Annotation of imach/src/imach.c, revision 1.109
1.109 ! brouard 1: /* $Id: imach.c,v 1.108 2006/01/19 18:05:42 lievre Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.109 ! brouard 4: Revision 1.108 2006/01/19 18:05:42 lievre
! 5: Gnuplot problem appeared...
! 6: To be fixed
! 7:
1.108 lievre 8: Revision 1.107 2006/01/19 16:20:37 brouard
9: Test existence of gnuplot in imach path
10:
1.107 brouard 11: Revision 1.106 2006/01/19 13:24:36 brouard
12: Some cleaning and links added in html output
13:
1.106 brouard 14: Revision 1.105 2006/01/05 20:23:19 lievre
15: *** empty log message ***
16:
1.105 lievre 17: Revision 1.104 2005/09/30 16:11:43 lievre
18: (Module): sump fixed, loop imx fixed, and simplifications.
19: (Module): If the status is missing at the last wave but we know
20: that the person is alive, then we can code his/her status as -2
21: (instead of missing=-1 in earlier versions) and his/her
22: contributions to the likelihood is 1 - Prob of dying from last
23: health status (= 1-p13= p11+p12 in the easiest case of somebody in
24: the healthy state at last known wave). Version is 0.98
25:
1.104 lievre 26: Revision 1.103 2005/09/30 15:54:49 lievre
27: (Module): sump fixed, loop imx fixed, and simplifications.
28:
1.103 lievre 29: Revision 1.102 2004/09/15 17:31:30 brouard
30: Add the possibility to read data file including tab characters.
31:
1.102 brouard 32: Revision 1.101 2004/09/15 10:38:38 brouard
33: Fix on curr_time
34:
1.101 brouard 35: Revision 1.100 2004/07/12 18:29:06 brouard
36: Add version for Mac OS X. Just define UNIX in Makefile
37:
1.100 brouard 38: Revision 1.99 2004/06/05 08:57:40 brouard
39: *** empty log message ***
40:
1.99 brouard 41: Revision 1.98 2004/05/16 15:05:56 brouard
42: New version 0.97 . First attempt to estimate force of mortality
43: directly from the data i.e. without the need of knowing the health
44: state at each age, but using a Gompertz model: log u =a + b*age .
45: This is the basic analysis of mortality and should be done before any
46: other analysis, in order to test if the mortality estimated from the
47: cross-longitudinal survey is different from the mortality estimated
48: from other sources like vital statistic data.
49:
50: The same imach parameter file can be used but the option for mle should be -3.
51:
52: Agnès, who wrote this part of the code, tried to keep most of the
53: former routines in order to include the new code within the former code.
54:
55: The output is very simple: only an estimate of the intercept and of
56: the slope with 95% confident intervals.
57:
58: Current limitations:
59: A) Even if you enter covariates, i.e. with the
60: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
61: B) There is no computation of Life Expectancy nor Life Table.
62:
1.98 brouard 63: Revision 1.97 2004/02/20 13:25:42 lievre
64: Version 0.96d. Population forecasting command line is (temporarily)
65: suppressed.
66:
1.97 lievre 67: Revision 1.96 2003/07/15 15:38:55 brouard
68: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
69: rewritten within the same printf. Workaround: many printfs.
70:
1.96 brouard 71: Revision 1.95 2003/07/08 07:54:34 brouard
72: * imach.c (Repository):
73: (Repository): Using imachwizard code to output a more meaningful covariance
74: matrix (cov(a12,c31) instead of numbers.
75:
1.95 brouard 76: Revision 1.94 2003/06/27 13:00:02 brouard
77: Just cleaning
78:
1.94 brouard 79: Revision 1.93 2003/06/25 16:33:55 brouard
80: (Module): On windows (cygwin) function asctime_r doesn't
81: exist so I changed back to asctime which exists.
82: (Module): Version 0.96b
83:
1.93 brouard 84: Revision 1.92 2003/06/25 16:30:45 brouard
85: (Module): On windows (cygwin) function asctime_r doesn't
86: exist so I changed back to asctime which exists.
87:
1.92 brouard 88: Revision 1.91 2003/06/25 15:30:29 brouard
89: * imach.c (Repository): Duplicated warning errors corrected.
90: (Repository): Elapsed time after each iteration is now output. It
91: helps to forecast when convergence will be reached. Elapsed time
92: is stamped in powell. We created a new html file for the graphs
93: concerning matrix of covariance. It has extension -cov.htm.
94:
1.91 brouard 95: Revision 1.90 2003/06/24 12:34:15 brouard
96: (Module): Some bugs corrected for windows. Also, when
97: mle=-1 a template is output in file "or"mypar.txt with the design
98: of the covariance matrix to be input.
99:
1.90 brouard 100: Revision 1.89 2003/06/24 12:30:52 brouard
101: (Module): Some bugs corrected for windows. Also, when
102: mle=-1 a template is output in file "or"mypar.txt with the design
103: of the covariance matrix to be input.
104:
1.89 brouard 105: Revision 1.88 2003/06/23 17:54:56 brouard
106: * 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.
107:
1.88 brouard 108: Revision 1.87 2003/06/18 12:26:01 brouard
109: Version 0.96
110:
1.87 brouard 111: Revision 1.86 2003/06/17 20:04:08 brouard
112: (Module): Change position of html and gnuplot routines and added
113: routine fileappend.
114:
1.86 brouard 115: Revision 1.85 2003/06/17 13:12:43 brouard
116: * imach.c (Repository): Check when date of death was earlier that
117: current date of interview. It may happen when the death was just
118: prior to the death. In this case, dh was negative and likelihood
119: was wrong (infinity). We still send an "Error" but patch by
120: assuming that the date of death was just one stepm after the
121: interview.
122: (Repository): Because some people have very long ID (first column)
123: we changed int to long in num[] and we added a new lvector for
124: memory allocation. But we also truncated to 8 characters (left
125: truncation)
126: (Repository): No more line truncation errors.
127:
1.85 brouard 128: Revision 1.84 2003/06/13 21:44:43 brouard
129: * imach.c (Repository): Replace "freqsummary" at a correct
130: place. It differs from routine "prevalence" which may be called
131: many times. Probs is memory consuming and must be used with
132: parcimony.
1.86 brouard 133: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 134:
1.84 brouard 135: Revision 1.83 2003/06/10 13:39:11 lievre
136: *** empty log message ***
137:
1.83 lievre 138: Revision 1.82 2003/06/05 15:57:20 brouard
139: Add log in imach.c and fullversion number is now printed.
140:
1.82 brouard 141: */
142: /*
1.53 brouard 143: Interpolated Markov Chain
144:
145: Short summary of the programme:
146:
147: This program computes Healthy Life Expectancies from
148: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
149: first survey ("cross") where individuals from different ages are
150: interviewed on their health status or degree of disability (in the
151: case of a health survey which is our main interest) -2- at least a
152: second wave of interviews ("longitudinal") which measure each change
153: (if any) in individual health status. Health expectancies are
154: computed from the time spent in each health state according to a
155: model. More health states you consider, more time is necessary to reach the
156: Maximum Likelihood of the parameters involved in the model. The
157: simplest model is the multinomial logistic model where pij is the
158: probability to be observed in state j at the second wave
159: conditional to be observed in state i at the first wave. Therefore
160: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
161: 'age' is age and 'sex' is a covariate. If you want to have a more
162: complex model than "constant and age", you should modify the program
163: where the markup *Covariates have to be included here again* invites
164: you to do it. More covariates you add, slower the
165: convergence.
166:
167: The advantage of this computer programme, compared to a simple
168: multinomial logistic model, is clear when the delay between waves is not
169: identical for each individual. Also, if a individual missed an
170: intermediate interview, the information is lost, but taken into
171: account using an interpolation or extrapolation.
172:
173: hPijx is the probability to be observed in state i at age x+h
174: conditional to the observed state i at age x. The delay 'h' can be
175: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 176: states. This elementary transition (by month, quarter,
177: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 178: matrix is simply the matrix product of nh*stepm elementary matrices
179: and the contribution of each individual to the likelihood is simply
180: hPijx.
181:
182: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 183: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 184:
185: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
186: Institut national d'études démographiques, Paris.
187: This software have been partly granted by Euro-REVES, a concerted action
188: from the European Union.
189: It is copyrighted identically to a GNU software product, ie programme and
190: software can be distributed freely for non commercial use. Latest version
191: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 192:
193: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
194: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
195:
1.53 brouard 196: **********************************************************************/
1.74 brouard 197: /*
198: main
199: read parameterfile
200: read datafile
201: concatwav
1.84 brouard 202: freqsummary
1.74 brouard 203: if (mle >= 1)
204: mlikeli
205: print results files
206: if mle==1
207: computes hessian
208: read end of parameter file: agemin, agemax, bage, fage, estepm
209: begin-prev-date,...
210: open gnuplot file
211: open html file
212: stable prevalence
213: for age prevalim()
214: h Pij x
215: variance of p varprob
216: forecasting if prevfcast==1 prevforecast call prevalence()
217: health expectancies
218: Variance-covariance of DFLE
219: prevalence()
220: movingaverage()
221: varevsij()
222: if popbased==1 varevsij(,popbased)
223: total life expectancies
224: Variance of stable prevalence
225: end
226: */
227:
228:
229:
1.53 brouard 230:
231: #include <math.h>
232: #include <stdio.h>
233: #include <stdlib.h>
1.106 brouard 234: #include <string.h>
1.53 brouard 235: #include <unistd.h>
236:
1.109 ! brouard 237: #include <limits.h>
1.107 brouard 238: #include <sys/types.h>
239: #include <sys/stat.h>
240: #include <errno.h>
241: extern int errno;
242:
1.99 brouard 243: /* #include <sys/time.h> */
1.86 brouard 244: #include <time.h>
245: #include "timeval.h"
246:
1.95 brouard 247: /* #include <libintl.h> */
248: /* #define _(String) gettext (String) */
249:
1.53 brouard 250: #define MAXLINE 256
1.108 lievre 251:
1.53 brouard 252: #define GNUPLOTPROGRAM "gnuplot"
253: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 254: #define FILENAMELENGTH 132
1.108 lievre 255:
1.53 brouard 256: #define GLOCK_ERROR_NOPATH -1 /* empty path */
257: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
258:
259: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
260: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
261:
262: #define NINTERVMAX 8
263: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
264: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
265: #define NCOVMAX 8 /* Maximum number of covariates */
266: #define MAXN 20000
267: #define YEARM 12. /* Number of months per year */
268: #define AGESUP 130
269: #define AGEBASE 40
1.98 brouard 270: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.100 brouard 271: #ifdef UNIX
1.85 brouard 272: #define DIRSEPARATOR '/'
1.107 brouard 273: #define CHARSEPARATOR "/"
1.85 brouard 274: #define ODIRSEPARATOR '\\'
275: #else
1.53 brouard 276: #define DIRSEPARATOR '\\'
1.107 brouard 277: #define CHARSEPARATOR "\\"
1.53 brouard 278: #define ODIRSEPARATOR '/'
279: #endif
280:
1.109 ! brouard 281: /* $Id: imach.c,v 1.108 2006/01/19 18:05:42 lievre Exp $ */
1.81 brouard 282: /* $State: Exp $ */
1.80 brouard 283:
1.106 brouard 284: char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
1.109 ! brouard 285: char fullversion[]="$Revision: 1.108 $ $Date: 2006/01/19 18:05:42 $";
1.91 brouard 286: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 287: int nvar;
288: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
289: int npar=NPARMAX;
290: int nlstate=2; /* Number of live states */
291: int ndeath=1; /* Number of dead states */
292: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
293: int popbased=0;
294:
295: int *wav; /* Number of waves for this individuual 0 is possible */
296: int maxwav; /* Maxim number of waves */
297: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 298: int gipmx, gsw; /* Global variables on the number of contributions
299: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 300: int mle, weightopt;
301: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
302: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 303: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
304: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 305: double jmean; /* Mean space between 2 waves */
306: double **oldm, **newm, **savm; /* Working pointers to matrices */
307: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
308: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 309: FILE *ficlog, *ficrespow;
1.85 brouard 310: int globpr; /* Global variable for printing or not */
311: double fretone; /* Only one call to likelihood */
312: long ipmx; /* Number of contributions */
313: double sw; /* Sum of weights */
1.98 brouard 314: char filerespow[FILENAMELENGTH];
1.85 brouard 315: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
316: FILE *ficresilk;
1.53 brouard 317: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
318: FILE *ficresprobmorprev;
1.91 brouard 319: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 320: FILE *ficreseij;
321: char filerese[FILENAMELENGTH];
322: FILE *ficresvij;
323: char fileresv[FILENAMELENGTH];
324: FILE *ficresvpl;
325: char fileresvpl[FILENAMELENGTH];
326: char title[MAXLINE];
327: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
328: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.96 brouard 329: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 330: char command[FILENAMELENGTH];
331: int outcmd=0;
1.53 brouard 332:
333: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 334:
1.53 brouard 335: char filelog[FILENAMELENGTH]; /* Log file */
336: char filerest[FILENAMELENGTH];
337: char fileregp[FILENAMELENGTH];
338: char popfile[FILENAMELENGTH];
339:
1.91 brouard 340: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
341:
342: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
343: struct timezone tzp;
344: extern int gettimeofday();
345: struct tm tmg, tm, tmf, *gmtime(), *localtime();
346: long time_value;
347: extern long time();
348: char strcurr[80], strfor[80];
1.53 brouard 349:
1.109 ! brouard 350: char *endptr;
! 351: long lval;
! 352:
1.53 brouard 353: #define NR_END 1
354: #define FREE_ARG char*
355: #define FTOL 1.0e-10
356:
357: #define NRANSI
358: #define ITMAX 200
359:
360: #define TOL 2.0e-4
361:
362: #define CGOLD 0.3819660
363: #define ZEPS 1.0e-10
364: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
365:
366: #define GOLD 1.618034
367: #define GLIMIT 100.0
368: #define TINY 1.0e-20
369:
370: static double maxarg1,maxarg2;
371: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
372: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
373:
374: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
375: #define rint(a) floor(a+0.5)
376:
377: static double sqrarg;
378: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
379: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 brouard 380: int agegomp= AGEGOMP;
1.53 brouard 381:
382: int imx;
1.98 brouard 383: int stepm=1;
1.53 brouard 384: /* Stepm, step in month: minimum step interpolation*/
385:
386: int estepm;
387: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
388:
389: int m,nb;
1.85 brouard 390: long *num;
1.98 brouard 391: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 392: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 393: double **pmmij, ***probs;
1.98 brouard 394: double *ageexmed,*agecens;
1.53 brouard 395: double dateintmean=0;
396:
397: double *weight;
398: int **s; /* Status */
399: double *agedc, **covar, idx;
400: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.105 lievre 401: double *lsurv, *lpop, *tpop;
1.53 brouard 402:
403: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
404: double ftolhess; /* Tolerance for computing hessian */
405:
406: /**************** split *************************/
407: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
408: {
1.107 brouard 409: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1.99 brouard 410: the name of the file (name), its extension only (ext) and its first part of the name (finame)
411: */
1.59 brouard 412: char *ss; /* pointer */
413: int l1, l2; /* length counters */
1.53 brouard 414:
1.59 brouard 415: l1 = strlen(path ); /* length of path */
416: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
417: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1.107 brouard 418: if ( ss == NULL ) { /* no directory, so determine current directory */
419: strcpy( name, path ); /* we got the fullname name because no directory */
1.59 brouard 420: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
421: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 422: /* get current working directory */
423: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 424: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
425: return( GLOCK_ERROR_GETCWD );
426: }
1.107 brouard 427: /* got dirc from getcwd*/
428: printf(" DIRC = %s \n",dirc);
1.59 brouard 429: } else { /* strip direcotry from path */
430: ss++; /* after this, the filename */
431: l2 = strlen( ss ); /* length of filename */
432: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
433: strcpy( name, ss ); /* save file name */
434: strncpy( dirc, path, l1 - l2 ); /* now the directory */
435: dirc[l1-l2] = 0; /* add zero */
1.107 brouard 436: printf(" DIRC2 = %s \n",dirc);
1.59 brouard 437: }
1.107 brouard 438: /* We add a separator at the end of dirc if not exists */
1.59 brouard 439: l1 = strlen( dirc ); /* length of directory */
1.107 brouard 440: if( dirc[l1-1] != DIRSEPARATOR ){
441: dirc[l1] = DIRSEPARATOR;
442: dirc[l1+1] = 0;
443: printf(" DIRC3 = %s \n",dirc);
444: }
1.59 brouard 445: ss = strrchr( name, '.' ); /* find last / */
1.99 brouard 446: if (ss >0){
447: ss++;
448: strcpy(ext,ss); /* save extension */
449: l1= strlen( name);
450: l2= strlen(ss)+1;
451: strncpy( finame, name, l1-l2);
452: finame[l1-l2]= 0;
453: }
1.107 brouard 454:
1.59 brouard 455: return( 0 ); /* we're done */
1.53 brouard 456: }
457:
458:
459: /******************************************/
460:
1.89 brouard 461: void replace_back_to_slash(char *s, char*t)
1.53 brouard 462: {
463: int i;
1.89 brouard 464: int lg=0;
1.53 brouard 465: i=0;
466: lg=strlen(t);
467: for(i=0; i<= lg; i++) {
468: (s[i] = t[i]);
469: if (t[i]== '\\') s[i]='/';
470: }
471: }
472:
473: int nbocc(char *s, char occ)
474: {
475: int i,j=0;
476: int lg=20;
477: i=0;
478: lg=strlen(s);
479: for(i=0; i<= lg; i++) {
480: if (s[i] == occ ) j++;
481: }
482: return j;
483: }
484:
485: void cutv(char *u,char *v, char*t, char occ)
486: {
1.102 brouard 487: /* cuts string t into u and v where u ends before first occurence of char 'occ'
488: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
1.53 brouard 489: gives u="abcedf" and v="ghi2j" */
490: int i,lg,j,p=0;
491: i=0;
492: for(j=0; j<=strlen(t)-1; j++) {
493: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
494: }
495:
496: lg=strlen(t);
497: for(j=0; j<p; j++) {
498: (u[j] = t[j]);
499: }
500: u[p]='\0';
501:
502: for(j=0; j<= lg; j++) {
503: if (j>=(p+1))(v[j-p-1] = t[j]);
504: }
505: }
506:
507: /********************** nrerror ********************/
508:
509: void nrerror(char error_text[])
510: {
511: fprintf(stderr,"ERREUR ...\n");
512: fprintf(stderr,"%s\n",error_text);
1.59 brouard 513: exit(EXIT_FAILURE);
1.53 brouard 514: }
515: /*********************** vector *******************/
516: double *vector(int nl, int nh)
517: {
518: double *v;
519: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
520: if (!v) nrerror("allocation failure in vector");
521: return v-nl+NR_END;
522: }
523:
524: /************************ free vector ******************/
525: void free_vector(double*v, int nl, int nh)
526: {
527: free((FREE_ARG)(v+nl-NR_END));
528: }
529:
530: /************************ivector *******************************/
1.85 brouard 531: int *ivector(long nl,long nh)
1.76 brouard 532: {
1.85 brouard 533: int *v;
534: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
535: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 536: return v-nl+NR_END;
537: }
538:
539: /******************free ivector **************************/
1.85 brouard 540: void free_ivector(int *v, long nl, long nh)
1.76 brouard 541: {
542: free((FREE_ARG)(v+nl-NR_END));
543: }
544:
1.85 brouard 545: /************************lvector *******************************/
546: long *lvector(long nl,long nh)
1.53 brouard 547: {
1.85 brouard 548: long *v;
549: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 550: if (!v) nrerror("allocation failure in ivector");
551: return v-nl+NR_END;
552: }
553:
1.85 brouard 554: /******************free lvector **************************/
555: void free_lvector(long *v, long nl, long nh)
1.53 brouard 556: {
557: free((FREE_ARG)(v+nl-NR_END));
558: }
559:
560: /******************* imatrix *******************************/
561: int **imatrix(long nrl, long nrh, long ncl, long nch)
562: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
563: {
564: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
565: int **m;
566:
567: /* allocate pointers to rows */
568: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
569: if (!m) nrerror("allocation failure 1 in matrix()");
570: m += NR_END;
571: m -= nrl;
572:
573:
574: /* allocate rows and set pointers to them */
575: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
576: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
577: m[nrl] += NR_END;
578: m[nrl] -= ncl;
579:
580: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
581:
582: /* return pointer to array of pointers to rows */
583: return m;
584: }
585:
586: /****************** free_imatrix *************************/
587: void free_imatrix(m,nrl,nrh,ncl,nch)
588: int **m;
589: long nch,ncl,nrh,nrl;
590: /* free an int matrix allocated by imatrix() */
591: {
592: free((FREE_ARG) (m[nrl]+ncl-NR_END));
593: free((FREE_ARG) (m+nrl-NR_END));
594: }
595:
596: /******************* matrix *******************************/
597: double **matrix(long nrl, long nrh, long ncl, long nch)
598: {
599: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
600: double **m;
601:
602: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
603: if (!m) nrerror("allocation failure 1 in matrix()");
604: m += NR_END;
605: m -= nrl;
606:
607: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
608: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
609: m[nrl] += NR_END;
610: m[nrl] -= ncl;
611:
612: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
613: return m;
1.85 brouard 614: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 615: */
1.53 brouard 616: }
617:
618: /*************************free matrix ************************/
619: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
620: {
621: free((FREE_ARG)(m[nrl]+ncl-NR_END));
622: free((FREE_ARG)(m+nrl-NR_END));
623: }
624:
625: /******************* ma3x *******************************/
626: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
627: {
628: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
629: double ***m;
630:
631: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
632: if (!m) nrerror("allocation failure 1 in matrix()");
633: m += NR_END;
634: m -= nrl;
635:
636: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
637: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
638: m[nrl] += NR_END;
639: m[nrl] -= ncl;
640:
641: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
642:
643: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
644: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
645: m[nrl][ncl] += NR_END;
646: m[nrl][ncl] -= nll;
647: for (j=ncl+1; j<=nch; j++)
648: m[nrl][j]=m[nrl][j-1]+nlay;
649:
650: for (i=nrl+1; i<=nrh; i++) {
651: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
652: for (j=ncl+1; j<=nch; j++)
653: m[i][j]=m[i][j-1]+nlay;
654: }
1.74 brouard 655: return m;
656: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
657: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
658: */
1.53 brouard 659: }
660:
661: /*************************free ma3x ************************/
662: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
663: {
664: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
665: free((FREE_ARG)(m[nrl]+ncl-NR_END));
666: free((FREE_ARG)(m+nrl-NR_END));
667: }
668:
1.94 brouard 669: /*************** function subdirf ***********/
670: char *subdirf(char fileres[])
671: {
672: /* Caution optionfilefiname is hidden */
673: strcpy(tmpout,optionfilefiname);
674: strcat(tmpout,"/"); /* Add to the right */
675: strcat(tmpout,fileres);
676: return tmpout;
677: }
678:
679: /*************** function subdirf2 ***********/
680: char *subdirf2(char fileres[], char *preop)
681: {
682:
683: /* Caution optionfilefiname is hidden */
684: strcpy(tmpout,optionfilefiname);
685: strcat(tmpout,"/");
686: strcat(tmpout,preop);
687: strcat(tmpout,fileres);
688: return tmpout;
689: }
690:
691: /*************** function subdirf3 ***********/
692: char *subdirf3(char fileres[], char *preop, char *preop2)
693: {
694:
695: /* Caution optionfilefiname is hidden */
696: strcpy(tmpout,optionfilefiname);
697: strcat(tmpout,"/");
698: strcat(tmpout,preop);
699: strcat(tmpout,preop2);
700: strcat(tmpout,fileres);
701: return tmpout;
702: }
703:
1.53 brouard 704: /***************** f1dim *************************/
705: extern int ncom;
706: extern double *pcom,*xicom;
707: extern double (*nrfunc)(double []);
708:
709: double f1dim(double x)
710: {
711: int j;
712: double f;
713: double *xt;
714:
715: xt=vector(1,ncom);
716: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
717: f=(*nrfunc)(xt);
718: free_vector(xt,1,ncom);
719: return f;
720: }
721:
722: /*****************brent *************************/
723: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
724: {
725: int iter;
726: double a,b,d,etemp;
727: double fu,fv,fw,fx;
728: double ftemp;
729: double p,q,r,tol1,tol2,u,v,w,x,xm;
730: double e=0.0;
731:
732: a=(ax < cx ? ax : cx);
733: b=(ax > cx ? ax : cx);
734: x=w=v=bx;
735: fw=fv=fx=(*f)(x);
736: for (iter=1;iter<=ITMAX;iter++) {
737: xm=0.5*(a+b);
738: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
739: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
740: printf(".");fflush(stdout);
741: fprintf(ficlog,".");fflush(ficlog);
742: #ifdef DEBUG
743: 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);
744: 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);
745: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
746: #endif
747: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
748: *xmin=x;
749: return fx;
750: }
751: ftemp=fu;
752: if (fabs(e) > tol1) {
753: r=(x-w)*(fx-fv);
754: q=(x-v)*(fx-fw);
755: p=(x-v)*q-(x-w)*r;
756: q=2.0*(q-r);
757: if (q > 0.0) p = -p;
758: q=fabs(q);
759: etemp=e;
760: e=d;
761: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
762: d=CGOLD*(e=(x >= xm ? a-x : b-x));
763: else {
764: d=p/q;
765: u=x+d;
766: if (u-a < tol2 || b-u < tol2)
767: d=SIGN(tol1,xm-x);
768: }
769: } else {
770: d=CGOLD*(e=(x >= xm ? a-x : b-x));
771: }
772: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
773: fu=(*f)(u);
774: if (fu <= fx) {
775: if (u >= x) a=x; else b=x;
776: SHFT(v,w,x,u)
777: SHFT(fv,fw,fx,fu)
778: } else {
779: if (u < x) a=u; else b=u;
780: if (fu <= fw || w == x) {
781: v=w;
782: w=u;
783: fv=fw;
784: fw=fu;
785: } else if (fu <= fv || v == x || v == w) {
786: v=u;
787: fv=fu;
788: }
789: }
790: }
791: nrerror("Too many iterations in brent");
792: *xmin=x;
793: return fx;
794: }
795:
796: /****************** mnbrak ***********************/
797:
798: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
799: double (*func)(double))
800: {
801: double ulim,u,r,q, dum;
802: double fu;
803:
804: *fa=(*func)(*ax);
805: *fb=(*func)(*bx);
806: if (*fb > *fa) {
807: SHFT(dum,*ax,*bx,dum)
808: SHFT(dum,*fb,*fa,dum)
809: }
810: *cx=(*bx)+GOLD*(*bx-*ax);
811: *fc=(*func)(*cx);
812: while (*fb > *fc) {
813: r=(*bx-*ax)*(*fb-*fc);
814: q=(*bx-*cx)*(*fb-*fa);
815: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
816: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
817: ulim=(*bx)+GLIMIT*(*cx-*bx);
818: if ((*bx-u)*(u-*cx) > 0.0) {
819: fu=(*func)(u);
820: } else if ((*cx-u)*(u-ulim) > 0.0) {
821: fu=(*func)(u);
822: if (fu < *fc) {
823: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
824: SHFT(*fb,*fc,fu,(*func)(u))
825: }
826: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
827: u=ulim;
828: fu=(*func)(u);
829: } else {
830: u=(*cx)+GOLD*(*cx-*bx);
831: fu=(*func)(u);
832: }
833: SHFT(*ax,*bx,*cx,u)
834: SHFT(*fa,*fb,*fc,fu)
835: }
836: }
837:
838: /*************** linmin ************************/
839:
840: int ncom;
841: double *pcom,*xicom;
842: double (*nrfunc)(double []);
843:
844: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
845: {
846: double brent(double ax, double bx, double cx,
847: double (*f)(double), double tol, double *xmin);
848: double f1dim(double x);
849: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
850: double *fc, double (*func)(double));
851: int j;
852: double xx,xmin,bx,ax;
853: double fx,fb,fa;
854:
855: ncom=n;
856: pcom=vector(1,n);
857: xicom=vector(1,n);
858: nrfunc=func;
859: for (j=1;j<=n;j++) {
860: pcom[j]=p[j];
861: xicom[j]=xi[j];
862: }
863: ax=0.0;
864: xx=1.0;
865: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
866: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
867: #ifdef DEBUG
868: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
869: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
870: #endif
871: for (j=1;j<=n;j++) {
872: xi[j] *= xmin;
873: p[j] += xi[j];
874: }
875: free_vector(xicom,1,n);
876: free_vector(pcom,1,n);
877: }
878:
1.91 brouard 879: char *asc_diff_time(long time_sec, char ascdiff[])
880: {
881: long sec_left, days, hours, minutes;
882: days = (time_sec) / (60*60*24);
883: sec_left = (time_sec) % (60*60*24);
884: hours = (sec_left) / (60*60) ;
885: sec_left = (sec_left) %(60*60);
886: minutes = (sec_left) /60;
887: sec_left = (sec_left) % (60);
888: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
889: return ascdiff;
890: }
891:
1.53 brouard 892: /*************** powell ************************/
893: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
894: double (*func)(double []))
895: {
896: void linmin(double p[], double xi[], int n, double *fret,
897: double (*func)(double []));
898: int i,ibig,j;
899: double del,t,*pt,*ptt,*xit;
900: double fp,fptt;
901: double *xits;
1.91 brouard 902: int niterf, itmp;
903:
1.53 brouard 904: pt=vector(1,n);
905: ptt=vector(1,n);
906: xit=vector(1,n);
907: xits=vector(1,n);
908: *fret=(*func)(p);
909: for (j=1;j<=n;j++) pt[j]=p[j];
910: for (*iter=1;;++(*iter)) {
911: fp=(*fret);
912: ibig=0;
913: del=0.0;
1.91 brouard 914: last_time=curr_time;
915: (void) gettimeofday(&curr_time,&tzp);
916: 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 917: /* 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 918: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.98 brouard 919: */
920: for (i=1;i<=n;i++) {
1.53 brouard 921: printf(" %d %.12f",i, p[i]);
1.76 brouard 922: fprintf(ficlog," %d %.12lf",i, p[i]);
923: fprintf(ficrespow," %.12lf", p[i]);
924: }
1.53 brouard 925: printf("\n");
926: fprintf(ficlog,"\n");
1.91 brouard 927: fprintf(ficrespow,"\n");fflush(ficrespow);
928: if(*iter <=3){
929: tm = *localtime(&curr_time.tv_sec);
1.101 brouard 930: strcpy(strcurr,asctime(&tm));
1.92 brouard 931: /* asctime_r(&tm,strcurr); */
1.101 brouard 932: forecast_time=curr_time;
1.91 brouard 933: itmp = strlen(strcurr);
1.101 brouard 934: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.91 brouard 935: strcurr[itmp-1]='\0';
936: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
937: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
938: for(niterf=10;niterf<=30;niterf+=10){
939: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
940: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 941: /* asctime_r(&tmf,strfor); */
942: strcpy(strfor,asctime(&tmf));
1.91 brouard 943: itmp = strlen(strfor);
944: if(strfor[itmp-1]=='\n')
945: strfor[itmp-1]='\0';
1.101 brouard 946: 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);
947: 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 948: }
949: }
1.53 brouard 950: for (i=1;i<=n;i++) {
951: for (j=1;j<=n;j++) xit[j]=xi[j][i];
952: fptt=(*fret);
953: #ifdef DEBUG
954: printf("fret=%lf \n",*fret);
955: fprintf(ficlog,"fret=%lf \n",*fret);
956: #endif
957: printf("%d",i);fflush(stdout);
958: fprintf(ficlog,"%d",i);fflush(ficlog);
959: linmin(p,xit,n,fret,func);
960: if (fabs(fptt-(*fret)) > del) {
961: del=fabs(fptt-(*fret));
962: ibig=i;
963: }
964: #ifdef DEBUG
965: printf("%d %.12e",i,(*fret));
966: fprintf(ficlog,"%d %.12e",i,(*fret));
967: for (j=1;j<=n;j++) {
968: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
969: printf(" x(%d)=%.12e",j,xit[j]);
970: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
971: }
972: for(j=1;j<=n;j++) {
973: printf(" p=%.12e",p[j]);
974: fprintf(ficlog," p=%.12e",p[j]);
975: }
976: printf("\n");
977: fprintf(ficlog,"\n");
978: #endif
979: }
980: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
981: #ifdef DEBUG
982: int k[2],l;
983: k[0]=1;
984: k[1]=-1;
985: printf("Max: %.12e",(*func)(p));
986: fprintf(ficlog,"Max: %.12e",(*func)(p));
987: for (j=1;j<=n;j++) {
988: printf(" %.12e",p[j]);
989: fprintf(ficlog," %.12e",p[j]);
990: }
991: printf("\n");
992: fprintf(ficlog,"\n");
993: for(l=0;l<=1;l++) {
994: for (j=1;j<=n;j++) {
995: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
996: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
997: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
998: }
999: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1000: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1001: }
1002: #endif
1003:
1004:
1005: free_vector(xit,1,n);
1006: free_vector(xits,1,n);
1007: free_vector(ptt,1,n);
1008: free_vector(pt,1,n);
1009: return;
1010: }
1011: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1012: for (j=1;j<=n;j++) {
1013: ptt[j]=2.0*p[j]-pt[j];
1014: xit[j]=p[j]-pt[j];
1015: pt[j]=p[j];
1016: }
1017: fptt=(*func)(ptt);
1018: if (fptt < fp) {
1019: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1020: if (t < 0.0) {
1021: linmin(p,xit,n,fret,func);
1022: for (j=1;j<=n;j++) {
1023: xi[j][ibig]=xi[j][n];
1024: xi[j][n]=xit[j];
1025: }
1026: #ifdef DEBUG
1027: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1028: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1029: for(j=1;j<=n;j++){
1030: printf(" %.12e",xit[j]);
1031: fprintf(ficlog," %.12e",xit[j]);
1032: }
1033: printf("\n");
1034: fprintf(ficlog,"\n");
1035: #endif
1.54 brouard 1036: }
1.53 brouard 1037: }
1038: }
1039: }
1040:
1.54 brouard 1041: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 1042:
1043: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1044: {
1045: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1046: matrix by transitions matrix until convergence is reached */
1047:
1048: int i, ii,j,k;
1049: double min, max, maxmin, maxmax,sumnew=0.;
1050: double **matprod2();
1051: double **out, cov[NCOVMAX], **pmij();
1052: double **newm;
1053: double agefin, delaymax=50 ; /* Max number of years to converge */
1054:
1055: for (ii=1;ii<=nlstate+ndeath;ii++)
1056: for (j=1;j<=nlstate+ndeath;j++){
1057: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1058: }
1059:
1060: cov[1]=1.;
1061:
1062: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1063: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1064: newm=savm;
1065: /* Covariates have to be included here again */
1066: cov[2]=agefin;
1067:
1068: for (k=1; k<=cptcovn;k++) {
1069: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1070: /* 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]]);*/
1071: }
1072: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1073: for (k=1; k<=cptcovprod;k++)
1074: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1075:
1076: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1077: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1078: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1079: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1080:
1081: savm=oldm;
1082: oldm=newm;
1083: maxmax=0.;
1084: for(j=1;j<=nlstate;j++){
1085: min=1.;
1086: max=0.;
1087: for(i=1; i<=nlstate; i++) {
1088: sumnew=0;
1089: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1090: prlim[i][j]= newm[i][j]/(1-sumnew);
1091: max=FMAX(max,prlim[i][j]);
1092: min=FMIN(min,prlim[i][j]);
1093: }
1094: maxmin=max-min;
1095: maxmax=FMAX(maxmax,maxmin);
1096: }
1097: if(maxmax < ftolpl){
1098: return prlim;
1099: }
1100: }
1101: }
1102:
1103: /*************** transition probabilities ***************/
1104:
1105: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1106: {
1107: double s1, s2;
1108: /*double t34;*/
1109: int i,j,j1, nc, ii, jj;
1110:
1111: for(i=1; i<= nlstate; i++){
1.99 brouard 1112: for(j=1; j<i;j++){
1113: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1114: /*s2 += param[i][j][nc]*cov[nc];*/
1115: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1116: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1117: }
1118: ps[i][j]=s2;
1119: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1120: }
1121: for(j=i+1; j<=nlstate+ndeath;j++){
1122: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1123: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1124: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1125: }
1126: ps[i][j]=s2;
1.53 brouard 1127: }
1128: }
1129: /*ps[3][2]=1;*/
1.99 brouard 1130:
1131: for(i=1; i<= nlstate; i++){
1132: s1=0;
1133: for(j=1; j<i; j++)
1134: s1+=exp(ps[i][j]);
1135: for(j=i+1; j<=nlstate+ndeath; j++)
1136: s1+=exp(ps[i][j]);
1137: ps[i][i]=1./(s1+1.);
1138: for(j=1; j<i; j++)
1139: ps[i][j]= exp(ps[i][j])*ps[i][i];
1140: for(j=i+1; j<=nlstate+ndeath; j++)
1141: ps[i][j]= exp(ps[i][j])*ps[i][i];
1142: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1143: } /* end i */
1144:
1145: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1146: for(jj=1; jj<= nlstate+ndeath; jj++){
1147: ps[ii][jj]=0;
1148: ps[ii][ii]=1;
1149: }
1.53 brouard 1150: }
1.99 brouard 1151:
1.53 brouard 1152:
1.99 brouard 1153: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1154: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1155: /* printf("ddd %lf ",ps[ii][jj]); */
1156: /* } */
1157: /* printf("\n "); */
1158: /* } */
1159: /* printf("\n ");printf("%lf ",cov[2]); */
1160: /*
1161: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1162: goto end;*/
1.53 brouard 1163: return ps;
1164: }
1165:
1166: /**************** Product of 2 matrices ******************/
1167:
1168: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1169: {
1170: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1171: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1172: /* in, b, out are matrice of pointers which should have been initialized
1173: before: only the contents of out is modified. The function returns
1174: a pointer to pointers identical to out */
1175: long i, j, k;
1176: for(i=nrl; i<= nrh; i++)
1177: for(k=ncolol; k<=ncoloh; k++)
1178: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1179: out[i][k] +=in[i][j]*b[j][k];
1180:
1181: return out;
1182: }
1183:
1184:
1185: /************* Higher Matrix Product ***************/
1186:
1187: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1188: {
1.66 brouard 1189: /* Computes the transition matrix starting at age 'age' over
1190: 'nhstepm*hstepm*stepm' months (i.e. until
1191: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1192: nhstepm*hstepm matrices.
1.53 brouard 1193: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1194: (typically every 2 years instead of every month which is too big
1195: for the memory).
1.53 brouard 1196: Model is determined by parameters x and covariates have to be
1197: included manually here.
1198:
1199: */
1200:
1201: int i, j, d, h, k;
1202: double **out, cov[NCOVMAX];
1203: double **newm;
1204:
1205: /* Hstepm could be zero and should return the unit matrix */
1206: for (i=1;i<=nlstate+ndeath;i++)
1207: for (j=1;j<=nlstate+ndeath;j++){
1208: oldm[i][j]=(i==j ? 1.0 : 0.0);
1209: po[i][j][0]=(i==j ? 1.0 : 0.0);
1210: }
1211: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1212: for(h=1; h <=nhstepm; h++){
1213: for(d=1; d <=hstepm; d++){
1214: newm=savm;
1215: /* Covariates have to be included here again */
1216: cov[1]=1.;
1217: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1218: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1219: for (k=1; k<=cptcovage;k++)
1220: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1221: for (k=1; k<=cptcovprod;k++)
1222: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1223:
1224:
1225: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1226: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1227: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1228: pmij(pmmij,cov,ncovmodel,x,nlstate));
1229: savm=oldm;
1230: oldm=newm;
1231: }
1232: for(i=1; i<=nlstate+ndeath; i++)
1233: for(j=1;j<=nlstate+ndeath;j++) {
1234: po[i][j][h]=newm[i][j];
1235: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1236: */
1237: }
1238: } /* end h */
1239: return po;
1240: }
1241:
1242:
1243: /*************** log-likelihood *************/
1244: double func( double *x)
1245: {
1246: int i, ii, j, k, mi, d, kk;
1247: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1248: double **out;
1249: double sw; /* Sum of weights */
1250: double lli; /* Individual log likelihood */
1.59 brouard 1251: int s1, s2;
1.68 lievre 1252: double bbh, survp;
1.53 brouard 1253: long ipmx;
1254: /*extern weight */
1255: /* We are differentiating ll according to initial status */
1256: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1257: /*for(i=1;i<imx;i++)
1258: printf(" %d\n",s[4][i]);
1259: */
1260: cov[1]=1.;
1261:
1262: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1263:
1264: if(mle==1){
1265: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1266: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1267: for(mi=1; mi<= wav[i]-1; mi++){
1268: for (ii=1;ii<=nlstate+ndeath;ii++)
1269: for (j=1;j<=nlstate+ndeath;j++){
1270: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1271: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1272: }
1273: for(d=0; d<dh[mi][i]; d++){
1274: newm=savm;
1275: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1276: for (kk=1; kk<=cptcovage;kk++) {
1277: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1278: }
1279: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1280: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1281: savm=oldm;
1282: oldm=newm;
1283: } /* end mult */
1.53 brouard 1284:
1.61 brouard 1285: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1.101 brouard 1286: /* But now since version 0.9 we anticipate for bias at large stepm.
1.61 brouard 1287: * If stepm is larger than one month (smallest stepm) and if the exact delay
1288: * (in months) between two waves is not a multiple of stepm, we rounded to
1289: * the nearest (and in case of equal distance, to the lowest) interval but now
1290: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1.101 brouard 1291: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1.61 brouard 1292: * probability in order to take into account the bias as a fraction of the way
1.101 brouard 1293: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1.61 brouard 1294: * -stepm/2 to stepm/2 .
1295: * For stepm=1 the results are the same as for previous versions of Imach.
1296: * For stepm > 1 the results are less biased than in previous versions.
1297: */
1298: s1=s[mw[mi][i]][i];
1299: s2=s[mw[mi+1][i]][i];
1.64 lievre 1300: bbh=(double)bh[mi][i]/(double)stepm;
1.101 brouard 1301: /* bias bh is positive if real duration
1.64 lievre 1302: * is higher than the multiple of stepm and negative otherwise.
1303: */
1304: /* 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 1305: if( s2 > nlstate){
1.104 lievre 1306: /* i.e. if s2 is a death state and if the date of death is known
1307: then the contribution to the likelihood is the probability to
1308: die between last step unit time and current step unit time,
1309: which is also equal to probability to die before dh
1.101 brouard 1310: minus probability to die before dh-stepm .
1.71 brouard 1311: In version up to 0.92 likelihood was computed
1312: as if date of death was unknown. Death was treated as any other
1313: health state: the date of the interview describes the actual state
1314: and not the date of a change in health state. The former idea was
1315: to consider that at each interview the state was recorded
1316: (healthy, disable or death) and IMaCh was corrected; but when we
1317: introduced the exact date of death then we should have modified
1318: the contribution of an exact death to the likelihood. This new
1319: contribution is smaller and very dependent of the step unit
1320: stepm. It is no more the probability to die between last interview
1321: and month of death but the probability to survive from last
1322: interview up to one month before death multiplied by the
1323: probability to die within a month. Thanks to Chris
1324: Jackson for correcting this bug. Former versions increased
1325: mortality artificially. The bad side is that we add another loop
1326: which slows down the processing. The difference can be up to 10%
1327: lower mortality.
1328: */
1329: lli=log(out[s1][s2] - savm[s1][s2]);
1.104 lievre 1330:
1331:
1332: } else if (s2==-2) {
1333: for (j=1,survp=0. ; j<=nlstate; j++)
1334: survp += out[s1][j];
1335: lli= survp;
1336: }
1.105 lievre 1337:
1338: else if (s2==-4) {
1339: for (j=3,survp=0. ; j<=nlstate; j++)
1340: survp += out[s1][j];
1341: lli= survp;
1342: }
1343:
1344: else if (s2==-5) {
1345: for (j=1,survp=0. ; j<=2; j++)
1346: survp += out[s1][j];
1347: lli= survp;
1348: }
1.104 lievre 1349:
1350:
1351: else{
1.71 brouard 1352: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1353: /* 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 */
1354: }
1.64 lievre 1355: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1356: /*if(lli ==000.0)*/
1357: /*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 1358: ipmx +=1;
1.64 lievre 1359: sw += weight[i];
1360: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1361: } /* end of wave */
1362: } /* end of individual */
1363: } else if(mle==2){
1364: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1365: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1366: for(mi=1; mi<= wav[i]-1; mi++){
1367: for (ii=1;ii<=nlstate+ndeath;ii++)
1368: for (j=1;j<=nlstate+ndeath;j++){
1369: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1370: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1371: }
1372: for(d=0; d<=dh[mi][i]; d++){
1373: newm=savm;
1374: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1375: for (kk=1; kk<=cptcovage;kk++) {
1376: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1377: }
1378: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1379: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1380: savm=oldm;
1381: oldm=newm;
1382: } /* end mult */
1383:
1384: s1=s[mw[mi][i]][i];
1385: s2=s[mw[mi+1][i]][i];
1386: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1387: 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 1388: ipmx +=1;
1389: sw += weight[i];
1390: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1391: } /* end of wave */
1392: } /* end of individual */
1393: } else if(mle==3){ /* exponential inter-extrapolation */
1394: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1395: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1396: for(mi=1; mi<= wav[i]-1; mi++){
1397: for (ii=1;ii<=nlstate+ndeath;ii++)
1398: for (j=1;j<=nlstate+ndeath;j++){
1399: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1400: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1401: }
1402: for(d=0; d<dh[mi][i]; d++){
1403: newm=savm;
1404: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1405: for (kk=1; kk<=cptcovage;kk++) {
1406: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1407: }
1408: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1409: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1410: savm=oldm;
1411: oldm=newm;
1412: } /* end mult */
1413:
1414: s1=s[mw[mi][i]][i];
1415: s2=s[mw[mi+1][i]][i];
1416: bbh=(double)bh[mi][i]/(double)stepm;
1417: 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 1418: ipmx +=1;
1419: sw += weight[i];
1420: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1421: } /* end of wave */
1422: } /* end of individual */
1.84 brouard 1423: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1424: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1425: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1426: for(mi=1; mi<= wav[i]-1; mi++){
1427: for (ii=1;ii<=nlstate+ndeath;ii++)
1428: for (j=1;j<=nlstate+ndeath;j++){
1429: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1430: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1431: }
1432: for(d=0; d<dh[mi][i]; d++){
1433: newm=savm;
1434: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1435: for (kk=1; kk<=cptcovage;kk++) {
1436: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1437: }
1438:
1439: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1440: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1441: savm=oldm;
1442: oldm=newm;
1443: } /* end mult */
1444:
1.84 brouard 1445: s1=s[mw[mi][i]][i];
1446: s2=s[mw[mi+1][i]][i];
1447: if( s2 > nlstate){
1448: lli=log(out[s1][s2] - savm[s1][s2]);
1449: }else{
1450: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1451: }
1452: ipmx +=1;
1453: sw += weight[i];
1454: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1455: /* 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 1456: } /* end of wave */
1457: } /* end of individual */
1458: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1459: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1460: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1461: for(mi=1; mi<= wav[i]-1; mi++){
1462: for (ii=1;ii<=nlstate+ndeath;ii++)
1463: for (j=1;j<=nlstate+ndeath;j++){
1464: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1465: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1466: }
1467: for(d=0; d<dh[mi][i]; d++){
1468: newm=savm;
1469: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1470: for (kk=1; kk<=cptcovage;kk++) {
1471: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1472: }
1473:
1474: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1475: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1476: savm=oldm;
1477: oldm=newm;
1478: } /* end mult */
1479:
1480: s1=s[mw[mi][i]][i];
1481: s2=s[mw[mi+1][i]][i];
1.61 brouard 1482: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1483: ipmx +=1;
1484: sw += weight[i];
1485: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1486: /*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 1487: } /* end of wave */
1488: } /* end of individual */
1489: } /* End of if */
1.53 brouard 1490: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1491: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1492: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1493: return -l;
1494: }
1495:
1496: /*************** log-likelihood *************/
1497: double funcone( double *x)
1498: {
1.87 brouard 1499: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1500: int i, ii, j, k, mi, d, kk;
1501: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1502: double **out;
1503: double lli; /* Individual log likelihood */
1.87 brouard 1504: double llt;
1.85 brouard 1505: int s1, s2;
1506: double bbh, survp;
1507: /*extern weight */
1508: /* We are differentiating ll according to initial status */
1509: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1510: /*for(i=1;i<imx;i++)
1511: printf(" %d\n",s[4][i]);
1512: */
1513: cov[1]=1.;
1514:
1515: for(k=1; k<=nlstate; k++) ll[k]=0.;
1516:
1517: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1518: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1519: for(mi=1; mi<= wav[i]-1; mi++){
1520: for (ii=1;ii<=nlstate+ndeath;ii++)
1521: for (j=1;j<=nlstate+ndeath;j++){
1522: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1523: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1524: }
1525: for(d=0; d<dh[mi][i]; d++){
1526: newm=savm;
1527: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1528: for (kk=1; kk<=cptcovage;kk++) {
1529: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1530: }
1531: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1532: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1533: savm=oldm;
1534: oldm=newm;
1535: } /* end mult */
1536:
1537: s1=s[mw[mi][i]][i];
1538: s2=s[mw[mi+1][i]][i];
1539: bbh=(double)bh[mi][i]/(double)stepm;
1540: /* bias is positive if real duration
1541: * is higher than the multiple of stepm and negative otherwise.
1542: */
1543: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1544: lli=log(out[s1][s2] - savm[s1][s2]);
1545: } else if (mle==1){
1546: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1547: } else if(mle==2){
1548: 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 */
1549: } else if(mle==3){ /* exponential inter-extrapolation */
1550: 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 */
1551: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1552: lli=log(out[s1][s2]); /* Original formula */
1553: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1554: lli=log(out[s1][s2]); /* Original formula */
1555: } /* End of if */
1556: ipmx +=1;
1557: sw += weight[i];
1558: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1559: /* 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]); */
1560: if(globpr){
1.88 brouard 1561: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1562: %10.6f %10.6f %10.6f ", \
1563: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1564: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1565: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1566: llt +=ll[k]*gipmx/gsw;
1567: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1568: }
1569: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1570: }
1571: } /* end of wave */
1572: } /* end of individual */
1573: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1574: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1575: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1576: if(globpr==0){ /* First time we count the contributions and weights */
1577: gipmx=ipmx;
1578: gsw=sw;
1579: }
1.53 brouard 1580: return -l;
1581: }
1582:
1583:
1.94 brouard 1584: /*************** function likelione ***********/
1.87 brouard 1585: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1586: {
1.87 brouard 1587: /* This routine should help understanding what is done with
1588: the selection of individuals/waves and
1.85 brouard 1589: to check the exact contribution to the likelihood.
1590: Plotting could be done.
1591: */
1592: int k;
1.87 brouard 1593:
1.88 brouard 1594: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1595: strcpy(fileresilk,"ilk");
1596: strcat(fileresilk,fileres);
1597: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1598: printf("Problem with resultfile: %s\n", fileresilk);
1599: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1600: }
1.87 brouard 1601: 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 1602: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1603: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1604: for(k=1; k<=nlstate; k++)
1.87 brouard 1605: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1606: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1607: }
1608:
1609: *fretone=(*funcone)(p);
1.87 brouard 1610: if(*globpri !=0){
1.85 brouard 1611: fclose(ficresilk);
1.88 brouard 1612: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1613: fflush(fichtm);
1614: }
1.85 brouard 1615: return;
1616: }
1617:
1.88 brouard 1618:
1.53 brouard 1619: /*********** Maximum Likelihood Estimation ***************/
1620:
1621: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1622: {
1623: int i,j, iter;
1.74 brouard 1624: double **xi;
1.53 brouard 1625: double fret;
1.85 brouard 1626: double fretone; /* Only one call to likelihood */
1.98 brouard 1627: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1628: xi=matrix(1,npar,1,npar);
1629: for (i=1;i<=npar;i++)
1630: for (j=1;j<=npar;j++)
1631: xi[i][j]=(i==j ? 1.0 : 0.0);
1632: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1633: strcpy(filerespow,"pow");
1634: strcat(filerespow,fileres);
1635: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1636: printf("Problem with resultfile: %s\n", filerespow);
1637: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1638: }
1639: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1640: for (i=1;i<=nlstate;i++)
1641: for(j=1;j<=nlstate+ndeath;j++)
1642: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1643: fprintf(ficrespow,"\n");
1.85 brouard 1644:
1.53 brouard 1645: powell(p,xi,npar,ftol,&iter,&fret,func);
1646:
1.76 brouard 1647: fclose(ficrespow);
1648: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1649: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1650: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1651:
1652: }
1653:
1654: /**** Computes Hessian and covariance matrix ***/
1655: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1656: {
1657: double **a,**y,*x,pd;
1658: double **hess;
1659: int i, j,jk;
1660: int *indx;
1661:
1.98 brouard 1662: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1663: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1664: void lubksb(double **a, int npar, int *indx, double b[]) ;
1665: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 brouard 1666: double gompertz(double p[]);
1.53 brouard 1667: hess=matrix(1,npar,1,npar);
1668:
1669: printf("\nCalculation of the hessian matrix. Wait...\n");
1670: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1671: for (i=1;i<=npar;i++){
1672: printf("%d",i);fflush(stdout);
1673: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 brouard 1674:
1675: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1676:
1677: /* printf(" %f ",p[i]);
1678: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1679: }
1680:
1681: for (i=1;i<=npar;i++) {
1682: for (j=1;j<=npar;j++) {
1683: if (j>i) {
1684: printf(".%d%d",i,j);fflush(stdout);
1685: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 brouard 1686: hess[i][j]=hessij(p,delti,i,j,func,npar);
1687:
1.53 brouard 1688: hess[j][i]=hess[i][j];
1689: /*printf(" %lf ",hess[i][j]);*/
1690: }
1691: }
1692: }
1693: printf("\n");
1694: fprintf(ficlog,"\n");
1695:
1696: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1697: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1698:
1699: a=matrix(1,npar,1,npar);
1700: y=matrix(1,npar,1,npar);
1701: x=vector(1,npar);
1702: indx=ivector(1,npar);
1703: for (i=1;i<=npar;i++)
1704: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1705: ludcmp(a,npar,indx,&pd);
1706:
1707: for (j=1;j<=npar;j++) {
1708: for (i=1;i<=npar;i++) x[i]=0;
1709: x[j]=1;
1710: lubksb(a,npar,indx,x);
1711: for (i=1;i<=npar;i++){
1712: matcov[i][j]=x[i];
1713: }
1714: }
1715:
1716: printf("\n#Hessian matrix#\n");
1717: fprintf(ficlog,"\n#Hessian matrix#\n");
1718: for (i=1;i<=npar;i++) {
1719: for (j=1;j<=npar;j++) {
1720: printf("%.3e ",hess[i][j]);
1721: fprintf(ficlog,"%.3e ",hess[i][j]);
1722: }
1723: printf("\n");
1724: fprintf(ficlog,"\n");
1725: }
1726:
1727: /* Recompute Inverse */
1728: for (i=1;i<=npar;i++)
1729: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1730: ludcmp(a,npar,indx,&pd);
1731:
1732: /* printf("\n#Hessian matrix recomputed#\n");
1733:
1734: for (j=1;j<=npar;j++) {
1735: for (i=1;i<=npar;i++) x[i]=0;
1736: x[j]=1;
1737: lubksb(a,npar,indx,x);
1738: for (i=1;i<=npar;i++){
1739: y[i][j]=x[i];
1740: printf("%.3e ",y[i][j]);
1741: fprintf(ficlog,"%.3e ",y[i][j]);
1742: }
1743: printf("\n");
1744: fprintf(ficlog,"\n");
1745: }
1746: */
1747:
1748: free_matrix(a,1,npar,1,npar);
1749: free_matrix(y,1,npar,1,npar);
1750: free_vector(x,1,npar);
1751: free_ivector(indx,1,npar);
1752: free_matrix(hess,1,npar,1,npar);
1753:
1754:
1755: }
1756:
1757: /*************** hessian matrix ****************/
1.98 brouard 1758: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1759: {
1760: int i;
1761: int l=1, lmax=20;
1762: double k1,k2;
1763: double p2[NPARMAX+1];
1764: double res;
1.98 brouard 1765: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1766: double fx;
1767: int k=0,kmax=10;
1768: double l1;
1769:
1770: fx=func(x);
1771: for (i=1;i<=npar;i++) p2[i]=x[i];
1772: for(l=0 ; l <=lmax; l++){
1773: l1=pow(10,l);
1774: delts=delt;
1775: for(k=1 ; k <kmax; k=k+1){
1776: delt = delta*(l1*k);
1777: p2[theta]=x[theta] +delt;
1778: k1=func(p2)-fx;
1779: p2[theta]=x[theta]-delt;
1780: k2=func(p2)-fx;
1781: /*res= (k1-2.0*fx+k2)/delt/delt; */
1782: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1783:
1784: #ifdef DEBUG
1785: 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);
1786: 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);
1787: #endif
1788: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1789: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1790: k=kmax;
1791: }
1792: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1793: k=kmax; l=lmax*10.;
1794: }
1795: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1796: delts=delt;
1797: }
1798: }
1799: }
1800: delti[theta]=delts;
1801: return res;
1802:
1803: }
1804:
1.98 brouard 1805: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1806: {
1807: int i;
1808: int l=1, l1, lmax=20;
1809: double k1,k2,k3,k4,res,fx;
1810: double p2[NPARMAX+1];
1811: int k;
1812:
1813: fx=func(x);
1814: for (k=1; k<=2; k++) {
1815: for (i=1;i<=npar;i++) p2[i]=x[i];
1816: p2[thetai]=x[thetai]+delti[thetai]/k;
1817: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1818: k1=func(p2)-fx;
1819:
1820: p2[thetai]=x[thetai]+delti[thetai]/k;
1821: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1822: k2=func(p2)-fx;
1823:
1824: p2[thetai]=x[thetai]-delti[thetai]/k;
1825: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1826: k3=func(p2)-fx;
1827:
1828: p2[thetai]=x[thetai]-delti[thetai]/k;
1829: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1830: k4=func(p2)-fx;
1831: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1832: #ifdef DEBUG
1833: 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);
1834: 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);
1835: #endif
1836: }
1837: return res;
1838: }
1839:
1840: /************** Inverse of matrix **************/
1841: void ludcmp(double **a, int n, int *indx, double *d)
1842: {
1843: int i,imax,j,k;
1844: double big,dum,sum,temp;
1845: double *vv;
1846:
1847: vv=vector(1,n);
1848: *d=1.0;
1849: for (i=1;i<=n;i++) {
1850: big=0.0;
1851: for (j=1;j<=n;j++)
1852: if ((temp=fabs(a[i][j])) > big) big=temp;
1853: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1854: vv[i]=1.0/big;
1855: }
1856: for (j=1;j<=n;j++) {
1857: for (i=1;i<j;i++) {
1858: sum=a[i][j];
1859: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1860: a[i][j]=sum;
1861: }
1862: big=0.0;
1863: for (i=j;i<=n;i++) {
1864: sum=a[i][j];
1865: for (k=1;k<j;k++)
1866: sum -= a[i][k]*a[k][j];
1867: a[i][j]=sum;
1868: if ( (dum=vv[i]*fabs(sum)) >= big) {
1869: big=dum;
1870: imax=i;
1871: }
1872: }
1873: if (j != imax) {
1874: for (k=1;k<=n;k++) {
1875: dum=a[imax][k];
1876: a[imax][k]=a[j][k];
1877: a[j][k]=dum;
1878: }
1879: *d = -(*d);
1880: vv[imax]=vv[j];
1881: }
1882: indx[j]=imax;
1883: if (a[j][j] == 0.0) a[j][j]=TINY;
1884: if (j != n) {
1885: dum=1.0/(a[j][j]);
1886: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1887: }
1888: }
1889: free_vector(vv,1,n); /* Doesn't work */
1890: ;
1891: }
1892:
1893: void lubksb(double **a, int n, int *indx, double b[])
1894: {
1895: int i,ii=0,ip,j;
1896: double sum;
1897:
1898: for (i=1;i<=n;i++) {
1899: ip=indx[i];
1900: sum=b[ip];
1901: b[ip]=b[i];
1902: if (ii)
1903: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1904: else if (sum) ii=i;
1905: b[i]=sum;
1906: }
1907: for (i=n;i>=1;i--) {
1908: sum=b[i];
1909: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1910: b[i]=sum/a[i][i];
1911: }
1912: }
1913:
1914: /************ Frequencies ********************/
1.105 lievre 1915: 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 1916: { /* Some frequencies */
1917:
1918: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1919: int first;
1920: double ***freq; /* Frequencies */
1.73 lievre 1921: double *pp, **prop;
1922: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1923: FILE *ficresp;
1924: char fileresp[FILENAMELENGTH];
1925:
1926: pp=vector(1,nlstate);
1.74 brouard 1927: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1928: strcpy(fileresp,"p");
1929: strcat(fileresp,fileres);
1930: if((ficresp=fopen(fileresp,"w"))==NULL) {
1931: printf("Problem with prevalence resultfile: %s\n", fileresp);
1932: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1933: exit(0);
1934: }
1.105 lievre 1935: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1936: j1=0;
1937:
1938: j=cptcoveff;
1939: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1940:
1941: first=1;
1942:
1943: for(k1=1; k1<=j;k1++){
1944: for(i1=1; i1<=ncodemax[k1];i1++){
1945: j1++;
1946: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1947: scanf("%d", i);*/
1.105 lievre 1948: for (i=-5; i<=nlstate+ndeath; i++)
1949: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.74 brouard 1950: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1951: freq[i][jk][m]=0;
1.73 lievre 1952:
1953: for (i=1; i<=nlstate; i++)
1.74 brouard 1954: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1955: prop[i][m]=0;
1.53 brouard 1956:
1957: dateintsum=0;
1958: k2cpt=0;
1959: for (i=1; i<=imx; i++) {
1960: bool=1;
1961: if (cptcovn>0) {
1962: for (z1=1; z1<=cptcoveff; z1++)
1963: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1964: bool=0;
1965: }
1.58 lievre 1966: if (bool==1){
1.53 brouard 1967: for(m=firstpass; m<=lastpass; m++){
1968: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1969: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1970: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1971: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1972: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1973: if (m<lastpass) {
1974: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1975: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1976: }
1977:
1.74 brouard 1978: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1979: dateintsum=dateintsum+k2;
1980: k2cpt++;
1981: }
1.84 brouard 1982: /*}*/
1.53 brouard 1983: }
1984: }
1985: }
1986:
1.84 brouard 1987: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.105 lievre 1988: fprintf(ficresp, "#Local time at start: %s", strstart);
1.53 brouard 1989: if (cptcovn>0) {
1990: fprintf(ficresp, "\n#********** Variable ");
1991: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1992: fprintf(ficresp, "**********\n#");
1993: }
1994: for(i=1; i<=nlstate;i++)
1995: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1996: fprintf(ficresp, "\n");
1997:
1.74 brouard 1998: for(i=iagemin; i <= iagemax+3; i++){
1999: if(i==iagemax+3){
1.53 brouard 2000: fprintf(ficlog,"Total");
2001: }else{
2002: if(first==1){
2003: first=0;
2004: printf("See log file for details...\n");
2005: }
2006: fprintf(ficlog,"Age %d", i);
2007: }
2008: for(jk=1; jk <=nlstate ; jk++){
2009: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2010: pp[jk] += freq[jk][m][i];
2011: }
2012: for(jk=1; jk <=nlstate ; jk++){
2013: for(m=-1, pos=0; m <=0 ; m++)
2014: pos += freq[jk][m][i];
2015: if(pp[jk]>=1.e-10){
2016: if(first==1){
2017: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2018: }
2019: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2020: }else{
2021: if(first==1)
2022: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2023: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2024: }
2025: }
2026:
2027: for(jk=1; jk <=nlstate ; jk++){
2028: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2029: pp[jk] += freq[jk][m][i];
1.73 lievre 2030: }
2031: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2032: pos += pp[jk];
2033: posprop += prop[jk][i];
1.53 brouard 2034: }
2035: for(jk=1; jk <=nlstate ; jk++){
2036: if(pos>=1.e-5){
2037: if(first==1)
2038: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2039: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2040: }else{
2041: if(first==1)
2042: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2043: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2044: }
1.74 brouard 2045: if( i <= iagemax){
1.53 brouard 2046: if(pos>=1.e-5){
1.73 lievre 2047: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 2048: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 2049: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2050: }
2051: else
1.73 lievre 2052: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 2053: }
2054: }
2055:
1.69 brouard 2056: for(jk=-1; jk <=nlstate+ndeath; jk++)
2057: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 2058: if(freq[jk][m][i] !=0 ) {
2059: if(first==1)
2060: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2061: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2062: }
1.74 brouard 2063: if(i <= iagemax)
1.53 brouard 2064: fprintf(ficresp,"\n");
2065: if(first==1)
2066: printf("Others in log...\n");
2067: fprintf(ficlog,"\n");
2068: }
2069: }
2070: }
2071: dateintmean=dateintsum/k2cpt;
2072:
2073: fclose(ficresp);
1.105 lievre 2074: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 2075: free_vector(pp,1,nlstate);
1.74 brouard 2076: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 2077: /* End of Freq */
2078: }
2079:
2080: /************ Prevalence ********************/
1.84 brouard 2081: 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 2082: {
2083: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2084: in each health status at the date of interview (if between dateprev1 and dateprev2).
2085: We still use firstpass and lastpass as another selection.
2086: */
1.53 brouard 2087:
2088: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2089: double ***freq; /* Frequencies */
1.73 lievre 2090: double *pp, **prop;
2091: double pos,posprop;
1.69 brouard 2092: double y2; /* in fractional years */
1.74 brouard 2093: int iagemin, iagemax;
1.53 brouard 2094:
1.74 brouard 2095: iagemin= (int) agemin;
2096: iagemax= (int) agemax;
2097: /*pp=vector(1,nlstate);*/
2098: prop=matrix(1,nlstate,iagemin,iagemax+3);
2099: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 2100: j1=0;
2101:
2102: j=cptcoveff;
2103: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2104:
2105: for(k1=1; k1<=j;k1++){
2106: for(i1=1; i1<=ncodemax[k1];i1++){
2107: j1++;
2108:
1.73 lievre 2109: for (i=1; i<=nlstate; i++)
1.74 brouard 2110: for(m=iagemin; m <= iagemax+3; m++)
2111: prop[i][m]=0.0;
1.53 brouard 2112:
1.69 brouard 2113: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2114: bool=1;
2115: if (cptcovn>0) {
2116: for (z1=1; z1<=cptcoveff; z1++)
2117: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2118: bool=0;
2119: }
2120: if (bool==1) {
1.69 brouard 2121: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2122: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2123: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2124: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2125: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2126: 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);
2127: if (s[m][i]>0 && s[m][i]<=nlstate) {
2128: /*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]]);*/
2129: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2130: prop[s[m][i]][iagemax+3] += weight[i];
2131: }
1.53 brouard 2132: }
1.69 brouard 2133: } /* end selection of waves */
1.53 brouard 2134: }
2135: }
1.74 brouard 2136: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2137:
1.74 brouard 2138: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2139: posprop += prop[jk][i];
2140: }
2141:
2142: for(jk=1; jk <=nlstate ; jk++){
2143: if( i <= iagemax){
2144: if(posprop>=1.e-5){
2145: probs[i][jk][j1]= prop[jk][i]/posprop;
2146: }
2147: }
2148: }/* end jk */
2149: }/* end i */
1.53 brouard 2150: } /* end i1 */
2151: } /* end k1 */
2152:
1.74 brouard 2153: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2154: /*free_vector(pp,1,nlstate);*/
2155: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2156: } /* End of prevalence */
1.53 brouard 2157:
2158: /************* Waves Concatenation ***************/
2159:
1.59 brouard 2160: 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 2161: {
2162: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2163: Death is a valid wave (if date is known).
2164: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2165: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2166: and mw[mi+1][i]. dh depends on stepm.
2167: */
2168:
2169: int i, mi, m;
2170: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2171: double sum=0., jmean=0.;*/
2172: int first;
2173: int j, k=0,jk, ju, jl;
2174: double sum=0.;
2175: first=0;
2176: jmin=1e+5;
2177: jmax=-1;
2178: jmean=0.;
2179: for(i=1; i<=imx; i++){
2180: mi=0;
2181: m=firstpass;
2182: while(s[m][i] <= nlstate){
1.105 lievre 2183: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
1.53 brouard 2184: mw[++mi][i]=m;
2185: if(m >=lastpass)
2186: break;
2187: else
2188: m++;
2189: }/* end while */
2190: if (s[m][i] > nlstate){
2191: mi++; /* Death is another wave */
2192: /* if(mi==0) never been interviewed correctly before death */
2193: /* Only death is a correct wave */
2194: mw[mi][i]=m;
2195: }
2196:
2197: wav[i]=mi;
2198: if(mi==0){
1.91 brouard 2199: nbwarn++;
1.53 brouard 2200: if(first==0){
1.85 brouard 2201: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2202: first=1;
2203: }
2204: if(first==1){
1.85 brouard 2205: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2206: }
2207: } /* end mi==0 */
1.77 brouard 2208: } /* End individuals */
1.53 brouard 2209:
2210: for(i=1; i<=imx; i++){
2211: for(mi=1; mi<wav[i];mi++){
2212: if (stepm <=0)
2213: dh[mi][i]=1;
2214: else{
1.77 brouard 2215: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2216: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2217: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2218: if(j==0) j=1; /* Survives at least one month after exam */
2219: else if(j<0){
1.91 brouard 2220: nberr++;
1.85 brouard 2221: 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 2222: j=1; /* Temporary Dangerous patch */
1.105 lievre 2223: 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 2224: 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 2225: 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 2226: }
2227: k=k+1;
2228: if (j >= jmax) jmax=j;
2229: if (j <= jmin) jmin=j;
2230: sum=sum+j;
2231: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2232: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2233: }
2234: }
2235: else{
2236: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.104 lievre 2237: /* 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]); */
2238:
1.53 brouard 2239: k=k+1;
2240: if (j >= jmax) jmax=j;
2241: else if (j <= jmin)jmin=j;
2242: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2243: /*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 2244: if(j<0){
1.91 brouard 2245: nberr++;
1.85 brouard 2246: 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]);
2247: 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]);
2248: }
1.53 brouard 2249: sum=sum+j;
2250: }
2251: jk= j/stepm;
2252: jl= j -jk*stepm;
2253: ju= j -(jk+1)*stepm;
1.85 brouard 2254: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2255: if(jl==0){
2256: dh[mi][i]=jk;
2257: bh[mi][i]=0;
2258: }else{ /* We want a negative bias in order to only have interpolation ie
2259: * at the price of an extra matrix product in likelihood */
2260: dh[mi][i]=jk+1;
2261: bh[mi][i]=ju;
2262: }
2263: }else{
2264: if(jl <= -ju){
2265: dh[mi][i]=jk;
2266: bh[mi][i]=jl; /* bias is positive if real duration
2267: * is higher than the multiple of stepm and negative otherwise.
2268: */
2269: }
2270: else{
2271: dh[mi][i]=jk+1;
2272: bh[mi][i]=ju;
2273: }
2274: if(dh[mi][i]==0){
2275: dh[mi][i]=1; /* At least one step */
2276: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2277: /* 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 2278: }
1.85 brouard 2279: } /* end if mle */
2280: }
1.64 lievre 2281: } /* end wave */
1.53 brouard 2282: }
2283: jmean=sum/k;
2284: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2285: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2286: }
2287:
2288: /*********** Tricode ****************************/
2289: void tricode(int *Tvar, int **nbcode, int imx)
2290: {
1.58 lievre 2291:
2292: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2293: int cptcode=0;
2294: cptcoveff=0;
2295:
1.58 lievre 2296: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2297: for (k=1; k<=7; k++) ncodemax[k]=0;
2298:
2299: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2300: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2301: modality*/
2302: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2303: Ndum[ij]++; /*store the modality */
1.53 brouard 2304: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2305: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2306: Tvar[j]. If V=sex and male is 0 and
2307: female is 1, then cptcode=1.*/
1.53 brouard 2308: }
2309:
2310: for (i=0; i<=cptcode; i++) {
1.58 lievre 2311: 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 2312: }
1.58 lievre 2313:
1.53 brouard 2314: ij=1;
2315: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2316: for (k=0; k<= maxncov; k++) {
1.53 brouard 2317: if (Ndum[k] != 0) {
2318: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2319: /* 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 2320:
2321: ij++;
2322: }
2323: if (ij > ncodemax[j]) break;
2324: }
2325: }
2326: }
2327:
1.58 lievre 2328: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2329:
1.58 lievre 2330: for (i=1; i<=ncovmodel-2; i++) {
1.104 lievre 2331: /* 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 2332: ij=Tvar[i];
1.58 lievre 2333: Ndum[ij]++;
1.53 brouard 2334: }
2335:
2336: ij=1;
1.58 lievre 2337: for (i=1; i<= maxncov; i++) {
1.53 brouard 2338: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2339: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2340: ij++;
2341: }
2342: }
2343:
1.58 lievre 2344: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2345: }
2346:
2347: /*********** Health Expectancies ****************/
2348:
1.105 lievre 2349: 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 2350:
2351: {
2352: /* Health expectancies */
2353: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2354: double age, agelim, hf;
2355: double ***p3mat,***varhe;
2356: double **dnewm,**doldm;
2357: double *xp;
2358: double **gp, **gm;
2359: double ***gradg, ***trgradg;
2360: int theta;
2361:
1.74 brouard 2362: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2363: xp=vector(1,npar);
1.74 brouard 2364: dnewm=matrix(1,nlstate*nlstate,1,npar);
2365: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2366:
1.105 lievre 2367: fprintf(ficreseij,"# Local time at start: %s", strstart);
1.53 brouard 2368: fprintf(ficreseij,"# Health expectancies\n");
2369: fprintf(ficreseij,"# Age");
2370: for(i=1; i<=nlstate;i++)
2371: for(j=1; j<=nlstate;j++)
2372: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2373: fprintf(ficreseij,"\n");
2374:
2375: if(estepm < stepm){
2376: printf ("Problem %d lower than %d\n",estepm, stepm);
2377: }
2378: else hstepm=estepm;
2379: /* We compute the life expectancy from trapezoids spaced every estepm months
2380: * This is mainly to measure the difference between two models: for example
2381: * if stepm=24 months pijx are given only every 2 years and by summing them
2382: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2383: * progression in between and thus overestimating or underestimating according
1.53 brouard 2384: * to the curvature of the survival function. If, for the same date, we
2385: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2386: * to compare the new estimate of Life expectancy with the same linear
2387: * hypothesis. A more precise result, taking into account a more precise
2388: * curvature will be obtained if estepm is as small as stepm. */
2389:
2390: /* For example we decided to compute the life expectancy with the smallest unit */
2391: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2392: nhstepm is the number of hstepm from age to agelim
2393: nstepm is the number of stepm from age to agelin.
2394: Look at hpijx to understand the reason of that which relies in memory size
2395: and note for a fixed period like estepm months */
2396: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2397: survival function given by stepm (the optimization length). Unfortunately it
2398: means that if the survival funtion is printed only each two years of age and if
2399: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2400: results. So we changed our mind and took the option of the best precision.
2401: */
2402: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2403:
2404: agelim=AGESUP;
2405: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2406: /* nhstepm age range expressed in number of stepm */
2407: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2408: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2409: /* if (stepm >= YEARM) hstepm=1;*/
2410: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2411: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2412: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2413: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2414: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2415:
2416: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2417: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2418: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2419:
2420:
2421: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2422:
1.95 brouard 2423: /* Computing Variances of health expectancies */
1.53 brouard 2424:
2425: for(theta=1; theta <=npar; theta++){
2426: for(i=1; i<=npar; i++){
2427: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2428: }
2429: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2430:
2431: cptj=0;
2432: for(j=1; j<= nlstate; j++){
2433: for(i=1; i<=nlstate; i++){
2434: cptj=cptj+1;
2435: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2436: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2437: }
2438: }
2439: }
2440:
2441:
2442: for(i=1; i<=npar; i++)
2443: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2444: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2445:
2446: cptj=0;
2447: for(j=1; j<= nlstate; j++){
2448: for(i=1;i<=nlstate;i++){
2449: cptj=cptj+1;
2450: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2451:
1.53 brouard 2452: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2453: }
2454: }
2455: }
1.74 brouard 2456: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2457: for(h=0; h<=nhstepm-1; h++){
2458: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2459: }
2460: }
2461:
2462: /* End theta */
2463:
1.74 brouard 2464: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2465:
2466: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2467: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2468: for(theta=1; theta <=npar; theta++)
2469: trgradg[h][j][theta]=gradg[h][theta][j];
2470:
2471:
1.74 brouard 2472: for(i=1;i<=nlstate*nlstate;i++)
2473: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2474: varhe[i][j][(int)age] =0.;
2475:
2476: printf("%d|",(int)age);fflush(stdout);
2477: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2478: for(h=0;h<=nhstepm-1;h++){
2479: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2480: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2481: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2482: for(i=1;i<=nlstate*nlstate;i++)
2483: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2484: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2485: }
2486: }
2487: /* Computing expectancies */
2488: for(i=1; i<=nlstate;i++)
2489: for(j=1; j<=nlstate;j++)
2490: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2491: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2492:
2493: /* 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]);*/
2494:
2495: }
2496:
2497: fprintf(ficreseij,"%3.0f",age );
2498: cptj=0;
2499: for(i=1; i<=nlstate;i++)
2500: for(j=1; j<=nlstate;j++){
2501: cptj++;
2502: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2503: }
2504: fprintf(ficreseij,"\n");
2505:
1.74 brouard 2506: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2507: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2508: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2509: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2510: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2511: }
2512: printf("\n");
2513: fprintf(ficlog,"\n");
2514:
2515: free_vector(xp,1,npar);
1.74 brouard 2516: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2517: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2518: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2519: }
2520:
2521: /************ Variance ******************/
1.105 lievre 2522: 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 2523: {
2524: /* Variance of health expectancies */
2525: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2526: /* double **newm;*/
2527: double **dnewm,**doldm;
2528: double **dnewmp,**doldmp;
2529: int i, j, nhstepm, hstepm, h, nstepm ;
2530: int k, cptcode;
2531: double *xp;
2532: double **gp, **gm; /* for var eij */
2533: double ***gradg, ***trgradg; /*for var eij */
2534: double **gradgp, **trgradgp; /* for var p point j */
2535: double *gpp, *gmp; /* for var p point j */
2536: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2537: double ***p3mat;
2538: double age,agelim, hf;
2539: double ***mobaverage;
2540: int theta;
2541: char digit[4];
1.55 lievre 2542: char digitp[25];
1.53 brouard 2543:
2544: char fileresprobmorprev[FILENAMELENGTH];
2545:
1.55 lievre 2546: if(popbased==1){
1.58 lievre 2547: if(mobilav!=0)
1.55 lievre 2548: strcpy(digitp,"-populbased-mobilav-");
2549: else strcpy(digitp,"-populbased-nomobil-");
2550: }
2551: else
1.53 brouard 2552: strcpy(digitp,"-stablbased-");
1.56 lievre 2553:
1.54 brouard 2554: if (mobilav!=0) {
1.53 brouard 2555: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2556: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2557: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2558: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2559: }
1.53 brouard 2560: }
2561:
2562: strcpy(fileresprobmorprev,"prmorprev");
2563: sprintf(digit,"%-d",ij);
2564: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2565: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2566: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2567: strcat(fileresprobmorprev,fileres);
2568: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2569: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2570: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2571: }
2572: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2573:
1.53 brouard 2574: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2575: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
1.66 brouard 2576: 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 2577: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2578: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2579: fprintf(ficresprobmorprev," p.%-d SE",j);
2580: for(i=1; i<=nlstate;i++)
2581: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2582: }
2583: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2584: fprintf(ficgp,"\n# Routine varevsij");
1.106 brouard 2585: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.87 brouard 2586: 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");
2587: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2588: /* } */
1.53 brouard 2589: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.105 lievre 2590: fprintf(ficresvij, "#Local time at start: %s", strstart);
1.53 brouard 2591: 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");
2592: fprintf(ficresvij,"# Age");
2593: for(i=1; i<=nlstate;i++)
2594: for(j=1; j<=nlstate;j++)
2595: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2596: fprintf(ficresvij,"\n");
2597:
2598: xp=vector(1,npar);
2599: dnewm=matrix(1,nlstate,1,npar);
2600: doldm=matrix(1,nlstate,1,nlstate);
2601: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2602: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2603:
2604: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2605: gpp=vector(nlstate+1,nlstate+ndeath);
2606: gmp=vector(nlstate+1,nlstate+ndeath);
2607: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2608:
2609: if(estepm < stepm){
2610: printf ("Problem %d lower than %d\n",estepm, stepm);
2611: }
2612: else hstepm=estepm;
2613: /* For example we decided to compute the life expectancy with the smallest unit */
2614: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2615: nhstepm is the number of hstepm from age to agelim
2616: nstepm is the number of stepm from age to agelin.
2617: Look at hpijx to understand the reason of that which relies in memory size
2618: and note for a fixed period like k years */
2619: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2620: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2621: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2622: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2623: results. So we changed our mind and took the option of the best precision.
2624: */
2625: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2626: agelim = AGESUP;
2627: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2628: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2629: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2630: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2631: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2632: gp=matrix(0,nhstepm,1,nlstate);
2633: gm=matrix(0,nhstepm,1,nlstate);
2634:
2635:
2636: for(theta=1; theta <=npar; theta++){
1.66 brouard 2637: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2638: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2639: }
2640: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2641: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2642:
2643: if (popbased==1) {
1.54 brouard 2644: if(mobilav ==0){
1.53 brouard 2645: for(i=1; i<=nlstate;i++)
2646: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2647: }else{ /* mobilav */
1.53 brouard 2648: for(i=1; i<=nlstate;i++)
2649: prlim[i][i]=mobaverage[(int)age][i][ij];
2650: }
2651: }
2652:
2653: for(j=1; j<= nlstate; j++){
2654: for(h=0; h<=nhstepm; h++){
2655: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2656: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2657: }
2658: }
1.66 brouard 2659: /* This for computing probability of death (h=1 means
2660: computed over hstepm matrices product = hstepm*stepm months)
2661: as a weighted average of prlim.
2662: */
1.69 brouard 2663: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2664: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2665: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2666: }
1.66 brouard 2667: /* end probability of death */
1.53 brouard 2668:
1.66 brouard 2669: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2670: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2671: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2672: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2673:
2674: if (popbased==1) {
1.54 brouard 2675: if(mobilav ==0){
1.53 brouard 2676: for(i=1; i<=nlstate;i++)
2677: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2678: }else{ /* mobilav */
1.53 brouard 2679: for(i=1; i<=nlstate;i++)
2680: prlim[i][i]=mobaverage[(int)age][i][ij];
2681: }
2682: }
2683:
2684: for(j=1; j<= nlstate; j++){
2685: for(h=0; h<=nhstepm; h++){
2686: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2687: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2688: }
2689: }
1.66 brouard 2690: /* This for computing probability of death (h=1 means
2691: computed over hstepm matrices product = hstepm*stepm months)
2692: as a weighted average of prlim.
2693: */
1.69 brouard 2694: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2695: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2696: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2697: }
1.66 brouard 2698: /* end probability of death */
1.53 brouard 2699:
2700: for(j=1; j<= nlstate; j++) /* vareij */
2701: for(h=0; h<=nhstepm; h++){
2702: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2703: }
1.68 lievre 2704:
1.53 brouard 2705: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2706: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2707: }
2708:
2709: } /* End theta */
2710:
2711: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2712:
2713: for(h=0; h<=nhstepm; h++) /* veij */
2714: for(j=1; j<=nlstate;j++)
2715: for(theta=1; theta <=npar; theta++)
2716: trgradg[h][j][theta]=gradg[h][theta][j];
2717:
2718: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2719: for(theta=1; theta <=npar; theta++)
1.53 brouard 2720: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2721:
1.53 brouard 2722:
2723: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2724: for(i=1;i<=nlstate;i++)
2725: for(j=1;j<=nlstate;j++)
2726: vareij[i][j][(int)age] =0.;
2727:
2728: for(h=0;h<=nhstepm;h++){
2729: for(k=0;k<=nhstepm;k++){
2730: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2731: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2732: for(i=1;i<=nlstate;i++)
2733: for(j=1;j<=nlstate;j++)
2734: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2735: }
2736: }
1.70 brouard 2737:
1.53 brouard 2738: /* pptj */
2739: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2740: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2741: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2742: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2743: varppt[j][i]=doldmp[j][i];
2744: /* end ppptj */
1.66 brouard 2745: /* x centered again */
1.53 brouard 2746: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2747: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2748:
2749: if (popbased==1) {
1.54 brouard 2750: if(mobilav ==0){
1.53 brouard 2751: for(i=1; i<=nlstate;i++)
2752: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2753: }else{ /* mobilav */
1.53 brouard 2754: for(i=1; i<=nlstate;i++)
2755: prlim[i][i]=mobaverage[(int)age][i][ij];
2756: }
2757: }
1.70 brouard 2758:
1.66 brouard 2759: /* This for computing probability of death (h=1 means
2760: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2761: as a weighted average of prlim.
2762: */
1.68 lievre 2763: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2764: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2765: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2766: }
1.66 brouard 2767: /* end probability of death */
1.53 brouard 2768:
2769: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2770: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2771: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2772: for(i=1; i<=nlstate;i++){
2773: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2774: }
2775: }
2776: fprintf(ficresprobmorprev,"\n");
2777:
2778: fprintf(ficresvij,"%.0f ",age );
2779: for(i=1; i<=nlstate;i++)
2780: for(j=1; j<=nlstate;j++){
2781: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2782: }
2783: fprintf(ficresvij,"\n");
2784: free_matrix(gp,0,nhstepm,1,nlstate);
2785: free_matrix(gm,0,nhstepm,1,nlstate);
2786: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2787: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2788: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2789: } /* End age */
2790: free_vector(gpp,nlstate+1,nlstate+ndeath);
2791: free_vector(gmp,nlstate+1,nlstate+ndeath);
2792: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2793: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2794: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2795: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2796: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2797: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2798: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2799: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2800: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2801: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2802: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2803: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2804: 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 2805: /* 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);
2806: */
1.88 brouard 2807: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2808: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2809:
2810: free_vector(xp,1,npar);
2811: free_matrix(doldm,1,nlstate,1,nlstate);
2812: free_matrix(dnewm,1,nlstate,1,npar);
2813: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2814: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2815: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2816: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2817: fclose(ficresprobmorprev);
1.88 brouard 2818: fflush(ficgp);
2819: fflush(fichtm);
1.84 brouard 2820: } /* end varevsij */
1.53 brouard 2821:
2822: /************ Variance of prevlim ******************/
1.105 lievre 2823: 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 2824: {
2825: /* Variance of prevalence limit */
1.59 brouard 2826: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2827: double **newm;
2828: double **dnewm,**doldm;
2829: int i, j, nhstepm, hstepm;
2830: int k, cptcode;
2831: double *xp;
2832: double *gp, *gm;
2833: double **gradg, **trgradg;
2834: double age,agelim;
2835: int theta;
1.105 lievre 2836: fprintf(ficresvpl, "#Local time at start: %s", strstart);
1.54 brouard 2837: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2838: fprintf(ficresvpl,"# Age");
2839: for(i=1; i<=nlstate;i++)
2840: fprintf(ficresvpl," %1d-%1d",i,i);
2841: fprintf(ficresvpl,"\n");
2842:
2843: xp=vector(1,npar);
2844: dnewm=matrix(1,nlstate,1,npar);
2845: doldm=matrix(1,nlstate,1,nlstate);
2846:
2847: hstepm=1*YEARM; /* Every year of age */
2848: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2849: agelim = AGESUP;
2850: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2851: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2852: if (stepm >= YEARM) hstepm=1;
2853: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2854: gradg=matrix(1,npar,1,nlstate);
2855: gp=vector(1,nlstate);
2856: gm=vector(1,nlstate);
2857:
2858: for(theta=1; theta <=npar; theta++){
2859: for(i=1; i<=npar; i++){ /* Computes gradient */
2860: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2861: }
2862: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2863: for(i=1;i<=nlstate;i++)
2864: gp[i] = prlim[i][i];
2865:
2866: for(i=1; i<=npar; i++) /* Computes gradient */
2867: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2868: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2869: for(i=1;i<=nlstate;i++)
2870: gm[i] = prlim[i][i];
2871:
2872: for(i=1;i<=nlstate;i++)
2873: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2874: } /* End theta */
2875:
2876: trgradg =matrix(1,nlstate,1,npar);
2877:
2878: for(j=1; j<=nlstate;j++)
2879: for(theta=1; theta <=npar; theta++)
2880: trgradg[j][theta]=gradg[theta][j];
2881:
2882: for(i=1;i<=nlstate;i++)
2883: varpl[i][(int)age] =0.;
2884: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2885: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2886: for(i=1;i<=nlstate;i++)
2887: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2888:
2889: fprintf(ficresvpl,"%.0f ",age );
2890: for(i=1; i<=nlstate;i++)
2891: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2892: fprintf(ficresvpl,"\n");
2893: free_vector(gp,1,nlstate);
2894: free_vector(gm,1,nlstate);
2895: free_matrix(gradg,1,npar,1,nlstate);
2896: free_matrix(trgradg,1,nlstate,1,npar);
2897: } /* End age */
2898:
2899: free_vector(xp,1,npar);
2900: free_matrix(doldm,1,nlstate,1,npar);
2901: free_matrix(dnewm,1,nlstate,1,nlstate);
2902:
2903: }
2904:
2905: /************ Variance of one-step probabilities ******************/
1.105 lievre 2906: 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 2907: {
2908: int i, j=0, i1, k1, l1, t, tj;
2909: int k2, l2, j1, z1;
2910: int k=0,l, cptcode;
2911: int first=1, first1;
2912: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2913: double **dnewm,**doldm;
2914: double *xp;
2915: double *gp, *gm;
2916: double **gradg, **trgradg;
2917: double **mu;
2918: double age,agelim, cov[NCOVMAX];
2919: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2920: int theta;
2921: char fileresprob[FILENAMELENGTH];
2922: char fileresprobcov[FILENAMELENGTH];
2923: char fileresprobcor[FILENAMELENGTH];
2924:
2925: double ***varpij;
2926:
2927: strcpy(fileresprob,"prob");
2928: strcat(fileresprob,fileres);
2929: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2930: printf("Problem with resultfile: %s\n", fileresprob);
2931: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2932: }
2933: strcpy(fileresprobcov,"probcov");
2934: strcat(fileresprobcov,fileres);
2935: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2936: printf("Problem with resultfile: %s\n", fileresprobcov);
2937: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2938: }
2939: strcpy(fileresprobcor,"probcor");
2940: strcat(fileresprobcor,fileres);
2941: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2942: printf("Problem with resultfile: %s\n", fileresprobcor);
2943: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2944: }
2945: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2946: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2947: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2948: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2949: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2950: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.105 lievre 2951: fprintf(ficresprob, "#Local time at start: %s", strstart);
1.53 brouard 2952: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2953: fprintf(ficresprob,"# Age");
1.105 lievre 2954: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
1.53 brouard 2955: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2956: fprintf(ficresprobcov,"# Age");
1.105 lievre 2957: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
1.53 brouard 2958: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2959: fprintf(ficresprobcov,"# Age");
2960:
2961:
2962: for(i=1; i<=nlstate;i++)
2963: for(j=1; j<=(nlstate+ndeath);j++){
2964: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2965: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2966: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2967: }
1.69 brouard 2968: /* fprintf(ficresprob,"\n");
1.53 brouard 2969: fprintf(ficresprobcov,"\n");
2970: fprintf(ficresprobcor,"\n");
1.69 brouard 2971: */
2972: xp=vector(1,npar);
1.53 brouard 2973: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2974: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2975: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2976: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2977: first=1;
1.88 brouard 2978: fprintf(ficgp,"\n# Routine varprob");
2979: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2980: fprintf(fichtm,"\n");
2981:
1.95 brouard 2982: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2983: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 2984: file %s<br>\n",optionfilehtmcov);
2985: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2986: and drawn. It helps understanding how is the covariance between two incidences.\
2987: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2988: 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. \
2989: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2990: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2991: standard deviations wide on each axis. <br>\
2992: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2993: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2994: 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 2995:
2996: cov[1]=1;
2997: tj=cptcoveff;
2998: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2999: j1=0;
3000: for(t=1; t<=tj;t++){
3001: for(i1=1; i1<=ncodemax[t];i1++){
3002: j1++;
3003: if (cptcovn>0) {
3004: fprintf(ficresprob, "\n#********** Variable ");
3005: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3006: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 3007: fprintf(ficresprobcov, "\n#********** Variable ");
3008: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3009: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 3010:
3011: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 3012: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3013: fprintf(ficgp, "**********\n#\n");
1.53 brouard 3014:
3015:
1.96 brouard 3016: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 3017: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 3018: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 3019:
3020: fprintf(ficresprobcor, "\n#********** Variable ");
3021: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3022: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 3023: }
3024:
3025: for (age=bage; age<=fage; age ++){
3026: cov[2]=age;
3027: for (k=1; k<=cptcovn;k++) {
3028: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3029: }
3030: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3031: for (k=1; k<=cptcovprod;k++)
3032: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3033:
3034: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3035: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3036: gp=vector(1,(nlstate)*(nlstate+ndeath));
3037: gm=vector(1,(nlstate)*(nlstate+ndeath));
3038:
3039: for(theta=1; theta <=npar; theta++){
3040: for(i=1; i<=npar; i++)
1.74 brouard 3041: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 3042:
3043: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3044:
3045: k=0;
3046: for(i=1; i<= (nlstate); i++){
3047: for(j=1; j<=(nlstate+ndeath);j++){
3048: k=k+1;
3049: gp[k]=pmmij[i][j];
3050: }
3051: }
3052:
3053: for(i=1; i<=npar; i++)
1.74 brouard 3054: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 3055:
3056: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3057: k=0;
3058: for(i=1; i<=(nlstate); i++){
3059: for(j=1; j<=(nlstate+ndeath);j++){
3060: k=k+1;
3061: gm[k]=pmmij[i][j];
3062: }
3063: }
3064:
3065: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 3066: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 3067: }
3068:
3069: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3070: for(theta=1; theta <=npar; theta++)
3071: trgradg[j][theta]=gradg[theta][j];
3072:
3073: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3074: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 3075: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3076: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3077: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3078: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3079:
1.53 brouard 3080: pmij(pmmij,cov,ncovmodel,x,nlstate);
3081:
3082: k=0;
3083: for(i=1; i<=(nlstate); i++){
3084: for(j=1; j<=(nlstate+ndeath);j++){
3085: k=k+1;
3086: mu[k][(int) age]=pmmij[i][j];
3087: }
3088: }
3089: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3090: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3091: varpij[i][j][(int)age] = doldm[i][j];
3092:
3093: /*printf("\n%d ",(int)age);
1.59 brouard 3094: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3095: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3096: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3097: }*/
1.53 brouard 3098:
3099: fprintf(ficresprob,"\n%d ",(int)age);
3100: fprintf(ficresprobcov,"\n%d ",(int)age);
3101: fprintf(ficresprobcor,"\n%d ",(int)age);
3102:
3103: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3104: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3105: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3106: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3107: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3108: }
3109: i=0;
3110: for (k=1; k<=(nlstate);k++){
3111: for (l=1; l<=(nlstate+ndeath);l++){
3112: i=i++;
3113: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3114: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3115: for (j=1; j<=i;j++){
3116: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3117: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3118: }
3119: }
3120: }/* end of loop for state */
3121: } /* end of loop for age */
3122:
3123: /* Confidence intervalle of pij */
3124: /*
1.59 brouard 3125: fprintf(ficgp,"\nset noparametric;unset label");
3126: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3127: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3128: 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);
3129: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3130: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3131: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3132: */
3133:
3134: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3135: first1=1;
3136: for (k2=1; k2<=(nlstate);k2++){
3137: for (l2=1; l2<=(nlstate+ndeath);l2++){
3138: if(l2==k2) continue;
3139: j=(k2-1)*(nlstate+ndeath)+l2;
3140: for (k1=1; k1<=(nlstate);k1++){
3141: for (l1=1; l1<=(nlstate+ndeath);l1++){
3142: if(l1==k1) continue;
3143: i=(k1-1)*(nlstate+ndeath)+l1;
3144: if(i<=j) continue;
3145: for (age=bage; age<=fage; age ++){
3146: if ((int)age %5==0){
3147: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3148: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3149: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3150: mu1=mu[i][(int) age]/stepm*YEARM ;
3151: mu2=mu[j][(int) age]/stepm*YEARM;
3152: c12=cv12/sqrt(v1*v2);
3153: /* Computing eigen value of matrix of covariance */
3154: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3155: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3156: /* Eigen vectors */
3157: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3158: /*v21=sqrt(1.-v11*v11); *//* error */
3159: v21=(lc1-v1)/cv12*v11;
3160: v12=-v21;
3161: v22=v11;
3162: tnalp=v21/v11;
3163: if(first1==1){
3164: first1=0;
3165: 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);
3166: }
3167: 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);
3168: /*printf(fignu*/
3169: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3170: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3171: if(first==1){
3172: first=0;
3173: fprintf(ficgp,"\nset parametric;unset label");
3174: 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);
3175: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3176: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3177: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3178: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3179: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3180: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3181: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3182: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3183: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3184: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3185: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3186: 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",\
3187: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3188: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3189: }else{
3190: first=0;
1.91 brouard 3191: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3192: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3193: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3194: 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",\
3195: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3196: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3197: }/* if first */
3198: } /* age mod 5 */
3199: } /* end loop age */
1.88 brouard 3200: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3201: first=1;
3202: } /*l12 */
3203: } /* k12 */
3204: } /*l1 */
3205: }/* k1 */
3206: } /* loop covariates */
3207: }
1.59 brouard 3208: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3209: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3210: free_vector(xp,1,npar);
3211: fclose(ficresprob);
3212: fclose(ficresprobcov);
3213: fclose(ficresprobcor);
1.91 brouard 3214: fflush(ficgp);
3215: fflush(fichtmcov);
1.53 brouard 3216: }
3217:
3218:
3219: /******************* Printing html file ***********/
3220: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3221: int lastpass, int stepm, int weightopt, char model[],\
3222: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3223: int popforecast, int estepm ,\
3224: double jprev1, double mprev1,double anprev1, \
3225: double jprev2, double mprev2,double anprev2){
3226: int jj1, k1, i1, cpt;
3227:
1.107 brouard 3228: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3229: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
1.106 brouard 3230: </ul>");
1.107 brouard 3231: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
1.96 brouard 3232: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3233: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3234: fprintf(fichtm,"\
3235: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3236: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3237: fprintf(fichtm,"\
3238: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3239: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3240: fprintf(fichtm,"\
1.85 brouard 3241: - Life expectancies by age and initial health status (estepm=%2d months): \
1.96 brouard 3242: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3243: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3244:
3245: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3246:
3247: m=cptcoveff;
3248: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3249:
3250: jj1=0;
3251: for(k1=1; k1<=m;k1++){
3252: for(i1=1; i1<=ncodemax[k1];i1++){
3253: jj1++;
3254: if (cptcovn > 0) {
3255: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3256: for (cpt=1; cpt<=cptcoveff;cpt++)
3257: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3258: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3259: }
3260: /* Pij */
1.88 brouard 3261: 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> \
3262: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3263: /* Quasi-incidences */
1.85 brouard 3264: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3265: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3266: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3267: /* Stable prevalence in each health state */
3268: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3269: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3270: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3271: }
3272: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3273: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3274: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3275: }
3276: } /* end i1 */
3277: }/* End k1 */
3278: fprintf(fichtm,"</ul>");
3279:
3280:
1.96 brouard 3281: fprintf(fichtm,"\
1.107 brouard 3282: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.96 brouard 3283: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3284:
3285: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3286: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3287: fprintf(fichtm,"\
3288: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3289: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3290:
3291: fprintf(fichtm,"\
3292: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3293: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3294: fprintf(fichtm,"\
3295: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3296: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3297: fprintf(fichtm,"\
3298: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3299: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3300: fprintf(fichtm,"\
1.88 brouard 3301: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3302: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3303:
1.76 brouard 3304: /* if(popforecast==1) fprintf(fichtm,"\n */
3305: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3306: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3307: /* <br>",fileres,fileres,fileres,fileres); */
3308: /* else */
3309: /* 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 3310: fflush(fichtm);
3311: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3312:
3313: m=cptcoveff;
3314: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3315:
3316: jj1=0;
3317: for(k1=1; k1<=m;k1++){
3318: for(i1=1; i1<=ncodemax[k1];i1++){
3319: jj1++;
3320: if (cptcovn > 0) {
3321: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3322: for (cpt=1; cpt<=cptcoveff;cpt++)
3323: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3324: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3325: }
3326: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3327: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3328: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3329: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3330: }
1.96 brouard 3331: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3332: health expectancies in states (1) and (2): %s%d.png<br>\
3333: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3334: } /* end i1 */
3335: }/* End k1 */
3336: fprintf(fichtm,"</ul>");
1.87 brouard 3337: fflush(fichtm);
1.53 brouard 3338: }
3339:
3340: /******************* Gnuplot file **************/
1.89 brouard 3341: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3342:
1.88 brouard 3343: char dirfileres[132],optfileres[132];
1.53 brouard 3344: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3345: int ng;
1.88 brouard 3346: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3347: /* printf("Problem with file %s",optionfilegnuplot); */
3348: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3349: /* } */
1.53 brouard 3350:
1.54 brouard 3351: /*#ifdef windows */
1.89 brouard 3352: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3353: /*#endif */
1.88 brouard 3354: m=pow(2,cptcoveff);
3355:
3356: strcpy(dirfileres,optionfilefiname);
3357: strcpy(optfileres,"vpl");
1.53 brouard 3358: /* 1eme*/
3359: for (cpt=1; cpt<= nlstate ; cpt ++) {
3360: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3361: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3362: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3363: fprintf(ficgp,"set xlabel \"Age\" \n\
3364: set ylabel \"Probability\" \n\
3365: set ter png small\n\
3366: set size 0.65,0.65\n\
3367: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3368:
3369: for (i=1; i<= nlstate ; i ++) {
3370: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3371: else fprintf(ficgp," \%%*lf (\%%*lf)");
3372: }
1.88 brouard 3373: 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 3374: for (i=1; i<= nlstate ; i ++) {
3375: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3376: else fprintf(ficgp," \%%*lf (\%%*lf)");
3377: }
1.88 brouard 3378: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3379: for (i=1; i<= nlstate ; i ++) {
3380: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3381: else fprintf(ficgp," \%%*lf (\%%*lf)");
3382: }
1.88 brouard 3383: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3384: }
3385: }
3386: /*2 eme*/
3387:
3388: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3389: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3390: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3391:
3392: for (i=1; i<= nlstate+1 ; i ++) {
3393: k=2*i;
1.88 brouard 3394: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3395: for (j=1; j<= nlstate+1 ; j ++) {
3396: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3397: else fprintf(ficgp," \%%*lf (\%%*lf)");
3398: }
3399: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3400: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3401: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3402: for (j=1; j<= nlstate+1 ; j ++) {
3403: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3404: else fprintf(ficgp," \%%*lf (\%%*lf)");
3405: }
3406: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3407: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3408: for (j=1; j<= nlstate+1 ; j ++) {
3409: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3410: else fprintf(ficgp," \%%*lf (\%%*lf)");
3411: }
3412: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3413: else fprintf(ficgp,"\" t\"\" w l 0,");
3414: }
3415: }
3416:
3417: /*3eme*/
3418:
3419: for (k1=1; k1<= m ; k1 ++) {
3420: for (cpt=1; cpt<= nlstate ; cpt ++) {
3421: k=2+nlstate*(2*cpt-2);
1.88 brouard 3422: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3423: fprintf(ficgp,"set ter png small\n\
3424: set size 0.65,0.65\n\
3425: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3426: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3427: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3428: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3429: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3430: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3431: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3432:
3433: */
3434: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3435: 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 3436:
3437: }
3438: }
3439: }
3440:
1.76 brouard 3441: /* CV preval stable (period) */
1.53 brouard 3442: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3443: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3444: k=3;
1.88 brouard 3445: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3446: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3447: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3448: unset log y\n\
1.88 brouard 3449: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3450:
1.83 lievre 3451: for (i=1; i< nlstate ; i ++)
1.53 brouard 3452: fprintf(ficgp,"+$%d",k+i+1);
3453: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3454:
3455: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3456: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3457: for (i=1; i< nlstate ; i ++) {
3458: l=3+(nlstate+ndeath)*cpt;
3459: fprintf(ficgp,"+$%d",l+i+1);
3460: }
3461: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3462: }
3463: }
3464:
3465: /* proba elementaires */
3466: for(i=1,jk=1; i <=nlstate; i++){
3467: for(k=1; k <=(nlstate+ndeath); k++){
3468: if (k != i) {
3469: for(j=1; j <=ncovmodel; j++){
3470: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3471: jk++;
3472: fprintf(ficgp,"\n");
3473: }
3474: }
3475: }
3476: }
3477:
3478: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3479: for(jk=1; jk <=m; jk++) {
1.88 brouard 3480: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3481: if (ng==2)
3482: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3483: else
3484: fprintf(ficgp,"\nset title \"Probability\"\n");
3485: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3486: i=1;
3487: for(k2=1; k2<=nlstate; k2++) {
3488: k3=i;
3489: for(k=1; k<=(nlstate+ndeath); k++) {
3490: if (k != k2){
3491: if(ng==2)
3492: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3493: else
3494: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3495: ij=1;
3496: for(j=3; j <=ncovmodel; j++) {
3497: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3498: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3499: ij++;
3500: }
3501: else
3502: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3503: }
3504: fprintf(ficgp,")/(1");
3505:
3506: for(k1=1; k1 <=nlstate; k1++){
3507: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3508: ij=1;
3509: for(j=3; j <=ncovmodel; j++){
3510: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3511: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3512: ij++;
3513: }
3514: else
3515: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3516: }
3517: fprintf(ficgp,")");
3518: }
3519: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3520: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3521: i=i+ncovmodel;
3522: }
3523: } /* end k */
3524: } /* end k2 */
3525: } /* end jk */
3526: } /* end ng */
1.88 brouard 3527: fflush(ficgp);
1.53 brouard 3528: } /* end gnuplot */
3529:
3530:
3531: /*************** Moving average **************/
1.54 brouard 3532: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3533:
3534: int i, cpt, cptcod;
1.58 lievre 3535: int modcovmax =1;
1.54 brouard 3536: int mobilavrange, mob;
1.53 brouard 3537: double age;
1.58 lievre 3538:
3539: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3540: a covariate has 2 modalities */
3541: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3542:
1.54 brouard 3543: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3544: if(mobilav==1) mobilavrange=5; /* default */
3545: else mobilavrange=mobilav;
3546: for (age=bage; age<=fage; age++)
3547: for (i=1; i<=nlstate;i++)
1.58 lievre 3548: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3549: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3550: /* We keep the original values on the extreme ages bage, fage and for
3551: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3552: we use a 5 terms etc. until the borders are no more concerned.
3553: */
3554: for (mob=3;mob <=mobilavrange;mob=mob+2){
3555: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3556: for (i=1; i<=nlstate;i++){
1.58 lievre 3557: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3558: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3559: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3560: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3561: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3562: }
3563: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3564: }
1.53 brouard 3565: }
1.54 brouard 3566: }/* end age */
3567: }/* end mob */
3568: }else return -1;
3569: return 0;
3570: }/* End movingaverage */
1.53 brouard 3571:
3572:
3573: /************** Forecasting ******************/
1.70 brouard 3574: 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 3575: /* proj1, year, month, day of starting projection
3576: agemin, agemax range of age
3577: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3578: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3579: */
1.73 lievre 3580: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3581: int *popage;
1.70 brouard 3582: double agec; /* generic age */
3583: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3584: double *popeffectif,*popcount;
3585: double ***p3mat;
1.55 lievre 3586: double ***mobaverage;
1.53 brouard 3587: char fileresf[FILENAMELENGTH];
3588:
1.69 brouard 3589: agelim=AGESUP;
1.84 brouard 3590: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3591:
3592: strcpy(fileresf,"f");
3593: strcat(fileresf,fileres);
3594: if((ficresf=fopen(fileresf,"w"))==NULL) {
3595: printf("Problem with forecast resultfile: %s\n", fileresf);
3596: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3597: }
3598: printf("Computing forecasting: result on file '%s' \n", fileresf);
3599: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3600:
3601: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3602:
1.54 brouard 3603: if (mobilav!=0) {
1.53 brouard 3604: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3605: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3606: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3607: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3608: }
1.53 brouard 3609: }
3610:
3611: stepsize=(int) (stepm+YEARM-1)/YEARM;
3612: if (stepm<=12) stepsize=1;
1.74 brouard 3613: if(estepm < stepm){
3614: printf ("Problem %d lower than %d\n",estepm, stepm);
3615: }
3616: else hstepm=estepm;
3617:
1.53 brouard 3618: hstepm=hstepm/stepm;
1.69 brouard 3619: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3620: fractional in yp1 */
1.53 brouard 3621: anprojmean=yp;
3622: yp2=modf((yp1*12),&yp);
3623: mprojmean=yp;
3624: yp1=modf((yp2*30.5),&yp);
3625: jprojmean=yp;
3626: if(jprojmean==0) jprojmean=1;
3627: if(mprojmean==0) jprojmean=1;
1.73 lievre 3628:
3629: i1=cptcoveff;
3630: if (cptcovn < 1){i1=1;}
1.53 brouard 3631:
1.70 brouard 3632: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3633:
1.70 brouard 3634: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3635:
1.75 brouard 3636: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3637: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3638: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3639: k=k+1;
3640: fprintf(ficresf,"\n#******");
3641: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3642: 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 3643: }
3644: fprintf(ficresf,"******\n");
1.70 brouard 3645: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3646: for(j=1; j<=nlstate+ndeath;j++){
3647: for(i=1; i<=nlstate;i++)
3648: fprintf(ficresf," p%d%d",i,j);
3649: fprintf(ficresf," p.%d",j);
3650: }
1.74 brouard 3651: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3652: fprintf(ficresf,"\n");
1.70 brouard 3653: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3654:
1.71 brouard 3655: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3656: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3657: nhstepm = nhstepm/hstepm;
3658: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3659: oldm=oldms;savm=savms;
1.70 brouard 3660: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3661:
3662: for (h=0; h<=nhstepm; h++){
1.75 brouard 3663: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3664: fprintf(ficresf,"\n");
3665: for(j=1;j<=cptcoveff;j++)
3666: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3667: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3668: }
3669: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3670: ppij=0.;
1.71 brouard 3671: for(i=1; i<=nlstate;i++) {
1.53 brouard 3672: if (mobilav==1)
1.71 brouard 3673: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3674: else {
1.71 brouard 3675: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3676: }
1.75 brouard 3677: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3678: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3679: }
3680: } /* end i */
3681: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3682: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3683: }
1.75 brouard 3684: }/* end j */
3685: } /* end h */
1.53 brouard 3686: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3687: } /* end agec */
3688: } /* end yearp */
3689: } /* end cptcod */
3690: } /* end cptcov */
1.53 brouard 3691:
1.54 brouard 3692: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3693:
3694: fclose(ficresf);
3695: }
1.70 brouard 3696:
3697: /************** Forecasting *****not tested NB*************/
1.53 brouard 3698: 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){
3699:
3700: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3701: int *popage;
1.69 brouard 3702: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3703: double *popeffectif,*popcount;
3704: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3705: double ***mobaverage;
1.53 brouard 3706: char filerespop[FILENAMELENGTH];
3707:
3708: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3709: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3710: agelim=AGESUP;
1.69 brouard 3711: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3712:
1.84 brouard 3713: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3714:
3715:
3716: strcpy(filerespop,"pop");
3717: strcat(filerespop,fileres);
3718: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3719: printf("Problem with forecast resultfile: %s\n", filerespop);
3720: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3721: }
3722: printf("Computing forecasting: result on file '%s' \n", filerespop);
3723: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3724:
3725: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3726:
1.54 brouard 3727: if (mobilav!=0) {
1.53 brouard 3728: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3729: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3730: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3731: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3732: }
1.53 brouard 3733: }
3734:
3735: stepsize=(int) (stepm+YEARM-1)/YEARM;
3736: if (stepm<=12) stepsize=1;
3737:
3738: agelim=AGESUP;
3739:
3740: hstepm=1;
3741: hstepm=hstepm/stepm;
3742:
3743: if (popforecast==1) {
3744: if((ficpop=fopen(popfile,"r"))==NULL) {
3745: printf("Problem with population file : %s\n",popfile);exit(0);
3746: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3747: }
3748: popage=ivector(0,AGESUP);
3749: popeffectif=vector(0,AGESUP);
3750: popcount=vector(0,AGESUP);
3751:
3752: i=1;
3753: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3754:
3755: imx=i;
3756: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3757: }
3758:
1.69 brouard 3759: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3760: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3761: k=k+1;
3762: fprintf(ficrespop,"\n#******");
3763: for(j=1;j<=cptcoveff;j++) {
3764: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3765: }
3766: fprintf(ficrespop,"******\n");
3767: fprintf(ficrespop,"# Age");
3768: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3769: if (popforecast==1) fprintf(ficrespop," [Population]");
3770:
3771: for (cpt=0; cpt<=0;cpt++) {
3772: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3773:
1.69 brouard 3774: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3775: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3776: nhstepm = nhstepm/hstepm;
3777:
3778: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3779: oldm=oldms;savm=savms;
3780: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3781:
3782: for (h=0; h<=nhstepm; h++){
1.69 brouard 3783: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3784: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3785: }
3786: for(j=1; j<=nlstate+ndeath;j++) {
3787: kk1=0.;kk2=0;
3788: for(i=1; i<=nlstate;i++) {
3789: if (mobilav==1)
3790: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3791: else {
3792: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3793: }
3794: }
1.69 brouard 3795: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3796: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3797: /*fprintf(ficrespop," %.3f", kk1);
3798: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3799: }
3800: }
3801: for(i=1; i<=nlstate;i++){
3802: kk1=0.;
3803: for(j=1; j<=nlstate;j++){
3804: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3805: }
1.69 brouard 3806: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3807: }
3808:
1.69 brouard 3809: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3810: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3811: }
3812: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3813: }
3814: }
3815:
3816: /******/
3817:
3818: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3819: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3820: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3821: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3822: nhstepm = nhstepm/hstepm;
3823:
3824: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3825: oldm=oldms;savm=savms;
3826: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3827: for (h=0; h<=nhstepm; h++){
1.69 brouard 3828: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3829: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3830: }
3831: for(j=1; j<=nlstate+ndeath;j++) {
3832: kk1=0.;kk2=0;
3833: for(i=1; i<=nlstate;i++) {
3834: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3835: }
1.69 brouard 3836: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3837: }
3838: }
3839: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3840: }
3841: }
3842: }
3843: }
3844:
1.54 brouard 3845: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3846:
3847: if (popforecast==1) {
3848: free_ivector(popage,0,AGESUP);
3849: free_vector(popeffectif,0,AGESUP);
3850: free_vector(popcount,0,AGESUP);
3851: }
3852: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3853: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3854: fclose(ficrespop);
1.84 brouard 3855: } /* End of popforecast */
1.53 brouard 3856:
1.87 brouard 3857: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3858: {
1.87 brouard 3859: if((fichier=fopen(optionfich,"a"))==NULL) {
3860: printf("Problem with file: %s\n", optionfich);
3861: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3862: return (0);
1.86 brouard 3863: }
1.87 brouard 3864: fflush(fichier);
3865: return (1);
1.86 brouard 3866: }
1.94 brouard 3867:
3868:
3869: /**************** function prwizard **********************/
1.88 brouard 3870: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3871: {
3872:
1.94 brouard 3873: /* Wizard to print covariance matrix template */
3874:
1.88 brouard 3875: char ca[32], cb[32], cc[32];
3876: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3877: int numlinepar;
3878:
3879: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3880: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3881: for(i=1; i <=nlstate; i++){
3882: jj=0;
3883: for(j=1; j <=nlstate+ndeath; j++){
3884: if(j==i) continue;
3885: jj++;
3886: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3887: printf("%1d%1d",i,j);
3888: fprintf(ficparo,"%1d%1d",i,j);
3889: for(k=1; k<=ncovmodel;k++){
3890: /* printf(" %lf",param[i][j][k]); */
3891: /* fprintf(ficparo," %lf",param[i][j][k]); */
3892: printf(" 0.");
3893: fprintf(ficparo," 0.");
3894: }
3895: printf("\n");
3896: fprintf(ficparo,"\n");
3897: }
3898: }
3899: printf("# Scales (for hessian or gradient estimation)\n");
3900: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3901: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3902: for(i=1; i <=nlstate; i++){
3903: jj=0;
3904: for(j=1; j <=nlstate+ndeath; j++){
3905: if(j==i) continue;
3906: jj++;
3907: fprintf(ficparo,"%1d%1d",i,j);
3908: printf("%1d%1d",i,j);
3909: fflush(stdout);
3910: for(k=1; k<=ncovmodel;k++){
3911: /* printf(" %le",delti3[i][j][k]); */
3912: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3913: printf(" 0.");
3914: fprintf(ficparo," 0.");
3915: }
3916: numlinepar++;
3917: printf("\n");
3918: fprintf(ficparo,"\n");
3919: }
3920: }
3921: printf("# Covariance matrix\n");
3922: /* # 121 Var(a12)\n\ */
3923: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3924: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3925: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3926: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3927: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3928: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3929: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3930: fflush(stdout);
3931: fprintf(ficparo,"# Covariance matrix\n");
3932: /* # 121 Var(a12)\n\ */
3933: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3934: /* # ...\n\ */
3935: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3936:
3937: for(itimes=1;itimes<=2;itimes++){
3938: jj=0;
3939: for(i=1; i <=nlstate; i++){
3940: for(j=1; j <=nlstate+ndeath; j++){
3941: if(j==i) continue;
3942: for(k=1; k<=ncovmodel;k++){
3943: jj++;
3944: ca[0]= k+'a'-1;ca[1]='\0';
3945: if(itimes==1){
3946: printf("#%1d%1d%d",i,j,k);
3947: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3948: }else{
3949: printf("%1d%1d%d",i,j,k);
3950: fprintf(ficparo,"%1d%1d%d",i,j,k);
3951: /* printf(" %.5le",matcov[i][j]); */
3952: }
3953: ll=0;
3954: for(li=1;li <=nlstate; li++){
3955: for(lj=1;lj <=nlstate+ndeath; lj++){
3956: if(lj==li) continue;
3957: for(lk=1;lk<=ncovmodel;lk++){
3958: ll++;
3959: if(ll<=jj){
3960: cb[0]= lk +'a'-1;cb[1]='\0';
3961: if(ll<jj){
3962: if(itimes==1){
3963: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3964: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3965: }else{
3966: printf(" 0.");
3967: fprintf(ficparo," 0.");
3968: }
3969: }else{
3970: if(itimes==1){
3971: printf(" Var(%s%1d%1d)",ca,i,j);
3972: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3973: }else{
3974: printf(" 0.");
3975: fprintf(ficparo," 0.");
3976: }
3977: }
3978: }
3979: } /* end lk */
3980: } /* end lj */
3981: } /* end li */
3982: printf("\n");
3983: fprintf(ficparo,"\n");
3984: numlinepar++;
3985: } /* end k*/
3986: } /*end j */
3987: } /* end i */
1.95 brouard 3988: } /* end itimes */
1.88 brouard 3989:
3990: } /* end of prwizard */
1.98 brouard 3991: /******************* Gompertz Likelihood ******************************/
3992: double gompertz(double x[])
3993: {
3994: double A,B,L=0.0,sump=0.,num=0.;
3995: int i,n=0; /* n is the size of the sample */
3996: for (i=0;i<=imx-1 ; i++) {
3997: sump=sump+weight[i];
1.103 lievre 3998: /* sump=sump+1;*/
1.98 brouard 3999: num=num+1;
4000: }
4001:
4002:
1.103 lievre 4003: /* for (i=0; i<=imx; i++)
1.98 brouard 4004: 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]);*/
4005:
1.103 lievre 4006: for (i=1;i<=imx ; i++)
1.98 brouard 4007: {
4008: if (cens[i]==1 & wav[i]>1)
1.103 lievre 4009: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
1.98 brouard 4010:
4011: if (cens[i]==0 & wav[i]>1)
1.103 lievre 4012: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4013: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
1.98 brouard 4014:
4015: if (wav[i]>1 & agecens[i]>15) {
4016: L=L+A*weight[i];
4017: /* 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]);*/
4018: }
4019: }
4020:
4021: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4022:
4023: return -2*L*num/sump;
4024: }
4025:
4026: /******************* Printing html file ***********/
4027: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4028: int lastpass, int stepm, int weightopt, char model[],\
1.105 lievre 4029: int imx, double p[],double **matcov,double agemortsup){
4030: int i,k;
1.98 brouard 4031:
4032: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4033: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4034: for (i=1;i<=2;i++)
4035: 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]));
4036: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4037: fprintf(fichtm,"</ul>");
1.105 lievre 4038:
4039: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4040:
1.106 brouard 4041: 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 4042:
4043: for (k=agegomp;k<(agemortsup-2);k++)
4044: 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]);
4045:
4046:
1.98 brouard 4047: fflush(fichtm);
4048: }
4049:
4050: /******************* Gnuplot file **************/
4051: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4052:
4053: char dirfileres[132],optfileres[132];
4054: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4055: int ng;
4056:
4057:
4058: /*#ifdef windows */
4059: fprintf(ficgp,"cd \"%s\" \n",pathc);
4060: /*#endif */
4061:
4062:
4063: strcpy(dirfileres,optionfilefiname);
4064: strcpy(optfileres,"vpl");
4065: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4066: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4067: fprintf(ficgp, "set ter png small\n set log y\n");
4068: fprintf(ficgp, "set size 0.65,0.65\n");
4069: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4070:
4071: }
4072:
4073:
1.88 brouard 4074:
1.91 brouard 4075:
1.53 brouard 4076: /***********************************************/
4077: /**************** Main Program *****************/
4078: /***********************************************/
4079:
4080: int main(int argc, char *argv[])
4081: {
1.61 brouard 4082: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 4083: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.109 ! brouard 4084: int linei;
1.95 brouard 4085: int jj, ll, li, lj, lk, imk;
1.85 brouard 4086: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 4087: int itimes;
1.98 brouard 4088: int NDIM=2;
1.95 brouard 4089:
4090: char ca[32], cb[32], cc[32];
1.87 brouard 4091: /* FILE *fichtm; *//* Html File */
4092: /* FILE *ficgp;*/ /*Gnuplot File */
1.107 brouard 4093: struct stat info;
1.53 brouard 4094: double agedeb, agefin,hf;
4095: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4096:
4097: double fret;
4098: double **xi,tmp,delta;
4099:
4100: double dum; /* Dummy variable */
4101: double ***p3mat;
4102: double ***mobaverage;
4103: int *indx;
4104: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 4105: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.99 brouard 4106: char pathr[MAXLINE], pathimach[MAXLINE];
1.53 brouard 4107: int firstobs=1, lastobs=10;
4108: int sdeb, sfin; /* Status at beginning and end */
4109: int c, h , cpt,l;
4110: int ju,jl, mi;
4111: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 4112: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 4113: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 4114: int mobilav=0,popforecast=0;
4115: int hstepm, nhstepm;
1.105 lievre 4116: int agemortsup;
4117: float sumlpop=0.;
1.74 brouard 4118: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4119: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 4120:
4121: double bage, fage, age, agelim, agebase;
4122: double ftolpl=FTOL;
4123: double **prlim;
4124: double *severity;
4125: double ***param; /* Matrix of parameters */
4126: double *p;
4127: double **matcov; /* Matrix of covariance */
4128: double ***delti3; /* Scale */
4129: double *delti; /* Scale */
4130: double ***eij, ***vareij;
4131: double **varpl; /* Variances of prevalence limits by age */
4132: double *epj, vepp;
4133: double kk1, kk2;
1.74 brouard 4134: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 brouard 4135: double **ximort;
1.53 brouard 4136: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 brouard 4137: int *dcwave;
1.53 brouard 4138:
4139: char z[1]="c", occ;
1.86 brouard 4140:
1.53 brouard 4141: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 4142: char strstart[80], *strt, strtend[80];
1.85 brouard 4143: char *stratrunc;
4144: int lstra;
4145:
4146: long total_usecs;
1.53 brouard 4147:
1.95 brouard 4148: /* setlocale (LC_ALL, ""); */
4149: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4150: /* textdomain (PACKAGE); */
4151: /* setlocale (LC_CTYPE, ""); */
4152: /* setlocale (LC_MESSAGES, ""); */
4153:
1.85 brouard 4154: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4155: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4156: curr_time=start_time;
1.85 brouard 4157: tm = *localtime(&start_time.tv_sec);
4158: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4159: strcpy(strstart,asctime(&tm));
1.86 brouard 4160:
1.88 brouard 4161: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4162: /* tp.tv_sec = tp.tv_sec +86400; */
4163: /* tm = *localtime(&start_time.tv_sec); */
4164: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4165: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4166: /* tmg.tm_hour=tmg.tm_hour + 1; */
4167: /* tp.tv_sec = mktime(&tmg); */
4168: /* strt=asctime(&tmg); */
1.88 brouard 4169: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4170: /* (void) time (&time_value);
4171: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4172: * tm = *localtime(&time_value);
1.88 brouard 4173: * strstart=asctime(&tm);
4174: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4175: */
4176:
1.91 brouard 4177: nberr=0; /* Number of errors and warnings */
4178: nbwarn=0;
1.53 brouard 4179: getcwd(pathcd, size);
4180:
1.81 brouard 4181: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4182: if(argc <=1){
4183: printf("\nEnter the parameter file name: ");
4184: scanf("%s",pathtot);
4185: }
4186: else{
4187: strcpy(pathtot,argv[1]);
4188: }
1.88 brouard 4189: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4190: /*cygwin_split_path(pathtot,path,optionfile);
4191: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4192: /* cutv(path,optionfile,pathtot,'\\');*/
4193:
1.107 brouard 4194: /* Split argv[0], imach program to get pathimach */
4195: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
1.99 brouard 4196: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4197: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.99 brouard 4198: /* strcpy(pathimach,argv[0]); */
1.107 brouard 4199: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
1.53 brouard 4200: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4201: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 4202: chdir(path);
1.88 brouard 4203: strcpy(command,"mkdir ");
4204: strcat(command,optionfilefiname);
4205: if((outcmd=system(command)) != 0){
4206: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4207: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4208: /* fclose(ficlog); */
4209: /* exit(1); */
4210: }
4211: /* if((imk=mkdir(optionfilefiname))<0){ */
4212: /* perror("mkdir"); */
4213: /* } */
1.53 brouard 4214:
1.59 brouard 4215: /*-------- arguments in the command line --------*/
1.53 brouard 4216:
4217: /* Log file */
4218: strcat(filelog, optionfilefiname);
4219: strcat(filelog,".log"); /* */
4220: if((ficlog=fopen(filelog,"w"))==NULL) {
4221: printf("Problem with logfile %s\n",filelog);
4222: goto end;
4223: }
4224: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4225: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.99 brouard 4226: fprintf(ficlog,"\nEnter the parameter file name: \n");
4227: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
1.88 brouard 4228: path=%s \n\
4229: optionfile=%s\n\
4230: optionfilext=%s\n\
1.99 brouard 4231: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4232:
1.94 brouard 4233: printf("Local time (at start):%s",strstart);
4234: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4235: fflush(ficlog);
1.91 brouard 4236: /* (void) gettimeofday(&curr_time,&tzp); */
4237: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4238:
4239: /* */
4240: strcpy(fileres,"r");
4241: strcat(fileres, optionfilefiname);
4242: strcat(fileres,".txt"); /* Other files have txt extension */
4243:
4244: /*---------arguments file --------*/
4245:
4246: if((ficpar=fopen(optionfile,"r"))==NULL) {
4247: printf("Problem with optionfile %s\n",optionfile);
4248: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4249: fflush(ficlog);
1.53 brouard 4250: goto end;
4251: }
4252:
1.88 brouard 4253:
4254:
1.53 brouard 4255: strcpy(filereso,"o");
4256: strcat(filereso,fileres);
1.88 brouard 4257: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4258: printf("Problem with Output resultfile: %s\n", filereso);
4259: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4260: fflush(ficlog);
1.53 brouard 4261: goto end;
4262: }
4263:
4264: /* Reads comments: lines beginning with '#' */
1.85 brouard 4265: numlinepar=0;
1.53 brouard 4266: while((c=getc(ficpar))=='#' && c!= EOF){
4267: ungetc(c,ficpar);
4268: fgets(line, MAXLINE, ficpar);
1.85 brouard 4269: numlinepar++;
1.53 brouard 4270: puts(line);
4271: fputs(line,ficparo);
1.85 brouard 4272: fputs(line,ficlog);
1.53 brouard 4273: }
4274: ungetc(c,ficpar);
4275:
4276: 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 4277: numlinepar++;
1.53 brouard 4278: 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);
4279: 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 4280: 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);
4281: fflush(ficlog);
1.59 brouard 4282: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4283: ungetc(c,ficpar);
4284: fgets(line, MAXLINE, ficpar);
1.85 brouard 4285: numlinepar++;
1.53 brouard 4286: puts(line);
4287: fputs(line,ficparo);
1.85 brouard 4288: fputs(line,ficlog);
1.53 brouard 4289: }
4290: ungetc(c,ficpar);
1.85 brouard 4291:
1.53 brouard 4292:
4293: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4294: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4295: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4296:
1.58 lievre 4297: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4298: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 brouard 4299: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4300:
4301: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4302: delti=delti3[1][1];
4303: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4304: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4305: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4306: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4307: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 brouard 4308: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4309: fclose (ficparo);
4310: fclose (ficlog);
4311: exit(0);
4312: }
1.98 brouard 4313: else if(mle==-3) {
4314: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4315: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4316: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4317: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4318: matcov=matrix(1,npar,1,npar);
1.53 brouard 4319: }
1.98 brouard 4320: else{
4321: /* Read guess parameters */
4322: /* Reads comments: lines beginning with '#' */
4323: while((c=getc(ficpar))=='#' && c!= EOF){
4324: ungetc(c,ficpar);
4325: fgets(line, MAXLINE, ficpar);
1.85 brouard 4326: numlinepar++;
1.98 brouard 4327: puts(line);
4328: fputs(line,ficparo);
4329: fputs(line,ficlog);
1.53 brouard 4330: }
1.98 brouard 4331: ungetc(c,ficpar);
4332:
4333: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4334: for(i=1; i <=nlstate; i++){
4335: j=0;
4336: for(jj=1; jj <=nlstate+ndeath; jj++){
4337: if(jj==i) continue;
4338: j++;
4339: fscanf(ficpar,"%1d%1d",&i1,&j1);
4340: if ((i1 != i) && (j1 != j)){
4341: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4342: exit(1);
4343: }
4344: fprintf(ficparo,"%1d%1d",i1,j1);
4345: if(mle==1)
4346: printf("%1d%1d",i,j);
4347: fprintf(ficlog,"%1d%1d",i,j);
4348: for(k=1; k<=ncovmodel;k++){
4349: fscanf(ficpar," %lf",¶m[i][j][k]);
4350: if(mle==1){
4351: printf(" %lf",param[i][j][k]);
4352: fprintf(ficlog," %lf",param[i][j][k]);
4353: }
4354: else
4355: fprintf(ficlog," %lf",param[i][j][k]);
4356: fprintf(ficparo," %lf",param[i][j][k]);
4357: }
4358: fscanf(ficpar,"\n");
4359: numlinepar++;
4360: if(mle==1)
4361: printf("\n");
4362: fprintf(ficlog,"\n");
4363: fprintf(ficparo,"\n");
4364: }
4365: }
4366: fflush(ficlog);
1.85 brouard 4367:
1.98 brouard 4368: p=param[1][1];
4369:
4370: /* Reads comments: lines beginning with '#' */
4371: while((c=getc(ficpar))=='#' && c!= EOF){
4372: ungetc(c,ficpar);
4373: fgets(line, MAXLINE, ficpar);
4374: numlinepar++;
4375: puts(line);
4376: fputs(line,ficparo);
4377: fputs(line,ficlog);
4378: }
1.53 brouard 4379: ungetc(c,ficpar);
4380:
1.98 brouard 4381: for(i=1; i <=nlstate; i++){
4382: for(j=1; j <=nlstate+ndeath-1; j++){
4383: fscanf(ficpar,"%1d%1d",&i1,&j1);
4384: if ((i1-i)*(j1-j)!=0){
4385: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4386: exit(1);
4387: }
4388: printf("%1d%1d",i,j);
4389: fprintf(ficparo,"%1d%1d",i1,j1);
4390: fprintf(ficlog,"%1d%1d",i1,j1);
4391: for(k=1; k<=ncovmodel;k++){
4392: fscanf(ficpar,"%le",&delti3[i][j][k]);
4393: printf(" %le",delti3[i][j][k]);
4394: fprintf(ficparo," %le",delti3[i][j][k]);
4395: fprintf(ficlog," %le",delti3[i][j][k]);
4396: }
4397: fscanf(ficpar,"\n");
4398: numlinepar++;
4399: printf("\n");
4400: fprintf(ficparo,"\n");
4401: fprintf(ficlog,"\n");
1.85 brouard 4402: }
1.53 brouard 4403: }
1.98 brouard 4404: fflush(ficlog);
1.85 brouard 4405:
1.98 brouard 4406: delti=delti3[1][1];
1.74 brouard 4407:
4408:
1.98 brouard 4409: /* 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 4410:
1.98 brouard 4411: /* Reads comments: lines beginning with '#' */
4412: while((c=getc(ficpar))=='#' && c!= EOF){
4413: ungetc(c,ficpar);
4414: fgets(line, MAXLINE, ficpar);
4415: numlinepar++;
4416: puts(line);
4417: fputs(line,ficparo);
4418: fputs(line,ficlog);
4419: }
1.53 brouard 4420: ungetc(c,ficpar);
4421:
1.98 brouard 4422: matcov=matrix(1,npar,1,npar);
4423: for(i=1; i <=npar; i++){
4424: fscanf(ficpar,"%s",&str);
4425: if(mle==1)
4426: printf("%s",str);
4427: fprintf(ficlog,"%s",str);
4428: fprintf(ficparo,"%s",str);
4429: for(j=1; j <=i; j++){
4430: fscanf(ficpar," %le",&matcov[i][j]);
4431: if(mle==1){
4432: printf(" %.5le",matcov[i][j]);
4433: }
4434: fprintf(ficlog," %.5le",matcov[i][j]);
4435: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4436: }
1.98 brouard 4437: fscanf(ficpar,"\n");
4438: numlinepar++;
4439: if(mle==1)
4440: printf("\n");
4441: fprintf(ficlog,"\n");
4442: fprintf(ficparo,"\n");
1.53 brouard 4443: }
1.98 brouard 4444: for(i=1; i <=npar; i++)
4445: for(j=i+1;j<=npar;j++)
4446: matcov[i][j]=matcov[j][i];
4447:
1.53 brouard 4448: if(mle==1)
4449: printf("\n");
4450: fprintf(ficlog,"\n");
1.98 brouard 4451:
4452: fflush(ficlog);
4453:
4454: /*-------- Rewriting parameter file ----------*/
4455: strcpy(rfileres,"r"); /* "Rparameterfile */
4456: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4457: strcat(rfileres,"."); /* */
4458: strcat(rfileres,optionfilext); /* Other files have txt extension */
4459: if((ficres =fopen(rfileres,"w"))==NULL) {
4460: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4461: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4462: }
4463: fprintf(ficres,"#%s\n",version);
4464: } /* End of mle != -3 */
1.53 brouard 4465:
1.59 brouard 4466: /*-------- data file ----------*/
4467: if((fic=fopen(datafile,"r"))==NULL) {
4468: printf("Problem with datafile: %s\n", datafile);goto end;
4469: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4470: }
4471:
4472: n= lastobs;
4473: severity = vector(1,maxwav);
4474: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4475: num=lvector(1,n);
1.59 brouard 4476: moisnais=vector(1,n);
4477: annais=vector(1,n);
4478: moisdc=vector(1,n);
4479: andc=vector(1,n);
4480: agedc=vector(1,n);
4481: cod=ivector(1,n);
4482: weight=vector(1,n);
4483: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4484: mint=matrix(1,maxwav,1,n);
4485: anint=matrix(1,maxwav,1,n);
4486: s=imatrix(1,maxwav+1,1,n);
4487: tab=ivector(1,NCOVMAX);
4488: ncodemax=ivector(1,8);
4489:
4490: i=1;
1.109 ! brouard 4491: linei=0;
! 4492: while ((fgets(line, MAXLINE, fic) != NULL) ||((i >= firstobs) && (i <=lastobs))) {
! 4493: linei=linei+1;
! 4494: printf("IIIII= %d linei=%d\n",i,linei);
! 4495: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
1.102 brouard 4496: if(line[j] == '\t')
4497: line[j] = ' ';
4498: }
1.109 ! brouard 4499: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10);j--){;};line[j+1]=0; /* Trims blanks at end of line */
! 4500: if(line[0]=='#'){
! 4501: fprintf(ficlog,"Comment line\n%s\n",line);
! 4502: printf("Comment line\n%s\n",line);
! 4503: continue;
! 4504: }
1.59 brouard 4505: for (j=maxwav;j>=1;j--){
1.109 ! brouard 4506: cutv(stra, strb,line,' ');
! 4507: errno=0;
! 4508: lval=strtol(strb,&endptr,10);
! 4509: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 4510: if( strb[0]=='\0' || (*endptr != '\0')){
! 4511: printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n",lval, i,line,linei,j,maxwav);
! 4512: exit(1);
! 4513: }
! 4514: s[j][i]=lval;
! 4515:
! 4516: strcpy(line,stra);
! 4517: cutv(stra, strb,line,'/');
! 4518: errno=0;
! 4519: lval=strtol(strb,&endptr,10);
! 4520: if( strb[0]=='\0' || (*endptr != '\0')){
! 4521: printf("Error reading data around '%d'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d. Exiting.\n",lval, i,line,linei,j);
! 4522: exit(1);
! 4523: }
! 4524: anint[j][i]=(double)(lval);
! 4525:
! 4526: strcpy(line,stra);
! 4527: cutv(stra, strb,line,' ');
! 4528: errno=0;
! 4529: lval=strtol(strb,&endptr,10);
! 4530: if( strb[0]=='\0' || (*endptr != '\0')){
! 4531: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of exam at wave %d. Exiting.\n",lval, i,line, linei,j);
! 4532: exit(1);
! 4533: }
! 4534: mint[j][i]=(double)(lval);
1.59 brouard 4535: strcpy(line,stra);
4536: }
1.53 brouard 4537:
1.109 ! brouard 4538: cutv(stra, strb,line,'/');
! 4539: errno=0;
! 4540: lval=strtol(strb,&endptr,10);
! 4541: if( strb[0]=='\0' || (*endptr != '\0')){
! 4542: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of death. Exiting.\n",lval, i,line,linei);
! 4543: exit(1);
! 4544: }
! 4545: andc[i]=(double)(lval);
! 4546: strcpy(line,stra);
! 4547:
! 4548: cutv(stra, strb,line,' ');
! 4549: errno=0;
! 4550: lval=strtol(strb,&endptr,10);
! 4551: if( strb[0]=='\0' || (*endptr != '\0')){
! 4552: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of death. Exiting.\n",lval,i,line, linei);
! 4553: exit(1);
! 4554: }
! 4555: moisdc[i]=(double)(lval);
! 4556:
! 4557: strcpy(line,stra);
! 4558: cutv(stra, strb,line,'/');
! 4559: errno=0;
! 4560: lval=strtol(strb,&endptr,10);
! 4561: if( strb[0]=='\0' || (*endptr != '\0')){
! 4562: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of birth. Exiting.\n",lval, i,line, linei);
! 4563: exit(1);
! 4564: }
! 4565: annais[i]=(double)(lval);
! 4566:
! 4567: strcpy(line,stra);
! 4568: cutv(stra, strb,line,' ');
! 4569: errno=0;
! 4570: lval=strtol(strb,&endptr,10);
! 4571: if( strb[0]=='\0' || (*endptr != '\0')){
! 4572: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of birth. Exiting.\n",lval,i,line,linei);
! 4573: exit(1);
! 4574: }
! 4575: moisnais[i]=(double)(lval);
! 4576: strcpy(line,stra);
! 4577:
! 4578: cutv(stra, strb,line,' ');
! 4579: errno=0;
! 4580: lval=strtol(strb,&endptr,10);
! 4581: if( strb[0]=='\0' || (*endptr != '\0')){
! 4582: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
! 4583: exit(1);
! 4584: }
! 4585: weight[i]=(double)(lval);
! 4586: strcpy(line,stra);
1.53 brouard 4587:
1.59 brouard 4588: for (j=ncovcol;j>=1;j--){
1.109 ! brouard 4589: cutv(stra, strb,line,' ');
! 4590: errno=0;
! 4591: lval=strtol(strb,&endptr,10);
! 4592: if( strb[0]=='\0' || (*endptr != '\0')){
! 4593: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, i,line,linei);
! 4594: exit(1);
! 4595: }
! 4596: if(lval <0 || lval >1){
! 4597: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,i,line,linei,j);
! 4598: exit(1);
! 4599: }
! 4600: covar[j][i]=(double)(lval);
! 4601: strcpy(line,stra);
1.59 brouard 4602: }
1.85 brouard 4603: lstra=strlen(stra);
1.109 ! brouard 4604:
1.85 brouard 4605: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4606: stratrunc = &(stra[lstra-9]);
4607: num[i]=atol(stratrunc);
4608: }
4609: else
4610: num[i]=atol(stra);
1.109 ! brouard 4611: printf ("num [i] %ld %d\n",i, num[i]);fflush(stdout);
1.59 brouard 4612: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4613: 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 4614:
1.59 brouard 4615: i=i+1;
1.109 ! brouard 4616: } /* End loop reading data */
1.59 brouard 4617: /* printf("ii=%d", ij);
4618: scanf("%d",i);*/
1.53 brouard 4619: imx=i-1; /* Number of individuals */
4620:
4621: /* for (i=1; i<=imx; i++){
4622: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4623: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4624: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4625: }*/
4626: /* for (i=1; i<=imx; i++){
4627: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4628: 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 4629:
1.106 brouard 4630: /* for (i=1; i<=imx; i++) */
1.53 brouard 4631:
1.71 brouard 4632: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4633: else weight[i]=1;*/
4634:
1.106 brouard 4635: /* Calculation of the number of parameters from char model */
1.53 brouard 4636: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4637: Tprod=ivector(1,15);
4638: Tvaraff=ivector(1,15);
4639: Tvard=imatrix(1,15,1,2);
4640: Tage=ivector(1,15);
4641:
1.58 lievre 4642: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4643: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4644: j=nbocc(model,'+'); /* j=Number of '+' */
4645: j1=nbocc(model,'*'); /* j1=Number of '*' */
4646: cptcovn=j+1;
4647: cptcovprod=j1; /*Number of products */
1.53 brouard 4648:
4649: strcpy(modelsav,model);
4650: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4651: printf("Error. Non available option model=%s ",model);
4652: fprintf(ficlog,"Error. Non available option model=%s ",model);
4653: goto end;
4654: }
4655:
1.59 brouard 4656: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4657:
1.53 brouard 4658: for(i=(j+1); i>=1;i--){
4659: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4660: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4661: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4662: /*scanf("%d",i);*/
4663: if (strchr(strb,'*')) { /* Model includes a product */
4664: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4665: if (strcmp(strc,"age")==0) { /* Vn*age */
4666: cptcovprod--;
4667: cutv(strb,stre,strd,'V');
4668: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4669: cptcovage++;
4670: Tage[cptcovage]=i;
4671: /*printf("stre=%s ", stre);*/
4672: }
4673: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4674: cptcovprod--;
4675: cutv(strb,stre,strc,'V');
4676: Tvar[i]=atoi(stre);
4677: cptcovage++;
4678: Tage[cptcovage]=i;
4679: }
4680: else { /* Age is not in the model */
4681: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4682: Tvar[i]=ncovcol+k1;
4683: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4684: Tprod[k1]=i;
4685: Tvard[k1][1]=atoi(strc); /* m*/
4686: Tvard[k1][2]=atoi(stre); /* n */
4687: Tvar[cptcovn+k2]=Tvard[k1][1];
4688: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4689: for (k=1; k<=lastobs;k++)
4690: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4691: k1++;
4692: k2=k2+2;
4693: }
4694: }
4695: else { /* no more sum */
4696: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4697: /* scanf("%d",i);*/
4698: cutv(strd,strc,strb,'V');
4699: Tvar[i]=atoi(strc);
4700: }
4701: strcpy(modelsav,stra);
4702: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4703: scanf("%d",i);*/
4704: } /* end of loop + */
4705: } /* end model */
4706:
1.58 lievre 4707: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4708: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4709:
1.53 brouard 4710: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4711: printf("cptcovprod=%d ", cptcovprod);
4712: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4713:
4714: scanf("%d ",i);
4715: fclose(fic);*/
1.53 brouard 4716:
4717: /* if(mle==1){*/
1.59 brouard 4718: if (weightopt != 1) { /* Maximisation without weights*/
4719: for(i=1;i<=n;i++) weight[i]=1.0;
4720: }
1.53 brouard 4721: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4722: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4723:
1.59 brouard 4724: for (i=1; i<=imx; i++) {
4725: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4726: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4727: anint[m][i]=9999;
4728: s[m][i]=-1;
4729: }
1.76 brouard 4730: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4731: nberr++;
1.85 brouard 4732: 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);
4733: 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 4734: s[m][i]=-1;
4735: }
4736: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4737: nberr++;
1.85 brouard 4738: 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]);
4739: 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 4740: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4741: }
1.53 brouard 4742: }
1.59 brouard 4743: }
1.53 brouard 4744:
1.59 brouard 4745: for (i=1; i<=imx; i++) {
4746: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4747: for(m=firstpass; (m<= lastpass); m++){
1.105 lievre 4748: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
1.59 brouard 4749: if (s[m][i] >= nlstate+1) {
4750: if(agedc[i]>0)
1.76 brouard 4751: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4752: agev[m][i]=agedc[i];
1.59 brouard 4753: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4754: else {
1.76 brouard 4755: if ((int)andc[i]!=9999){
1.91 brouard 4756: nbwarn++;
1.85 brouard 4757: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4758: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4759: agev[m][i]=-1;
1.53 brouard 4760: }
4761: }
1.70 brouard 4762: }
1.69 brouard 4763: else if(s[m][i] !=9){ /* Standard case, age in fractional
1.108 lievre 4764: years but with the precision of a month */
1.59 brouard 4765: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4766: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4767: agev[m][i]=1;
4768: else if(agev[m][i] <agemin){
4769: agemin=agev[m][i];
4770: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4771: }
1.59 brouard 4772: else if(agev[m][i] >agemax){
4773: agemax=agev[m][i];
4774: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4775: }
1.59 brouard 4776: /*agev[m][i]=anint[m][i]-annais[i];*/
4777: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4778: }
1.59 brouard 4779: else { /* =9 */
1.53 brouard 4780: agev[m][i]=1;
1.59 brouard 4781: s[m][i]=-1;
4782: }
1.53 brouard 4783: }
1.59 brouard 4784: else /*= 0 Unknown */
4785: agev[m][i]=1;
4786: }
1.53 brouard 4787:
1.59 brouard 4788: }
4789: for (i=1; i<=imx; i++) {
1.71 brouard 4790: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4791: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4792: nberr++;
1.59 brouard 4793: 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);
4794: 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);
4795: goto end;
1.53 brouard 4796: }
4797: }
1.59 brouard 4798: }
1.53 brouard 4799:
1.71 brouard 4800: /*for (i=1; i<=imx; i++){
4801: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4802: 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 4803: }
4804:
4805: }*/
4806:
1.97 lievre 4807:
1.59 brouard 4808: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4809: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4810:
1.98 brouard 4811: agegomp=(int)agemin;
1.59 brouard 4812: free_vector(severity,1,maxwav);
4813: free_imatrix(outcome,1,maxwav+1,1,n);
4814: free_vector(moisnais,1,n);
4815: free_vector(annais,1,n);
4816: /* free_matrix(mint,1,maxwav,1,n);
4817: free_matrix(anint,1,maxwav,1,n);*/
4818: free_vector(moisdc,1,n);
4819: free_vector(andc,1,n);
1.53 brouard 4820:
4821:
1.59 brouard 4822: wav=ivector(1,imx);
4823: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4824: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4825: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4826:
1.59 brouard 4827: /* Concatenates waves */
4828: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4829:
1.59 brouard 4830: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4831:
1.59 brouard 4832: Tcode=ivector(1,100);
4833: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4834: ncodemax[1]=1;
4835: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4836:
1.59 brouard 4837: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4838: the estimations*/
4839: h=0;
4840: m=pow(2,cptcoveff);
1.53 brouard 4841:
1.59 brouard 4842: for(k=1;k<=cptcoveff; k++){
4843: for(i=1; i <=(m/pow(2,k));i++){
4844: for(j=1; j <= ncodemax[k]; j++){
4845: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4846: h++;
4847: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4848: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4849: }
4850: }
4851: }
4852: }
4853: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4854: codtab[1][2]=1;codtab[2][2]=2; */
4855: /* for(i=1; i <=m ;i++){
4856: for(k=1; k <=cptcovn; k++){
4857: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4858: }
4859: printf("\n");
1.53 brouard 4860: }
1.59 brouard 4861: scanf("%d",i);*/
1.53 brouard 4862:
1.86 brouard 4863: /*------------ gnuplot -------------*/
4864: strcpy(optionfilegnuplot,optionfilefiname);
1.98 brouard 4865: if(mle==-3)
4866: strcat(optionfilegnuplot,"-mort");
1.86 brouard 4867: strcat(optionfilegnuplot,".gp");
1.98 brouard 4868:
1.86 brouard 4869: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4870: printf("Problem with file %s",optionfilegnuplot);
4871: }
4872: else{
4873: fprintf(ficgp,"\n# %s\n", version);
4874: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4875: fprintf(ficgp,"set missing 'NaNq'\n");
4876: }
1.88 brouard 4877: /* fclose(ficgp);*/
1.86 brouard 4878: /*--------- index.htm --------*/
4879:
1.91 brouard 4880: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 brouard 4881: if(mle==-3)
4882: strcat(optionfilehtm,"-mort");
1.86 brouard 4883: strcat(optionfilehtm,".htm");
4884: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4885: printf("Problem with %s \n",optionfilehtm), exit(0);
4886: }
4887:
1.91 brouard 4888: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4889: strcat(optionfilehtmcov,"-cov.htm");
4890: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4891: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4892: }
4893: else{
4894: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4895: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4896: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4897: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4898: }
4899:
1.87 brouard 4900: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4901: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4902: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4903: \n\
4904: <hr size=\"2\" color=\"#EC5E5E\">\
4905: <ul><li><h4>Parameter files</h4>\n\
4906: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4907: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4908: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4909: - Date and time at start: %s</ul>\n",\
1.91 brouard 4910: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4911: fileres,fileres,\
1.88 brouard 4912: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4913: fflush(fichtm);
1.86 brouard 4914:
1.88 brouard 4915: strcpy(pathr,path);
4916: strcat(pathr,optionfilefiname);
4917: chdir(optionfilefiname); /* Move to directory named optionfile */
4918:
1.59 brouard 4919: /* Calculates basic frequencies. Computes observed prevalence at single age
4920: and prints on file fileres'p'. */
1.105 lievre 4921: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
1.53 brouard 4922:
1.88 brouard 4923: fprintf(fichtm,"\n");
4924: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4925: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4926: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4927: imx,agemin,agemax,jmin,jmax,jmean);
4928: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4929: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4930: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4931: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4932: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4933:
4934:
1.59 brouard 4935: /* For Powell, parameters are in a vector p[] starting at p[1]
4936: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4937: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4938:
1.86 brouard 4939: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.98 brouard 4940: if (mle==-3){
4941: ximort=matrix(1,NDIM,1,NDIM);
4942: cens=ivector(1,n);
4943: ageexmed=vector(1,n);
4944: agecens=vector(1,n);
4945: dcwave=ivector(1,n);
4946:
4947: for (i=1; i<=imx; i++){
4948: dcwave[i]=-1;
4949: for (j=1; j<=lastpass; j++)
4950: if (s[j][i]>nlstate) {
4951: dcwave[i]=j;
4952: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4953: break;
4954: }
4955: }
4956:
4957: for (i=1; i<=imx; i++) {
4958: if (wav[i]>0){
4959: ageexmed[i]=agev[mw[1][i]][i];
4960: j=wav[i];agecens[i]=1.;
4961: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4962: cens[i]=1;
4963:
4964: if (ageexmed[i]<1) cens[i]=-1;
4965: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4966: }
4967: else cens[i]=-1;
4968: }
4969:
4970: for (i=1;i<=NDIM;i++) {
4971: for (j=1;j<=NDIM;j++)
4972: ximort[i][j]=(i == j ? 1.0 : 0.0);
4973: }
4974:
4975: p[1]=0.1; p[2]=0.1;
4976: /*printf("%lf %lf", p[1], p[2]);*/
4977:
4978:
4979: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4980: strcpy(filerespow,"pow-mort");
4981: strcat(filerespow,fileres);
4982: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4983: printf("Problem with resultfile: %s\n", filerespow);
4984: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1.59 brouard 4985: }
1.98 brouard 4986: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4987: /* for (i=1;i<=nlstate;i++)
4988: for(j=1;j<=nlstate+ndeath;j++)
4989: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4990: */
4991: fprintf(ficrespow,"\n");
4992:
4993: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4994: fclose(ficrespow);
1.53 brouard 4995:
1.98 brouard 4996: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
1.53 brouard 4997:
1.98 brouard 4998: for(i=1; i <=NDIM; i++)
4999: for(j=i+1;j<=NDIM;j++)
5000: matcov[i][j]=matcov[j][i];
5001:
5002: printf("\nCovariance matrix\n ");
5003: for(i=1; i <=NDIM; i++) {
5004: for(j=1;j<=NDIM;j++){
5005: printf("%f ",matcov[i][j]);
1.95 brouard 5006: }
1.98 brouard 5007: printf("\n ");
5008: }
5009:
5010: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5011: for (i=1;i<=NDIM;i++)
5012: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.105 lievre 5013:
5014: lsurv=vector(1,AGESUP);
5015: lpop=vector(1,AGESUP);
5016: tpop=vector(1,AGESUP);
5017: lsurv[agegomp]=100000;
5018:
5019: for (k=agegomp;k<=AGESUP;k++) {
5020: agemortsup=k;
5021: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5022: }
5023:
5024: for (k=agegomp;k<agemortsup;k++)
5025: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5026:
5027: for (k=agegomp;k<agemortsup;k++){
5028: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5029: sumlpop=sumlpop+lpop[k];
5030: }
5031:
5032: tpop[agegomp]=sumlpop;
5033: for (k=agegomp;k<(agemortsup-3);k++){
5034: /* tpop[k+1]=2;*/
5035: tpop[k+1]=tpop[k]-lpop[k];
5036: }
5037:
5038:
5039: printf("\nAge lx qx dx Lx Tx e(x)\n");
5040: for (k=agegomp;k<(agemortsup-2);k++)
5041: 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]);
5042:
5043:
1.98 brouard 5044: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5045: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5046:
5047: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5048: stepm, weightopt,\
1.105 lievre 5049: model,imx,p,matcov,agemortsup);
5050:
5051: free_vector(lsurv,1,AGESUP);
5052: free_vector(lpop,1,AGESUP);
5053: free_vector(tpop,1,AGESUP);
1.98 brouard 5054: } /* Endof if mle==-3 */
5055:
5056: else{ /* For mle >=1 */
5057:
5058: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5059: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5060: for (k=1; k<=npar;k++)
5061: printf(" %d %8.5f",k,p[k]);
5062: printf("\n");
5063: globpr=1; /* to print the contributions */
5064: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5065: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5066: for (k=1; k<=npar;k++)
5067: printf(" %d %8.5f",k,p[k]);
5068: printf("\n");
5069: if(mle>=1){ /* Could be 1 or 2 */
5070: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 5071: }
1.98 brouard 5072:
5073: /*--------- results files --------------*/
5074: 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);
5075:
5076:
5077: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5078: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5079: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5080: for(i=1,jk=1; i <=nlstate; i++){
5081: for(k=1; k <=(nlstate+ndeath); k++){
5082: if (k != i) {
5083: printf("%d%d ",i,k);
5084: fprintf(ficlog,"%d%d ",i,k);
5085: fprintf(ficres,"%1d%1d ",i,k);
5086: for(j=1; j <=ncovmodel; j++){
5087: printf("%f ",p[jk]);
5088: fprintf(ficlog,"%f ",p[jk]);
5089: fprintf(ficres,"%f ",p[jk]);
5090: jk++;
5091: }
5092: printf("\n");
5093: fprintf(ficlog,"\n");
5094: fprintf(ficres,"\n");
1.59 brouard 5095: }
5096: }
5097: }
1.98 brouard 5098: if(mle!=0){
5099: /* Computing hessian and covariance matrix */
5100: ftolhess=ftol; /* Usually correct */
5101: hesscov(matcov, p, npar, delti, ftolhess, func);
5102: }
5103: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5104: printf("# Scales (for hessian or gradient estimation)\n");
5105: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5106: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 5107: for(j=1; j <=nlstate+ndeath; j++){
1.98 brouard 5108: if (j!=i) {
5109: fprintf(ficres,"%1d%1d",i,j);
5110: printf("%1d%1d",i,j);
5111: fprintf(ficlog,"%1d%1d",i,j);
5112: for(k=1; k<=ncovmodel;k++){
5113: printf(" %.5e",delti[jk]);
5114: fprintf(ficlog," %.5e",delti[jk]);
5115: fprintf(ficres," %.5e",delti[jk]);
5116: jk++;
1.95 brouard 5117: }
1.98 brouard 5118: printf("\n");
5119: fprintf(ficlog,"\n");
5120: fprintf(ficres,"\n");
5121: }
5122: }
5123: }
5124:
5125: 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");
5126: if(mle>=1)
5127: 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");
5128: 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");
5129: /* # 121 Var(a12)\n\ */
5130: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5131: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5132: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5133: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5134: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5135: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5136: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5137:
5138:
5139: /* Just to have a covariance matrix which will be more understandable
5140: even is we still don't want to manage dictionary of variables
5141: */
5142: for(itimes=1;itimes<=2;itimes++){
5143: jj=0;
5144: for(i=1; i <=nlstate; i++){
5145: for(j=1; j <=nlstate+ndeath; j++){
5146: if(j==i) continue;
5147: for(k=1; k<=ncovmodel;k++){
5148: jj++;
5149: ca[0]= k+'a'-1;ca[1]='\0';
5150: if(itimes==1){
5151: if(mle>=1)
5152: printf("#%1d%1d%d",i,j,k);
5153: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5154: fprintf(ficres,"#%1d%1d%d",i,j,k);
5155: }else{
5156: if(mle>=1)
5157: printf("%1d%1d%d",i,j,k);
5158: fprintf(ficlog,"%1d%1d%d",i,j,k);
5159: fprintf(ficres,"%1d%1d%d",i,j,k);
5160: }
5161: ll=0;
5162: for(li=1;li <=nlstate; li++){
5163: for(lj=1;lj <=nlstate+ndeath; lj++){
5164: if(lj==li) continue;
5165: for(lk=1;lk<=ncovmodel;lk++){
5166: ll++;
5167: if(ll<=jj){
5168: cb[0]= lk +'a'-1;cb[1]='\0';
5169: if(ll<jj){
5170: if(itimes==1){
5171: if(mle>=1)
5172: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5173: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5174: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5175: }else{
5176: if(mle>=1)
5177: printf(" %.5e",matcov[jj][ll]);
5178: fprintf(ficlog," %.5e",matcov[jj][ll]);
5179: fprintf(ficres," %.5e",matcov[jj][ll]);
5180: }
1.95 brouard 5181: }else{
1.98 brouard 5182: if(itimes==1){
5183: if(mle>=1)
5184: printf(" Var(%s%1d%1d)",ca,i,j);
5185: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5186: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5187: }else{
5188: if(mle>=1)
5189: printf(" %.5e",matcov[jj][ll]);
5190: fprintf(ficlog," %.5e",matcov[jj][ll]);
5191: fprintf(ficres," %.5e",matcov[jj][ll]);
5192: }
1.95 brouard 5193: }
5194: }
1.98 brouard 5195: } /* end lk */
5196: } /* end lj */
5197: } /* end li */
5198: if(mle>=1)
5199: printf("\n");
5200: fprintf(ficlog,"\n");
5201: fprintf(ficres,"\n");
5202: numlinepar++;
5203: } /* end k*/
5204: } /*end j */
5205: } /* end i */
5206: } /* end itimes */
5207:
5208: fflush(ficlog);
5209: fflush(ficres);
5210:
5211: while((c=getc(ficpar))=='#' && c!= EOF){
5212: ungetc(c,ficpar);
5213: fgets(line, MAXLINE, ficpar);
5214: puts(line);
5215: fputs(line,ficparo);
5216: }
1.59 brouard 5217: ungetc(c,ficpar);
1.98 brouard 5218:
5219: estepm=0;
5220: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5221: if (estepm==0 || estepm < stepm) estepm=stepm;
5222: if (fage <= 2) {
5223: bage = ageminpar;
5224: fage = agemaxpar;
5225: }
5226:
5227: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5228: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5229: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5230:
5231: while((c=getc(ficpar))=='#' && c!= EOF){
5232: ungetc(c,ficpar);
5233: fgets(line, MAXLINE, ficpar);
5234: puts(line);
5235: fputs(line,ficparo);
5236: }
1.59 brouard 5237: ungetc(c,ficpar);
1.98 brouard 5238:
5239: 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);
5240: 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);
5241: 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);
5242: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5243: 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);
5244:
5245: while((c=getc(ficpar))=='#' && c!= EOF){
5246: ungetc(c,ficpar);
5247: fgets(line, MAXLINE, ficpar);
5248: puts(line);
5249: fputs(line,ficparo);
5250: }
1.59 brouard 5251: ungetc(c,ficpar);
1.98 brouard 5252:
5253:
5254: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5255: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5256:
5257: fscanf(ficpar,"pop_based=%d\n",&popbased);
5258: fprintf(ficparo,"pop_based=%d\n",popbased);
5259: fprintf(ficres,"pop_based=%d\n",popbased);
5260:
5261: while((c=getc(ficpar))=='#' && c!= EOF){
5262: ungetc(c,ficpar);
5263: fgets(line, MAXLINE, ficpar);
5264: puts(line);
5265: fputs(line,ficparo);
5266: }
1.53 brouard 5267: ungetc(c,ficpar);
1.98 brouard 5268:
5269: 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);
5270: 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);
5271: 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);
5272: 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);
5273: 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);
5274: /* day and month of proj2 are not used but only year anproj2.*/
5275:
5276:
5277:
5278: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5279: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5280:
5281: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5282: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5283:
5284: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5285: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5286: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5287:
5288: /*------------ free_vector -------------*/
5289: /* chdir(path); */
1.53 brouard 5290:
1.98 brouard 5291: free_ivector(wav,1,imx);
5292: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5293: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5294: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5295: free_lvector(num,1,n);
5296: free_vector(agedc,1,n);
5297: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5298: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5299: fclose(ficparo);
5300: fclose(ficres);
5301:
5302:
5303: /*--------------- Prevalence limit (stable prevalence) --------------*/
5304:
5305: strcpy(filerespl,"pl");
5306: strcat(filerespl,fileres);
5307: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5308: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5309: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5310: }
5311: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5312: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
1.105 lievre 5313: fprintf(ficrespl, "#Local time at start: %s", strstart);
1.98 brouard 5314: fprintf(ficrespl,"#Stable prevalence \n");
5315: fprintf(ficrespl,"#Age ");
5316: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5317: fprintf(ficrespl,"\n");
5318:
5319: prlim=matrix(1,nlstate,1,nlstate);
5320:
5321: agebase=ageminpar;
5322: agelim=agemaxpar;
5323: ftolpl=1.e-10;
5324: i1=cptcoveff;
5325: if (cptcovn < 1){i1=1;}
5326:
5327: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5328: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5329: k=k+1;
5330: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5331: fprintf(ficrespl,"\n#******");
5332: printf("\n#******");
5333: fprintf(ficlog,"\n#******");
5334: for(j=1;j<=cptcoveff;j++) {
5335: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5336: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5337: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5338: }
5339: fprintf(ficrespl,"******\n");
5340: printf("******\n");
5341: fprintf(ficlog,"******\n");
1.53 brouard 5342:
1.98 brouard 5343: for (age=agebase; age<=agelim; age++){
5344: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5345: fprintf(ficrespl,"%.0f ",age );
5346: for(j=1;j<=cptcoveff;j++)
5347: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5348: for(i=1; i<=nlstate;i++)
5349: fprintf(ficrespl," %.5f", prlim[i][i]);
5350: fprintf(ficrespl,"\n");
5351: }
1.53 brouard 5352: }
5353: }
1.98 brouard 5354: fclose(ficrespl);
1.53 brouard 5355:
1.98 brouard 5356: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5357:
1.98 brouard 5358: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5359: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5360: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5361: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5362: }
5363: printf("Computing pij: result on file '%s' \n", filerespij);
5364: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5365:
1.98 brouard 5366: stepsize=(int) (stepm+YEARM-1)/YEARM;
5367: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5368:
1.98 brouard 5369: agelim=AGESUP;
5370: hstepm=stepsize*YEARM; /* Every year of age */
5371: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5372:
1.98 brouard 5373: /* hstepm=1; aff par mois*/
1.105 lievre 5374: fprintf(ficrespij, "#Local time at start: %s", strstart);
1.98 brouard 5375: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5376: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5377: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5378: k=k+1;
5379: fprintf(ficrespij,"\n#****** ");
5380: for(j=1;j<=cptcoveff;j++)
5381: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5382: fprintf(ficrespij,"******\n");
1.53 brouard 5383:
1.98 brouard 5384: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5385: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5386: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5387:
1.98 brouard 5388: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5389:
1.98 brouard 5390: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5391: oldm=oldms;savm=savms;
5392: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5393: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5394: for(i=1; i<=nlstate;i++)
5395: for(j=1; j<=nlstate+ndeath;j++)
1.98 brouard 5396: fprintf(ficrespij," %1d-%1d",i,j);
5397: fprintf(ficrespij,"\n");
5398: for (h=0; h<=nhstepm; h++){
5399: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5400: for(i=1; i<=nlstate;i++)
5401: for(j=1; j<=nlstate+ndeath;j++)
5402: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5403: fprintf(ficrespij,"\n");
5404: }
5405: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5406: fprintf(ficrespij,"\n");
5407: }
1.59 brouard 5408: }
1.53 brouard 5409: }
5410:
1.105 lievre 5411: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.53 brouard 5412:
1.98 brouard 5413: fclose(ficrespij);
1.53 brouard 5414:
1.98 brouard 5415: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5416: for(i=1;i<=AGESUP;i++)
5417: for(j=1;j<=NCOVMAX;j++)
5418: for(k=1;k<=NCOVMAX;k++)
5419: probs[i][j][k]=0.;
5420:
5421: /*---------- Forecasting ------------------*/
5422: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5423: if(prevfcast==1){
5424: /* if(stepm ==1){*/
1.70 brouard 5425: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5426: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 brouard 5427: /* } */
5428: /* else{ */
5429: /* erreur=108; */
5430: /* 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); */
5431: /* 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); */
5432: /* } */
5433: }
1.53 brouard 5434:
5435:
1.98 brouard 5436: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5437:
1.98 brouard 5438: strcpy(filerest,"t");
5439: strcat(filerest,fileres);
5440: if((ficrest=fopen(filerest,"w"))==NULL) {
5441: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5442: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5443: }
5444: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5445: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
1.53 brouard 5446:
5447:
1.98 brouard 5448: strcpy(filerese,"e");
5449: strcat(filerese,fileres);
5450: if((ficreseij=fopen(filerese,"w"))==NULL) {
5451: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5452: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5453: }
5454: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5455: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5456:
1.98 brouard 5457: strcpy(fileresv,"v");
5458: strcat(fileresv,fileres);
5459: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5460: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5461: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5462: }
5463: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5464: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5465:
1.98 brouard 5466: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5467: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5468: /* 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",\
5469: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5470: */
1.58 lievre 5471:
1.98 brouard 5472: if (mobilav!=0) {
5473: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5474: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5475: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5476: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5477: }
1.54 brouard 5478: }
1.53 brouard 5479:
1.98 brouard 5480: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5481: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5482: k=k+1;
5483: fprintf(ficrest,"\n#****** ");
5484: for(j=1;j<=cptcoveff;j++)
5485: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5486: fprintf(ficrest,"******\n");
5487:
5488: fprintf(ficreseij,"\n#****** ");
5489: for(j=1;j<=cptcoveff;j++)
5490: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5491: fprintf(ficreseij,"******\n");
5492:
5493: fprintf(ficresvij,"\n#****** ");
5494: for(j=1;j<=cptcoveff;j++)
5495: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5496: fprintf(ficresvij,"******\n");
5497:
5498: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5499: oldm=oldms;savm=savms;
1.105 lievre 5500: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.53 brouard 5501:
1.98 brouard 5502: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5503: oldm=oldms;savm=savms;
1.105 lievre 5504: 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 5505: if(popbased==1){
1.105 lievre 5506: 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 5507: }
1.53 brouard 5508:
1.105 lievre 5509: fprintf(ficrest, "#Local time at start: %s", strstart);
1.98 brouard 5510: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5511: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5512: fprintf(ficrest,"\n");
5513:
5514: epj=vector(1,nlstate+1);
5515: for(age=bage; age <=fage ;age++){
5516: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5517: if (popbased==1) {
5518: if(mobilav ==0){
5519: for(i=1; i<=nlstate;i++)
5520: prlim[i][i]=probs[(int)age][i][k];
5521: }else{ /* mobilav */
5522: for(i=1; i<=nlstate;i++)
5523: prlim[i][i]=mobaverage[(int)age][i][k];
5524: }
1.53 brouard 5525: }
5526:
1.98 brouard 5527: fprintf(ficrest," %4.0f",age);
5528: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5529: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5530: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5531: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5532: }
5533: epj[nlstate+1] +=epj[j];
1.53 brouard 5534: }
5535:
1.98 brouard 5536: for(i=1, vepp=0.;i <=nlstate;i++)
5537: for(j=1;j <=nlstate;j++)
5538: vepp += vareij[i][j][(int)age];
5539: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5540: for(j=1;j <=nlstate;j++){
5541: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5542: }
5543: fprintf(ficrest,"\n");
1.53 brouard 5544: }
1.98 brouard 5545: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5546: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5547: free_vector(epj,1,nlstate+1);
5548: }
5549: }
5550: free_vector(weight,1,n);
5551: free_imatrix(Tvard,1,15,1,2);
5552: free_imatrix(s,1,maxwav+1,1,n);
5553: free_matrix(anint,1,maxwav,1,n);
5554: free_matrix(mint,1,maxwav,1,n);
5555: free_ivector(cod,1,n);
5556: free_ivector(tab,1,NCOVMAX);
5557: fclose(ficreseij);
5558: fclose(ficresvij);
5559: fclose(ficrest);
5560: fclose(ficpar);
5561:
5562: /*------- Variance of stable prevalence------*/
5563:
5564: strcpy(fileresvpl,"vpl");
5565: strcat(fileresvpl,fileres);
5566: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5567: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5568: exit(0);
5569: }
5570: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5571:
5572: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5573: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5574: k=k+1;
5575: fprintf(ficresvpl,"\n#****** ");
5576: for(j=1;j<=cptcoveff;j++)
5577: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5578: fprintf(ficresvpl,"******\n");
5579:
5580: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5581: oldm=oldms;savm=savms;
1.105 lievre 5582: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
1.98 brouard 5583: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5584: }
1.98 brouard 5585: }
1.53 brouard 5586:
1.98 brouard 5587: fclose(ficresvpl);
1.53 brouard 5588:
1.98 brouard 5589: /*---------- End : free ----------------*/
5590: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5591: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5592:
5593: } /* mle==-3 arrives here for freeing */
5594: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5595: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5596: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5597: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5598:
5599: free_matrix(covar,0,NCOVMAX,1,n);
5600: free_matrix(matcov,1,npar,1,npar);
5601: /*free_vector(delti,1,npar);*/
5602: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5603: free_matrix(agev,1,maxwav,1,imx);
5604: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5605:
5606: free_ivector(ncodemax,1,8);
5607: free_ivector(Tvar,1,15);
5608: free_ivector(Tprod,1,15);
5609: free_ivector(Tvaraff,1,15);
5610: free_ivector(Tage,1,15);
5611: free_ivector(Tcode,1,100);
1.74 brouard 5612:
1.53 brouard 5613:
1.88 brouard 5614: fflush(fichtm);
5615: fflush(ficgp);
1.53 brouard 5616:
5617:
1.91 brouard 5618: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5619: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5620: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5621: }else{
1.91 brouard 5622: printf("End of Imach\n");
5623: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5624: }
5625: printf("See log file on %s\n",filelog);
5626: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5627: (void) gettimeofday(&end_time,&tzp);
5628: tm = *localtime(&end_time.tv_sec);
5629: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5630: strcpy(strtend,asctime(&tm));
1.105 lievre 5631: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
1.94 brouard 5632: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5633: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5634:
1.91 brouard 5635: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5636: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5637: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5638: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5639: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5640: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5641: fclose(fichtm);
1.91 brouard 5642: fclose(fichtmcov);
1.88 brouard 5643: fclose(ficgp);
1.91 brouard 5644: fclose(ficlog);
1.53 brouard 5645: /*------ End -----------*/
5646:
1.88 brouard 5647: chdir(path);
1.107 brouard 5648: #ifndef UNIX
1.108 lievre 5649: /* strcpy(plotcmd,"\""); */
1.107 brouard 5650: #endif
1.108 lievre 5651: strcpy(plotcmd,pathimach);
1.107 brouard 5652: /*strcat(plotcmd,CHARSEPARATOR);*/
1.99 brouard 5653: strcat(plotcmd,GNUPLOTPROGRAM);
1.107 brouard 5654: #ifndef UNIX
1.108 lievre 5655: strcat(plotcmd,".exe");
5656: /* strcat(plotcmd,"\"");*/
1.107 brouard 5657: #endif
5658: if(stat(plotcmd,&info)){
5659: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5660: }
1.108 lievre 5661:
5662: #ifndef UNIX
5663: strcpy(plotcmd,"\"");
5664: #endif
5665: strcat(plotcmd,pathimach);
5666: strcat(plotcmd,GNUPLOTPROGRAM);
5667: #ifndef UNIX
5668: strcat(plotcmd,".exe");
5669: strcat(plotcmd,"\"");
5670: #endif
1.59 brouard 5671: strcat(plotcmd," ");
5672: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5673: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.107 brouard 5674:
1.91 brouard 5675: if((outcmd=system(plotcmd)) != 0){
1.108 lievre 5676: printf("\n Problem with gnuplot\n");
1.91 brouard 5677: }
1.75 brouard 5678: printf(" Wait...");
1.53 brouard 5679: while (z[0] != 'q') {
5680: /* chdir(path); */
1.91 brouard 5681: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5682: scanf("%s",z);
1.91 brouard 5683: /* if (z[0] == 'c') system("./imach"); */
1.99 brouard 5684: if (z[0] == 'e') {
5685: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5686: system(optionfilehtm);
5687: }
1.53 brouard 5688: else if (z[0] == 'g') system(plotcmd);
5689: else if (z[0] == 'q') exit(0);
5690: }
1.91 brouard 5691: end:
5692: while (z[0] != 'q') {
5693: printf("\nType q for exiting: ");
5694: scanf("%s",z);
5695: }
1.53 brouard 5696: }
1.88 brouard 5697:
1.53 brouard 5698:
5699:
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