/ 4328: /*------ End -----------*/ 4329: 4330: end: 4331: #ifdef windows 4332: /* chdir(pathcd);*/ 4333: #endif 4334: /*system("wgnuplot graph.plt");*/ 4335: /*system("../gp37mgw/wgnuplot graph.plt");*/ 4336: /*system("cd ../gp37mgw");*/ 4337: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ 4338: strcpy(plotcmd,GNUPLOTPROGRAM); 4339: strcat(plotcmd," "); 4340: strcat(plotcmd,optionfilegnuplot); 4341: printf("Starting: %s\n",plotcmd);fflush(stdout); 4342: system(plotcmd); 4343: 4344: /*#ifdef windows*/ 4345: while (z[0] != 'q') { 4346: /* chdir(path); */ 4347: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); 4348: scanf("%s",z); 4349: if (z[0] == 'c') system("./imach"); 4350: else if (z[0] == 'e') system(optionfilehtm); 4351: else if (z[0] == 'g') system(plotcmd); 4352: else if (z[0] == 'q') exit(0); 4353: } 4354: /*#endif */ 4355: } 4356: 4357: