Annotation of imach/src/imach.c, revision 1.106
1.106 ! brouard 1: /* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.106 ! brouard 4: Revision 1.105 2006/01/05 20:23:19 lievre
! 5: *** empty log message ***
! 6:
1.105 lievre 7: Revision 1.104 2005/09/30 16:11:43 lievre
8: (Module): sump fixed, loop imx fixed, and simplifications.
9: (Module): If the status is missing at the last wave but we know
10: that the person is alive, then we can code his/her status as -2
11: (instead of missing=-1 in earlier versions) and his/her
12: contributions to the likelihood is 1 - Prob of dying from last
13: health status (= 1-p13= p11+p12 in the easiest case of somebody in
14: the healthy state at last known wave). Version is 0.98
15:
1.104 lievre 16: Revision 1.103 2005/09/30 15:54:49 lievre
17: (Module): sump fixed, loop imx fixed, and simplifications.
18:
1.103 lievre 19: Revision 1.102 2004/09/15 17:31:30 brouard
20: Add the possibility to read data file including tab characters.
21:
1.102 brouard 22: Revision 1.101 2004/09/15 10:38:38 brouard
23: Fix on curr_time
24:
1.101 brouard 25: Revision 1.100 2004/07/12 18:29:06 brouard
26: Add version for Mac OS X. Just define UNIX in Makefile
27:
1.100 brouard 28: Revision 1.99 2004/06/05 08:57:40 brouard
29: *** empty log message ***
30:
1.99 brouard 31: Revision 1.98 2004/05/16 15:05:56 brouard
32: New version 0.97 . First attempt to estimate force of mortality
33: directly from the data i.e. without the need of knowing the health
34: state at each age, but using a Gompertz model: log u =a + b*age .
35: This is the basic analysis of mortality and should be done before any
36: other analysis, in order to test if the mortality estimated from the
37: cross-longitudinal survey is different from the mortality estimated
38: from other sources like vital statistic data.
39:
40: The same imach parameter file can be used but the option for mle should be -3.
41:
42: Agnès, who wrote this part of the code, tried to keep most of the
43: former routines in order to include the new code within the former code.
44:
45: The output is very simple: only an estimate of the intercept and of
46: the slope with 95% confident intervals.
47:
48: Current limitations:
49: A) Even if you enter covariates, i.e. with the
50: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
51: B) There is no computation of Life Expectancy nor Life Table.
52:
1.98 brouard 53: Revision 1.97 2004/02/20 13:25:42 lievre
54: Version 0.96d. Population forecasting command line is (temporarily)
55: suppressed.
56:
1.97 lievre 57: Revision 1.96 2003/07/15 15:38:55 brouard
58: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
59: rewritten within the same printf. Workaround: many printfs.
60:
1.96 brouard 61: Revision 1.95 2003/07/08 07:54:34 brouard
62: * imach.c (Repository):
63: (Repository): Using imachwizard code to output a more meaningful covariance
64: matrix (cov(a12,c31) instead of numbers.
65:
1.95 brouard 66: Revision 1.94 2003/06/27 13:00:02 brouard
67: Just cleaning
68:
1.94 brouard 69: Revision 1.93 2003/06/25 16:33:55 brouard
70: (Module): On windows (cygwin) function asctime_r doesn't
71: exist so I changed back to asctime which exists.
72: (Module): Version 0.96b
73:
1.93 brouard 74: Revision 1.92 2003/06/25 16:30:45 brouard
75: (Module): On windows (cygwin) function asctime_r doesn't
76: exist so I changed back to asctime which exists.
77:
1.92 brouard 78: Revision 1.91 2003/06/25 15:30:29 brouard
79: * imach.c (Repository): Duplicated warning errors corrected.
80: (Repository): Elapsed time after each iteration is now output. It
81: helps to forecast when convergence will be reached. Elapsed time
82: is stamped in powell. We created a new html file for the graphs
83: concerning matrix of covariance. It has extension -cov.htm.
84:
1.91 brouard 85: Revision 1.90 2003/06/24 12:34:15 brouard
86: (Module): Some bugs corrected for windows. Also, when
87: mle=-1 a template is output in file "or"mypar.txt with the design
88: of the covariance matrix to be input.
89:
1.90 brouard 90: Revision 1.89 2003/06/24 12:30:52 brouard
91: (Module): Some bugs corrected for windows. Also, when
92: mle=-1 a template is output in file "or"mypar.txt with the design
93: of the covariance matrix to be input.
94:
1.89 brouard 95: Revision 1.88 2003/06/23 17:54:56 brouard
96: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
97:
1.88 brouard 98: Revision 1.87 2003/06/18 12:26:01 brouard
99: Version 0.96
100:
1.87 brouard 101: Revision 1.86 2003/06/17 20:04:08 brouard
102: (Module): Change position of html and gnuplot routines and added
103: routine fileappend.
104:
1.86 brouard 105: Revision 1.85 2003/06/17 13:12:43 brouard
106: * imach.c (Repository): Check when date of death was earlier that
107: current date of interview. It may happen when the death was just
108: prior to the death. In this case, dh was negative and likelihood
109: was wrong (infinity). We still send an "Error" but patch by
110: assuming that the date of death was just one stepm after the
111: interview.
112: (Repository): Because some people have very long ID (first column)
113: we changed int to long in num[] and we added a new lvector for
114: memory allocation. But we also truncated to 8 characters (left
115: truncation)
116: (Repository): No more line truncation errors.
117:
1.85 brouard 118: Revision 1.84 2003/06/13 21:44:43 brouard
119: * imach.c (Repository): Replace "freqsummary" at a correct
120: place. It differs from routine "prevalence" which may be called
121: many times. Probs is memory consuming and must be used with
122: parcimony.
1.86 brouard 123: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 124:
1.84 brouard 125: Revision 1.83 2003/06/10 13:39:11 lievre
126: *** empty log message ***
127:
1.83 lievre 128: Revision 1.82 2003/06/05 15:57:20 brouard
129: Add log in imach.c and fullversion number is now printed.
130:
1.82 brouard 131: */
132: /*
1.53 brouard 133: Interpolated Markov Chain
134:
135: Short summary of the programme:
136:
137: This program computes Healthy Life Expectancies from
138: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
139: first survey ("cross") where individuals from different ages are
140: interviewed on their health status or degree of disability (in the
141: case of a health survey which is our main interest) -2- at least a
142: second wave of interviews ("longitudinal") which measure each change
143: (if any) in individual health status. Health expectancies are
144: computed from the time spent in each health state according to a
145: model. More health states you consider, more time is necessary to reach the
146: Maximum Likelihood of the parameters involved in the model. The
147: simplest model is the multinomial logistic model where pij is the
148: probability to be observed in state j at the second wave
149: conditional to be observed in state i at the first wave. Therefore
150: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
151: 'age' is age and 'sex' is a covariate. If you want to have a more
152: complex model than "constant and age", you should modify the program
153: where the markup *Covariates have to be included here again* invites
154: you to do it. More covariates you add, slower the
155: convergence.
156:
157: The advantage of this computer programme, compared to a simple
158: multinomial logistic model, is clear when the delay between waves is not
159: identical for each individual. Also, if a individual missed an
160: intermediate interview, the information is lost, but taken into
161: account using an interpolation or extrapolation.
162:
163: hPijx is the probability to be observed in state i at age x+h
164: conditional to the observed state i at age x. The delay 'h' can be
165: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 166: states. This elementary transition (by month, quarter,
167: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 168: matrix is simply the matrix product of nh*stepm elementary matrices
169: and the contribution of each individual to the likelihood is simply
170: hPijx.
171:
172: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 173: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 174:
175: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
176: Institut national d'études démographiques, Paris.
177: This software have been partly granted by Euro-REVES, a concerted action
178: from the European Union.
179: It is copyrighted identically to a GNU software product, ie programme and
180: software can be distributed freely for non commercial use. Latest version
181: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 182:
183: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
184: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
185:
1.53 brouard 186: **********************************************************************/
1.74 brouard 187: /*
188: main
189: read parameterfile
190: read datafile
191: concatwav
1.84 brouard 192: freqsummary
1.74 brouard 193: if (mle >= 1)
194: mlikeli
195: print results files
196: if mle==1
197: computes hessian
198: read end of parameter file: agemin, agemax, bage, fage, estepm
199: begin-prev-date,...
200: open gnuplot file
201: open html file
202: stable prevalence
203: for age prevalim()
204: h Pij x
205: variance of p varprob
206: forecasting if prevfcast==1 prevforecast call prevalence()
207: health expectancies
208: Variance-covariance of DFLE
209: prevalence()
210: movingaverage()
211: varevsij()
212: if popbased==1 varevsij(,popbased)
213: total life expectancies
214: Variance of stable prevalence
215: end
216: */
217:
218:
219:
1.53 brouard 220:
221: #include <math.h>
222: #include <stdio.h>
223: #include <stdlib.h>
1.106 ! brouard 224: #include <string.h>
1.53 brouard 225: #include <unistd.h>
226:
1.99 brouard 227: /* #include <sys/time.h> */
1.86 brouard 228: #include <time.h>
229: #include "timeval.h"
230:
1.95 brouard 231: /* #include <libintl.h> */
232: /* #define _(String) gettext (String) */
233:
1.53 brouard 234: #define MAXLINE 256
235: #define GNUPLOTPROGRAM "gnuplot"
236: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 237: #define FILENAMELENGTH 132
1.53 brouard 238: /*#define DEBUG*/
1.85 brouard 239: /*#define windows*/
1.53 brouard 240: #define GLOCK_ERROR_NOPATH -1 /* empty path */
241: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
242:
243: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
244: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
245:
246: #define NINTERVMAX 8
247: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
248: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
249: #define NCOVMAX 8 /* Maximum number of covariates */
250: #define MAXN 20000
251: #define YEARM 12. /* Number of months per year */
252: #define AGESUP 130
253: #define AGEBASE 40
1.98 brouard 254: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.100 brouard 255: #ifdef UNIX
1.85 brouard 256: #define DIRSEPARATOR '/'
257: #define ODIRSEPARATOR '\\'
258: #else
1.53 brouard 259: #define DIRSEPARATOR '\\'
260: #define ODIRSEPARATOR '/'
261: #endif
262:
1.106 ! brouard 263: /* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ */
1.81 brouard 264: /* $State: Exp $ */
1.80 brouard 265:
1.106 ! brouard 266: char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
! 267: char fullversion[]="$Revision: 1.105 $ $Date: 2006/01/05 20:23:19 $";
1.91 brouard 268: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 269: int nvar;
270: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
271: int npar=NPARMAX;
272: int nlstate=2; /* Number of live states */
273: int ndeath=1; /* Number of dead states */
274: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
275: int popbased=0;
276:
277: int *wav; /* Number of waves for this individuual 0 is possible */
278: int maxwav; /* Maxim number of waves */
279: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 280: int gipmx, gsw; /* Global variables on the number of contributions
281: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 282: int mle, weightopt;
283: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
284: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 285: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
286: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 287: double jmean; /* Mean space between 2 waves */
288: double **oldm, **newm, **savm; /* Working pointers to matrices */
289: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
290: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 291: FILE *ficlog, *ficrespow;
1.85 brouard 292: int globpr; /* Global variable for printing or not */
293: double fretone; /* Only one call to likelihood */
294: long ipmx; /* Number of contributions */
295: double sw; /* Sum of weights */
1.98 brouard 296: char filerespow[FILENAMELENGTH];
1.85 brouard 297: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
298: FILE *ficresilk;
1.53 brouard 299: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
300: FILE *ficresprobmorprev;
1.91 brouard 301: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 302: FILE *ficreseij;
303: char filerese[FILENAMELENGTH];
304: FILE *ficresvij;
305: char fileresv[FILENAMELENGTH];
306: FILE *ficresvpl;
307: char fileresvpl[FILENAMELENGTH];
308: char title[MAXLINE];
309: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
310: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.96 brouard 311: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 312: char command[FILENAMELENGTH];
313: int outcmd=0;
1.53 brouard 314:
315: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 316:
1.53 brouard 317: char filelog[FILENAMELENGTH]; /* Log file */
318: char filerest[FILENAMELENGTH];
319: char fileregp[FILENAMELENGTH];
320: char popfile[FILENAMELENGTH];
321:
1.91 brouard 322: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
323:
324: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
325: struct timezone tzp;
326: extern int gettimeofday();
327: struct tm tmg, tm, tmf, *gmtime(), *localtime();
328: long time_value;
329: extern long time();
330: char strcurr[80], strfor[80];
1.53 brouard 331:
332: #define NR_END 1
333: #define FREE_ARG char*
334: #define FTOL 1.0e-10
335:
336: #define NRANSI
337: #define ITMAX 200
338:
339: #define TOL 2.0e-4
340:
341: #define CGOLD 0.3819660
342: #define ZEPS 1.0e-10
343: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
344:
345: #define GOLD 1.618034
346: #define GLIMIT 100.0
347: #define TINY 1.0e-20
348:
349: static double maxarg1,maxarg2;
350: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
351: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
352:
353: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
354: #define rint(a) floor(a+0.5)
355:
356: static double sqrarg;
357: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
358: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 brouard 359: int agegomp= AGEGOMP;
1.53 brouard 360:
361: int imx;
1.98 brouard 362: int stepm=1;
1.53 brouard 363: /* Stepm, step in month: minimum step interpolation*/
364:
365: int estepm;
366: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
367:
368: int m,nb;
1.85 brouard 369: long *num;
1.98 brouard 370: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 371: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 372: double **pmmij, ***probs;
1.98 brouard 373: double *ageexmed,*agecens;
1.53 brouard 374: double dateintmean=0;
375:
376: double *weight;
377: int **s; /* Status */
378: double *agedc, **covar, idx;
379: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.105 lievre 380: double *lsurv, *lpop, *tpop;
1.53 brouard 381:
382: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
383: double ftolhess; /* Tolerance for computing hessian */
384:
385: /**************** split *************************/
386: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
387: {
1.99 brouard 388: /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
389: the name of the file (name), its extension only (ext) and its first part of the name (finame)
390: */
1.59 brouard 391: char *ss; /* pointer */
392: int l1, l2; /* length counters */
1.53 brouard 393:
1.59 brouard 394: l1 = strlen(path ); /* length of path */
395: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
396: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
397: if ( ss == NULL ) { /* no directory, so use current */
398: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
399: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 400: /* get current working directory */
401: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 402: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
403: return( GLOCK_ERROR_GETCWD );
404: }
405: strcpy( name, path ); /* we've got it */
406: } else { /* strip direcotry from path */
407: ss++; /* after this, the filename */
408: l2 = strlen( ss ); /* length of filename */
409: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
410: strcpy( name, ss ); /* save file name */
411: strncpy( dirc, path, l1 - l2 ); /* now the directory */
412: dirc[l1-l2] = 0; /* add zero */
413: }
414: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 415: /*#ifdef windows
1.59 brouard 416: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 417: #else
1.59 brouard 418: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 419: #endif
1.85 brouard 420: */
1.59 brouard 421: ss = strrchr( name, '.' ); /* find last / */
1.99 brouard 422: if (ss >0){
423: ss++;
424: strcpy(ext,ss); /* save extension */
425: l1= strlen( name);
426: l2= strlen(ss)+1;
427: strncpy( finame, name, l1-l2);
428: finame[l1-l2]= 0;
429: }
1.59 brouard 430: return( 0 ); /* we're done */
1.53 brouard 431: }
432:
433:
434: /******************************************/
435:
1.89 brouard 436: void replace_back_to_slash(char *s, char*t)
1.53 brouard 437: {
438: int i;
1.89 brouard 439: int lg=0;
1.53 brouard 440: i=0;
441: lg=strlen(t);
442: for(i=0; i<= lg; i++) {
443: (s[i] = t[i]);
444: if (t[i]== '\\') s[i]='/';
445: }
446: }
447:
448: int nbocc(char *s, char occ)
449: {
450: int i,j=0;
451: int lg=20;
452: i=0;
453: lg=strlen(s);
454: for(i=0; i<= lg; i++) {
455: if (s[i] == occ ) j++;
456: }
457: return j;
458: }
459:
460: void cutv(char *u,char *v, char*t, char occ)
461: {
1.102 brouard 462: /* cuts string t into u and v where u ends before first occurence of char 'occ'
463: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
1.53 brouard 464: gives u="abcedf" and v="ghi2j" */
465: int i,lg,j,p=0;
466: i=0;
467: for(j=0; j<=strlen(t)-1; j++) {
468: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
469: }
470:
471: lg=strlen(t);
472: for(j=0; j<p; j++) {
473: (u[j] = t[j]);
474: }
475: u[p]='\0';
476:
477: for(j=0; j<= lg; j++) {
478: if (j>=(p+1))(v[j-p-1] = t[j]);
479: }
480: }
481:
482: /********************** nrerror ********************/
483:
484: void nrerror(char error_text[])
485: {
486: fprintf(stderr,"ERREUR ...\n");
487: fprintf(stderr,"%s\n",error_text);
1.59 brouard 488: exit(EXIT_FAILURE);
1.53 brouard 489: }
490: /*********************** vector *******************/
491: double *vector(int nl, int nh)
492: {
493: double *v;
494: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
495: if (!v) nrerror("allocation failure in vector");
496: return v-nl+NR_END;
497: }
498:
499: /************************ free vector ******************/
500: void free_vector(double*v, int nl, int nh)
501: {
502: free((FREE_ARG)(v+nl-NR_END));
503: }
504:
505: /************************ivector *******************************/
1.85 brouard 506: int *ivector(long nl,long nh)
1.76 brouard 507: {
1.85 brouard 508: int *v;
509: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
510: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 511: return v-nl+NR_END;
512: }
513:
514: /******************free ivector **************************/
1.85 brouard 515: void free_ivector(int *v, long nl, long nh)
1.76 brouard 516: {
517: free((FREE_ARG)(v+nl-NR_END));
518: }
519:
1.85 brouard 520: /************************lvector *******************************/
521: long *lvector(long nl,long nh)
1.53 brouard 522: {
1.85 brouard 523: long *v;
524: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 525: if (!v) nrerror("allocation failure in ivector");
526: return v-nl+NR_END;
527: }
528:
1.85 brouard 529: /******************free lvector **************************/
530: void free_lvector(long *v, long nl, long nh)
1.53 brouard 531: {
532: free((FREE_ARG)(v+nl-NR_END));
533: }
534:
535: /******************* imatrix *******************************/
536: int **imatrix(long nrl, long nrh, long ncl, long nch)
537: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
538: {
539: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
540: int **m;
541:
542: /* allocate pointers to rows */
543: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
544: if (!m) nrerror("allocation failure 1 in matrix()");
545: m += NR_END;
546: m -= nrl;
547:
548:
549: /* allocate rows and set pointers to them */
550: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
551: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
552: m[nrl] += NR_END;
553: m[nrl] -= ncl;
554:
555: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
556:
557: /* return pointer to array of pointers to rows */
558: return m;
559: }
560:
561: /****************** free_imatrix *************************/
562: void free_imatrix(m,nrl,nrh,ncl,nch)
563: int **m;
564: long nch,ncl,nrh,nrl;
565: /* free an int matrix allocated by imatrix() */
566: {
567: free((FREE_ARG) (m[nrl]+ncl-NR_END));
568: free((FREE_ARG) (m+nrl-NR_END));
569: }
570:
571: /******************* matrix *******************************/
572: double **matrix(long nrl, long nrh, long ncl, long nch)
573: {
574: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
575: double **m;
576:
577: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
578: if (!m) nrerror("allocation failure 1 in matrix()");
579: m += NR_END;
580: m -= nrl;
581:
582: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
583: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
584: m[nrl] += NR_END;
585: m[nrl] -= ncl;
586:
587: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
588: return m;
1.85 brouard 589: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 590: */
1.53 brouard 591: }
592:
593: /*************************free matrix ************************/
594: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
595: {
596: free((FREE_ARG)(m[nrl]+ncl-NR_END));
597: free((FREE_ARG)(m+nrl-NR_END));
598: }
599:
600: /******************* ma3x *******************************/
601: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
602: {
603: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
604: double ***m;
605:
606: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
607: if (!m) nrerror("allocation failure 1 in matrix()");
608: m += NR_END;
609: m -= nrl;
610:
611: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
612: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
613: m[nrl] += NR_END;
614: m[nrl] -= ncl;
615:
616: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
617:
618: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
619: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
620: m[nrl][ncl] += NR_END;
621: m[nrl][ncl] -= nll;
622: for (j=ncl+1; j<=nch; j++)
623: m[nrl][j]=m[nrl][j-1]+nlay;
624:
625: for (i=nrl+1; i<=nrh; i++) {
626: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
627: for (j=ncl+1; j<=nch; j++)
628: m[i][j]=m[i][j-1]+nlay;
629: }
1.74 brouard 630: return m;
631: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
632: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
633: */
1.53 brouard 634: }
635:
636: /*************************free ma3x ************************/
637: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
638: {
639: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
640: free((FREE_ARG)(m[nrl]+ncl-NR_END));
641: free((FREE_ARG)(m+nrl-NR_END));
642: }
643:
1.94 brouard 644: /*************** function subdirf ***********/
645: char *subdirf(char fileres[])
646: {
647: /* Caution optionfilefiname is hidden */
648: strcpy(tmpout,optionfilefiname);
649: strcat(tmpout,"/"); /* Add to the right */
650: strcat(tmpout,fileres);
651: return tmpout;
652: }
653:
654: /*************** function subdirf2 ***********/
655: char *subdirf2(char fileres[], char *preop)
656: {
657:
658: /* Caution optionfilefiname is hidden */
659: strcpy(tmpout,optionfilefiname);
660: strcat(tmpout,"/");
661: strcat(tmpout,preop);
662: strcat(tmpout,fileres);
663: return tmpout;
664: }
665:
666: /*************** function subdirf3 ***********/
667: char *subdirf3(char fileres[], char *preop, char *preop2)
668: {
669:
670: /* Caution optionfilefiname is hidden */
671: strcpy(tmpout,optionfilefiname);
672: strcat(tmpout,"/");
673: strcat(tmpout,preop);
674: strcat(tmpout,preop2);
675: strcat(tmpout,fileres);
676: return tmpout;
677: }
678:
1.53 brouard 679: /***************** f1dim *************************/
680: extern int ncom;
681: extern double *pcom,*xicom;
682: extern double (*nrfunc)(double []);
683:
684: double f1dim(double x)
685: {
686: int j;
687: double f;
688: double *xt;
689:
690: xt=vector(1,ncom);
691: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
692: f=(*nrfunc)(xt);
693: free_vector(xt,1,ncom);
694: return f;
695: }
696:
697: /*****************brent *************************/
698: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
699: {
700: int iter;
701: double a,b,d,etemp;
702: double fu,fv,fw,fx;
703: double ftemp;
704: double p,q,r,tol1,tol2,u,v,w,x,xm;
705: double e=0.0;
706:
707: a=(ax < cx ? ax : cx);
708: b=(ax > cx ? ax : cx);
709: x=w=v=bx;
710: fw=fv=fx=(*f)(x);
711: for (iter=1;iter<=ITMAX;iter++) {
712: xm=0.5*(a+b);
713: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
714: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
715: printf(".");fflush(stdout);
716: fprintf(ficlog,".");fflush(ficlog);
717: #ifdef DEBUG
718: 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);
719: 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);
720: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
721: #endif
722: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
723: *xmin=x;
724: return fx;
725: }
726: ftemp=fu;
727: if (fabs(e) > tol1) {
728: r=(x-w)*(fx-fv);
729: q=(x-v)*(fx-fw);
730: p=(x-v)*q-(x-w)*r;
731: q=2.0*(q-r);
732: if (q > 0.0) p = -p;
733: q=fabs(q);
734: etemp=e;
735: e=d;
736: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
737: d=CGOLD*(e=(x >= xm ? a-x : b-x));
738: else {
739: d=p/q;
740: u=x+d;
741: if (u-a < tol2 || b-u < tol2)
742: d=SIGN(tol1,xm-x);
743: }
744: } else {
745: d=CGOLD*(e=(x >= xm ? a-x : b-x));
746: }
747: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
748: fu=(*f)(u);
749: if (fu <= fx) {
750: if (u >= x) a=x; else b=x;
751: SHFT(v,w,x,u)
752: SHFT(fv,fw,fx,fu)
753: } else {
754: if (u < x) a=u; else b=u;
755: if (fu <= fw || w == x) {
756: v=w;
757: w=u;
758: fv=fw;
759: fw=fu;
760: } else if (fu <= fv || v == x || v == w) {
761: v=u;
762: fv=fu;
763: }
764: }
765: }
766: nrerror("Too many iterations in brent");
767: *xmin=x;
768: return fx;
769: }
770:
771: /****************** mnbrak ***********************/
772:
773: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
774: double (*func)(double))
775: {
776: double ulim,u,r,q, dum;
777: double fu;
778:
779: *fa=(*func)(*ax);
780: *fb=(*func)(*bx);
781: if (*fb > *fa) {
782: SHFT(dum,*ax,*bx,dum)
783: SHFT(dum,*fb,*fa,dum)
784: }
785: *cx=(*bx)+GOLD*(*bx-*ax);
786: *fc=(*func)(*cx);
787: while (*fb > *fc) {
788: r=(*bx-*ax)*(*fb-*fc);
789: q=(*bx-*cx)*(*fb-*fa);
790: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
791: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
792: ulim=(*bx)+GLIMIT*(*cx-*bx);
793: if ((*bx-u)*(u-*cx) > 0.0) {
794: fu=(*func)(u);
795: } else if ((*cx-u)*(u-ulim) > 0.0) {
796: fu=(*func)(u);
797: if (fu < *fc) {
798: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
799: SHFT(*fb,*fc,fu,(*func)(u))
800: }
801: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
802: u=ulim;
803: fu=(*func)(u);
804: } else {
805: u=(*cx)+GOLD*(*cx-*bx);
806: fu=(*func)(u);
807: }
808: SHFT(*ax,*bx,*cx,u)
809: SHFT(*fa,*fb,*fc,fu)
810: }
811: }
812:
813: /*************** linmin ************************/
814:
815: int ncom;
816: double *pcom,*xicom;
817: double (*nrfunc)(double []);
818:
819: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
820: {
821: double brent(double ax, double bx, double cx,
822: double (*f)(double), double tol, double *xmin);
823: double f1dim(double x);
824: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
825: double *fc, double (*func)(double));
826: int j;
827: double xx,xmin,bx,ax;
828: double fx,fb,fa;
829:
830: ncom=n;
831: pcom=vector(1,n);
832: xicom=vector(1,n);
833: nrfunc=func;
834: for (j=1;j<=n;j++) {
835: pcom[j]=p[j];
836: xicom[j]=xi[j];
837: }
838: ax=0.0;
839: xx=1.0;
840: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
841: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
842: #ifdef DEBUG
843: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
844: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
845: #endif
846: for (j=1;j<=n;j++) {
847: xi[j] *= xmin;
848: p[j] += xi[j];
849: }
850: free_vector(xicom,1,n);
851: free_vector(pcom,1,n);
852: }
853:
1.91 brouard 854: char *asc_diff_time(long time_sec, char ascdiff[])
855: {
856: long sec_left, days, hours, minutes;
857: days = (time_sec) / (60*60*24);
858: sec_left = (time_sec) % (60*60*24);
859: hours = (sec_left) / (60*60) ;
860: sec_left = (sec_left) %(60*60);
861: minutes = (sec_left) /60;
862: sec_left = (sec_left) % (60);
863: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
864: return ascdiff;
865: }
866:
1.53 brouard 867: /*************** powell ************************/
868: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
869: double (*func)(double []))
870: {
871: void linmin(double p[], double xi[], int n, double *fret,
872: double (*func)(double []));
873: int i,ibig,j;
874: double del,t,*pt,*ptt,*xit;
875: double fp,fptt;
876: double *xits;
1.91 brouard 877: int niterf, itmp;
878:
1.53 brouard 879: pt=vector(1,n);
880: ptt=vector(1,n);
881: xit=vector(1,n);
882: xits=vector(1,n);
883: *fret=(*func)(p);
884: for (j=1;j<=n;j++) pt[j]=p[j];
885: for (*iter=1;;++(*iter)) {
886: fp=(*fret);
887: ibig=0;
888: del=0.0;
1.91 brouard 889: last_time=curr_time;
890: (void) gettimeofday(&curr_time,&tzp);
891: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
1.98 brouard 892: /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
1.91 brouard 893: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.98 brouard 894: */
895: for (i=1;i<=n;i++) {
1.53 brouard 896: printf(" %d %.12f",i, p[i]);
1.76 brouard 897: fprintf(ficlog," %d %.12lf",i, p[i]);
898: fprintf(ficrespow," %.12lf", p[i]);
899: }
1.53 brouard 900: printf("\n");
901: fprintf(ficlog,"\n");
1.91 brouard 902: fprintf(ficrespow,"\n");fflush(ficrespow);
903: if(*iter <=3){
904: tm = *localtime(&curr_time.tv_sec);
1.101 brouard 905: strcpy(strcurr,asctime(&tm));
1.92 brouard 906: /* asctime_r(&tm,strcurr); */
1.101 brouard 907: forecast_time=curr_time;
1.91 brouard 908: itmp = strlen(strcurr);
1.101 brouard 909: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.91 brouard 910: strcurr[itmp-1]='\0';
911: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
912: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
913: for(niterf=10;niterf<=30;niterf+=10){
914: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
915: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 916: /* asctime_r(&tmf,strfor); */
917: strcpy(strfor,asctime(&tmf));
1.91 brouard 918: itmp = strlen(strfor);
919: if(strfor[itmp-1]=='\n')
920: strfor[itmp-1]='\0';
1.101 brouard 921: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
922: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
1.91 brouard 923: }
924: }
1.53 brouard 925: for (i=1;i<=n;i++) {
926: for (j=1;j<=n;j++) xit[j]=xi[j][i];
927: fptt=(*fret);
928: #ifdef DEBUG
929: printf("fret=%lf \n",*fret);
930: fprintf(ficlog,"fret=%lf \n",*fret);
931: #endif
932: printf("%d",i);fflush(stdout);
933: fprintf(ficlog,"%d",i);fflush(ficlog);
934: linmin(p,xit,n,fret,func);
935: if (fabs(fptt-(*fret)) > del) {
936: del=fabs(fptt-(*fret));
937: ibig=i;
938: }
939: #ifdef DEBUG
940: printf("%d %.12e",i,(*fret));
941: fprintf(ficlog,"%d %.12e",i,(*fret));
942: for (j=1;j<=n;j++) {
943: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
944: printf(" x(%d)=%.12e",j,xit[j]);
945: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
946: }
947: for(j=1;j<=n;j++) {
948: printf(" p=%.12e",p[j]);
949: fprintf(ficlog," p=%.12e",p[j]);
950: }
951: printf("\n");
952: fprintf(ficlog,"\n");
953: #endif
954: }
955: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
956: #ifdef DEBUG
957: int k[2],l;
958: k[0]=1;
959: k[1]=-1;
960: printf("Max: %.12e",(*func)(p));
961: fprintf(ficlog,"Max: %.12e",(*func)(p));
962: for (j=1;j<=n;j++) {
963: printf(" %.12e",p[j]);
964: fprintf(ficlog," %.12e",p[j]);
965: }
966: printf("\n");
967: fprintf(ficlog,"\n");
968: for(l=0;l<=1;l++) {
969: for (j=1;j<=n;j++) {
970: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
971: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
972: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
973: }
974: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
975: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
976: }
977: #endif
978:
979:
980: free_vector(xit,1,n);
981: free_vector(xits,1,n);
982: free_vector(ptt,1,n);
983: free_vector(pt,1,n);
984: return;
985: }
986: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
987: for (j=1;j<=n;j++) {
988: ptt[j]=2.0*p[j]-pt[j];
989: xit[j]=p[j]-pt[j];
990: pt[j]=p[j];
991: }
992: fptt=(*func)(ptt);
993: if (fptt < fp) {
994: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
995: if (t < 0.0) {
996: linmin(p,xit,n,fret,func);
997: for (j=1;j<=n;j++) {
998: xi[j][ibig]=xi[j][n];
999: xi[j][n]=xit[j];
1000: }
1001: #ifdef DEBUG
1002: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1003: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1004: for(j=1;j<=n;j++){
1005: printf(" %.12e",xit[j]);
1006: fprintf(ficlog," %.12e",xit[j]);
1007: }
1008: printf("\n");
1009: fprintf(ficlog,"\n");
1010: #endif
1.54 brouard 1011: }
1.53 brouard 1012: }
1013: }
1014: }
1015:
1.54 brouard 1016: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 1017:
1018: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1019: {
1020: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1021: matrix by transitions matrix until convergence is reached */
1022:
1023: int i, ii,j,k;
1024: double min, max, maxmin, maxmax,sumnew=0.;
1025: double **matprod2();
1026: double **out, cov[NCOVMAX], **pmij();
1027: double **newm;
1028: double agefin, delaymax=50 ; /* Max number of years to converge */
1029:
1030: for (ii=1;ii<=nlstate+ndeath;ii++)
1031: for (j=1;j<=nlstate+ndeath;j++){
1032: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1033: }
1034:
1035: cov[1]=1.;
1036:
1037: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1038: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1039: newm=savm;
1040: /* Covariates have to be included here again */
1041: cov[2]=agefin;
1042:
1043: for (k=1; k<=cptcovn;k++) {
1044: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1045: /* 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]]);*/
1046: }
1047: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1048: for (k=1; k<=cptcovprod;k++)
1049: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1050:
1051: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1052: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1053: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1054: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1055:
1056: savm=oldm;
1057: oldm=newm;
1058: maxmax=0.;
1059: for(j=1;j<=nlstate;j++){
1060: min=1.;
1061: max=0.;
1062: for(i=1; i<=nlstate; i++) {
1063: sumnew=0;
1064: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1065: prlim[i][j]= newm[i][j]/(1-sumnew);
1066: max=FMAX(max,prlim[i][j]);
1067: min=FMIN(min,prlim[i][j]);
1068: }
1069: maxmin=max-min;
1070: maxmax=FMAX(maxmax,maxmin);
1071: }
1072: if(maxmax < ftolpl){
1073: return prlim;
1074: }
1075: }
1076: }
1077:
1078: /*************** transition probabilities ***************/
1079:
1080: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1081: {
1082: double s1, s2;
1083: /*double t34;*/
1084: int i,j,j1, nc, ii, jj;
1085:
1086: for(i=1; i<= nlstate; i++){
1.99 brouard 1087: for(j=1; j<i;j++){
1088: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1089: /*s2 += param[i][j][nc]*cov[nc];*/
1090: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1091: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1092: }
1093: ps[i][j]=s2;
1094: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1095: }
1096: for(j=i+1; j<=nlstate+ndeath;j++){
1097: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1098: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1099: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1100: }
1101: ps[i][j]=s2;
1.53 brouard 1102: }
1103: }
1104: /*ps[3][2]=1;*/
1.99 brouard 1105:
1106: for(i=1; i<= nlstate; i++){
1107: s1=0;
1108: for(j=1; j<i; j++)
1109: s1+=exp(ps[i][j]);
1110: for(j=i+1; j<=nlstate+ndeath; j++)
1111: s1+=exp(ps[i][j]);
1112: ps[i][i]=1./(s1+1.);
1113: for(j=1; j<i; j++)
1114: ps[i][j]= exp(ps[i][j])*ps[i][i];
1115: for(j=i+1; j<=nlstate+ndeath; j++)
1116: ps[i][j]= exp(ps[i][j])*ps[i][i];
1117: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1118: } /* end i */
1119:
1120: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1121: for(jj=1; jj<= nlstate+ndeath; jj++){
1122: ps[ii][jj]=0;
1123: ps[ii][ii]=1;
1124: }
1.53 brouard 1125: }
1.99 brouard 1126:
1.53 brouard 1127:
1.99 brouard 1128: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1129: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1130: /* printf("ddd %lf ",ps[ii][jj]); */
1131: /* } */
1132: /* printf("\n "); */
1133: /* } */
1134: /* printf("\n ");printf("%lf ",cov[2]); */
1135: /*
1136: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1137: goto end;*/
1.53 brouard 1138: return ps;
1139: }
1140:
1141: /**************** Product of 2 matrices ******************/
1142:
1143: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1144: {
1145: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1146: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1147: /* in, b, out are matrice of pointers which should have been initialized
1148: before: only the contents of out is modified. The function returns
1149: a pointer to pointers identical to out */
1150: long i, j, k;
1151: for(i=nrl; i<= nrh; i++)
1152: for(k=ncolol; k<=ncoloh; k++)
1153: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1154: out[i][k] +=in[i][j]*b[j][k];
1155:
1156: return out;
1157: }
1158:
1159:
1160: /************* Higher Matrix Product ***************/
1161:
1162: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1163: {
1.66 brouard 1164: /* Computes the transition matrix starting at age 'age' over
1165: 'nhstepm*hstepm*stepm' months (i.e. until
1166: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1167: nhstepm*hstepm matrices.
1.53 brouard 1168: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1169: (typically every 2 years instead of every month which is too big
1170: for the memory).
1.53 brouard 1171: Model is determined by parameters x and covariates have to be
1172: included manually here.
1173:
1174: */
1175:
1176: int i, j, d, h, k;
1177: double **out, cov[NCOVMAX];
1178: double **newm;
1179:
1180: /* Hstepm could be zero and should return the unit matrix */
1181: for (i=1;i<=nlstate+ndeath;i++)
1182: for (j=1;j<=nlstate+ndeath;j++){
1183: oldm[i][j]=(i==j ? 1.0 : 0.0);
1184: po[i][j][0]=(i==j ? 1.0 : 0.0);
1185: }
1186: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1187: for(h=1; h <=nhstepm; h++){
1188: for(d=1; d <=hstepm; d++){
1189: newm=savm;
1190: /* Covariates have to be included here again */
1191: cov[1]=1.;
1192: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1193: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1194: for (k=1; k<=cptcovage;k++)
1195: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1196: for (k=1; k<=cptcovprod;k++)
1197: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1198:
1199:
1200: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1201: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1202: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1203: pmij(pmmij,cov,ncovmodel,x,nlstate));
1204: savm=oldm;
1205: oldm=newm;
1206: }
1207: for(i=1; i<=nlstate+ndeath; i++)
1208: for(j=1;j<=nlstate+ndeath;j++) {
1209: po[i][j][h]=newm[i][j];
1210: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1211: */
1212: }
1213: } /* end h */
1214: return po;
1215: }
1216:
1217:
1218: /*************** log-likelihood *************/
1219: double func( double *x)
1220: {
1221: int i, ii, j, k, mi, d, kk;
1222: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1223: double **out;
1224: double sw; /* Sum of weights */
1225: double lli; /* Individual log likelihood */
1.59 brouard 1226: int s1, s2;
1.68 lievre 1227: double bbh, survp;
1.53 brouard 1228: long ipmx;
1229: /*extern weight */
1230: /* We are differentiating ll according to initial status */
1231: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1232: /*for(i=1;i<imx;i++)
1233: printf(" %d\n",s[4][i]);
1234: */
1235: cov[1]=1.;
1236:
1237: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1238:
1239: if(mle==1){
1240: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1241: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1242: for(mi=1; mi<= wav[i]-1; mi++){
1243: for (ii=1;ii<=nlstate+ndeath;ii++)
1244: for (j=1;j<=nlstate+ndeath;j++){
1245: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1246: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1247: }
1248: for(d=0; d<dh[mi][i]; d++){
1249: newm=savm;
1250: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1251: for (kk=1; kk<=cptcovage;kk++) {
1252: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1253: }
1254: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1255: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1256: savm=oldm;
1257: oldm=newm;
1258: } /* end mult */
1.53 brouard 1259:
1.61 brouard 1260: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1.101 brouard 1261: /* But now since version 0.9 we anticipate for bias at large stepm.
1.61 brouard 1262: * If stepm is larger than one month (smallest stepm) and if the exact delay
1263: * (in months) between two waves is not a multiple of stepm, we rounded to
1264: * the nearest (and in case of equal distance, to the lowest) interval but now
1265: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1.101 brouard 1266: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1.61 brouard 1267: * probability in order to take into account the bias as a fraction of the way
1.101 brouard 1268: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1.61 brouard 1269: * -stepm/2 to stepm/2 .
1270: * For stepm=1 the results are the same as for previous versions of Imach.
1271: * For stepm > 1 the results are less biased than in previous versions.
1272: */
1273: s1=s[mw[mi][i]][i];
1274: s2=s[mw[mi+1][i]][i];
1.64 lievre 1275: bbh=(double)bh[mi][i]/(double)stepm;
1.101 brouard 1276: /* bias bh is positive if real duration
1.64 lievre 1277: * is higher than the multiple of stepm and negative otherwise.
1278: */
1279: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1.71 brouard 1280: if( s2 > nlstate){
1.104 lievre 1281: /* i.e. if s2 is a death state and if the date of death is known
1282: then the contribution to the likelihood is the probability to
1283: die between last step unit time and current step unit time,
1284: which is also equal to probability to die before dh
1.101 brouard 1285: minus probability to die before dh-stepm .
1.71 brouard 1286: In version up to 0.92 likelihood was computed
1287: as if date of death was unknown. Death was treated as any other
1288: health state: the date of the interview describes the actual state
1289: and not the date of a change in health state. The former idea was
1290: to consider that at each interview the state was recorded
1291: (healthy, disable or death) and IMaCh was corrected; but when we
1292: introduced the exact date of death then we should have modified
1293: the contribution of an exact death to the likelihood. This new
1294: contribution is smaller and very dependent of the step unit
1295: stepm. It is no more the probability to die between last interview
1296: and month of death but the probability to survive from last
1297: interview up to one month before death multiplied by the
1298: probability to die within a month. Thanks to Chris
1299: Jackson for correcting this bug. Former versions increased
1300: mortality artificially. The bad side is that we add another loop
1301: which slows down the processing. The difference can be up to 10%
1302: lower mortality.
1303: */
1304: lli=log(out[s1][s2] - savm[s1][s2]);
1.104 lievre 1305:
1306:
1307: } else if (s2==-2) {
1308: for (j=1,survp=0. ; j<=nlstate; j++)
1309: survp += out[s1][j];
1310: lli= survp;
1311: }
1.105 lievre 1312:
1313: else if (s2==-4) {
1314: for (j=3,survp=0. ; j<=nlstate; j++)
1315: survp += out[s1][j];
1316: lli= survp;
1317: }
1318:
1319: else if (s2==-5) {
1320: for (j=1,survp=0. ; j<=2; j++)
1321: survp += out[s1][j];
1322: lli= survp;
1323: }
1.104 lievre 1324:
1325:
1326: else{
1.71 brouard 1327: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1328: /* 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 */
1329: }
1.64 lievre 1330: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1331: /*if(lli ==000.0)*/
1332: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1.71 brouard 1333: ipmx +=1;
1.64 lievre 1334: sw += weight[i];
1335: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1336: } /* end of wave */
1337: } /* end of individual */
1338: } else if(mle==2){
1339: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1340: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1341: for(mi=1; mi<= wav[i]-1; mi++){
1342: for (ii=1;ii<=nlstate+ndeath;ii++)
1343: for (j=1;j<=nlstate+ndeath;j++){
1344: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1345: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1346: }
1347: for(d=0; d<=dh[mi][i]; d++){
1348: newm=savm;
1349: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1350: for (kk=1; kk<=cptcovage;kk++) {
1351: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1352: }
1353: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1354: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1355: savm=oldm;
1356: oldm=newm;
1357: } /* end mult */
1358:
1359: s1=s[mw[mi][i]][i];
1360: s2=s[mw[mi+1][i]][i];
1361: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1362: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.64 lievre 1363: ipmx +=1;
1364: sw += weight[i];
1365: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1366: } /* end of wave */
1367: } /* end of individual */
1368: } else if(mle==3){ /* exponential inter-extrapolation */
1369: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1370: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1371: for(mi=1; mi<= wav[i]-1; mi++){
1372: for (ii=1;ii<=nlstate+ndeath;ii++)
1373: for (j=1;j<=nlstate+ndeath;j++){
1374: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1375: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1376: }
1377: for(d=0; d<dh[mi][i]; d++){
1378: newm=savm;
1379: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1380: for (kk=1; kk<=cptcovage;kk++) {
1381: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1382: }
1383: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1384: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1385: savm=oldm;
1386: oldm=newm;
1387: } /* end mult */
1388:
1389: s1=s[mw[mi][i]][i];
1390: s2=s[mw[mi+1][i]][i];
1391: bbh=(double)bh[mi][i]/(double)stepm;
1392: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.61 brouard 1393: ipmx +=1;
1394: sw += weight[i];
1395: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1396: } /* end of wave */
1397: } /* end of individual */
1.84 brouard 1398: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1399: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1400: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1401: for(mi=1; mi<= wav[i]-1; mi++){
1402: for (ii=1;ii<=nlstate+ndeath;ii++)
1403: for (j=1;j<=nlstate+ndeath;j++){
1404: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1405: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1406: }
1407: for(d=0; d<dh[mi][i]; d++){
1408: newm=savm;
1409: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1410: for (kk=1; kk<=cptcovage;kk++) {
1411: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1412: }
1413:
1414: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1415: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1416: savm=oldm;
1417: oldm=newm;
1418: } /* end mult */
1419:
1.84 brouard 1420: s1=s[mw[mi][i]][i];
1421: s2=s[mw[mi+1][i]][i];
1422: if( s2 > nlstate){
1423: lli=log(out[s1][s2] - savm[s1][s2]);
1424: }else{
1425: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1426: }
1427: ipmx +=1;
1428: sw += weight[i];
1429: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1430: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.84 brouard 1431: } /* end of wave */
1432: } /* end of individual */
1433: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1434: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1435: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1436: for(mi=1; mi<= wav[i]-1; mi++){
1437: for (ii=1;ii<=nlstate+ndeath;ii++)
1438: for (j=1;j<=nlstate+ndeath;j++){
1439: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1440: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1441: }
1442: for(d=0; d<dh[mi][i]; d++){
1443: newm=savm;
1444: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1445: for (kk=1; kk<=cptcovage;kk++) {
1446: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1447: }
1448:
1449: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1450: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1451: savm=oldm;
1452: oldm=newm;
1453: } /* end mult */
1454:
1455: s1=s[mw[mi][i]][i];
1456: s2=s[mw[mi+1][i]][i];
1.61 brouard 1457: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1458: ipmx +=1;
1459: sw += weight[i];
1460: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1461: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1.61 brouard 1462: } /* end of wave */
1463: } /* end of individual */
1464: } /* End of if */
1.53 brouard 1465: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1466: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1467: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1468: return -l;
1469: }
1470:
1471: /*************** log-likelihood *************/
1472: double funcone( double *x)
1473: {
1.87 brouard 1474: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1475: int i, ii, j, k, mi, d, kk;
1476: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1477: double **out;
1478: double lli; /* Individual log likelihood */
1.87 brouard 1479: double llt;
1.85 brouard 1480: int s1, s2;
1481: double bbh, survp;
1482: /*extern weight */
1483: /* We are differentiating ll according to initial status */
1484: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1485: /*for(i=1;i<imx;i++)
1486: printf(" %d\n",s[4][i]);
1487: */
1488: cov[1]=1.;
1489:
1490: for(k=1; k<=nlstate; k++) ll[k]=0.;
1491:
1492: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1493: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1494: for(mi=1; mi<= wav[i]-1; mi++){
1495: for (ii=1;ii<=nlstate+ndeath;ii++)
1496: for (j=1;j<=nlstate+ndeath;j++){
1497: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1498: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1499: }
1500: for(d=0; d<dh[mi][i]; d++){
1501: newm=savm;
1502: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1503: for (kk=1; kk<=cptcovage;kk++) {
1504: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1505: }
1506: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1507: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1508: savm=oldm;
1509: oldm=newm;
1510: } /* end mult */
1511:
1512: s1=s[mw[mi][i]][i];
1513: s2=s[mw[mi+1][i]][i];
1514: bbh=(double)bh[mi][i]/(double)stepm;
1515: /* bias is positive if real duration
1516: * is higher than the multiple of stepm and negative otherwise.
1517: */
1518: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1519: lli=log(out[s1][s2] - savm[s1][s2]);
1520: } else if (mle==1){
1521: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1522: } else if(mle==2){
1523: 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 */
1524: } else if(mle==3){ /* exponential inter-extrapolation */
1525: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1526: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1527: lli=log(out[s1][s2]); /* Original formula */
1528: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1529: lli=log(out[s1][s2]); /* Original formula */
1530: } /* End of if */
1531: ipmx +=1;
1532: sw += weight[i];
1533: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1534: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1535: if(globpr){
1.88 brouard 1536: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1537: %10.6f %10.6f %10.6f ", \
1538: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1539: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1540: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1541: llt +=ll[k]*gipmx/gsw;
1542: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1543: }
1544: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1545: }
1546: } /* end of wave */
1547: } /* end of individual */
1548: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1549: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1550: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1551: if(globpr==0){ /* First time we count the contributions and weights */
1552: gipmx=ipmx;
1553: gsw=sw;
1554: }
1.53 brouard 1555: return -l;
1556: }
1557:
1558:
1.94 brouard 1559: /*************** function likelione ***********/
1.87 brouard 1560: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1561: {
1.87 brouard 1562: /* This routine should help understanding what is done with
1563: the selection of individuals/waves and
1.85 brouard 1564: to check the exact contribution to the likelihood.
1565: Plotting could be done.
1566: */
1567: int k;
1.87 brouard 1568:
1.88 brouard 1569: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1570: strcpy(fileresilk,"ilk");
1571: strcat(fileresilk,fileres);
1572: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1573: printf("Problem with resultfile: %s\n", fileresilk);
1574: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1575: }
1.87 brouard 1576: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.88 brouard 1577: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1578: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1579: for(k=1; k<=nlstate; k++)
1.87 brouard 1580: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1581: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1582: }
1583:
1584: *fretone=(*funcone)(p);
1.87 brouard 1585: if(*globpri !=0){
1.85 brouard 1586: fclose(ficresilk);
1.88 brouard 1587: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1588: fflush(fichtm);
1589: }
1.85 brouard 1590: return;
1591: }
1592:
1.88 brouard 1593:
1.53 brouard 1594: /*********** Maximum Likelihood Estimation ***************/
1595:
1596: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1597: {
1598: int i,j, iter;
1.74 brouard 1599: double **xi;
1.53 brouard 1600: double fret;
1.85 brouard 1601: double fretone; /* Only one call to likelihood */
1.98 brouard 1602: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1603: xi=matrix(1,npar,1,npar);
1604: for (i=1;i<=npar;i++)
1605: for (j=1;j<=npar;j++)
1606: xi[i][j]=(i==j ? 1.0 : 0.0);
1607: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1608: strcpy(filerespow,"pow");
1609: strcat(filerespow,fileres);
1610: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1611: printf("Problem with resultfile: %s\n", filerespow);
1612: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1613: }
1614: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1615: for (i=1;i<=nlstate;i++)
1616: for(j=1;j<=nlstate+ndeath;j++)
1617: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1618: fprintf(ficrespow,"\n");
1.85 brouard 1619:
1.53 brouard 1620: powell(p,xi,npar,ftol,&iter,&fret,func);
1621:
1.76 brouard 1622: fclose(ficrespow);
1623: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1624: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1625: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1626:
1627: }
1628:
1629: /**** Computes Hessian and covariance matrix ***/
1630: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1631: {
1632: double **a,**y,*x,pd;
1633: double **hess;
1634: int i, j,jk;
1635: int *indx;
1636:
1.98 brouard 1637: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1638: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1639: void lubksb(double **a, int npar, int *indx, double b[]) ;
1640: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 brouard 1641: double gompertz(double p[]);
1.53 brouard 1642: hess=matrix(1,npar,1,npar);
1643:
1644: printf("\nCalculation of the hessian matrix. Wait...\n");
1645: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1646: for (i=1;i<=npar;i++){
1647: printf("%d",i);fflush(stdout);
1648: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 brouard 1649:
1650: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1651:
1652: /* printf(" %f ",p[i]);
1653: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1654: }
1655:
1656: for (i=1;i<=npar;i++) {
1657: for (j=1;j<=npar;j++) {
1658: if (j>i) {
1659: printf(".%d%d",i,j);fflush(stdout);
1660: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 brouard 1661: hess[i][j]=hessij(p,delti,i,j,func,npar);
1662:
1.53 brouard 1663: hess[j][i]=hess[i][j];
1664: /*printf(" %lf ",hess[i][j]);*/
1665: }
1666: }
1667: }
1668: printf("\n");
1669: fprintf(ficlog,"\n");
1670:
1671: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1672: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1673:
1674: a=matrix(1,npar,1,npar);
1675: y=matrix(1,npar,1,npar);
1676: x=vector(1,npar);
1677: indx=ivector(1,npar);
1678: for (i=1;i<=npar;i++)
1679: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1680: ludcmp(a,npar,indx,&pd);
1681:
1682: for (j=1;j<=npar;j++) {
1683: for (i=1;i<=npar;i++) x[i]=0;
1684: x[j]=1;
1685: lubksb(a,npar,indx,x);
1686: for (i=1;i<=npar;i++){
1687: matcov[i][j]=x[i];
1688: }
1689: }
1690:
1691: printf("\n#Hessian matrix#\n");
1692: fprintf(ficlog,"\n#Hessian matrix#\n");
1693: for (i=1;i<=npar;i++) {
1694: for (j=1;j<=npar;j++) {
1695: printf("%.3e ",hess[i][j]);
1696: fprintf(ficlog,"%.3e ",hess[i][j]);
1697: }
1698: printf("\n");
1699: fprintf(ficlog,"\n");
1700: }
1701:
1702: /* Recompute Inverse */
1703: for (i=1;i<=npar;i++)
1704: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1705: ludcmp(a,npar,indx,&pd);
1706:
1707: /* printf("\n#Hessian matrix recomputed#\n");
1708:
1709: for (j=1;j<=npar;j++) {
1710: for (i=1;i<=npar;i++) x[i]=0;
1711: x[j]=1;
1712: lubksb(a,npar,indx,x);
1713: for (i=1;i<=npar;i++){
1714: y[i][j]=x[i];
1715: printf("%.3e ",y[i][j]);
1716: fprintf(ficlog,"%.3e ",y[i][j]);
1717: }
1718: printf("\n");
1719: fprintf(ficlog,"\n");
1720: }
1721: */
1722:
1723: free_matrix(a,1,npar,1,npar);
1724: free_matrix(y,1,npar,1,npar);
1725: free_vector(x,1,npar);
1726: free_ivector(indx,1,npar);
1727: free_matrix(hess,1,npar,1,npar);
1728:
1729:
1730: }
1731:
1732: /*************** hessian matrix ****************/
1.98 brouard 1733: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1734: {
1735: int i;
1736: int l=1, lmax=20;
1737: double k1,k2;
1738: double p2[NPARMAX+1];
1739: double res;
1.98 brouard 1740: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1741: double fx;
1742: int k=0,kmax=10;
1743: double l1;
1744:
1745: fx=func(x);
1746: for (i=1;i<=npar;i++) p2[i]=x[i];
1747: for(l=0 ; l <=lmax; l++){
1748: l1=pow(10,l);
1749: delts=delt;
1750: for(k=1 ; k <kmax; k=k+1){
1751: delt = delta*(l1*k);
1752: p2[theta]=x[theta] +delt;
1753: k1=func(p2)-fx;
1754: p2[theta]=x[theta]-delt;
1755: k2=func(p2)-fx;
1756: /*res= (k1-2.0*fx+k2)/delt/delt; */
1757: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1758:
1759: #ifdef DEBUG
1760: 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);
1761: 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);
1762: #endif
1763: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1764: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1765: k=kmax;
1766: }
1767: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1768: k=kmax; l=lmax*10.;
1769: }
1770: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1771: delts=delt;
1772: }
1773: }
1774: }
1775: delti[theta]=delts;
1776: return res;
1777:
1778: }
1779:
1.98 brouard 1780: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1781: {
1782: int i;
1783: int l=1, l1, lmax=20;
1784: double k1,k2,k3,k4,res,fx;
1785: double p2[NPARMAX+1];
1786: int k;
1787:
1788: fx=func(x);
1789: for (k=1; k<=2; k++) {
1790: for (i=1;i<=npar;i++) p2[i]=x[i];
1791: p2[thetai]=x[thetai]+delti[thetai]/k;
1792: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1793: k1=func(p2)-fx;
1794:
1795: p2[thetai]=x[thetai]+delti[thetai]/k;
1796: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1797: k2=func(p2)-fx;
1798:
1799: p2[thetai]=x[thetai]-delti[thetai]/k;
1800: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1801: k3=func(p2)-fx;
1802:
1803: p2[thetai]=x[thetai]-delti[thetai]/k;
1804: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1805: k4=func(p2)-fx;
1806: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1807: #ifdef DEBUG
1808: 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);
1809: 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);
1810: #endif
1811: }
1812: return res;
1813: }
1814:
1815: /************** Inverse of matrix **************/
1816: void ludcmp(double **a, int n, int *indx, double *d)
1817: {
1818: int i,imax,j,k;
1819: double big,dum,sum,temp;
1820: double *vv;
1821:
1822: vv=vector(1,n);
1823: *d=1.0;
1824: for (i=1;i<=n;i++) {
1825: big=0.0;
1826: for (j=1;j<=n;j++)
1827: if ((temp=fabs(a[i][j])) > big) big=temp;
1828: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1829: vv[i]=1.0/big;
1830: }
1831: for (j=1;j<=n;j++) {
1832: for (i=1;i<j;i++) {
1833: sum=a[i][j];
1834: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1835: a[i][j]=sum;
1836: }
1837: big=0.0;
1838: for (i=j;i<=n;i++) {
1839: sum=a[i][j];
1840: for (k=1;k<j;k++)
1841: sum -= a[i][k]*a[k][j];
1842: a[i][j]=sum;
1843: if ( (dum=vv[i]*fabs(sum)) >= big) {
1844: big=dum;
1845: imax=i;
1846: }
1847: }
1848: if (j != imax) {
1849: for (k=1;k<=n;k++) {
1850: dum=a[imax][k];
1851: a[imax][k]=a[j][k];
1852: a[j][k]=dum;
1853: }
1854: *d = -(*d);
1855: vv[imax]=vv[j];
1856: }
1857: indx[j]=imax;
1858: if (a[j][j] == 0.0) a[j][j]=TINY;
1859: if (j != n) {
1860: dum=1.0/(a[j][j]);
1861: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1862: }
1863: }
1864: free_vector(vv,1,n); /* Doesn't work */
1865: ;
1866: }
1867:
1868: void lubksb(double **a, int n, int *indx, double b[])
1869: {
1870: int i,ii=0,ip,j;
1871: double sum;
1872:
1873: for (i=1;i<=n;i++) {
1874: ip=indx[i];
1875: sum=b[ip];
1876: b[ip]=b[i];
1877: if (ii)
1878: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1879: else if (sum) ii=i;
1880: b[i]=sum;
1881: }
1882: for (i=n;i>=1;i--) {
1883: sum=b[i];
1884: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1885: b[i]=sum/a[i][i];
1886: }
1887: }
1888:
1889: /************ Frequencies ********************/
1.105 lievre 1890: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
1.53 brouard 1891: { /* Some frequencies */
1892:
1893: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1894: int first;
1895: double ***freq; /* Frequencies */
1.73 lievre 1896: double *pp, **prop;
1897: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1898: FILE *ficresp;
1899: char fileresp[FILENAMELENGTH];
1900:
1901: pp=vector(1,nlstate);
1.74 brouard 1902: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1903: strcpy(fileresp,"p");
1904: strcat(fileresp,fileres);
1905: if((ficresp=fopen(fileresp,"w"))==NULL) {
1906: printf("Problem with prevalence resultfile: %s\n", fileresp);
1907: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1908: exit(0);
1909: }
1.105 lievre 1910: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1911: j1=0;
1912:
1913: j=cptcoveff;
1914: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1915:
1916: first=1;
1917:
1918: for(k1=1; k1<=j;k1++){
1919: for(i1=1; i1<=ncodemax[k1];i1++){
1920: j1++;
1921: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1922: scanf("%d", i);*/
1.105 lievre 1923: for (i=-5; i<=nlstate+ndeath; i++)
1924: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.74 brouard 1925: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1926: freq[i][jk][m]=0;
1.73 lievre 1927:
1928: for (i=1; i<=nlstate; i++)
1.74 brouard 1929: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1930: prop[i][m]=0;
1.53 brouard 1931:
1932: dateintsum=0;
1933: k2cpt=0;
1934: for (i=1; i<=imx; i++) {
1935: bool=1;
1936: if (cptcovn>0) {
1937: for (z1=1; z1<=cptcoveff; z1++)
1938: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1939: bool=0;
1940: }
1.58 lievre 1941: if (bool==1){
1.53 brouard 1942: for(m=firstpass; m<=lastpass; m++){
1943: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1944: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1945: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1946: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1947: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1948: if (m<lastpass) {
1949: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1950: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1951: }
1952:
1.74 brouard 1953: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1954: dateintsum=dateintsum+k2;
1955: k2cpt++;
1956: }
1.84 brouard 1957: /*}*/
1.53 brouard 1958: }
1959: }
1960: }
1961:
1.84 brouard 1962: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.105 lievre 1963: fprintf(ficresp, "#Local time at start: %s", strstart);
1.53 brouard 1964: if (cptcovn>0) {
1965: fprintf(ficresp, "\n#********** Variable ");
1966: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1967: fprintf(ficresp, "**********\n#");
1968: }
1969: for(i=1; i<=nlstate;i++)
1970: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1971: fprintf(ficresp, "\n");
1972:
1.74 brouard 1973: for(i=iagemin; i <= iagemax+3; i++){
1974: if(i==iagemax+3){
1.53 brouard 1975: fprintf(ficlog,"Total");
1976: }else{
1977: if(first==1){
1978: first=0;
1979: printf("See log file for details...\n");
1980: }
1981: fprintf(ficlog,"Age %d", i);
1982: }
1983: for(jk=1; jk <=nlstate ; jk++){
1984: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1985: pp[jk] += freq[jk][m][i];
1986: }
1987: for(jk=1; jk <=nlstate ; jk++){
1988: for(m=-1, pos=0; m <=0 ; m++)
1989: pos += freq[jk][m][i];
1990: if(pp[jk]>=1.e-10){
1991: if(first==1){
1992: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1993: }
1994: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1995: }else{
1996: if(first==1)
1997: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1998: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1999: }
2000: }
2001:
2002: for(jk=1; jk <=nlstate ; jk++){
2003: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2004: pp[jk] += freq[jk][m][i];
1.73 lievre 2005: }
2006: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2007: pos += pp[jk];
2008: posprop += prop[jk][i];
1.53 brouard 2009: }
2010: for(jk=1; jk <=nlstate ; jk++){
2011: if(pos>=1.e-5){
2012: if(first==1)
2013: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2014: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2015: }else{
2016: if(first==1)
2017: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2018: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2019: }
1.74 brouard 2020: if( i <= iagemax){
1.53 brouard 2021: if(pos>=1.e-5){
1.73 lievre 2022: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 2023: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 2024: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2025: }
2026: else
1.73 lievre 2027: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 2028: }
2029: }
2030:
1.69 brouard 2031: for(jk=-1; jk <=nlstate+ndeath; jk++)
2032: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 2033: if(freq[jk][m][i] !=0 ) {
2034: if(first==1)
2035: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2036: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2037: }
1.74 brouard 2038: if(i <= iagemax)
1.53 brouard 2039: fprintf(ficresp,"\n");
2040: if(first==1)
2041: printf("Others in log...\n");
2042: fprintf(ficlog,"\n");
2043: }
2044: }
2045: }
2046: dateintmean=dateintsum/k2cpt;
2047:
2048: fclose(ficresp);
1.105 lievre 2049: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 2050: free_vector(pp,1,nlstate);
1.74 brouard 2051: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 2052: /* End of Freq */
2053: }
2054:
2055: /************ Prevalence ********************/
1.84 brouard 2056: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
1.69 brouard 2057: {
2058: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2059: in each health status at the date of interview (if between dateprev1 and dateprev2).
2060: We still use firstpass and lastpass as another selection.
2061: */
1.53 brouard 2062:
2063: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2064: double ***freq; /* Frequencies */
1.73 lievre 2065: double *pp, **prop;
2066: double pos,posprop;
1.69 brouard 2067: double y2; /* in fractional years */
1.74 brouard 2068: int iagemin, iagemax;
1.53 brouard 2069:
1.74 brouard 2070: iagemin= (int) agemin;
2071: iagemax= (int) agemax;
2072: /*pp=vector(1,nlstate);*/
2073: prop=matrix(1,nlstate,iagemin,iagemax+3);
2074: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 2075: j1=0;
2076:
2077: j=cptcoveff;
2078: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2079:
2080: for(k1=1; k1<=j;k1++){
2081: for(i1=1; i1<=ncodemax[k1];i1++){
2082: j1++;
2083:
1.73 lievre 2084: for (i=1; i<=nlstate; i++)
1.74 brouard 2085: for(m=iagemin; m <= iagemax+3; m++)
2086: prop[i][m]=0.0;
1.53 brouard 2087:
1.69 brouard 2088: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2089: bool=1;
2090: if (cptcovn>0) {
2091: for (z1=1; z1<=cptcoveff; z1++)
2092: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2093: bool=0;
2094: }
2095: if (bool==1) {
1.69 brouard 2096: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2097: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2098: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2099: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2100: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2101: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
2102: if (s[m][i]>0 && s[m][i]<=nlstate) {
2103: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
2104: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2105: prop[s[m][i]][iagemax+3] += weight[i];
2106: }
1.53 brouard 2107: }
1.69 brouard 2108: } /* end selection of waves */
1.53 brouard 2109: }
2110: }
1.74 brouard 2111: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2112:
1.74 brouard 2113: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2114: posprop += prop[jk][i];
2115: }
2116:
2117: for(jk=1; jk <=nlstate ; jk++){
2118: if( i <= iagemax){
2119: if(posprop>=1.e-5){
2120: probs[i][jk][j1]= prop[jk][i]/posprop;
2121: }
2122: }
2123: }/* end jk */
2124: }/* end i */
1.53 brouard 2125: } /* end i1 */
2126: } /* end k1 */
2127:
1.74 brouard 2128: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2129: /*free_vector(pp,1,nlstate);*/
2130: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2131: } /* End of prevalence */
1.53 brouard 2132:
2133: /************* Waves Concatenation ***************/
2134:
1.59 brouard 2135: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1.53 brouard 2136: {
2137: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2138: Death is a valid wave (if date is known).
2139: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2140: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2141: and mw[mi+1][i]. dh depends on stepm.
2142: */
2143:
2144: int i, mi, m;
2145: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2146: double sum=0., jmean=0.;*/
2147: int first;
2148: int j, k=0,jk, ju, jl;
2149: double sum=0.;
2150: first=0;
2151: jmin=1e+5;
2152: jmax=-1;
2153: jmean=0.;
2154: for(i=1; i<=imx; i++){
2155: mi=0;
2156: m=firstpass;
2157: while(s[m][i] <= nlstate){
1.105 lievre 2158: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
1.53 brouard 2159: mw[++mi][i]=m;
2160: if(m >=lastpass)
2161: break;
2162: else
2163: m++;
2164: }/* end while */
2165: if (s[m][i] > nlstate){
2166: mi++; /* Death is another wave */
2167: /* if(mi==0) never been interviewed correctly before death */
2168: /* Only death is a correct wave */
2169: mw[mi][i]=m;
2170: }
2171:
2172: wav[i]=mi;
2173: if(mi==0){
1.91 brouard 2174: nbwarn++;
1.53 brouard 2175: if(first==0){
1.85 brouard 2176: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2177: first=1;
2178: }
2179: if(first==1){
1.85 brouard 2180: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2181: }
2182: } /* end mi==0 */
1.77 brouard 2183: } /* End individuals */
1.53 brouard 2184:
2185: for(i=1; i<=imx; i++){
2186: for(mi=1; mi<wav[i];mi++){
2187: if (stepm <=0)
2188: dh[mi][i]=1;
2189: else{
1.77 brouard 2190: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2191: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2192: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2193: if(j==0) j=1; /* Survives at least one month after exam */
2194: else if(j<0){
1.91 brouard 2195: nberr++;
1.85 brouard 2196: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1.91 brouard 2197: j=1; /* Temporary Dangerous patch */
1.105 lievre 2198: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
1.91 brouard 2199: fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1.105 lievre 2200: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
1.85 brouard 2201: }
2202: k=k+1;
2203: if (j >= jmax) jmax=j;
2204: if (j <= jmin) jmin=j;
2205: sum=sum+j;
2206: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2207: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2208: }
2209: }
2210: else{
2211: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.104 lievre 2212: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
2213:
1.53 brouard 2214: k=k+1;
2215: if (j >= jmax) jmax=j;
2216: else if (j <= jmin)jmin=j;
2217: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2218: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1.85 brouard 2219: if(j<0){
1.91 brouard 2220: nberr++;
1.85 brouard 2221: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2222: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2223: }
1.53 brouard 2224: sum=sum+j;
2225: }
2226: jk= j/stepm;
2227: jl= j -jk*stepm;
2228: ju= j -(jk+1)*stepm;
1.85 brouard 2229: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2230: if(jl==0){
2231: dh[mi][i]=jk;
2232: bh[mi][i]=0;
2233: }else{ /* We want a negative bias in order to only have interpolation ie
2234: * at the price of an extra matrix product in likelihood */
2235: dh[mi][i]=jk+1;
2236: bh[mi][i]=ju;
2237: }
2238: }else{
2239: if(jl <= -ju){
2240: dh[mi][i]=jk;
2241: bh[mi][i]=jl; /* bias is positive if real duration
2242: * is higher than the multiple of stepm and negative otherwise.
2243: */
2244: }
2245: else{
2246: dh[mi][i]=jk+1;
2247: bh[mi][i]=ju;
2248: }
2249: if(dh[mi][i]==0){
2250: dh[mi][i]=1; /* At least one step */
2251: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2252: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
1.64 lievre 2253: }
1.85 brouard 2254: } /* end if mle */
2255: }
1.64 lievre 2256: } /* end wave */
1.53 brouard 2257: }
2258: jmean=sum/k;
2259: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2260: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2261: }
2262:
2263: /*********** Tricode ****************************/
2264: void tricode(int *Tvar, int **nbcode, int imx)
2265: {
1.58 lievre 2266:
2267: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2268: int cptcode=0;
2269: cptcoveff=0;
2270:
1.58 lievre 2271: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2272: for (k=1; k<=7; k++) ncodemax[k]=0;
2273:
2274: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2275: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2276: modality*/
2277: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2278: Ndum[ij]++; /*store the modality */
1.53 brouard 2279: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2280: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2281: Tvar[j]. If V=sex and male is 0 and
2282: female is 1, then cptcode=1.*/
1.53 brouard 2283: }
2284:
2285: for (i=0; i<=cptcode; i++) {
1.58 lievre 2286: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1.53 brouard 2287: }
1.58 lievre 2288:
1.53 brouard 2289: ij=1;
2290: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2291: for (k=0; k<= maxncov; k++) {
1.53 brouard 2292: if (Ndum[k] != 0) {
2293: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2294: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.53 brouard 2295:
2296: ij++;
2297: }
2298: if (ij > ncodemax[j]) break;
2299: }
2300: }
2301: }
2302:
1.58 lievre 2303: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2304:
1.58 lievre 2305: for (i=1; i<=ncovmodel-2; i++) {
1.104 lievre 2306: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 2307: ij=Tvar[i];
1.58 lievre 2308: Ndum[ij]++;
1.53 brouard 2309: }
2310:
2311: ij=1;
1.58 lievre 2312: for (i=1; i<= maxncov; i++) {
1.53 brouard 2313: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2314: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2315: ij++;
2316: }
2317: }
2318:
1.58 lievre 2319: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2320: }
2321:
2322: /*********** Health Expectancies ****************/
2323:
1.105 lievre 2324: 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,char strstart[] )
1.53 brouard 2325:
2326: {
2327: /* Health expectancies */
2328: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2329: double age, agelim, hf;
2330: double ***p3mat,***varhe;
2331: double **dnewm,**doldm;
2332: double *xp;
2333: double **gp, **gm;
2334: double ***gradg, ***trgradg;
2335: int theta;
2336:
1.74 brouard 2337: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2338: xp=vector(1,npar);
1.74 brouard 2339: dnewm=matrix(1,nlstate*nlstate,1,npar);
2340: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2341:
1.105 lievre 2342: fprintf(ficreseij,"# Local time at start: %s", strstart);
1.53 brouard 2343: fprintf(ficreseij,"# Health expectancies\n");
2344: fprintf(ficreseij,"# Age");
2345: for(i=1; i<=nlstate;i++)
2346: for(j=1; j<=nlstate;j++)
2347: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2348: fprintf(ficreseij,"\n");
2349:
2350: if(estepm < stepm){
2351: printf ("Problem %d lower than %d\n",estepm, stepm);
2352: }
2353: else hstepm=estepm;
2354: /* We compute the life expectancy from trapezoids spaced every estepm months
2355: * This is mainly to measure the difference between two models: for example
2356: * if stepm=24 months pijx are given only every 2 years and by summing them
2357: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2358: * progression in between and thus overestimating or underestimating according
1.53 brouard 2359: * to the curvature of the survival function. If, for the same date, we
2360: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2361: * to compare the new estimate of Life expectancy with the same linear
2362: * hypothesis. A more precise result, taking into account a more precise
2363: * curvature will be obtained if estepm is as small as stepm. */
2364:
2365: /* For example we decided to compute the life expectancy with the smallest unit */
2366: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2367: nhstepm is the number of hstepm from age to agelim
2368: nstepm is the number of stepm from age to agelin.
2369: Look at hpijx to understand the reason of that which relies in memory size
2370: and note for a fixed period like estepm months */
2371: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2372: survival function given by stepm (the optimization length). Unfortunately it
2373: means that if the survival funtion is printed only each two years of age and if
2374: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2375: results. So we changed our mind and took the option of the best precision.
2376: */
2377: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2378:
2379: agelim=AGESUP;
2380: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2381: /* nhstepm age range expressed in number of stepm */
2382: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2383: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2384: /* if (stepm >= YEARM) hstepm=1;*/
2385: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2386: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2387: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2388: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2389: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2390:
2391: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2392: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2393: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2394:
2395:
2396: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2397:
1.95 brouard 2398: /* Computing Variances of health expectancies */
1.53 brouard 2399:
2400: for(theta=1; theta <=npar; theta++){
2401: for(i=1; i<=npar; i++){
2402: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2403: }
2404: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2405:
2406: cptj=0;
2407: for(j=1; j<= nlstate; j++){
2408: for(i=1; i<=nlstate; i++){
2409: cptj=cptj+1;
2410: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2411: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2412: }
2413: }
2414: }
2415:
2416:
2417: for(i=1; i<=npar; i++)
2418: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2419: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2420:
2421: cptj=0;
2422: for(j=1; j<= nlstate; j++){
2423: for(i=1;i<=nlstate;i++){
2424: cptj=cptj+1;
2425: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2426:
1.53 brouard 2427: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2428: }
2429: }
2430: }
1.74 brouard 2431: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2432: for(h=0; h<=nhstepm-1; h++){
2433: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2434: }
2435: }
2436:
2437: /* End theta */
2438:
1.74 brouard 2439: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2440:
2441: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2442: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2443: for(theta=1; theta <=npar; theta++)
2444: trgradg[h][j][theta]=gradg[h][theta][j];
2445:
2446:
1.74 brouard 2447: for(i=1;i<=nlstate*nlstate;i++)
2448: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2449: varhe[i][j][(int)age] =0.;
2450:
2451: printf("%d|",(int)age);fflush(stdout);
2452: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2453: for(h=0;h<=nhstepm-1;h++){
2454: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2455: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2456: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2457: for(i=1;i<=nlstate*nlstate;i++)
2458: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2459: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2460: }
2461: }
2462: /* Computing expectancies */
2463: for(i=1; i<=nlstate;i++)
2464: for(j=1; j<=nlstate;j++)
2465: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2466: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2467:
2468: /* 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]);*/
2469:
2470: }
2471:
2472: fprintf(ficreseij,"%3.0f",age );
2473: cptj=0;
2474: for(i=1; i<=nlstate;i++)
2475: for(j=1; j<=nlstate;j++){
2476: cptj++;
2477: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2478: }
2479: fprintf(ficreseij,"\n");
2480:
1.74 brouard 2481: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2482: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2483: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2484: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2485: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2486: }
2487: printf("\n");
2488: fprintf(ficlog,"\n");
2489:
2490: free_vector(xp,1,npar);
1.74 brouard 2491: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2492: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2493: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2494: }
2495:
2496: /************ Variance ******************/
1.105 lievre 2497: 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, char strstart[])
1.53 brouard 2498: {
2499: /* Variance of health expectancies */
2500: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2501: /* double **newm;*/
2502: double **dnewm,**doldm;
2503: double **dnewmp,**doldmp;
2504: int i, j, nhstepm, hstepm, h, nstepm ;
2505: int k, cptcode;
2506: double *xp;
2507: double **gp, **gm; /* for var eij */
2508: double ***gradg, ***trgradg; /*for var eij */
2509: double **gradgp, **trgradgp; /* for var p point j */
2510: double *gpp, *gmp; /* for var p point j */
2511: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2512: double ***p3mat;
2513: double age,agelim, hf;
2514: double ***mobaverage;
2515: int theta;
2516: char digit[4];
1.55 lievre 2517: char digitp[25];
1.53 brouard 2518:
2519: char fileresprobmorprev[FILENAMELENGTH];
2520:
1.55 lievre 2521: if(popbased==1){
1.58 lievre 2522: if(mobilav!=0)
1.55 lievre 2523: strcpy(digitp,"-populbased-mobilav-");
2524: else strcpy(digitp,"-populbased-nomobil-");
2525: }
2526: else
1.53 brouard 2527: strcpy(digitp,"-stablbased-");
1.56 lievre 2528:
1.54 brouard 2529: if (mobilav!=0) {
1.53 brouard 2530: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2531: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2532: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2533: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2534: }
1.53 brouard 2535: }
2536:
2537: strcpy(fileresprobmorprev,"prmorprev");
2538: sprintf(digit,"%-d",ij);
2539: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2540: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2541: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2542: strcat(fileresprobmorprev,fileres);
2543: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2544: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2545: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2546: }
2547: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2548:
1.53 brouard 2549: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2550: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
1.66 brouard 2551: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.53 brouard 2552: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2553: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2554: fprintf(ficresprobmorprev," p.%-d SE",j);
2555: for(i=1; i<=nlstate;i++)
2556: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2557: }
2558: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2559: fprintf(ficgp,"\n# Routine varevsij");
1.106 ! brouard 2560: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.87 brouard 2561: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2562: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2563: /* } */
1.53 brouard 2564: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.105 lievre 2565: fprintf(ficresvij, "#Local time at start: %s", strstart);
1.53 brouard 2566: 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");
2567: fprintf(ficresvij,"# Age");
2568: for(i=1; i<=nlstate;i++)
2569: for(j=1; j<=nlstate;j++)
2570: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2571: fprintf(ficresvij,"\n");
2572:
2573: xp=vector(1,npar);
2574: dnewm=matrix(1,nlstate,1,npar);
2575: doldm=matrix(1,nlstate,1,nlstate);
2576: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2577: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2578:
2579: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2580: gpp=vector(nlstate+1,nlstate+ndeath);
2581: gmp=vector(nlstate+1,nlstate+ndeath);
2582: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2583:
2584: if(estepm < stepm){
2585: printf ("Problem %d lower than %d\n",estepm, stepm);
2586: }
2587: else hstepm=estepm;
2588: /* For example we decided to compute the life expectancy with the smallest unit */
2589: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2590: nhstepm is the number of hstepm from age to agelim
2591: nstepm is the number of stepm from age to agelin.
2592: Look at hpijx to understand the reason of that which relies in memory size
2593: and note for a fixed period like k years */
2594: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2595: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2596: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2597: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2598: results. So we changed our mind and took the option of the best precision.
2599: */
2600: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2601: agelim = AGESUP;
2602: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2603: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2604: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2605: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2606: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2607: gp=matrix(0,nhstepm,1,nlstate);
2608: gm=matrix(0,nhstepm,1,nlstate);
2609:
2610:
2611: for(theta=1; theta <=npar; theta++){
1.66 brouard 2612: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2613: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2614: }
2615: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2616: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2617:
2618: if (popbased==1) {
1.54 brouard 2619: if(mobilav ==0){
1.53 brouard 2620: for(i=1; i<=nlstate;i++)
2621: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2622: }else{ /* mobilav */
1.53 brouard 2623: for(i=1; i<=nlstate;i++)
2624: prlim[i][i]=mobaverage[(int)age][i][ij];
2625: }
2626: }
2627:
2628: for(j=1; j<= nlstate; j++){
2629: for(h=0; h<=nhstepm; h++){
2630: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2631: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2632: }
2633: }
1.66 brouard 2634: /* This for computing probability of death (h=1 means
2635: computed over hstepm matrices product = hstepm*stepm months)
2636: as a weighted average of prlim.
2637: */
1.69 brouard 2638: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2639: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2640: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2641: }
1.66 brouard 2642: /* end probability of death */
1.53 brouard 2643:
1.66 brouard 2644: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2645: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2646: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2647: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2648:
2649: if (popbased==1) {
1.54 brouard 2650: if(mobilav ==0){
1.53 brouard 2651: for(i=1; i<=nlstate;i++)
2652: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2653: }else{ /* mobilav */
1.53 brouard 2654: for(i=1; i<=nlstate;i++)
2655: prlim[i][i]=mobaverage[(int)age][i][ij];
2656: }
2657: }
2658:
2659: for(j=1; j<= nlstate; j++){
2660: for(h=0; h<=nhstepm; h++){
2661: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2662: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2663: }
2664: }
1.66 brouard 2665: /* This for computing probability of death (h=1 means
2666: computed over hstepm matrices product = hstepm*stepm months)
2667: as a weighted average of prlim.
2668: */
1.69 brouard 2669: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2670: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2671: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2672: }
1.66 brouard 2673: /* end probability of death */
1.53 brouard 2674:
2675: for(j=1; j<= nlstate; j++) /* vareij */
2676: for(h=0; h<=nhstepm; h++){
2677: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2678: }
1.68 lievre 2679:
1.53 brouard 2680: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2681: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2682: }
2683:
2684: } /* End theta */
2685:
2686: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2687:
2688: for(h=0; h<=nhstepm; h++) /* veij */
2689: for(j=1; j<=nlstate;j++)
2690: for(theta=1; theta <=npar; theta++)
2691: trgradg[h][j][theta]=gradg[h][theta][j];
2692:
2693: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2694: for(theta=1; theta <=npar; theta++)
1.53 brouard 2695: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2696:
1.53 brouard 2697:
2698: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2699: for(i=1;i<=nlstate;i++)
2700: for(j=1;j<=nlstate;j++)
2701: vareij[i][j][(int)age] =0.;
2702:
2703: for(h=0;h<=nhstepm;h++){
2704: for(k=0;k<=nhstepm;k++){
2705: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2706: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2707: for(i=1;i<=nlstate;i++)
2708: for(j=1;j<=nlstate;j++)
2709: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2710: }
2711: }
1.70 brouard 2712:
1.53 brouard 2713: /* pptj */
2714: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2715: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2716: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2717: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2718: varppt[j][i]=doldmp[j][i];
2719: /* end ppptj */
1.66 brouard 2720: /* x centered again */
1.53 brouard 2721: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2722: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2723:
2724: if (popbased==1) {
1.54 brouard 2725: if(mobilav ==0){
1.53 brouard 2726: for(i=1; i<=nlstate;i++)
2727: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2728: }else{ /* mobilav */
1.53 brouard 2729: for(i=1; i<=nlstate;i++)
2730: prlim[i][i]=mobaverage[(int)age][i][ij];
2731: }
2732: }
1.70 brouard 2733:
1.66 brouard 2734: /* This for computing probability of death (h=1 means
2735: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2736: as a weighted average of prlim.
2737: */
1.68 lievre 2738: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2739: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2740: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2741: }
1.66 brouard 2742: /* end probability of death */
1.53 brouard 2743:
2744: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2745: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2746: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2747: for(i=1; i<=nlstate;i++){
2748: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2749: }
2750: }
2751: fprintf(ficresprobmorprev,"\n");
2752:
2753: fprintf(ficresvij,"%.0f ",age );
2754: for(i=1; i<=nlstate;i++)
2755: for(j=1; j<=nlstate;j++){
2756: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2757: }
2758: fprintf(ficresvij,"\n");
2759: free_matrix(gp,0,nhstepm,1,nlstate);
2760: free_matrix(gm,0,nhstepm,1,nlstate);
2761: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2762: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2763: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2764: } /* End age */
2765: free_vector(gpp,nlstate+1,nlstate+ndeath);
2766: free_vector(gmp,nlstate+1,nlstate+ndeath);
2767: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2768: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2769: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2770: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2771: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2772: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2773: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2774: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2775: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2776: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2777: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2778: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2779: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2780: /* 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);
2781: */
1.88 brouard 2782: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2783: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2784:
2785: free_vector(xp,1,npar);
2786: free_matrix(doldm,1,nlstate,1,nlstate);
2787: free_matrix(dnewm,1,nlstate,1,npar);
2788: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2789: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2790: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2791: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2792: fclose(ficresprobmorprev);
1.88 brouard 2793: fflush(ficgp);
2794: fflush(fichtm);
1.84 brouard 2795: } /* end varevsij */
1.53 brouard 2796:
2797: /************ Variance of prevlim ******************/
1.105 lievre 2798: 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, char strstart[])
1.53 brouard 2799: {
2800: /* Variance of prevalence limit */
1.59 brouard 2801: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2802: double **newm;
2803: double **dnewm,**doldm;
2804: int i, j, nhstepm, hstepm;
2805: int k, cptcode;
2806: double *xp;
2807: double *gp, *gm;
2808: double **gradg, **trgradg;
2809: double age,agelim;
2810: int theta;
1.105 lievre 2811: fprintf(ficresvpl, "#Local time at start: %s", strstart);
1.54 brouard 2812: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2813: fprintf(ficresvpl,"# Age");
2814: for(i=1; i<=nlstate;i++)
2815: fprintf(ficresvpl," %1d-%1d",i,i);
2816: fprintf(ficresvpl,"\n");
2817:
2818: xp=vector(1,npar);
2819: dnewm=matrix(1,nlstate,1,npar);
2820: doldm=matrix(1,nlstate,1,nlstate);
2821:
2822: hstepm=1*YEARM; /* Every year of age */
2823: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2824: agelim = AGESUP;
2825: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2826: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2827: if (stepm >= YEARM) hstepm=1;
2828: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2829: gradg=matrix(1,npar,1,nlstate);
2830: gp=vector(1,nlstate);
2831: gm=vector(1,nlstate);
2832:
2833: for(theta=1; theta <=npar; theta++){
2834: for(i=1; i<=npar; i++){ /* Computes gradient */
2835: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2836: }
2837: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2838: for(i=1;i<=nlstate;i++)
2839: gp[i] = prlim[i][i];
2840:
2841: for(i=1; i<=npar; i++) /* Computes gradient */
2842: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2843: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2844: for(i=1;i<=nlstate;i++)
2845: gm[i] = prlim[i][i];
2846:
2847: for(i=1;i<=nlstate;i++)
2848: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2849: } /* End theta */
2850:
2851: trgradg =matrix(1,nlstate,1,npar);
2852:
2853: for(j=1; j<=nlstate;j++)
2854: for(theta=1; theta <=npar; theta++)
2855: trgradg[j][theta]=gradg[theta][j];
2856:
2857: for(i=1;i<=nlstate;i++)
2858: varpl[i][(int)age] =0.;
2859: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2860: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2861: for(i=1;i<=nlstate;i++)
2862: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2863:
2864: fprintf(ficresvpl,"%.0f ",age );
2865: for(i=1; i<=nlstate;i++)
2866: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2867: fprintf(ficresvpl,"\n");
2868: free_vector(gp,1,nlstate);
2869: free_vector(gm,1,nlstate);
2870: free_matrix(gradg,1,npar,1,nlstate);
2871: free_matrix(trgradg,1,nlstate,1,npar);
2872: } /* End age */
2873:
2874: free_vector(xp,1,npar);
2875: free_matrix(doldm,1,nlstate,1,npar);
2876: free_matrix(dnewm,1,nlstate,1,nlstate);
2877:
2878: }
2879:
2880: /************ Variance of one-step probabilities ******************/
1.105 lievre 2881: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
1.53 brouard 2882: {
2883: int i, j=0, i1, k1, l1, t, tj;
2884: int k2, l2, j1, z1;
2885: int k=0,l, cptcode;
2886: int first=1, first1;
2887: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2888: double **dnewm,**doldm;
2889: double *xp;
2890: double *gp, *gm;
2891: double **gradg, **trgradg;
2892: double **mu;
2893: double age,agelim, cov[NCOVMAX];
2894: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2895: int theta;
2896: char fileresprob[FILENAMELENGTH];
2897: char fileresprobcov[FILENAMELENGTH];
2898: char fileresprobcor[FILENAMELENGTH];
2899:
2900: double ***varpij;
2901:
2902: strcpy(fileresprob,"prob");
2903: strcat(fileresprob,fileres);
2904: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2905: printf("Problem with resultfile: %s\n", fileresprob);
2906: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2907: }
2908: strcpy(fileresprobcov,"probcov");
2909: strcat(fileresprobcov,fileres);
2910: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2911: printf("Problem with resultfile: %s\n", fileresprobcov);
2912: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2913: }
2914: strcpy(fileresprobcor,"probcor");
2915: strcat(fileresprobcor,fileres);
2916: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2917: printf("Problem with resultfile: %s\n", fileresprobcor);
2918: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2919: }
2920: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2921: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2922: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2923: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2924: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2925: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.105 lievre 2926: fprintf(ficresprob, "#Local time at start: %s", strstart);
1.53 brouard 2927: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2928: fprintf(ficresprob,"# Age");
1.105 lievre 2929: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
1.53 brouard 2930: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2931: fprintf(ficresprobcov,"# Age");
1.105 lievre 2932: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
1.53 brouard 2933: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2934: fprintf(ficresprobcov,"# Age");
2935:
2936:
2937: for(i=1; i<=nlstate;i++)
2938: for(j=1; j<=(nlstate+ndeath);j++){
2939: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2940: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2941: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2942: }
1.69 brouard 2943: /* fprintf(ficresprob,"\n");
1.53 brouard 2944: fprintf(ficresprobcov,"\n");
2945: fprintf(ficresprobcor,"\n");
1.69 brouard 2946: */
2947: xp=vector(1,npar);
1.53 brouard 2948: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2949: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2950: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2951: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2952: first=1;
1.88 brouard 2953: fprintf(ficgp,"\n# Routine varprob");
2954: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2955: fprintf(fichtm,"\n");
2956:
1.95 brouard 2957: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2958: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 2959: file %s<br>\n",optionfilehtmcov);
2960: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2961: and drawn. It helps understanding how is the covariance between two incidences.\
2962: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2963: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
2964: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2965: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2966: standard deviations wide on each axis. <br>\
2967: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2968: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2969: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
1.53 brouard 2970:
2971: cov[1]=1;
2972: tj=cptcoveff;
2973: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2974: j1=0;
2975: for(t=1; t<=tj;t++){
2976: for(i1=1; i1<=ncodemax[t];i1++){
2977: j1++;
2978: if (cptcovn>0) {
2979: fprintf(ficresprob, "\n#********** Variable ");
2980: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2981: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2982: fprintf(ficresprobcov, "\n#********** Variable ");
2983: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2984: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2985:
2986: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2987: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2988: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2989:
2990:
1.96 brouard 2991: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 2992: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 2993: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 2994:
2995: fprintf(ficresprobcor, "\n#********** Variable ");
2996: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2997: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2998: }
2999:
3000: for (age=bage; age<=fage; age ++){
3001: cov[2]=age;
3002: for (k=1; k<=cptcovn;k++) {
3003: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3004: }
3005: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3006: for (k=1; k<=cptcovprod;k++)
3007: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3008:
3009: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3010: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3011: gp=vector(1,(nlstate)*(nlstate+ndeath));
3012: gm=vector(1,(nlstate)*(nlstate+ndeath));
3013:
3014: for(theta=1; theta <=npar; theta++){
3015: for(i=1; i<=npar; i++)
1.74 brouard 3016: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 3017:
3018: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3019:
3020: k=0;
3021: for(i=1; i<= (nlstate); i++){
3022: for(j=1; j<=(nlstate+ndeath);j++){
3023: k=k+1;
3024: gp[k]=pmmij[i][j];
3025: }
3026: }
3027:
3028: for(i=1; i<=npar; i++)
1.74 brouard 3029: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 3030:
3031: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3032: k=0;
3033: for(i=1; i<=(nlstate); i++){
3034: for(j=1; j<=(nlstate+ndeath);j++){
3035: k=k+1;
3036: gm[k]=pmmij[i][j];
3037: }
3038: }
3039:
3040: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 3041: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 3042: }
3043:
3044: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3045: for(theta=1; theta <=npar; theta++)
3046: trgradg[j][theta]=gradg[theta][j];
3047:
3048: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3049: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 3050: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3051: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3052: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3053: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3054:
1.53 brouard 3055: pmij(pmmij,cov,ncovmodel,x,nlstate);
3056:
3057: k=0;
3058: for(i=1; i<=(nlstate); i++){
3059: for(j=1; j<=(nlstate+ndeath);j++){
3060: k=k+1;
3061: mu[k][(int) age]=pmmij[i][j];
3062: }
3063: }
3064: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3065: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3066: varpij[i][j][(int)age] = doldm[i][j];
3067:
3068: /*printf("\n%d ",(int)age);
1.59 brouard 3069: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3070: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3071: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3072: }*/
1.53 brouard 3073:
3074: fprintf(ficresprob,"\n%d ",(int)age);
3075: fprintf(ficresprobcov,"\n%d ",(int)age);
3076: fprintf(ficresprobcor,"\n%d ",(int)age);
3077:
3078: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3079: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3080: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3081: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3082: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3083: }
3084: i=0;
3085: for (k=1; k<=(nlstate);k++){
3086: for (l=1; l<=(nlstate+ndeath);l++){
3087: i=i++;
3088: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3089: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3090: for (j=1; j<=i;j++){
3091: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3092: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3093: }
3094: }
3095: }/* end of loop for state */
3096: } /* end of loop for age */
3097:
3098: /* Confidence intervalle of pij */
3099: /*
1.59 brouard 3100: fprintf(ficgp,"\nset noparametric;unset label");
3101: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3102: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3103: 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);
3104: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3105: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3106: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3107: */
3108:
3109: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3110: first1=1;
3111: for (k2=1; k2<=(nlstate);k2++){
3112: for (l2=1; l2<=(nlstate+ndeath);l2++){
3113: if(l2==k2) continue;
3114: j=(k2-1)*(nlstate+ndeath)+l2;
3115: for (k1=1; k1<=(nlstate);k1++){
3116: for (l1=1; l1<=(nlstate+ndeath);l1++){
3117: if(l1==k1) continue;
3118: i=(k1-1)*(nlstate+ndeath)+l1;
3119: if(i<=j) continue;
3120: for (age=bage; age<=fage; age ++){
3121: if ((int)age %5==0){
3122: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3123: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3124: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3125: mu1=mu[i][(int) age]/stepm*YEARM ;
3126: mu2=mu[j][(int) age]/stepm*YEARM;
3127: c12=cv12/sqrt(v1*v2);
3128: /* Computing eigen value of matrix of covariance */
3129: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3130: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3131: /* Eigen vectors */
3132: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3133: /*v21=sqrt(1.-v11*v11); *//* error */
3134: v21=(lc1-v1)/cv12*v11;
3135: v12=-v21;
3136: v22=v11;
3137: tnalp=v21/v11;
3138: if(first1==1){
3139: first1=0;
3140: 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);
3141: }
3142: 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);
3143: /*printf(fignu*/
3144: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3145: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3146: if(first==1){
3147: first=0;
3148: fprintf(ficgp,"\nset parametric;unset label");
3149: 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);
3150: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3151: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3152: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3153: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3154: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3155: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3156: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3157: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3158: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3159: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3160: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3161: 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",\
3162: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3163: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3164: }else{
3165: first=0;
1.91 brouard 3166: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3167: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3168: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3169: 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",\
3170: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3171: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3172: }/* if first */
3173: } /* age mod 5 */
3174: } /* end loop age */
1.88 brouard 3175: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3176: first=1;
3177: } /*l12 */
3178: } /* k12 */
3179: } /*l1 */
3180: }/* k1 */
3181: } /* loop covariates */
3182: }
1.59 brouard 3183: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3184: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3185: free_vector(xp,1,npar);
3186: fclose(ficresprob);
3187: fclose(ficresprobcov);
3188: fclose(ficresprobcor);
1.91 brouard 3189: fflush(ficgp);
3190: fflush(fichtmcov);
1.53 brouard 3191: }
3192:
3193:
3194: /******************* Printing html file ***********/
3195: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3196: int lastpass, int stepm, int weightopt, char model[],\
3197: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3198: int popforecast, int estepm ,\
3199: double jprev1, double mprev1,double anprev1, \
3200: double jprev2, double mprev2,double anprev2){
3201: int jj1, k1, i1, cpt;
3202:
1.106 ! brouard 3203: fprintf(fichtm,"<ul><li><a> href="#firstorder">Result files (first order: no variance)</a>\n \
! 3204: <li><a> href="#secondorder">Result files (second order (variance)</a>\n \
! 3205: </ul>");
! 3206: fprintf(fichtm,"<ul><li><h4><a name="firstorder">Result files (first order: no variance)</a></h4>\n \
1.96 brouard 3207: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3208: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3209: fprintf(fichtm,"\
3210: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3211: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3212: fprintf(fichtm,"\
3213: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3214: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3215: fprintf(fichtm,"\
1.85 brouard 3216: - Life expectancies by age and initial health status (estepm=%2d months): \
1.96 brouard 3217: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3218: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3219:
3220: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3221:
3222: m=cptcoveff;
3223: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3224:
3225: jj1=0;
3226: for(k1=1; k1<=m;k1++){
3227: for(i1=1; i1<=ncodemax[k1];i1++){
3228: jj1++;
3229: if (cptcovn > 0) {
3230: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3231: for (cpt=1; cpt<=cptcoveff;cpt++)
3232: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3233: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3234: }
3235: /* Pij */
1.88 brouard 3236: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
3237: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3238: /* Quasi-incidences */
1.85 brouard 3239: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3240: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3241: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3242: /* Stable prevalence in each health state */
3243: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3244: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3245: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3246: }
3247: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3248: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3249: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3250: }
3251: } /* end i1 */
3252: }/* End k1 */
3253: fprintf(fichtm,"</ul>");
3254:
3255:
1.96 brouard 3256: fprintf(fichtm,"\
1.106 ! brouard 3257: \n<br><li><h4> <a name="secondorder">Result files (second order: variances)</a></h4>\n\
1.96 brouard 3258: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3259:
3260: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3261: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3262: fprintf(fichtm,"\
3263: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3264: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3265:
3266: fprintf(fichtm,"\
3267: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3268: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3269: fprintf(fichtm,"\
3270: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3271: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3272: fprintf(fichtm,"\
3273: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3274: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3275: fprintf(fichtm,"\
1.88 brouard 3276: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3277: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3278:
1.76 brouard 3279: /* if(popforecast==1) fprintf(fichtm,"\n */
3280: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3281: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3282: /* <br>",fileres,fileres,fileres,fileres); */
3283: /* else */
3284: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
1.96 brouard 3285: fflush(fichtm);
3286: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3287:
3288: m=cptcoveff;
3289: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3290:
3291: jj1=0;
3292: for(k1=1; k1<=m;k1++){
3293: for(i1=1; i1<=ncodemax[k1];i1++){
3294: jj1++;
3295: if (cptcovn > 0) {
3296: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3297: for (cpt=1; cpt<=cptcoveff;cpt++)
3298: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3299: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3300: }
3301: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3302: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3303: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3304: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3305: }
1.96 brouard 3306: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3307: health expectancies in states (1) and (2): %s%d.png<br>\
3308: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3309: } /* end i1 */
3310: }/* End k1 */
3311: fprintf(fichtm,"</ul>");
1.87 brouard 3312: fflush(fichtm);
1.53 brouard 3313: }
3314:
3315: /******************* Gnuplot file **************/
1.89 brouard 3316: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3317:
1.88 brouard 3318: char dirfileres[132],optfileres[132];
1.53 brouard 3319: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3320: int ng;
1.88 brouard 3321: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3322: /* printf("Problem with file %s",optionfilegnuplot); */
3323: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3324: /* } */
1.53 brouard 3325:
1.54 brouard 3326: /*#ifdef windows */
1.89 brouard 3327: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3328: /*#endif */
1.88 brouard 3329: m=pow(2,cptcoveff);
3330:
3331: strcpy(dirfileres,optionfilefiname);
3332: strcpy(optfileres,"vpl");
1.53 brouard 3333: /* 1eme*/
3334: for (cpt=1; cpt<= nlstate ; cpt ++) {
3335: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3336: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3337: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3338: fprintf(ficgp,"set xlabel \"Age\" \n\
3339: set ylabel \"Probability\" \n\
3340: set ter png small\n\
3341: set size 0.65,0.65\n\
3342: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3343:
3344: for (i=1; i<= nlstate ; i ++) {
3345: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3346: else fprintf(ficgp," \%%*lf (\%%*lf)");
3347: }
1.88 brouard 3348: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3349: for (i=1; i<= nlstate ; i ++) {
3350: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3351: else fprintf(ficgp," \%%*lf (\%%*lf)");
3352: }
1.88 brouard 3353: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3354: for (i=1; i<= nlstate ; i ++) {
3355: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3356: else fprintf(ficgp," \%%*lf (\%%*lf)");
3357: }
1.88 brouard 3358: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3359: }
3360: }
3361: /*2 eme*/
3362:
3363: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3364: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3365: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3366:
3367: for (i=1; i<= nlstate+1 ; i ++) {
3368: k=2*i;
1.88 brouard 3369: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3370: for (j=1; j<= nlstate+1 ; j ++) {
3371: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3372: else fprintf(ficgp," \%%*lf (\%%*lf)");
3373: }
3374: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3375: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3376: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3377: for (j=1; j<= nlstate+1 ; j ++) {
3378: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3379: else fprintf(ficgp," \%%*lf (\%%*lf)");
3380: }
3381: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3382: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3383: for (j=1; j<= nlstate+1 ; j ++) {
3384: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3385: else fprintf(ficgp," \%%*lf (\%%*lf)");
3386: }
3387: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3388: else fprintf(ficgp,"\" t\"\" w l 0,");
3389: }
3390: }
3391:
3392: /*3eme*/
3393:
3394: for (k1=1; k1<= m ; k1 ++) {
3395: for (cpt=1; cpt<= nlstate ; cpt ++) {
3396: k=2+nlstate*(2*cpt-2);
1.88 brouard 3397: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3398: fprintf(ficgp,"set ter png small\n\
3399: set size 0.65,0.65\n\
3400: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3401: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3402: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3403: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3404: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3405: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3406: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3407:
3408: */
3409: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3410: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
1.53 brouard 3411:
3412: }
3413: }
3414: }
3415:
1.76 brouard 3416: /* CV preval stable (period) */
1.53 brouard 3417: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3418: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3419: k=3;
1.88 brouard 3420: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3421: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3422: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3423: unset log y\n\
1.88 brouard 3424: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3425:
1.83 lievre 3426: for (i=1; i< nlstate ; i ++)
1.53 brouard 3427: fprintf(ficgp,"+$%d",k+i+1);
3428: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3429:
3430: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3431: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3432: for (i=1; i< nlstate ; i ++) {
3433: l=3+(nlstate+ndeath)*cpt;
3434: fprintf(ficgp,"+$%d",l+i+1);
3435: }
3436: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3437: }
3438: }
3439:
3440: /* proba elementaires */
3441: for(i=1,jk=1; i <=nlstate; i++){
3442: for(k=1; k <=(nlstate+ndeath); k++){
3443: if (k != i) {
3444: for(j=1; j <=ncovmodel; j++){
3445: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3446: jk++;
3447: fprintf(ficgp,"\n");
3448: }
3449: }
3450: }
3451: }
3452:
3453: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3454: for(jk=1; jk <=m; jk++) {
1.88 brouard 3455: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3456: if (ng==2)
3457: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3458: else
3459: fprintf(ficgp,"\nset title \"Probability\"\n");
3460: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3461: i=1;
3462: for(k2=1; k2<=nlstate; k2++) {
3463: k3=i;
3464: for(k=1; k<=(nlstate+ndeath); k++) {
3465: if (k != k2){
3466: if(ng==2)
3467: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3468: else
3469: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3470: ij=1;
3471: for(j=3; j <=ncovmodel; j++) {
3472: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3473: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3474: ij++;
3475: }
3476: else
3477: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3478: }
3479: fprintf(ficgp,")/(1");
3480:
3481: for(k1=1; k1 <=nlstate; k1++){
3482: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3483: ij=1;
3484: for(j=3; j <=ncovmodel; j++){
3485: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3486: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3487: ij++;
3488: }
3489: else
3490: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3491: }
3492: fprintf(ficgp,")");
3493: }
3494: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3495: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3496: i=i+ncovmodel;
3497: }
3498: } /* end k */
3499: } /* end k2 */
3500: } /* end jk */
3501: } /* end ng */
1.88 brouard 3502: fflush(ficgp);
1.53 brouard 3503: } /* end gnuplot */
3504:
3505:
3506: /*************** Moving average **************/
1.54 brouard 3507: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3508:
3509: int i, cpt, cptcod;
1.58 lievre 3510: int modcovmax =1;
1.54 brouard 3511: int mobilavrange, mob;
1.53 brouard 3512: double age;
1.58 lievre 3513:
3514: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3515: a covariate has 2 modalities */
3516: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3517:
1.54 brouard 3518: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3519: if(mobilav==1) mobilavrange=5; /* default */
3520: else mobilavrange=mobilav;
3521: for (age=bage; age<=fage; age++)
3522: for (i=1; i<=nlstate;i++)
1.58 lievre 3523: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3524: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3525: /* We keep the original values on the extreme ages bage, fage and for
3526: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3527: we use a 5 terms etc. until the borders are no more concerned.
3528: */
3529: for (mob=3;mob <=mobilavrange;mob=mob+2){
3530: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3531: for (i=1; i<=nlstate;i++){
1.58 lievre 3532: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3533: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3534: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3535: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3536: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3537: }
3538: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3539: }
1.53 brouard 3540: }
1.54 brouard 3541: }/* end age */
3542: }/* end mob */
3543: }else return -1;
3544: return 0;
3545: }/* End movingaverage */
1.53 brouard 3546:
3547:
3548: /************** Forecasting ******************/
1.70 brouard 3549: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.69 brouard 3550: /* proj1, year, month, day of starting projection
3551: agemin, agemax range of age
3552: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3553: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3554: */
1.73 lievre 3555: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3556: int *popage;
1.70 brouard 3557: double agec; /* generic age */
3558: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3559: double *popeffectif,*popcount;
3560: double ***p3mat;
1.55 lievre 3561: double ***mobaverage;
1.53 brouard 3562: char fileresf[FILENAMELENGTH];
3563:
1.69 brouard 3564: agelim=AGESUP;
1.84 brouard 3565: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3566:
3567: strcpy(fileresf,"f");
3568: strcat(fileresf,fileres);
3569: if((ficresf=fopen(fileresf,"w"))==NULL) {
3570: printf("Problem with forecast resultfile: %s\n", fileresf);
3571: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3572: }
3573: printf("Computing forecasting: result on file '%s' \n", fileresf);
3574: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3575:
3576: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3577:
1.54 brouard 3578: if (mobilav!=0) {
1.53 brouard 3579: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3580: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3581: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3582: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3583: }
1.53 brouard 3584: }
3585:
3586: stepsize=(int) (stepm+YEARM-1)/YEARM;
3587: if (stepm<=12) stepsize=1;
1.74 brouard 3588: if(estepm < stepm){
3589: printf ("Problem %d lower than %d\n",estepm, stepm);
3590: }
3591: else hstepm=estepm;
3592:
1.53 brouard 3593: hstepm=hstepm/stepm;
1.69 brouard 3594: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3595: fractional in yp1 */
1.53 brouard 3596: anprojmean=yp;
3597: yp2=modf((yp1*12),&yp);
3598: mprojmean=yp;
3599: yp1=modf((yp2*30.5),&yp);
3600: jprojmean=yp;
3601: if(jprojmean==0) jprojmean=1;
3602: if(mprojmean==0) jprojmean=1;
1.73 lievre 3603:
3604: i1=cptcoveff;
3605: if (cptcovn < 1){i1=1;}
1.53 brouard 3606:
1.70 brouard 3607: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3608:
1.70 brouard 3609: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3610:
1.75 brouard 3611: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3612: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3613: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3614: k=k+1;
3615: fprintf(ficresf,"\n#******");
3616: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3617: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.53 brouard 3618: }
3619: fprintf(ficresf,"******\n");
1.70 brouard 3620: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3621: for(j=1; j<=nlstate+ndeath;j++){
3622: for(i=1; i<=nlstate;i++)
3623: fprintf(ficresf," p%d%d",i,j);
3624: fprintf(ficresf," p.%d",j);
3625: }
1.74 brouard 3626: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3627: fprintf(ficresf,"\n");
1.70 brouard 3628: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3629:
1.71 brouard 3630: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3631: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3632: nhstepm = nhstepm/hstepm;
3633: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3634: oldm=oldms;savm=savms;
1.70 brouard 3635: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3636:
3637: for (h=0; h<=nhstepm; h++){
1.75 brouard 3638: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3639: fprintf(ficresf,"\n");
3640: for(j=1;j<=cptcoveff;j++)
3641: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3642: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3643: }
3644: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3645: ppij=0.;
1.71 brouard 3646: for(i=1; i<=nlstate;i++) {
1.53 brouard 3647: if (mobilav==1)
1.71 brouard 3648: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3649: else {
1.71 brouard 3650: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3651: }
1.75 brouard 3652: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3653: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3654: }
3655: } /* end i */
3656: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3657: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3658: }
1.75 brouard 3659: }/* end j */
3660: } /* end h */
1.53 brouard 3661: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3662: } /* end agec */
3663: } /* end yearp */
3664: } /* end cptcod */
3665: } /* end cptcov */
1.53 brouard 3666:
1.54 brouard 3667: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3668:
3669: fclose(ficresf);
3670: }
1.70 brouard 3671:
3672: /************** Forecasting *****not tested NB*************/
1.53 brouard 3673: 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){
3674:
3675: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3676: int *popage;
1.69 brouard 3677: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3678: double *popeffectif,*popcount;
3679: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3680: double ***mobaverage;
1.53 brouard 3681: char filerespop[FILENAMELENGTH];
3682:
3683: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3684: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3685: agelim=AGESUP;
1.69 brouard 3686: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3687:
1.84 brouard 3688: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3689:
3690:
3691: strcpy(filerespop,"pop");
3692: strcat(filerespop,fileres);
3693: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3694: printf("Problem with forecast resultfile: %s\n", filerespop);
3695: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3696: }
3697: printf("Computing forecasting: result on file '%s' \n", filerespop);
3698: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3699:
3700: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3701:
1.54 brouard 3702: if (mobilav!=0) {
1.53 brouard 3703: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3704: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3705: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3706: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3707: }
1.53 brouard 3708: }
3709:
3710: stepsize=(int) (stepm+YEARM-1)/YEARM;
3711: if (stepm<=12) stepsize=1;
3712:
3713: agelim=AGESUP;
3714:
3715: hstepm=1;
3716: hstepm=hstepm/stepm;
3717:
3718: if (popforecast==1) {
3719: if((ficpop=fopen(popfile,"r"))==NULL) {
3720: printf("Problem with population file : %s\n",popfile);exit(0);
3721: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3722: }
3723: popage=ivector(0,AGESUP);
3724: popeffectif=vector(0,AGESUP);
3725: popcount=vector(0,AGESUP);
3726:
3727: i=1;
3728: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3729:
3730: imx=i;
3731: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3732: }
3733:
1.69 brouard 3734: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3735: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3736: k=k+1;
3737: fprintf(ficrespop,"\n#******");
3738: for(j=1;j<=cptcoveff;j++) {
3739: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3740: }
3741: fprintf(ficrespop,"******\n");
3742: fprintf(ficrespop,"# Age");
3743: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3744: if (popforecast==1) fprintf(ficrespop," [Population]");
3745:
3746: for (cpt=0; cpt<=0;cpt++) {
3747: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3748:
1.69 brouard 3749: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3750: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3751: nhstepm = nhstepm/hstepm;
3752:
3753: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3754: oldm=oldms;savm=savms;
3755: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3756:
3757: for (h=0; h<=nhstepm; h++){
1.69 brouard 3758: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3759: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3760: }
3761: for(j=1; j<=nlstate+ndeath;j++) {
3762: kk1=0.;kk2=0;
3763: for(i=1; i<=nlstate;i++) {
3764: if (mobilav==1)
3765: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3766: else {
3767: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3768: }
3769: }
1.69 brouard 3770: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3771: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3772: /*fprintf(ficrespop," %.3f", kk1);
3773: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3774: }
3775: }
3776: for(i=1; i<=nlstate;i++){
3777: kk1=0.;
3778: for(j=1; j<=nlstate;j++){
3779: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3780: }
1.69 brouard 3781: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3782: }
3783:
1.69 brouard 3784: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3785: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3786: }
3787: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3788: }
3789: }
3790:
3791: /******/
3792:
3793: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3794: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3795: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3796: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3797: nhstepm = nhstepm/hstepm;
3798:
3799: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3800: oldm=oldms;savm=savms;
3801: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3802: for (h=0; h<=nhstepm; h++){
1.69 brouard 3803: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3804: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3805: }
3806: for(j=1; j<=nlstate+ndeath;j++) {
3807: kk1=0.;kk2=0;
3808: for(i=1; i<=nlstate;i++) {
3809: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3810: }
1.69 brouard 3811: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3812: }
3813: }
3814: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3815: }
3816: }
3817: }
3818: }
3819:
1.54 brouard 3820: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3821:
3822: if (popforecast==1) {
3823: free_ivector(popage,0,AGESUP);
3824: free_vector(popeffectif,0,AGESUP);
3825: free_vector(popcount,0,AGESUP);
3826: }
3827: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3828: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3829: fclose(ficrespop);
1.84 brouard 3830: } /* End of popforecast */
1.53 brouard 3831:
1.87 brouard 3832: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3833: {
1.87 brouard 3834: if((fichier=fopen(optionfich,"a"))==NULL) {
3835: printf("Problem with file: %s\n", optionfich);
3836: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3837: return (0);
1.86 brouard 3838: }
1.87 brouard 3839: fflush(fichier);
3840: return (1);
1.86 brouard 3841: }
1.94 brouard 3842:
3843:
3844: /**************** function prwizard **********************/
1.88 brouard 3845: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3846: {
3847:
1.94 brouard 3848: /* Wizard to print covariance matrix template */
3849:
1.88 brouard 3850: char ca[32], cb[32], cc[32];
3851: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3852: int numlinepar;
3853:
3854: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3855: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3856: for(i=1; i <=nlstate; i++){
3857: jj=0;
3858: for(j=1; j <=nlstate+ndeath; j++){
3859: if(j==i) continue;
3860: jj++;
3861: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3862: printf("%1d%1d",i,j);
3863: fprintf(ficparo,"%1d%1d",i,j);
3864: for(k=1; k<=ncovmodel;k++){
3865: /* printf(" %lf",param[i][j][k]); */
3866: /* fprintf(ficparo," %lf",param[i][j][k]); */
3867: printf(" 0.");
3868: fprintf(ficparo," 0.");
3869: }
3870: printf("\n");
3871: fprintf(ficparo,"\n");
3872: }
3873: }
3874: printf("# Scales (for hessian or gradient estimation)\n");
3875: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3876: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3877: for(i=1; i <=nlstate; i++){
3878: jj=0;
3879: for(j=1; j <=nlstate+ndeath; j++){
3880: if(j==i) continue;
3881: jj++;
3882: fprintf(ficparo,"%1d%1d",i,j);
3883: printf("%1d%1d",i,j);
3884: fflush(stdout);
3885: for(k=1; k<=ncovmodel;k++){
3886: /* printf(" %le",delti3[i][j][k]); */
3887: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3888: printf(" 0.");
3889: fprintf(ficparo," 0.");
3890: }
3891: numlinepar++;
3892: printf("\n");
3893: fprintf(ficparo,"\n");
3894: }
3895: }
3896: printf("# Covariance matrix\n");
3897: /* # 121 Var(a12)\n\ */
3898: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3899: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3900: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3901: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3902: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3903: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3904: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3905: fflush(stdout);
3906: fprintf(ficparo,"# Covariance matrix\n");
3907: /* # 121 Var(a12)\n\ */
3908: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3909: /* # ...\n\ */
3910: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3911:
3912: for(itimes=1;itimes<=2;itimes++){
3913: jj=0;
3914: for(i=1; i <=nlstate; i++){
3915: for(j=1; j <=nlstate+ndeath; j++){
3916: if(j==i) continue;
3917: for(k=1; k<=ncovmodel;k++){
3918: jj++;
3919: ca[0]= k+'a'-1;ca[1]='\0';
3920: if(itimes==1){
3921: printf("#%1d%1d%d",i,j,k);
3922: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3923: }else{
3924: printf("%1d%1d%d",i,j,k);
3925: fprintf(ficparo,"%1d%1d%d",i,j,k);
3926: /* printf(" %.5le",matcov[i][j]); */
3927: }
3928: ll=0;
3929: for(li=1;li <=nlstate; li++){
3930: for(lj=1;lj <=nlstate+ndeath; lj++){
3931: if(lj==li) continue;
3932: for(lk=1;lk<=ncovmodel;lk++){
3933: ll++;
3934: if(ll<=jj){
3935: cb[0]= lk +'a'-1;cb[1]='\0';
3936: if(ll<jj){
3937: if(itimes==1){
3938: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3939: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3940: }else{
3941: printf(" 0.");
3942: fprintf(ficparo," 0.");
3943: }
3944: }else{
3945: if(itimes==1){
3946: printf(" Var(%s%1d%1d)",ca,i,j);
3947: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3948: }else{
3949: printf(" 0.");
3950: fprintf(ficparo," 0.");
3951: }
3952: }
3953: }
3954: } /* end lk */
3955: } /* end lj */
3956: } /* end li */
3957: printf("\n");
3958: fprintf(ficparo,"\n");
3959: numlinepar++;
3960: } /* end k*/
3961: } /*end j */
3962: } /* end i */
1.95 brouard 3963: } /* end itimes */
1.88 brouard 3964:
3965: } /* end of prwizard */
1.98 brouard 3966: /******************* Gompertz Likelihood ******************************/
3967: double gompertz(double x[])
3968: {
3969: double A,B,L=0.0,sump=0.,num=0.;
3970: int i,n=0; /* n is the size of the sample */
3971: for (i=0;i<=imx-1 ; i++) {
3972: sump=sump+weight[i];
1.103 lievre 3973: /* sump=sump+1;*/
1.98 brouard 3974: num=num+1;
3975: }
3976:
3977:
1.103 lievre 3978: /* for (i=0; i<=imx; i++)
1.98 brouard 3979: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
3980:
1.103 lievre 3981: for (i=1;i<=imx ; i++)
1.98 brouard 3982: {
3983: if (cens[i]==1 & wav[i]>1)
1.103 lievre 3984: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
1.98 brouard 3985:
3986: if (cens[i]==0 & wav[i]>1)
1.103 lievre 3987: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
3988: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
1.98 brouard 3989:
3990: if (wav[i]>1 & agecens[i]>15) {
3991: L=L+A*weight[i];
3992: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
3993: }
3994: }
3995:
3996: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
3997:
3998: return -2*L*num/sump;
3999: }
4000:
4001: /******************* Printing html file ***********/
4002: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4003: int lastpass, int stepm, int weightopt, char model[],\
1.105 lievre 4004: int imx, double p[],double **matcov,double agemortsup){
4005: int i,k;
1.98 brouard 4006:
4007: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4008: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4009: for (i=1;i<=2;i++)
4010: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4011: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4012: fprintf(fichtm,"</ul>");
1.105 lievre 4013:
4014: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4015:
1.106 ! brouard 4016: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
1.105 lievre 4017:
4018: for (k=agegomp;k<(agemortsup-2);k++)
4019: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4020:
4021:
1.98 brouard 4022: fflush(fichtm);
4023: }
4024:
4025: /******************* Gnuplot file **************/
4026: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4027:
4028: char dirfileres[132],optfileres[132];
4029: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4030: int ng;
4031:
4032:
4033: /*#ifdef windows */
4034: fprintf(ficgp,"cd \"%s\" \n",pathc);
4035: /*#endif */
4036:
4037:
4038: strcpy(dirfileres,optionfilefiname);
4039: strcpy(optfileres,"vpl");
4040: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4041: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4042: fprintf(ficgp, "set ter png small\n set log y\n");
4043: fprintf(ficgp, "set size 0.65,0.65\n");
4044: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4045:
4046: }
4047:
4048:
1.88 brouard 4049:
1.91 brouard 4050:
1.53 brouard 4051: /***********************************************/
4052: /**************** Main Program *****************/
4053: /***********************************************/
4054:
4055: int main(int argc, char *argv[])
4056: {
1.61 brouard 4057: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 4058: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.95 brouard 4059: int jj, ll, li, lj, lk, imk;
1.85 brouard 4060: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 4061: int itimes;
1.98 brouard 4062: int NDIM=2;
1.95 brouard 4063:
4064: char ca[32], cb[32], cc[32];
1.87 brouard 4065: /* FILE *fichtm; *//* Html File */
4066: /* FILE *ficgp;*/ /*Gnuplot File */
1.53 brouard 4067: double agedeb, agefin,hf;
4068: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4069:
4070: double fret;
4071: double **xi,tmp,delta;
4072:
4073: double dum; /* Dummy variable */
4074: double ***p3mat;
4075: double ***mobaverage;
4076: int *indx;
4077: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 4078: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.99 brouard 4079: char pathr[MAXLINE], pathimach[MAXLINE];
1.53 brouard 4080: int firstobs=1, lastobs=10;
4081: int sdeb, sfin; /* Status at beginning and end */
4082: int c, h , cpt,l;
4083: int ju,jl, mi;
4084: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 4085: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 4086: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 4087: int mobilav=0,popforecast=0;
4088: int hstepm, nhstepm;
1.105 lievre 4089: int agemortsup;
4090: float sumlpop=0.;
1.74 brouard 4091: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4092: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 4093:
4094: double bage, fage, age, agelim, agebase;
4095: double ftolpl=FTOL;
4096: double **prlim;
4097: double *severity;
4098: double ***param; /* Matrix of parameters */
4099: double *p;
4100: double **matcov; /* Matrix of covariance */
4101: double ***delti3; /* Scale */
4102: double *delti; /* Scale */
4103: double ***eij, ***vareij;
4104: double **varpl; /* Variances of prevalence limits by age */
4105: double *epj, vepp;
4106: double kk1, kk2;
1.74 brouard 4107: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 brouard 4108: double **ximort;
1.53 brouard 4109: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 brouard 4110: int *dcwave;
1.53 brouard 4111:
4112: char z[1]="c", occ;
1.86 brouard 4113:
1.53 brouard 4114: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 4115: char strstart[80], *strt, strtend[80];
1.85 brouard 4116: char *stratrunc;
4117: int lstra;
4118:
4119: long total_usecs;
1.53 brouard 4120:
1.95 brouard 4121: /* setlocale (LC_ALL, ""); */
4122: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4123: /* textdomain (PACKAGE); */
4124: /* setlocale (LC_CTYPE, ""); */
4125: /* setlocale (LC_MESSAGES, ""); */
4126:
1.85 brouard 4127: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4128: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4129: curr_time=start_time;
1.85 brouard 4130: tm = *localtime(&start_time.tv_sec);
4131: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4132: strcpy(strstart,asctime(&tm));
1.86 brouard 4133:
1.88 brouard 4134: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4135: /* tp.tv_sec = tp.tv_sec +86400; */
4136: /* tm = *localtime(&start_time.tv_sec); */
4137: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4138: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4139: /* tmg.tm_hour=tmg.tm_hour + 1; */
4140: /* tp.tv_sec = mktime(&tmg); */
4141: /* strt=asctime(&tmg); */
1.88 brouard 4142: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4143: /* (void) time (&time_value);
4144: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4145: * tm = *localtime(&time_value);
1.88 brouard 4146: * strstart=asctime(&tm);
4147: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4148: */
4149:
1.91 brouard 4150: nberr=0; /* Number of errors and warnings */
4151: nbwarn=0;
1.53 brouard 4152: getcwd(pathcd, size);
4153:
1.81 brouard 4154: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4155: if(argc <=1){
4156: printf("\nEnter the parameter file name: ");
4157: scanf("%s",pathtot);
4158: }
4159: else{
4160: strcpy(pathtot,argv[1]);
4161: }
1.88 brouard 4162: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4163: /*cygwin_split_path(pathtot,path,optionfile);
4164: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4165: /* cutv(path,optionfile,pathtot,'\\');*/
4166:
1.99 brouard 4167: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4168: /* strcpy(pathimach,argv[0]); */
1.53 brouard 4169: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.99 brouard 4170: printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 4171: chdir(path);
1.88 brouard 4172: strcpy(command,"mkdir ");
4173: strcat(command,optionfilefiname);
4174: if((outcmd=system(command)) != 0){
4175: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4176: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4177: /* fclose(ficlog); */
4178: /* exit(1); */
4179: }
4180: /* if((imk=mkdir(optionfilefiname))<0){ */
4181: /* perror("mkdir"); */
4182: /* } */
1.53 brouard 4183:
1.59 brouard 4184: /*-------- arguments in the command line --------*/
1.53 brouard 4185:
4186: /* Log file */
4187: strcat(filelog, optionfilefiname);
4188: strcat(filelog,".log"); /* */
4189: if((ficlog=fopen(filelog,"w"))==NULL) {
4190: printf("Problem with logfile %s\n",filelog);
4191: goto end;
4192: }
4193: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4194: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.99 brouard 4195: fprintf(ficlog,"\nEnter the parameter file name: \n");
4196: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
1.88 brouard 4197: path=%s \n\
4198: optionfile=%s\n\
4199: optionfilext=%s\n\
1.99 brouard 4200: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4201:
1.94 brouard 4202: printf("Local time (at start):%s",strstart);
4203: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4204: fflush(ficlog);
1.91 brouard 4205: /* (void) gettimeofday(&curr_time,&tzp); */
4206: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4207:
4208: /* */
4209: strcpy(fileres,"r");
4210: strcat(fileres, optionfilefiname);
4211: strcat(fileres,".txt"); /* Other files have txt extension */
4212:
4213: /*---------arguments file --------*/
4214:
4215: if((ficpar=fopen(optionfile,"r"))==NULL) {
4216: printf("Problem with optionfile %s\n",optionfile);
4217: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4218: fflush(ficlog);
1.53 brouard 4219: goto end;
4220: }
4221:
1.88 brouard 4222:
4223:
1.53 brouard 4224: strcpy(filereso,"o");
4225: strcat(filereso,fileres);
1.88 brouard 4226: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4227: printf("Problem with Output resultfile: %s\n", filereso);
4228: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4229: fflush(ficlog);
1.53 brouard 4230: goto end;
4231: }
4232:
4233: /* Reads comments: lines beginning with '#' */
1.85 brouard 4234: numlinepar=0;
1.53 brouard 4235: while((c=getc(ficpar))=='#' && c!= EOF){
4236: ungetc(c,ficpar);
4237: fgets(line, MAXLINE, ficpar);
1.85 brouard 4238: numlinepar++;
1.53 brouard 4239: puts(line);
4240: fputs(line,ficparo);
1.85 brouard 4241: fputs(line,ficlog);
1.53 brouard 4242: }
4243: ungetc(c,ficpar);
4244:
4245: 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);
1.85 brouard 4246: numlinepar++;
1.53 brouard 4247: 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);
4248: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.85 brouard 4249: fprintf(ficlog,"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);
4250: fflush(ficlog);
1.59 brouard 4251: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4252: ungetc(c,ficpar);
4253: fgets(line, MAXLINE, ficpar);
1.85 brouard 4254: numlinepar++;
1.53 brouard 4255: puts(line);
4256: fputs(line,ficparo);
1.85 brouard 4257: fputs(line,ficlog);
1.53 brouard 4258: }
4259: ungetc(c,ficpar);
1.85 brouard 4260:
1.53 brouard 4261:
4262: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4263: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4264: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4265:
1.58 lievre 4266: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4267: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 brouard 4268: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4269:
4270: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4271: delti=delti3[1][1];
4272: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4273: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4274: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4275: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4276: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 brouard 4277: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4278: fclose (ficparo);
4279: fclose (ficlog);
4280: exit(0);
4281: }
1.98 brouard 4282: else if(mle==-3) {
4283: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4284: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4285: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4286: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4287: matcov=matrix(1,npar,1,npar);
1.53 brouard 4288: }
1.98 brouard 4289: else{
4290: /* Read guess parameters */
4291: /* Reads comments: lines beginning with '#' */
4292: while((c=getc(ficpar))=='#' && c!= EOF){
4293: ungetc(c,ficpar);
4294: fgets(line, MAXLINE, ficpar);
1.85 brouard 4295: numlinepar++;
1.98 brouard 4296: puts(line);
4297: fputs(line,ficparo);
4298: fputs(line,ficlog);
1.53 brouard 4299: }
1.98 brouard 4300: ungetc(c,ficpar);
4301:
4302: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4303: for(i=1; i <=nlstate; i++){
4304: j=0;
4305: for(jj=1; jj <=nlstate+ndeath; jj++){
4306: if(jj==i) continue;
4307: j++;
4308: fscanf(ficpar,"%1d%1d",&i1,&j1);
4309: if ((i1 != i) && (j1 != j)){
4310: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4311: exit(1);
4312: }
4313: fprintf(ficparo,"%1d%1d",i1,j1);
4314: if(mle==1)
4315: printf("%1d%1d",i,j);
4316: fprintf(ficlog,"%1d%1d",i,j);
4317: for(k=1; k<=ncovmodel;k++){
4318: fscanf(ficpar," %lf",¶m[i][j][k]);
4319: if(mle==1){
4320: printf(" %lf",param[i][j][k]);
4321: fprintf(ficlog," %lf",param[i][j][k]);
4322: }
4323: else
4324: fprintf(ficlog," %lf",param[i][j][k]);
4325: fprintf(ficparo," %lf",param[i][j][k]);
4326: }
4327: fscanf(ficpar,"\n");
4328: numlinepar++;
4329: if(mle==1)
4330: printf("\n");
4331: fprintf(ficlog,"\n");
4332: fprintf(ficparo,"\n");
4333: }
4334: }
4335: fflush(ficlog);
1.85 brouard 4336:
1.53 brouard 4337:
1.98 brouard 4338: p=param[1][1];
4339:
4340: /* Reads comments: lines beginning with '#' */
4341: while((c=getc(ficpar))=='#' && c!= EOF){
4342: ungetc(c,ficpar);
4343: fgets(line, MAXLINE, ficpar);
4344: numlinepar++;
4345: puts(line);
4346: fputs(line,ficparo);
4347: fputs(line,ficlog);
4348: }
1.53 brouard 4349: ungetc(c,ficpar);
4350:
1.98 brouard 4351: for(i=1; i <=nlstate; i++){
4352: for(j=1; j <=nlstate+ndeath-1; j++){
4353: fscanf(ficpar,"%1d%1d",&i1,&j1);
4354: if ((i1-i)*(j1-j)!=0){
4355: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4356: exit(1);
4357: }
4358: printf("%1d%1d",i,j);
4359: fprintf(ficparo,"%1d%1d",i1,j1);
4360: fprintf(ficlog,"%1d%1d",i1,j1);
4361: for(k=1; k<=ncovmodel;k++){
4362: fscanf(ficpar,"%le",&delti3[i][j][k]);
4363: printf(" %le",delti3[i][j][k]);
4364: fprintf(ficparo," %le",delti3[i][j][k]);
4365: fprintf(ficlog," %le",delti3[i][j][k]);
4366: }
4367: fscanf(ficpar,"\n");
4368: numlinepar++;
4369: printf("\n");
4370: fprintf(ficparo,"\n");
4371: fprintf(ficlog,"\n");
1.85 brouard 4372: }
1.53 brouard 4373: }
1.98 brouard 4374: fflush(ficlog);
1.85 brouard 4375:
1.98 brouard 4376: delti=delti3[1][1];
1.74 brouard 4377:
4378:
1.98 brouard 4379: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.53 brouard 4380:
1.98 brouard 4381: /* Reads comments: lines beginning with '#' */
4382: while((c=getc(ficpar))=='#' && c!= EOF){
4383: ungetc(c,ficpar);
4384: fgets(line, MAXLINE, ficpar);
4385: numlinepar++;
4386: puts(line);
4387: fputs(line,ficparo);
4388: fputs(line,ficlog);
4389: }
1.53 brouard 4390: ungetc(c,ficpar);
4391:
1.98 brouard 4392: matcov=matrix(1,npar,1,npar);
4393: for(i=1; i <=npar; i++){
4394: fscanf(ficpar,"%s",&str);
4395: if(mle==1)
4396: printf("%s",str);
4397: fprintf(ficlog,"%s",str);
4398: fprintf(ficparo,"%s",str);
4399: for(j=1; j <=i; j++){
4400: fscanf(ficpar," %le",&matcov[i][j]);
4401: if(mle==1){
4402: printf(" %.5le",matcov[i][j]);
4403: }
4404: fprintf(ficlog," %.5le",matcov[i][j]);
4405: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4406: }
1.98 brouard 4407: fscanf(ficpar,"\n");
4408: numlinepar++;
4409: if(mle==1)
4410: printf("\n");
4411: fprintf(ficlog,"\n");
4412: fprintf(ficparo,"\n");
1.53 brouard 4413: }
1.98 brouard 4414: for(i=1; i <=npar; i++)
4415: for(j=i+1;j<=npar;j++)
4416: matcov[i][j]=matcov[j][i];
4417:
1.53 brouard 4418: if(mle==1)
4419: printf("\n");
4420: fprintf(ficlog,"\n");
1.98 brouard 4421:
4422: fflush(ficlog);
4423:
4424: /*-------- Rewriting parameter file ----------*/
4425: strcpy(rfileres,"r"); /* "Rparameterfile */
4426: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4427: strcat(rfileres,"."); /* */
4428: strcat(rfileres,optionfilext); /* Other files have txt extension */
4429: if((ficres =fopen(rfileres,"w"))==NULL) {
4430: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4431: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4432: }
4433: fprintf(ficres,"#%s\n",version);
4434: } /* End of mle != -3 */
1.53 brouard 4435:
1.59 brouard 4436: /*-------- data file ----------*/
4437: if((fic=fopen(datafile,"r"))==NULL) {
4438: printf("Problem with datafile: %s\n", datafile);goto end;
4439: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4440: }
4441:
4442: n= lastobs;
4443: severity = vector(1,maxwav);
4444: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4445: num=lvector(1,n);
1.59 brouard 4446: moisnais=vector(1,n);
4447: annais=vector(1,n);
4448: moisdc=vector(1,n);
4449: andc=vector(1,n);
4450: agedc=vector(1,n);
4451: cod=ivector(1,n);
4452: weight=vector(1,n);
4453: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4454: mint=matrix(1,maxwav,1,n);
4455: anint=matrix(1,maxwav,1,n);
4456: s=imatrix(1,maxwav+1,1,n);
4457: tab=ivector(1,NCOVMAX);
4458: ncodemax=ivector(1,8);
4459:
4460: i=1;
4461: while (fgets(line, MAXLINE, fic) != NULL) {
4462: if ((i >= firstobs) && (i <=lastobs)) {
1.102 brouard 4463: for(j=0; line[j] != '\n';j++){ /* Untabifies line */
4464: if(line[j] == '\t')
4465: line[j] = ' ';
4466: }
1.59 brouard 4467: for (j=maxwav;j>=1;j--){
4468: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4469: strcpy(line,stra);
4470: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4471: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4472: }
1.53 brouard 4473:
1.59 brouard 4474: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4475: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4476:
1.59 brouard 4477: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4478: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4479:
1.59 brouard 4480: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4481: for (j=ncovcol;j>=1;j--){
4482: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4483: }
1.85 brouard 4484: lstra=strlen(stra);
4485: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4486: stratrunc = &(stra[lstra-9]);
4487: num[i]=atol(stratrunc);
4488: }
4489: else
4490: num[i]=atol(stra);
1.53 brouard 4491:
1.59 brouard 4492: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4493: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
1.53 brouard 4494:
1.59 brouard 4495: i=i+1;
4496: }
4497: }
4498: /* printf("ii=%d", ij);
4499: scanf("%d",i);*/
1.53 brouard 4500: imx=i-1; /* Number of individuals */
4501:
4502: /* for (i=1; i<=imx; i++){
4503: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4504: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4505: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4506: }*/
4507: /* for (i=1; i<=imx; i++){
4508: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4509: printf("%ld %.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]));}*/
1.53 brouard 4510:
1.106 ! brouard 4511: /* for (i=1; i<=imx; i++) */
1.53 brouard 4512:
1.71 brouard 4513: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4514: else weight[i]=1;*/
4515:
1.106 ! brouard 4516: /* Calculation of the number of parameters from char model */
1.53 brouard 4517: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4518: Tprod=ivector(1,15);
4519: Tvaraff=ivector(1,15);
4520: Tvard=imatrix(1,15,1,2);
4521: Tage=ivector(1,15);
4522:
1.58 lievre 4523: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4524: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4525: j=nbocc(model,'+'); /* j=Number of '+' */
4526: j1=nbocc(model,'*'); /* j1=Number of '*' */
4527: cptcovn=j+1;
4528: cptcovprod=j1; /*Number of products */
1.53 brouard 4529:
4530: strcpy(modelsav,model);
4531: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4532: printf("Error. Non available option model=%s ",model);
4533: fprintf(ficlog,"Error. Non available option model=%s ",model);
4534: goto end;
4535: }
4536:
1.59 brouard 4537: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4538:
1.53 brouard 4539: for(i=(j+1); i>=1;i--){
4540: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4541: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4542: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4543: /*scanf("%d",i);*/
4544: if (strchr(strb,'*')) { /* Model includes a product */
4545: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4546: if (strcmp(strc,"age")==0) { /* Vn*age */
4547: cptcovprod--;
4548: cutv(strb,stre,strd,'V');
4549: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4550: cptcovage++;
4551: Tage[cptcovage]=i;
4552: /*printf("stre=%s ", stre);*/
4553: }
4554: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4555: cptcovprod--;
4556: cutv(strb,stre,strc,'V');
4557: Tvar[i]=atoi(stre);
4558: cptcovage++;
4559: Tage[cptcovage]=i;
4560: }
4561: else { /* Age is not in the model */
4562: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4563: Tvar[i]=ncovcol+k1;
4564: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4565: Tprod[k1]=i;
4566: Tvard[k1][1]=atoi(strc); /* m*/
4567: Tvard[k1][2]=atoi(stre); /* n */
4568: Tvar[cptcovn+k2]=Tvard[k1][1];
4569: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4570: for (k=1; k<=lastobs;k++)
4571: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4572: k1++;
4573: k2=k2+2;
4574: }
4575: }
4576: else { /* no more sum */
4577: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4578: /* scanf("%d",i);*/
4579: cutv(strd,strc,strb,'V');
4580: Tvar[i]=atoi(strc);
4581: }
4582: strcpy(modelsav,stra);
4583: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4584: scanf("%d",i);*/
4585: } /* end of loop + */
4586: } /* end model */
4587:
1.58 lievre 4588: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4589: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4590:
1.53 brouard 4591: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4592: printf("cptcovprod=%d ", cptcovprod);
4593: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4594:
4595: scanf("%d ",i);
4596: fclose(fic);*/
1.53 brouard 4597:
4598: /* if(mle==1){*/
1.59 brouard 4599: if (weightopt != 1) { /* Maximisation without weights*/
4600: for(i=1;i<=n;i++) weight[i]=1.0;
4601: }
1.53 brouard 4602: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4603: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4604:
1.59 brouard 4605: for (i=1; i<=imx; i++) {
4606: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4607: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4608: anint[m][i]=9999;
4609: s[m][i]=-1;
4610: }
1.76 brouard 4611: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4612: nberr++;
1.85 brouard 4613: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
4614: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
1.76 brouard 4615: s[m][i]=-1;
4616: }
4617: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4618: nberr++;
1.85 brouard 4619: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
4620: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
1.84 brouard 4621: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4622: }
1.53 brouard 4623: }
1.59 brouard 4624: }
1.53 brouard 4625:
1.59 brouard 4626: for (i=1; i<=imx; i++) {
4627: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4628: for(m=firstpass; (m<= lastpass); m++){
1.105 lievre 4629: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
1.59 brouard 4630: if (s[m][i] >= nlstate+1) {
4631: if(agedc[i]>0)
1.76 brouard 4632: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4633: agev[m][i]=agedc[i];
1.59 brouard 4634: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4635: else {
1.76 brouard 4636: if ((int)andc[i]!=9999){
1.91 brouard 4637: nbwarn++;
1.85 brouard 4638: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4639: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4640: agev[m][i]=-1;
1.53 brouard 4641: }
4642: }
1.70 brouard 4643: }
1.69 brouard 4644: else if(s[m][i] !=9){ /* Standard case, age in fractional
4645: years but with the precision of a
4646: month */
1.59 brouard 4647: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4648: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4649: agev[m][i]=1;
4650: else if(agev[m][i] <agemin){
4651: agemin=agev[m][i];
4652: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4653: }
1.59 brouard 4654: else if(agev[m][i] >agemax){
4655: agemax=agev[m][i];
4656: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4657: }
1.59 brouard 4658: /*agev[m][i]=anint[m][i]-annais[i];*/
4659: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4660: }
1.59 brouard 4661: else { /* =9 */
1.53 brouard 4662: agev[m][i]=1;
1.59 brouard 4663: s[m][i]=-1;
4664: }
1.53 brouard 4665: }
1.59 brouard 4666: else /*= 0 Unknown */
4667: agev[m][i]=1;
4668: }
1.53 brouard 4669:
1.59 brouard 4670: }
4671: for (i=1; i<=imx; i++) {
1.71 brouard 4672: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4673: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4674: nberr++;
1.59 brouard 4675: 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);
4676: 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);
4677: goto end;
1.53 brouard 4678: }
4679: }
1.59 brouard 4680: }
1.53 brouard 4681:
1.71 brouard 4682: /*for (i=1; i<=imx; i++){
4683: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4684: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
1.71 brouard 4685: }
4686:
4687: }*/
4688:
1.97 lievre 4689:
1.59 brouard 4690: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4691: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4692:
1.98 brouard 4693: agegomp=(int)agemin;
1.59 brouard 4694: free_vector(severity,1,maxwav);
4695: free_imatrix(outcome,1,maxwav+1,1,n);
4696: free_vector(moisnais,1,n);
4697: free_vector(annais,1,n);
4698: /* free_matrix(mint,1,maxwav,1,n);
4699: free_matrix(anint,1,maxwav,1,n);*/
4700: free_vector(moisdc,1,n);
4701: free_vector(andc,1,n);
1.53 brouard 4702:
4703:
1.59 brouard 4704: wav=ivector(1,imx);
4705: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4706: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4707: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4708:
1.59 brouard 4709: /* Concatenates waves */
4710: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4711:
1.59 brouard 4712: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4713:
1.59 brouard 4714: Tcode=ivector(1,100);
4715: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4716: ncodemax[1]=1;
4717: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4718:
1.59 brouard 4719: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4720: the estimations*/
4721: h=0;
4722: m=pow(2,cptcoveff);
1.53 brouard 4723:
1.59 brouard 4724: for(k=1;k<=cptcoveff; k++){
4725: for(i=1; i <=(m/pow(2,k));i++){
4726: for(j=1; j <= ncodemax[k]; j++){
4727: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4728: h++;
4729: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4730: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4731: }
4732: }
4733: }
4734: }
4735: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4736: codtab[1][2]=1;codtab[2][2]=2; */
4737: /* for(i=1; i <=m ;i++){
4738: for(k=1; k <=cptcovn; k++){
4739: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4740: }
4741: printf("\n");
1.53 brouard 4742: }
1.59 brouard 4743: scanf("%d",i);*/
1.53 brouard 4744:
1.86 brouard 4745: /*------------ gnuplot -------------*/
4746: strcpy(optionfilegnuplot,optionfilefiname);
1.98 brouard 4747: if(mle==-3)
4748: strcat(optionfilegnuplot,"-mort");
1.86 brouard 4749: strcat(optionfilegnuplot,".gp");
1.98 brouard 4750:
1.86 brouard 4751: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4752: printf("Problem with file %s",optionfilegnuplot);
4753: }
4754: else{
4755: fprintf(ficgp,"\n# %s\n", version);
4756: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4757: fprintf(ficgp,"set missing 'NaNq'\n");
4758: }
1.88 brouard 4759: /* fclose(ficgp);*/
1.86 brouard 4760: /*--------- index.htm --------*/
4761:
1.91 brouard 4762: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 brouard 4763: if(mle==-3)
4764: strcat(optionfilehtm,"-mort");
1.86 brouard 4765: strcat(optionfilehtm,".htm");
4766: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4767: printf("Problem with %s \n",optionfilehtm), exit(0);
4768: }
4769:
1.91 brouard 4770: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4771: strcat(optionfilehtmcov,"-cov.htm");
4772: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4773: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4774: }
4775: else{
4776: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4777: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4778: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4779: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4780: }
4781:
1.87 brouard 4782: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4783: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4784: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4785: \n\
4786: <hr size=\"2\" color=\"#EC5E5E\">\
4787: <ul><li><h4>Parameter files</h4>\n\
4788: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4789: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4790: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4791: - Date and time at start: %s</ul>\n",\
1.91 brouard 4792: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4793: fileres,fileres,\
1.88 brouard 4794: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4795: fflush(fichtm);
1.86 brouard 4796:
1.88 brouard 4797: strcpy(pathr,path);
4798: strcat(pathr,optionfilefiname);
4799: chdir(optionfilefiname); /* Move to directory named optionfile */
4800:
1.59 brouard 4801: /* Calculates basic frequencies. Computes observed prevalence at single age
4802: and prints on file fileres'p'. */
1.105 lievre 4803: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
1.53 brouard 4804:
1.88 brouard 4805: fprintf(fichtm,"\n");
4806: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4807: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4808: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4809: imx,agemin,agemax,jmin,jmax,jmean);
4810: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4811: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4812: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4813: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4814: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4815:
4816:
1.59 brouard 4817: /* For Powell, parameters are in a vector p[] starting at p[1]
4818: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4819: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4820:
1.86 brouard 4821: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.98 brouard 4822: if (mle==-3){
4823: ximort=matrix(1,NDIM,1,NDIM);
4824: cens=ivector(1,n);
4825: ageexmed=vector(1,n);
4826: agecens=vector(1,n);
4827: dcwave=ivector(1,n);
4828:
4829: for (i=1; i<=imx; i++){
4830: dcwave[i]=-1;
4831: for (j=1; j<=lastpass; j++)
4832: if (s[j][i]>nlstate) {
4833: dcwave[i]=j;
4834: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4835: break;
4836: }
4837: }
4838:
4839: for (i=1; i<=imx; i++) {
4840: if (wav[i]>0){
4841: ageexmed[i]=agev[mw[1][i]][i];
4842: j=wav[i];agecens[i]=1.;
4843: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4844: cens[i]=1;
4845:
4846: if (ageexmed[i]<1) cens[i]=-1;
4847: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4848: }
4849: else cens[i]=-1;
4850: }
4851:
4852: for (i=1;i<=NDIM;i++) {
4853: for (j=1;j<=NDIM;j++)
4854: ximort[i][j]=(i == j ? 1.0 : 0.0);
4855: }
4856:
4857: p[1]=0.1; p[2]=0.1;
4858: /*printf("%lf %lf", p[1], p[2]);*/
4859:
4860:
4861: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4862: strcpy(filerespow,"pow-mort");
4863: strcat(filerespow,fileres);
4864: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4865: printf("Problem with resultfile: %s\n", filerespow);
4866: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1.59 brouard 4867: }
1.98 brouard 4868: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4869: /* for (i=1;i<=nlstate;i++)
4870: for(j=1;j<=nlstate+ndeath;j++)
4871: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4872: */
4873: fprintf(ficrespow,"\n");
4874:
4875: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4876: fclose(ficrespow);
1.53 brouard 4877:
1.98 brouard 4878: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
1.53 brouard 4879:
1.98 brouard 4880: for(i=1; i <=NDIM; i++)
4881: for(j=i+1;j<=NDIM;j++)
4882: matcov[i][j]=matcov[j][i];
4883:
4884: printf("\nCovariance matrix\n ");
4885: for(i=1; i <=NDIM; i++) {
4886: for(j=1;j<=NDIM;j++){
4887: printf("%f ",matcov[i][j]);
1.95 brouard 4888: }
1.98 brouard 4889: printf("\n ");
4890: }
4891:
4892: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
4893: for (i=1;i<=NDIM;i++)
4894: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.105 lievre 4895:
4896: lsurv=vector(1,AGESUP);
4897: lpop=vector(1,AGESUP);
4898: tpop=vector(1,AGESUP);
4899: lsurv[agegomp]=100000;
4900:
4901: for (k=agegomp;k<=AGESUP;k++) {
4902: agemortsup=k;
4903: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
4904: }
4905:
4906: for (k=agegomp;k<agemortsup;k++)
4907: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
4908:
4909: for (k=agegomp;k<agemortsup;k++){
4910: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
4911: sumlpop=sumlpop+lpop[k];
4912: }
4913:
4914: tpop[agegomp]=sumlpop;
4915: for (k=agegomp;k<(agemortsup-3);k++){
4916: /* tpop[k+1]=2;*/
4917: tpop[k+1]=tpop[k]-lpop[k];
4918: }
4919:
4920:
4921: printf("\nAge lx qx dx Lx Tx e(x)\n");
4922: for (k=agegomp;k<(agemortsup-2);k++)
4923: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4924:
4925:
1.98 brouard 4926: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4927: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4928:
4929: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
4930: stepm, weightopt,\
1.105 lievre 4931: model,imx,p,matcov,agemortsup);
4932:
4933: free_vector(lsurv,1,AGESUP);
4934: free_vector(lpop,1,AGESUP);
4935: free_vector(tpop,1,AGESUP);
1.98 brouard 4936: } /* Endof if mle==-3 */
4937:
4938: else{ /* For mle >=1 */
4939:
4940: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4941: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4942: for (k=1; k<=npar;k++)
4943: printf(" %d %8.5f",k,p[k]);
4944: printf("\n");
4945: globpr=1; /* to print the contributions */
4946: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4947: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4948: for (k=1; k<=npar;k++)
4949: printf(" %d %8.5f",k,p[k]);
4950: printf("\n");
4951: if(mle>=1){ /* Could be 1 or 2 */
4952: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4953: }
1.98 brouard 4954:
4955: /*--------- results files --------------*/
4956: 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);
4957:
4958:
4959: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4960: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4961: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4962: for(i=1,jk=1; i <=nlstate; i++){
4963: for(k=1; k <=(nlstate+ndeath); k++){
4964: if (k != i) {
4965: printf("%d%d ",i,k);
4966: fprintf(ficlog,"%d%d ",i,k);
4967: fprintf(ficres,"%1d%1d ",i,k);
4968: for(j=1; j <=ncovmodel; j++){
4969: printf("%f ",p[jk]);
4970: fprintf(ficlog,"%f ",p[jk]);
4971: fprintf(ficres,"%f ",p[jk]);
4972: jk++;
4973: }
4974: printf("\n");
4975: fprintf(ficlog,"\n");
4976: fprintf(ficres,"\n");
1.59 brouard 4977: }
4978: }
4979: }
1.98 brouard 4980: if(mle!=0){
4981: /* Computing hessian and covariance matrix */
4982: ftolhess=ftol; /* Usually correct */
4983: hesscov(matcov, p, npar, delti, ftolhess, func);
4984: }
4985: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4986: printf("# Scales (for hessian or gradient estimation)\n");
4987: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4988: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 4989: for(j=1; j <=nlstate+ndeath; j++){
1.98 brouard 4990: if (j!=i) {
4991: fprintf(ficres,"%1d%1d",i,j);
4992: printf("%1d%1d",i,j);
4993: fprintf(ficlog,"%1d%1d",i,j);
4994: for(k=1; k<=ncovmodel;k++){
4995: printf(" %.5e",delti[jk]);
4996: fprintf(ficlog," %.5e",delti[jk]);
4997: fprintf(ficres," %.5e",delti[jk]);
4998: jk++;
1.95 brouard 4999: }
1.98 brouard 5000: printf("\n");
5001: fprintf(ficlog,"\n");
5002: fprintf(ficres,"\n");
5003: }
5004: }
5005: }
5006:
5007: 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");
5008: if(mle>=1)
5009: 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");
5010: 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");
5011: /* # 121 Var(a12)\n\ */
5012: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5013: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5014: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5015: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5016: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5017: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5018: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5019:
5020:
5021: /* Just to have a covariance matrix which will be more understandable
5022: even is we still don't want to manage dictionary of variables
5023: */
5024: for(itimes=1;itimes<=2;itimes++){
5025: jj=0;
5026: for(i=1; i <=nlstate; i++){
5027: for(j=1; j <=nlstate+ndeath; j++){
5028: if(j==i) continue;
5029: for(k=1; k<=ncovmodel;k++){
5030: jj++;
5031: ca[0]= k+'a'-1;ca[1]='\0';
5032: if(itimes==1){
5033: if(mle>=1)
5034: printf("#%1d%1d%d",i,j,k);
5035: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5036: fprintf(ficres,"#%1d%1d%d",i,j,k);
5037: }else{
5038: if(mle>=1)
5039: printf("%1d%1d%d",i,j,k);
5040: fprintf(ficlog,"%1d%1d%d",i,j,k);
5041: fprintf(ficres,"%1d%1d%d",i,j,k);
5042: }
5043: ll=0;
5044: for(li=1;li <=nlstate; li++){
5045: for(lj=1;lj <=nlstate+ndeath; lj++){
5046: if(lj==li) continue;
5047: for(lk=1;lk<=ncovmodel;lk++){
5048: ll++;
5049: if(ll<=jj){
5050: cb[0]= lk +'a'-1;cb[1]='\0';
5051: if(ll<jj){
5052: if(itimes==1){
5053: if(mle>=1)
5054: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5055: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5056: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5057: }else{
5058: if(mle>=1)
5059: printf(" %.5e",matcov[jj][ll]);
5060: fprintf(ficlog," %.5e",matcov[jj][ll]);
5061: fprintf(ficres," %.5e",matcov[jj][ll]);
5062: }
1.95 brouard 5063: }else{
1.98 brouard 5064: if(itimes==1){
5065: if(mle>=1)
5066: printf(" Var(%s%1d%1d)",ca,i,j);
5067: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5068: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5069: }else{
5070: if(mle>=1)
5071: printf(" %.5e",matcov[jj][ll]);
5072: fprintf(ficlog," %.5e",matcov[jj][ll]);
5073: fprintf(ficres," %.5e",matcov[jj][ll]);
5074: }
1.95 brouard 5075: }
5076: }
1.98 brouard 5077: } /* end lk */
5078: } /* end lj */
5079: } /* end li */
5080: if(mle>=1)
5081: printf("\n");
5082: fprintf(ficlog,"\n");
5083: fprintf(ficres,"\n");
5084: numlinepar++;
5085: } /* end k*/
5086: } /*end j */
5087: } /* end i */
5088: } /* end itimes */
5089:
5090: fflush(ficlog);
5091: fflush(ficres);
5092:
5093: while((c=getc(ficpar))=='#' && c!= EOF){
5094: ungetc(c,ficpar);
5095: fgets(line, MAXLINE, ficpar);
5096: puts(line);
5097: fputs(line,ficparo);
5098: }
1.59 brouard 5099: ungetc(c,ficpar);
1.98 brouard 5100:
5101: estepm=0;
5102: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5103: if (estepm==0 || estepm < stepm) estepm=stepm;
5104: if (fage <= 2) {
5105: bage = ageminpar;
5106: fage = agemaxpar;
5107: }
5108:
5109: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5110: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5111: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5112:
5113: while((c=getc(ficpar))=='#' && c!= EOF){
5114: ungetc(c,ficpar);
5115: fgets(line, MAXLINE, ficpar);
5116: puts(line);
5117: fputs(line,ficparo);
5118: }
1.59 brouard 5119: ungetc(c,ficpar);
1.98 brouard 5120:
5121: 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);
5122: 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);
5123: 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);
5124: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5125: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5126:
5127: while((c=getc(ficpar))=='#' && c!= EOF){
5128: ungetc(c,ficpar);
5129: fgets(line, MAXLINE, ficpar);
5130: puts(line);
5131: fputs(line,ficparo);
5132: }
1.59 brouard 5133: ungetc(c,ficpar);
1.98 brouard 5134:
5135:
5136: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5137: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5138:
5139: fscanf(ficpar,"pop_based=%d\n",&popbased);
5140: fprintf(ficparo,"pop_based=%d\n",popbased);
5141: fprintf(ficres,"pop_based=%d\n",popbased);
5142:
5143: while((c=getc(ficpar))=='#' && c!= EOF){
5144: ungetc(c,ficpar);
5145: fgets(line, MAXLINE, ficpar);
5146: puts(line);
5147: fputs(line,ficparo);
5148: }
1.53 brouard 5149: ungetc(c,ficpar);
1.98 brouard 5150:
5151: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
5152: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
5153: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
5154: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
5155: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
5156: /* day and month of proj2 are not used but only year anproj2.*/
5157:
5158:
5159:
5160: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5161: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5162:
5163: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5164: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5165:
5166: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5167: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5168: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5169:
5170: /*------------ free_vector -------------*/
5171: /* chdir(path); */
1.53 brouard 5172:
1.98 brouard 5173: free_ivector(wav,1,imx);
5174: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5175: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5176: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5177: free_lvector(num,1,n);
5178: free_vector(agedc,1,n);
5179: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5180: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5181: fclose(ficparo);
5182: fclose(ficres);
5183:
5184:
5185: /*--------------- Prevalence limit (stable prevalence) --------------*/
5186:
5187: strcpy(filerespl,"pl");
5188: strcat(filerespl,fileres);
5189: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5190: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5191: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5192: }
5193: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5194: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
1.105 lievre 5195: fprintf(ficrespl, "#Local time at start: %s", strstart);
1.98 brouard 5196: fprintf(ficrespl,"#Stable prevalence \n");
5197: fprintf(ficrespl,"#Age ");
5198: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5199: fprintf(ficrespl,"\n");
5200:
5201: prlim=matrix(1,nlstate,1,nlstate);
5202:
5203: agebase=ageminpar;
5204: agelim=agemaxpar;
5205: ftolpl=1.e-10;
5206: i1=cptcoveff;
5207: if (cptcovn < 1){i1=1;}
5208:
5209: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5210: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5211: k=k+1;
5212: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5213: fprintf(ficrespl,"\n#******");
5214: printf("\n#******");
5215: fprintf(ficlog,"\n#******");
5216: for(j=1;j<=cptcoveff;j++) {
5217: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5218: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5219: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5220: }
5221: fprintf(ficrespl,"******\n");
5222: printf("******\n");
5223: fprintf(ficlog,"******\n");
1.53 brouard 5224:
1.98 brouard 5225: for (age=agebase; age<=agelim; age++){
5226: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5227: fprintf(ficrespl,"%.0f ",age );
5228: for(j=1;j<=cptcoveff;j++)
5229: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5230: for(i=1; i<=nlstate;i++)
5231: fprintf(ficrespl," %.5f", prlim[i][i]);
5232: fprintf(ficrespl,"\n");
5233: }
1.53 brouard 5234: }
5235: }
1.98 brouard 5236: fclose(ficrespl);
1.53 brouard 5237:
1.98 brouard 5238: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5239:
1.98 brouard 5240: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5241: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5242: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5243: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5244: }
5245: printf("Computing pij: result on file '%s' \n", filerespij);
5246: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5247:
1.98 brouard 5248: stepsize=(int) (stepm+YEARM-1)/YEARM;
5249: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5250:
1.98 brouard 5251: agelim=AGESUP;
5252: hstepm=stepsize*YEARM; /* Every year of age */
5253: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5254:
1.98 brouard 5255: /* hstepm=1; aff par mois*/
1.105 lievre 5256: fprintf(ficrespij, "#Local time at start: %s", strstart);
1.98 brouard 5257: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5258: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5259: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5260: k=k+1;
5261: fprintf(ficrespij,"\n#****** ");
5262: for(j=1;j<=cptcoveff;j++)
5263: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5264: fprintf(ficrespij,"******\n");
1.53 brouard 5265:
1.98 brouard 5266: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5267: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5268: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5269:
1.98 brouard 5270: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5271:
1.98 brouard 5272: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5273: oldm=oldms;savm=savms;
5274: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5275: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5276: for(i=1; i<=nlstate;i++)
5277: for(j=1; j<=nlstate+ndeath;j++)
1.98 brouard 5278: fprintf(ficrespij," %1d-%1d",i,j);
5279: fprintf(ficrespij,"\n");
5280: for (h=0; h<=nhstepm; h++){
5281: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5282: for(i=1; i<=nlstate;i++)
5283: for(j=1; j<=nlstate+ndeath;j++)
5284: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5285: fprintf(ficrespij,"\n");
5286: }
5287: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5288: fprintf(ficrespij,"\n");
5289: }
1.59 brouard 5290: }
1.53 brouard 5291: }
5292:
1.105 lievre 5293: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.53 brouard 5294:
1.98 brouard 5295: fclose(ficrespij);
1.53 brouard 5296:
1.98 brouard 5297: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5298: for(i=1;i<=AGESUP;i++)
5299: for(j=1;j<=NCOVMAX;j++)
5300: for(k=1;k<=NCOVMAX;k++)
5301: probs[i][j][k]=0.;
5302:
5303: /*---------- Forecasting ------------------*/
5304: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5305: if(prevfcast==1){
5306: /* if(stepm ==1){*/
1.70 brouard 5307: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5308: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 brouard 5309: /* } */
5310: /* else{ */
5311: /* erreur=108; */
5312: /* 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); */
5313: /* 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); */
5314: /* } */
5315: }
1.53 brouard 5316:
5317:
1.98 brouard 5318: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5319:
1.98 brouard 5320: strcpy(filerest,"t");
5321: strcat(filerest,fileres);
5322: if((ficrest=fopen(filerest,"w"))==NULL) {
5323: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5324: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5325: }
5326: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5327: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
1.53 brouard 5328:
5329:
1.98 brouard 5330: strcpy(filerese,"e");
5331: strcat(filerese,fileres);
5332: if((ficreseij=fopen(filerese,"w"))==NULL) {
5333: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5334: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5335: }
5336: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5337: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5338:
1.98 brouard 5339: strcpy(fileresv,"v");
5340: strcat(fileresv,fileres);
5341: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5342: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5343: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5344: }
5345: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5346: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5347:
1.98 brouard 5348: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5349: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5350: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
5351: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5352: */
1.58 lievre 5353:
1.98 brouard 5354: if (mobilav!=0) {
5355: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5356: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5357: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5358: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5359: }
1.54 brouard 5360: }
1.53 brouard 5361:
1.98 brouard 5362: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5363: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5364: k=k+1;
5365: fprintf(ficrest,"\n#****** ");
5366: for(j=1;j<=cptcoveff;j++)
5367: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5368: fprintf(ficrest,"******\n");
5369:
5370: fprintf(ficreseij,"\n#****** ");
5371: for(j=1;j<=cptcoveff;j++)
5372: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5373: fprintf(ficreseij,"******\n");
5374:
5375: fprintf(ficresvij,"\n#****** ");
5376: for(j=1;j<=cptcoveff;j++)
5377: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5378: fprintf(ficresvij,"******\n");
5379:
5380: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5381: oldm=oldms;savm=savms;
1.105 lievre 5382: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.53 brouard 5383:
1.98 brouard 5384: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5385: oldm=oldms;savm=savms;
1.105 lievre 5386: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
1.98 brouard 5387: if(popbased==1){
1.105 lievre 5388: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
1.98 brouard 5389: }
1.53 brouard 5390:
1.105 lievre 5391: fprintf(ficrest, "#Local time at start: %s", strstart);
1.98 brouard 5392: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5393: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5394: fprintf(ficrest,"\n");
5395:
5396: epj=vector(1,nlstate+1);
5397: for(age=bage; age <=fage ;age++){
5398: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5399: if (popbased==1) {
5400: if(mobilav ==0){
5401: for(i=1; i<=nlstate;i++)
5402: prlim[i][i]=probs[(int)age][i][k];
5403: }else{ /* mobilav */
5404: for(i=1; i<=nlstate;i++)
5405: prlim[i][i]=mobaverage[(int)age][i][k];
5406: }
1.53 brouard 5407: }
5408:
1.98 brouard 5409: fprintf(ficrest," %4.0f",age);
5410: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5411: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5412: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5413: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5414: }
5415: epj[nlstate+1] +=epj[j];
1.53 brouard 5416: }
5417:
1.98 brouard 5418: for(i=1, vepp=0.;i <=nlstate;i++)
5419: for(j=1;j <=nlstate;j++)
5420: vepp += vareij[i][j][(int)age];
5421: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5422: for(j=1;j <=nlstate;j++){
5423: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5424: }
5425: fprintf(ficrest,"\n");
1.53 brouard 5426: }
1.98 brouard 5427: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5428: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5429: free_vector(epj,1,nlstate+1);
5430: }
5431: }
5432: free_vector(weight,1,n);
5433: free_imatrix(Tvard,1,15,1,2);
5434: free_imatrix(s,1,maxwav+1,1,n);
5435: free_matrix(anint,1,maxwav,1,n);
5436: free_matrix(mint,1,maxwav,1,n);
5437: free_ivector(cod,1,n);
5438: free_ivector(tab,1,NCOVMAX);
5439: fclose(ficreseij);
5440: fclose(ficresvij);
5441: fclose(ficrest);
5442: fclose(ficpar);
5443:
5444: /*------- Variance of stable prevalence------*/
5445:
5446: strcpy(fileresvpl,"vpl");
5447: strcat(fileresvpl,fileres);
5448: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5449: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5450: exit(0);
5451: }
5452: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5453:
5454: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5455: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5456: k=k+1;
5457: fprintf(ficresvpl,"\n#****** ");
5458: for(j=1;j<=cptcoveff;j++)
5459: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5460: fprintf(ficresvpl,"******\n");
5461:
5462: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5463: oldm=oldms;savm=savms;
1.105 lievre 5464: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
1.98 brouard 5465: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5466: }
1.98 brouard 5467: }
1.53 brouard 5468:
1.98 brouard 5469: fclose(ficresvpl);
1.53 brouard 5470:
1.98 brouard 5471: /*---------- End : free ----------------*/
5472: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5473: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5474:
5475: } /* mle==-3 arrives here for freeing */
5476: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5477: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5478: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5479: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5480:
5481: free_matrix(covar,0,NCOVMAX,1,n);
5482: free_matrix(matcov,1,npar,1,npar);
5483: /*free_vector(delti,1,npar);*/
5484: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5485: free_matrix(agev,1,maxwav,1,imx);
5486: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5487:
5488: free_ivector(ncodemax,1,8);
5489: free_ivector(Tvar,1,15);
5490: free_ivector(Tprod,1,15);
5491: free_ivector(Tvaraff,1,15);
5492: free_ivector(Tage,1,15);
5493: free_ivector(Tcode,1,100);
1.74 brouard 5494:
1.53 brouard 5495:
1.88 brouard 5496: fflush(fichtm);
5497: fflush(ficgp);
1.53 brouard 5498:
5499:
1.91 brouard 5500: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5501: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5502: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5503: }else{
1.91 brouard 5504: printf("End of Imach\n");
5505: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5506: }
5507: printf("See log file on %s\n",filelog);
5508: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5509: (void) gettimeofday(&end_time,&tzp);
5510: tm = *localtime(&end_time.tv_sec);
5511: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5512: strcpy(strtend,asctime(&tm));
1.105 lievre 5513: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
1.94 brouard 5514: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5515: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5516:
1.91 brouard 5517: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5518: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5519: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5520: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5521: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5522: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5523: fclose(fichtm);
1.91 brouard 5524: fclose(fichtmcov);
1.88 brouard 5525: fclose(ficgp);
1.91 brouard 5526: fclose(ficlog);
1.53 brouard 5527: /*------ End -----------*/
5528:
1.88 brouard 5529: chdir(path);
1.99 brouard 5530: strcpy(plotcmd,"\"");
5531: strcat(plotcmd,pathimach);
5532: strcat(plotcmd,GNUPLOTPROGRAM);
5533: strcat(plotcmd,"\"");
1.59 brouard 5534: strcat(plotcmd," ");
5535: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5536: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.91 brouard 5537: if((outcmd=system(plotcmd)) != 0){
5538: printf(" Problem with gnuplot\n");
5539: }
1.75 brouard 5540: printf(" Wait...");
1.53 brouard 5541: while (z[0] != 'q') {
5542: /* chdir(path); */
1.91 brouard 5543: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5544: scanf("%s",z);
1.91 brouard 5545: /* if (z[0] == 'c') system("./imach"); */
1.99 brouard 5546: if (z[0] == 'e') {
5547: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5548: system(optionfilehtm);
5549: }
1.53 brouard 5550: else if (z[0] == 'g') system(plotcmd);
5551: else if (z[0] == 'q') exit(0);
5552: }
1.91 brouard 5553: end:
5554: while (z[0] != 'q') {
5555: printf("\nType q for exiting: ");
5556: scanf("%s",z);
5557: }
1.53 brouard 5558: }
1.88 brouard 5559:
1.53 brouard 5560:
5561:
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