Annotation of imach/src/imach.c, revision 1.115
1.115 ! brouard 1: /* $Id: imach.c,v 1.114 2006/02/26 12:57:58 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.115 ! brouard 4: Revision 1.114 2006/02/26 12:57:58 brouard
! 5: (Module): Some improvements in processing parameter
! 6: filename with strsep.
! 7:
1.114 brouard 8: Revision 1.113 2006/02/24 14:20:24 brouard
9: (Module): Memory leaks checks with valgrind and:
10: datafile was not closed, some imatrix were not freed and on matrix
11: allocation too.
12:
1.113 brouard 13: Revision 1.112 2006/01/30 09:55:26 brouard
14: (Module): Back to gnuplot.exe instead of wgnuplot.exe
15:
1.112 brouard 16: Revision 1.111 2006/01/25 20:38:18 brouard
17: (Module): Lots of cleaning and bugs added (Gompertz)
18: (Module): Comments can be added in data file. Missing date values
19: can be a simple dot '.'.
20:
1.111 brouard 21: Revision 1.110 2006/01/25 00:51:50 brouard
22: (Module): Lots of cleaning and bugs added (Gompertz)
23:
1.110 brouard 24: Revision 1.109 2006/01/24 19:37:15 brouard
25: (Module): Comments (lines starting with a #) are allowed in data.
26:
1.109 brouard 27: Revision 1.108 2006/01/19 18:05:42 lievre
28: Gnuplot problem appeared...
29: To be fixed
30:
1.108 lievre 31: Revision 1.107 2006/01/19 16:20:37 brouard
32: Test existence of gnuplot in imach path
33:
1.107 brouard 34: Revision 1.106 2006/01/19 13:24:36 brouard
35: Some cleaning and links added in html output
36:
1.106 brouard 37: Revision 1.105 2006/01/05 20:23:19 lievre
38: *** empty log message ***
39:
1.105 lievre 40: Revision 1.104 2005/09/30 16:11:43 lievre
41: (Module): sump fixed, loop imx fixed, and simplifications.
42: (Module): If the status is missing at the last wave but we know
43: that the person is alive, then we can code his/her status as -2
44: (instead of missing=-1 in earlier versions) and his/her
45: contributions to the likelihood is 1 - Prob of dying from last
46: health status (= 1-p13= p11+p12 in the easiest case of somebody in
47: the healthy state at last known wave). Version is 0.98
48:
1.104 lievre 49: Revision 1.103 2005/09/30 15:54:49 lievre
50: (Module): sump fixed, loop imx fixed, and simplifications.
51:
1.103 lievre 52: Revision 1.102 2004/09/15 17:31:30 brouard
53: Add the possibility to read data file including tab characters.
54:
1.102 brouard 55: Revision 1.101 2004/09/15 10:38:38 brouard
56: Fix on curr_time
57:
1.101 brouard 58: Revision 1.100 2004/07/12 18:29:06 brouard
59: Add version for Mac OS X. Just define UNIX in Makefile
60:
1.100 brouard 61: Revision 1.99 2004/06/05 08:57:40 brouard
62: *** empty log message ***
63:
1.99 brouard 64: Revision 1.98 2004/05/16 15:05:56 brouard
65: New version 0.97 . First attempt to estimate force of mortality
66: directly from the data i.e. without the need of knowing the health
67: state at each age, but using a Gompertz model: log u =a + b*age .
68: This is the basic analysis of mortality and should be done before any
69: other analysis, in order to test if the mortality estimated from the
70: cross-longitudinal survey is different from the mortality estimated
71: from other sources like vital statistic data.
72:
73: The same imach parameter file can be used but the option for mle should be -3.
74:
75: Agnès, who wrote this part of the code, tried to keep most of the
76: former routines in order to include the new code within the former code.
77:
78: The output is very simple: only an estimate of the intercept and of
79: the slope with 95% confident intervals.
80:
81: Current limitations:
82: A) Even if you enter covariates, i.e. with the
83: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
84: B) There is no computation of Life Expectancy nor Life Table.
85:
1.98 brouard 86: Revision 1.97 2004/02/20 13:25:42 lievre
87: Version 0.96d. Population forecasting command line is (temporarily)
88: suppressed.
89:
1.97 lievre 90: Revision 1.96 2003/07/15 15:38:55 brouard
91: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
92: rewritten within the same printf. Workaround: many printfs.
93:
1.96 brouard 94: Revision 1.95 2003/07/08 07:54:34 brouard
95: * imach.c (Repository):
96: (Repository): Using imachwizard code to output a more meaningful covariance
97: matrix (cov(a12,c31) instead of numbers.
98:
1.95 brouard 99: Revision 1.94 2003/06/27 13:00:02 brouard
100: Just cleaning
101:
1.94 brouard 102: Revision 1.93 2003/06/25 16:33:55 brouard
103: (Module): On windows (cygwin) function asctime_r doesn't
104: exist so I changed back to asctime which exists.
105: (Module): Version 0.96b
106:
1.93 brouard 107: Revision 1.92 2003/06/25 16:30:45 brouard
108: (Module): On windows (cygwin) function asctime_r doesn't
109: exist so I changed back to asctime which exists.
110:
1.92 brouard 111: Revision 1.91 2003/06/25 15:30:29 brouard
112: * imach.c (Repository): Duplicated warning errors corrected.
113: (Repository): Elapsed time after each iteration is now output. It
114: helps to forecast when convergence will be reached. Elapsed time
115: is stamped in powell. We created a new html file for the graphs
116: concerning matrix of covariance. It has extension -cov.htm.
117:
1.91 brouard 118: Revision 1.90 2003/06/24 12:34:15 brouard
119: (Module): Some bugs corrected for windows. Also, when
120: mle=-1 a template is output in file "or"mypar.txt with the design
121: of the covariance matrix to be input.
122:
1.90 brouard 123: Revision 1.89 2003/06/24 12:30:52 brouard
124: (Module): Some bugs corrected for windows. Also, when
125: mle=-1 a template is output in file "or"mypar.txt with the design
126: of the covariance matrix to be input.
127:
1.89 brouard 128: Revision 1.88 2003/06/23 17:54:56 brouard
129: * 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.
130:
1.88 brouard 131: Revision 1.87 2003/06/18 12:26:01 brouard
132: Version 0.96
133:
1.87 brouard 134: Revision 1.86 2003/06/17 20:04:08 brouard
135: (Module): Change position of html and gnuplot routines and added
136: routine fileappend.
137:
1.86 brouard 138: Revision 1.85 2003/06/17 13:12:43 brouard
139: * imach.c (Repository): Check when date of death was earlier that
140: current date of interview. It may happen when the death was just
141: prior to the death. In this case, dh was negative and likelihood
142: was wrong (infinity). We still send an "Error" but patch by
143: assuming that the date of death was just one stepm after the
144: interview.
145: (Repository): Because some people have very long ID (first column)
146: we changed int to long in num[] and we added a new lvector for
147: memory allocation. But we also truncated to 8 characters (left
148: truncation)
149: (Repository): No more line truncation errors.
150:
1.85 brouard 151: Revision 1.84 2003/06/13 21:44:43 brouard
152: * imach.c (Repository): Replace "freqsummary" at a correct
153: place. It differs from routine "prevalence" which may be called
154: many times. Probs is memory consuming and must be used with
155: parcimony.
1.86 brouard 156: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 157:
1.84 brouard 158: Revision 1.83 2003/06/10 13:39:11 lievre
159: *** empty log message ***
160:
1.83 lievre 161: Revision 1.82 2003/06/05 15:57:20 brouard
162: Add log in imach.c and fullversion number is now printed.
163:
1.82 brouard 164: */
165: /*
1.53 brouard 166: Interpolated Markov Chain
167:
168: Short summary of the programme:
169:
170: This program computes Healthy Life Expectancies from
171: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
172: first survey ("cross") where individuals from different ages are
173: interviewed on their health status or degree of disability (in the
174: case of a health survey which is our main interest) -2- at least a
175: second wave of interviews ("longitudinal") which measure each change
176: (if any) in individual health status. Health expectancies are
177: computed from the time spent in each health state according to a
178: model. More health states you consider, more time is necessary to reach the
179: Maximum Likelihood of the parameters involved in the model. The
180: simplest model is the multinomial logistic model where pij is the
181: probability to be observed in state j at the second wave
182: conditional to be observed in state i at the first wave. Therefore
183: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
184: 'age' is age and 'sex' is a covariate. If you want to have a more
185: complex model than "constant and age", you should modify the program
186: where the markup *Covariates have to be included here again* invites
187: you to do it. More covariates you add, slower the
188: convergence.
189:
190: The advantage of this computer programme, compared to a simple
191: multinomial logistic model, is clear when the delay between waves is not
192: identical for each individual. Also, if a individual missed an
193: intermediate interview, the information is lost, but taken into
194: account using an interpolation or extrapolation.
195:
196: hPijx is the probability to be observed in state i at age x+h
197: conditional to the observed state i at age x. The delay 'h' can be
198: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 199: states. This elementary transition (by month, quarter,
200: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 201: matrix is simply the matrix product of nh*stepm elementary matrices
202: and the contribution of each individual to the likelihood is simply
203: hPijx.
204:
205: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 206: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 207:
208: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
209: Institut national d'études démographiques, Paris.
210: This software have been partly granted by Euro-REVES, a concerted action
211: from the European Union.
212: It is copyrighted identically to a GNU software product, ie programme and
213: software can be distributed freely for non commercial use. Latest version
214: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 215:
216: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
217: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
218:
1.53 brouard 219: **********************************************************************/
1.74 brouard 220: /*
221: main
222: read parameterfile
223: read datafile
224: concatwav
1.84 brouard 225: freqsummary
1.74 brouard 226: if (mle >= 1)
227: mlikeli
228: print results files
229: if mle==1
230: computes hessian
231: read end of parameter file: agemin, agemax, bage, fage, estepm
232: begin-prev-date,...
233: open gnuplot file
234: open html file
235: stable prevalence
236: for age prevalim()
237: h Pij x
238: variance of p varprob
239: forecasting if prevfcast==1 prevforecast call prevalence()
240: health expectancies
241: Variance-covariance of DFLE
242: prevalence()
243: movingaverage()
244: varevsij()
245: if popbased==1 varevsij(,popbased)
246: total life expectancies
247: Variance of stable prevalence
248: end
249: */
250:
251:
252:
1.53 brouard 253:
254: #include <math.h>
255: #include <stdio.h>
256: #include <stdlib.h>
1.106 brouard 257: #include <string.h>
1.53 brouard 258: #include <unistd.h>
259:
1.109 brouard 260: #include <limits.h>
1.107 brouard 261: #include <sys/types.h>
262: #include <sys/stat.h>
263: #include <errno.h>
264: extern int errno;
265:
1.99 brouard 266: /* #include <sys/time.h> */
1.86 brouard 267: #include <time.h>
268: #include "timeval.h"
269:
1.95 brouard 270: /* #include <libintl.h> */
271: /* #define _(String) gettext (String) */
272:
1.53 brouard 273: #define MAXLINE 256
1.108 lievre 274:
1.53 brouard 275: #define GNUPLOTPROGRAM "gnuplot"
276: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 277: #define FILENAMELENGTH 132
1.108 lievre 278:
1.53 brouard 279: #define GLOCK_ERROR_NOPATH -1 /* empty path */
280: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
281:
282: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
283: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
284:
285: #define NINTERVMAX 8
286: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
287: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
288: #define NCOVMAX 8 /* Maximum number of covariates */
289: #define MAXN 20000
290: #define YEARM 12. /* Number of months per year */
291: #define AGESUP 130
292: #define AGEBASE 40
1.98 brouard 293: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.100 brouard 294: #ifdef UNIX
1.85 brouard 295: #define DIRSEPARATOR '/'
1.107 brouard 296: #define CHARSEPARATOR "/"
1.85 brouard 297: #define ODIRSEPARATOR '\\'
298: #else
1.53 brouard 299: #define DIRSEPARATOR '\\'
1.107 brouard 300: #define CHARSEPARATOR "\\"
1.53 brouard 301: #define ODIRSEPARATOR '/'
302: #endif
303:
1.115 ! brouard 304: /* $Id: imach.c,v 1.114 2006/02/26 12:57:58 brouard Exp $ */
1.81 brouard 305: /* $State: Exp $ */
1.80 brouard 306:
1.115 ! brouard 307: char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
! 308: char fullversion[]="$Revision: 1.114 $ $Date: 2006/02/26 12:57:58 $";
1.91 brouard 309: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 310: int nvar;
311: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
312: int npar=NPARMAX;
313: int nlstate=2; /* Number of live states */
314: int ndeath=1; /* Number of dead states */
315: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
316: int popbased=0;
317:
318: int *wav; /* Number of waves for this individuual 0 is possible */
319: int maxwav; /* Maxim number of waves */
320: int jmin, jmax; /* min, max spacing between 2 waves */
1.110 brouard 321: int ijmin, ijmax; /* Individuals having jmin and jmax */
1.87 brouard 322: int gipmx, gsw; /* Global variables on the number of contributions
323: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 324: int mle, weightopt;
325: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
326: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 327: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
328: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 329: double jmean; /* Mean space between 2 waves */
330: double **oldm, **newm, **savm; /* Working pointers to matrices */
331: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
332: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 333: FILE *ficlog, *ficrespow;
1.85 brouard 334: int globpr; /* Global variable for printing or not */
335: double fretone; /* Only one call to likelihood */
336: long ipmx; /* Number of contributions */
337: double sw; /* Sum of weights */
1.98 brouard 338: char filerespow[FILENAMELENGTH];
1.85 brouard 339: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
340: FILE *ficresilk;
1.53 brouard 341: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
342: FILE *ficresprobmorprev;
1.91 brouard 343: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 344: FILE *ficreseij;
345: char filerese[FILENAMELENGTH];
346: FILE *ficresvij;
347: char fileresv[FILENAMELENGTH];
348: FILE *ficresvpl;
349: char fileresvpl[FILENAMELENGTH];
350: char title[MAXLINE];
351: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
1.111 brouard 352: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1.96 brouard 353: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 354: char command[FILENAMELENGTH];
355: int outcmd=0;
1.53 brouard 356:
357: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 358:
1.53 brouard 359: char filelog[FILENAMELENGTH]; /* Log file */
360: char filerest[FILENAMELENGTH];
361: char fileregp[FILENAMELENGTH];
362: char popfile[FILENAMELENGTH];
363:
1.91 brouard 364: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
365:
366: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
367: struct timezone tzp;
368: extern int gettimeofday();
369: struct tm tmg, tm, tmf, *gmtime(), *localtime();
370: long time_value;
371: extern long time();
372: char strcurr[80], strfor[80];
1.53 brouard 373:
1.109 brouard 374: char *endptr;
375: long lval;
376:
1.53 brouard 377: #define NR_END 1
378: #define FREE_ARG char*
379: #define FTOL 1.0e-10
380:
381: #define NRANSI
382: #define ITMAX 200
383:
384: #define TOL 2.0e-4
385:
386: #define CGOLD 0.3819660
387: #define ZEPS 1.0e-10
388: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
389:
390: #define GOLD 1.618034
391: #define GLIMIT 100.0
392: #define TINY 1.0e-20
393:
394: static double maxarg1,maxarg2;
395: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
396: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
397:
398: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
399: #define rint(a) floor(a+0.5)
400:
401: static double sqrarg;
402: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
403: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 brouard 404: int agegomp= AGEGOMP;
1.53 brouard 405:
406: int imx;
1.98 brouard 407: int stepm=1;
1.53 brouard 408: /* Stepm, step in month: minimum step interpolation*/
409:
410: int estepm;
411: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
412:
413: int m,nb;
1.85 brouard 414: long *num;
1.98 brouard 415: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 416: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 417: double **pmmij, ***probs;
1.98 brouard 418: double *ageexmed,*agecens;
1.53 brouard 419: double dateintmean=0;
420:
421: double *weight;
422: int **s; /* Status */
423: double *agedc, **covar, idx;
424: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.105 lievre 425: double *lsurv, *lpop, *tpop;
1.53 brouard 426:
427: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
428: double ftolhess; /* Tolerance for computing hessian */
429:
430: /**************** split *************************/
431: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
432: {
1.107 brouard 433: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1.99 brouard 434: the name of the file (name), its extension only (ext) and its first part of the name (finame)
435: */
1.59 brouard 436: char *ss; /* pointer */
437: int l1, l2; /* length counters */
1.53 brouard 438:
1.59 brouard 439: l1 = strlen(path ); /* length of path */
440: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
441: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1.107 brouard 442: if ( ss == NULL ) { /* no directory, so determine current directory */
443: strcpy( name, path ); /* we got the fullname name because no directory */
1.59 brouard 444: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
445: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 446: /* get current working directory */
447: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 448: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
449: return( GLOCK_ERROR_GETCWD );
450: }
1.107 brouard 451: /* got dirc from getcwd*/
452: printf(" DIRC = %s \n",dirc);
1.59 brouard 453: } else { /* strip direcotry from path */
454: ss++; /* after this, the filename */
455: l2 = strlen( ss ); /* length of filename */
456: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
457: strcpy( name, ss ); /* save file name */
458: strncpy( dirc, path, l1 - l2 ); /* now the directory */
459: dirc[l1-l2] = 0; /* add zero */
1.107 brouard 460: printf(" DIRC2 = %s \n",dirc);
1.59 brouard 461: }
1.107 brouard 462: /* We add a separator at the end of dirc if not exists */
1.59 brouard 463: l1 = strlen( dirc ); /* length of directory */
1.107 brouard 464: if( dirc[l1-1] != DIRSEPARATOR ){
465: dirc[l1] = DIRSEPARATOR;
466: dirc[l1+1] = 0;
467: printf(" DIRC3 = %s \n",dirc);
468: }
1.59 brouard 469: ss = strrchr( name, '.' ); /* find last / */
1.99 brouard 470: if (ss >0){
471: ss++;
472: strcpy(ext,ss); /* save extension */
473: l1= strlen( name);
474: l2= strlen(ss)+1;
475: strncpy( finame, name, l1-l2);
476: finame[l1-l2]= 0;
477: }
1.107 brouard 478:
1.59 brouard 479: return( 0 ); /* we're done */
1.53 brouard 480: }
481:
482:
483: /******************************************/
484:
1.89 brouard 485: void replace_back_to_slash(char *s, char*t)
1.53 brouard 486: {
487: int i;
1.89 brouard 488: int lg=0;
1.53 brouard 489: i=0;
490: lg=strlen(t);
491: for(i=0; i<= lg; i++) {
492: (s[i] = t[i]);
493: if (t[i]== '\\') s[i]='/';
494: }
495: }
496:
497: int nbocc(char *s, char occ)
498: {
499: int i,j=0;
500: int lg=20;
501: i=0;
502: lg=strlen(s);
503: for(i=0; i<= lg; i++) {
504: if (s[i] == occ ) j++;
505: }
506: return j;
507: }
508:
509: void cutv(char *u,char *v, char*t, char occ)
510: {
1.102 brouard 511: /* cuts string t into u and v where u ends before first occurence of char 'occ'
512: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
1.53 brouard 513: gives u="abcedf" and v="ghi2j" */
514: int i,lg,j,p=0;
515: i=0;
516: for(j=0; j<=strlen(t)-1; j++) {
517: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
518: }
519:
520: lg=strlen(t);
521: for(j=0; j<p; j++) {
522: (u[j] = t[j]);
523: }
524: u[p]='\0';
525:
526: for(j=0; j<= lg; j++) {
527: if (j>=(p+1))(v[j-p-1] = t[j]);
528: }
529: }
530:
531: /********************** nrerror ********************/
532:
533: void nrerror(char error_text[])
534: {
535: fprintf(stderr,"ERREUR ...\n");
536: fprintf(stderr,"%s\n",error_text);
1.59 brouard 537: exit(EXIT_FAILURE);
1.53 brouard 538: }
539: /*********************** vector *******************/
540: double *vector(int nl, int nh)
541: {
542: double *v;
543: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
544: if (!v) nrerror("allocation failure in vector");
545: return v-nl+NR_END;
546: }
547:
548: /************************ free vector ******************/
549: void free_vector(double*v, int nl, int nh)
550: {
551: free((FREE_ARG)(v+nl-NR_END));
552: }
553:
554: /************************ivector *******************************/
1.85 brouard 555: int *ivector(long nl,long nh)
1.76 brouard 556: {
1.85 brouard 557: int *v;
558: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
559: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 560: return v-nl+NR_END;
561: }
562:
563: /******************free ivector **************************/
1.85 brouard 564: void free_ivector(int *v, long nl, long nh)
1.76 brouard 565: {
566: free((FREE_ARG)(v+nl-NR_END));
567: }
568:
1.85 brouard 569: /************************lvector *******************************/
570: long *lvector(long nl,long nh)
1.53 brouard 571: {
1.85 brouard 572: long *v;
573: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 574: if (!v) nrerror("allocation failure in ivector");
575: return v-nl+NR_END;
576: }
577:
1.85 brouard 578: /******************free lvector **************************/
579: void free_lvector(long *v, long nl, long nh)
1.53 brouard 580: {
581: free((FREE_ARG)(v+nl-NR_END));
582: }
583:
584: /******************* imatrix *******************************/
585: int **imatrix(long nrl, long nrh, long ncl, long nch)
586: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
587: {
588: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
589: int **m;
590:
591: /* allocate pointers to rows */
592: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
593: if (!m) nrerror("allocation failure 1 in matrix()");
594: m += NR_END;
595: m -= nrl;
596:
597:
598: /* allocate rows and set pointers to them */
599: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
600: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
601: m[nrl] += NR_END;
602: m[nrl] -= ncl;
603:
604: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
605:
606: /* return pointer to array of pointers to rows */
607: return m;
608: }
609:
610: /****************** free_imatrix *************************/
611: void free_imatrix(m,nrl,nrh,ncl,nch)
612: int **m;
613: long nch,ncl,nrh,nrl;
614: /* free an int matrix allocated by imatrix() */
615: {
616: free((FREE_ARG) (m[nrl]+ncl-NR_END));
617: free((FREE_ARG) (m+nrl-NR_END));
618: }
619:
620: /******************* matrix *******************************/
621: double **matrix(long nrl, long nrh, long ncl, long nch)
622: {
623: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
624: double **m;
625:
626: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
627: if (!m) nrerror("allocation failure 1 in matrix()");
628: m += NR_END;
629: m -= nrl;
630:
631: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
632: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
633: m[nrl] += NR_END;
634: m[nrl] -= ncl;
635:
636: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
637: return m;
1.85 brouard 638: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 639: */
1.53 brouard 640: }
641:
642: /*************************free matrix ************************/
643: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
644: {
645: free((FREE_ARG)(m[nrl]+ncl-NR_END));
646: free((FREE_ARG)(m+nrl-NR_END));
647: }
648:
649: /******************* ma3x *******************************/
650: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
651: {
652: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
653: double ***m;
654:
655: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
656: if (!m) nrerror("allocation failure 1 in matrix()");
657: m += NR_END;
658: m -= nrl;
659:
660: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
661: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
662: m[nrl] += NR_END;
663: m[nrl] -= ncl;
664:
665: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
666:
667: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
668: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
669: m[nrl][ncl] += NR_END;
670: m[nrl][ncl] -= nll;
671: for (j=ncl+1; j<=nch; j++)
672: m[nrl][j]=m[nrl][j-1]+nlay;
673:
674: for (i=nrl+1; i<=nrh; i++) {
675: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
676: for (j=ncl+1; j<=nch; j++)
677: m[i][j]=m[i][j-1]+nlay;
678: }
1.74 brouard 679: return m;
680: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
681: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
682: */
1.53 brouard 683: }
684:
685: /*************************free ma3x ************************/
686: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
687: {
688: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
689: free((FREE_ARG)(m[nrl]+ncl-NR_END));
690: free((FREE_ARG)(m+nrl-NR_END));
691: }
692:
1.94 brouard 693: /*************** function subdirf ***********/
694: char *subdirf(char fileres[])
695: {
696: /* Caution optionfilefiname is hidden */
697: strcpy(tmpout,optionfilefiname);
698: strcat(tmpout,"/"); /* Add to the right */
699: strcat(tmpout,fileres);
700: return tmpout;
701: }
702:
703: /*************** function subdirf2 ***********/
704: char *subdirf2(char fileres[], char *preop)
705: {
706:
707: /* Caution optionfilefiname is hidden */
708: strcpy(tmpout,optionfilefiname);
709: strcat(tmpout,"/");
710: strcat(tmpout,preop);
711: strcat(tmpout,fileres);
712: return tmpout;
713: }
714:
715: /*************** function subdirf3 ***********/
716: char *subdirf3(char fileres[], char *preop, char *preop2)
717: {
718:
719: /* Caution optionfilefiname is hidden */
720: strcpy(tmpout,optionfilefiname);
721: strcat(tmpout,"/");
722: strcat(tmpout,preop);
723: strcat(tmpout,preop2);
724: strcat(tmpout,fileres);
725: return tmpout;
726: }
727:
1.53 brouard 728: /***************** f1dim *************************/
729: extern int ncom;
730: extern double *pcom,*xicom;
731: extern double (*nrfunc)(double []);
732:
733: double f1dim(double x)
734: {
735: int j;
736: double f;
737: double *xt;
738:
739: xt=vector(1,ncom);
740: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
741: f=(*nrfunc)(xt);
742: free_vector(xt,1,ncom);
743: return f;
744: }
745:
746: /*****************brent *************************/
747: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
748: {
749: int iter;
750: double a,b,d,etemp;
751: double fu,fv,fw,fx;
752: double ftemp;
753: double p,q,r,tol1,tol2,u,v,w,x,xm;
754: double e=0.0;
755:
756: a=(ax < cx ? ax : cx);
757: b=(ax > cx ? ax : cx);
758: x=w=v=bx;
759: fw=fv=fx=(*f)(x);
760: for (iter=1;iter<=ITMAX;iter++) {
761: xm=0.5*(a+b);
762: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
763: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
764: printf(".");fflush(stdout);
765: fprintf(ficlog,".");fflush(ficlog);
766: #ifdef DEBUG
767: 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);
768: 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);
769: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
770: #endif
771: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
772: *xmin=x;
773: return fx;
774: }
775: ftemp=fu;
776: if (fabs(e) > tol1) {
777: r=(x-w)*(fx-fv);
778: q=(x-v)*(fx-fw);
779: p=(x-v)*q-(x-w)*r;
780: q=2.0*(q-r);
781: if (q > 0.0) p = -p;
782: q=fabs(q);
783: etemp=e;
784: e=d;
785: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
786: d=CGOLD*(e=(x >= xm ? a-x : b-x));
787: else {
788: d=p/q;
789: u=x+d;
790: if (u-a < tol2 || b-u < tol2)
791: d=SIGN(tol1,xm-x);
792: }
793: } else {
794: d=CGOLD*(e=(x >= xm ? a-x : b-x));
795: }
796: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
797: fu=(*f)(u);
798: if (fu <= fx) {
799: if (u >= x) a=x; else b=x;
800: SHFT(v,w,x,u)
801: SHFT(fv,fw,fx,fu)
802: } else {
803: if (u < x) a=u; else b=u;
804: if (fu <= fw || w == x) {
805: v=w;
806: w=u;
807: fv=fw;
808: fw=fu;
809: } else if (fu <= fv || v == x || v == w) {
810: v=u;
811: fv=fu;
812: }
813: }
814: }
815: nrerror("Too many iterations in brent");
816: *xmin=x;
817: return fx;
818: }
819:
820: /****************** mnbrak ***********************/
821:
822: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
823: double (*func)(double))
824: {
825: double ulim,u,r,q, dum;
826: double fu;
827:
828: *fa=(*func)(*ax);
829: *fb=(*func)(*bx);
830: if (*fb > *fa) {
831: SHFT(dum,*ax,*bx,dum)
832: SHFT(dum,*fb,*fa,dum)
833: }
834: *cx=(*bx)+GOLD*(*bx-*ax);
835: *fc=(*func)(*cx);
836: while (*fb > *fc) {
837: r=(*bx-*ax)*(*fb-*fc);
838: q=(*bx-*cx)*(*fb-*fa);
839: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
840: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
841: ulim=(*bx)+GLIMIT*(*cx-*bx);
842: if ((*bx-u)*(u-*cx) > 0.0) {
843: fu=(*func)(u);
844: } else if ((*cx-u)*(u-ulim) > 0.0) {
845: fu=(*func)(u);
846: if (fu < *fc) {
847: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
848: SHFT(*fb,*fc,fu,(*func)(u))
849: }
850: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
851: u=ulim;
852: fu=(*func)(u);
853: } else {
854: u=(*cx)+GOLD*(*cx-*bx);
855: fu=(*func)(u);
856: }
857: SHFT(*ax,*bx,*cx,u)
858: SHFT(*fa,*fb,*fc,fu)
859: }
860: }
861:
862: /*************** linmin ************************/
863:
864: int ncom;
865: double *pcom,*xicom;
866: double (*nrfunc)(double []);
867:
868: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
869: {
870: double brent(double ax, double bx, double cx,
871: double (*f)(double), double tol, double *xmin);
872: double f1dim(double x);
873: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
874: double *fc, double (*func)(double));
875: int j;
876: double xx,xmin,bx,ax;
877: double fx,fb,fa;
878:
879: ncom=n;
880: pcom=vector(1,n);
881: xicom=vector(1,n);
882: nrfunc=func;
883: for (j=1;j<=n;j++) {
884: pcom[j]=p[j];
885: xicom[j]=xi[j];
886: }
887: ax=0.0;
888: xx=1.0;
889: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
890: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
891: #ifdef DEBUG
892: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
893: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
894: #endif
895: for (j=1;j<=n;j++) {
896: xi[j] *= xmin;
897: p[j] += xi[j];
898: }
899: free_vector(xicom,1,n);
900: free_vector(pcom,1,n);
901: }
902:
1.91 brouard 903: char *asc_diff_time(long time_sec, char ascdiff[])
904: {
905: long sec_left, days, hours, minutes;
906: days = (time_sec) / (60*60*24);
907: sec_left = (time_sec) % (60*60*24);
908: hours = (sec_left) / (60*60) ;
909: sec_left = (sec_left) %(60*60);
910: minutes = (sec_left) /60;
911: sec_left = (sec_left) % (60);
912: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
913: return ascdiff;
914: }
915:
1.53 brouard 916: /*************** powell ************************/
917: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
918: double (*func)(double []))
919: {
920: void linmin(double p[], double xi[], int n, double *fret,
921: double (*func)(double []));
922: int i,ibig,j;
923: double del,t,*pt,*ptt,*xit;
924: double fp,fptt;
925: double *xits;
1.91 brouard 926: int niterf, itmp;
927:
1.53 brouard 928: pt=vector(1,n);
929: ptt=vector(1,n);
930: xit=vector(1,n);
931: xits=vector(1,n);
932: *fret=(*func)(p);
933: for (j=1;j<=n;j++) pt[j]=p[j];
934: for (*iter=1;;++(*iter)) {
935: fp=(*fret);
936: ibig=0;
937: del=0.0;
1.91 brouard 938: last_time=curr_time;
939: (void) gettimeofday(&curr_time,&tzp);
940: 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 941: /* 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 942: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.98 brouard 943: */
944: for (i=1;i<=n;i++) {
1.53 brouard 945: printf(" %d %.12f",i, p[i]);
1.76 brouard 946: fprintf(ficlog," %d %.12lf",i, p[i]);
947: fprintf(ficrespow," %.12lf", p[i]);
948: }
1.53 brouard 949: printf("\n");
950: fprintf(ficlog,"\n");
1.91 brouard 951: fprintf(ficrespow,"\n");fflush(ficrespow);
952: if(*iter <=3){
953: tm = *localtime(&curr_time.tv_sec);
1.101 brouard 954: strcpy(strcurr,asctime(&tm));
1.92 brouard 955: /* asctime_r(&tm,strcurr); */
1.101 brouard 956: forecast_time=curr_time;
1.91 brouard 957: itmp = strlen(strcurr);
1.101 brouard 958: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.91 brouard 959: strcurr[itmp-1]='\0';
960: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
961: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
962: for(niterf=10;niterf<=30;niterf+=10){
963: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
964: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 965: /* asctime_r(&tmf,strfor); */
966: strcpy(strfor,asctime(&tmf));
1.91 brouard 967: itmp = strlen(strfor);
968: if(strfor[itmp-1]=='\n')
969: strfor[itmp-1]='\0';
1.101 brouard 970: 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);
971: 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 972: }
973: }
1.53 brouard 974: for (i=1;i<=n;i++) {
975: for (j=1;j<=n;j++) xit[j]=xi[j][i];
976: fptt=(*fret);
977: #ifdef DEBUG
978: printf("fret=%lf \n",*fret);
979: fprintf(ficlog,"fret=%lf \n",*fret);
980: #endif
981: printf("%d",i);fflush(stdout);
982: fprintf(ficlog,"%d",i);fflush(ficlog);
983: linmin(p,xit,n,fret,func);
984: if (fabs(fptt-(*fret)) > del) {
985: del=fabs(fptt-(*fret));
986: ibig=i;
987: }
988: #ifdef DEBUG
989: printf("%d %.12e",i,(*fret));
990: fprintf(ficlog,"%d %.12e",i,(*fret));
991: for (j=1;j<=n;j++) {
992: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
993: printf(" x(%d)=%.12e",j,xit[j]);
994: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
995: }
996: for(j=1;j<=n;j++) {
997: printf(" p=%.12e",p[j]);
998: fprintf(ficlog," p=%.12e",p[j]);
999: }
1000: printf("\n");
1001: fprintf(ficlog,"\n");
1002: #endif
1003: }
1004: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1005: #ifdef DEBUG
1006: int k[2],l;
1007: k[0]=1;
1008: k[1]=-1;
1009: printf("Max: %.12e",(*func)(p));
1010: fprintf(ficlog,"Max: %.12e",(*func)(p));
1011: for (j=1;j<=n;j++) {
1012: printf(" %.12e",p[j]);
1013: fprintf(ficlog," %.12e",p[j]);
1014: }
1015: printf("\n");
1016: fprintf(ficlog,"\n");
1017: for(l=0;l<=1;l++) {
1018: for (j=1;j<=n;j++) {
1019: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1020: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1021: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1022: }
1023: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1024: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1025: }
1026: #endif
1027:
1028:
1029: free_vector(xit,1,n);
1030: free_vector(xits,1,n);
1031: free_vector(ptt,1,n);
1032: free_vector(pt,1,n);
1033: return;
1034: }
1035: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1036: for (j=1;j<=n;j++) {
1037: ptt[j]=2.0*p[j]-pt[j];
1038: xit[j]=p[j]-pt[j];
1039: pt[j]=p[j];
1040: }
1041: fptt=(*func)(ptt);
1042: if (fptt < fp) {
1043: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1044: if (t < 0.0) {
1045: linmin(p,xit,n,fret,func);
1046: for (j=1;j<=n;j++) {
1047: xi[j][ibig]=xi[j][n];
1048: xi[j][n]=xit[j];
1049: }
1050: #ifdef DEBUG
1051: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1052: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1053: for(j=1;j<=n;j++){
1054: printf(" %.12e",xit[j]);
1055: fprintf(ficlog," %.12e",xit[j]);
1056: }
1057: printf("\n");
1058: fprintf(ficlog,"\n");
1059: #endif
1.54 brouard 1060: }
1.53 brouard 1061: }
1062: }
1063: }
1064:
1.54 brouard 1065: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 1066:
1067: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1068: {
1069: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1070: matrix by transitions matrix until convergence is reached */
1071:
1072: int i, ii,j,k;
1073: double min, max, maxmin, maxmax,sumnew=0.;
1074: double **matprod2();
1075: double **out, cov[NCOVMAX], **pmij();
1076: double **newm;
1077: double agefin, delaymax=50 ; /* Max number of years to converge */
1078:
1079: for (ii=1;ii<=nlstate+ndeath;ii++)
1080: for (j=1;j<=nlstate+ndeath;j++){
1081: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1082: }
1083:
1084: cov[1]=1.;
1085:
1086: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1087: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1088: newm=savm;
1089: /* Covariates have to be included here again */
1090: cov[2]=agefin;
1091:
1092: for (k=1; k<=cptcovn;k++) {
1093: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1094: /* 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]]);*/
1095: }
1096: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1097: for (k=1; k<=cptcovprod;k++)
1098: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1099:
1100: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1101: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1102: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1103: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1104:
1105: savm=oldm;
1106: oldm=newm;
1107: maxmax=0.;
1108: for(j=1;j<=nlstate;j++){
1109: min=1.;
1110: max=0.;
1111: for(i=1; i<=nlstate; i++) {
1112: sumnew=0;
1113: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1114: prlim[i][j]= newm[i][j]/(1-sumnew);
1115: max=FMAX(max,prlim[i][j]);
1116: min=FMIN(min,prlim[i][j]);
1117: }
1118: maxmin=max-min;
1119: maxmax=FMAX(maxmax,maxmin);
1120: }
1121: if(maxmax < ftolpl){
1122: return prlim;
1123: }
1124: }
1125: }
1126:
1127: /*************** transition probabilities ***************/
1128:
1129: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1130: {
1131: double s1, s2;
1132: /*double t34;*/
1133: int i,j,j1, nc, ii, jj;
1134:
1135: for(i=1; i<= nlstate; i++){
1.99 brouard 1136: for(j=1; j<i;j++){
1137: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1138: /*s2 += param[i][j][nc]*cov[nc];*/
1139: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1140: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1141: }
1142: ps[i][j]=s2;
1143: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1144: }
1145: for(j=i+1; j<=nlstate+ndeath;j++){
1146: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1147: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1148: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1149: }
1150: ps[i][j]=s2;
1.53 brouard 1151: }
1152: }
1153: /*ps[3][2]=1;*/
1.99 brouard 1154:
1155: for(i=1; i<= nlstate; i++){
1156: s1=0;
1157: for(j=1; j<i; j++)
1158: s1+=exp(ps[i][j]);
1159: for(j=i+1; j<=nlstate+ndeath; j++)
1160: s1+=exp(ps[i][j]);
1161: ps[i][i]=1./(s1+1.);
1162: for(j=1; j<i; j++)
1163: ps[i][j]= exp(ps[i][j])*ps[i][i];
1164: for(j=i+1; j<=nlstate+ndeath; j++)
1165: ps[i][j]= exp(ps[i][j])*ps[i][i];
1166: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1167: } /* end i */
1168:
1169: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1170: for(jj=1; jj<= nlstate+ndeath; jj++){
1171: ps[ii][jj]=0;
1172: ps[ii][ii]=1;
1173: }
1.53 brouard 1174: }
1.99 brouard 1175:
1.53 brouard 1176:
1.99 brouard 1177: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1178: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1179: /* printf("ddd %lf ",ps[ii][jj]); */
1180: /* } */
1181: /* printf("\n "); */
1182: /* } */
1183: /* printf("\n ");printf("%lf ",cov[2]); */
1184: /*
1185: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1186: goto end;*/
1.53 brouard 1187: return ps;
1188: }
1189:
1190: /**************** Product of 2 matrices ******************/
1191:
1192: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1193: {
1194: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1195: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1196: /* in, b, out are matrice of pointers which should have been initialized
1197: before: only the contents of out is modified. The function returns
1198: a pointer to pointers identical to out */
1199: long i, j, k;
1200: for(i=nrl; i<= nrh; i++)
1201: for(k=ncolol; k<=ncoloh; k++)
1202: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1203: out[i][k] +=in[i][j]*b[j][k];
1204:
1205: return out;
1206: }
1207:
1208:
1209: /************* Higher Matrix Product ***************/
1210:
1211: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1212: {
1.66 brouard 1213: /* Computes the transition matrix starting at age 'age' over
1214: 'nhstepm*hstepm*stepm' months (i.e. until
1215: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1216: nhstepm*hstepm matrices.
1.53 brouard 1217: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1218: (typically every 2 years instead of every month which is too big
1219: for the memory).
1.53 brouard 1220: Model is determined by parameters x and covariates have to be
1221: included manually here.
1222:
1223: */
1224:
1225: int i, j, d, h, k;
1226: double **out, cov[NCOVMAX];
1227: double **newm;
1228:
1229: /* Hstepm could be zero and should return the unit matrix */
1230: for (i=1;i<=nlstate+ndeath;i++)
1231: for (j=1;j<=nlstate+ndeath;j++){
1232: oldm[i][j]=(i==j ? 1.0 : 0.0);
1233: po[i][j][0]=(i==j ? 1.0 : 0.0);
1234: }
1235: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1236: for(h=1; h <=nhstepm; h++){
1237: for(d=1; d <=hstepm; d++){
1238: newm=savm;
1239: /* Covariates have to be included here again */
1240: cov[1]=1.;
1241: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1242: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1243: for (k=1; k<=cptcovage;k++)
1244: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1245: for (k=1; k<=cptcovprod;k++)
1246: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1247:
1248:
1249: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1250: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1251: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1252: pmij(pmmij,cov,ncovmodel,x,nlstate));
1253: savm=oldm;
1254: oldm=newm;
1255: }
1256: for(i=1; i<=nlstate+ndeath; i++)
1257: for(j=1;j<=nlstate+ndeath;j++) {
1258: po[i][j][h]=newm[i][j];
1259: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1260: */
1261: }
1262: } /* end h */
1263: return po;
1264: }
1265:
1266:
1267: /*************** log-likelihood *************/
1268: double func( double *x)
1269: {
1270: int i, ii, j, k, mi, d, kk;
1271: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1272: double **out;
1273: double sw; /* Sum of weights */
1274: double lli; /* Individual log likelihood */
1.59 brouard 1275: int s1, s2;
1.68 lievre 1276: double bbh, survp;
1.53 brouard 1277: long ipmx;
1278: /*extern weight */
1279: /* We are differentiating ll according to initial status */
1280: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1281: /*for(i=1;i<imx;i++)
1282: printf(" %d\n",s[4][i]);
1283: */
1284: cov[1]=1.;
1285:
1286: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1287:
1288: if(mle==1){
1289: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1290: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1291: for(mi=1; mi<= wav[i]-1; mi++){
1292: for (ii=1;ii<=nlstate+ndeath;ii++)
1293: for (j=1;j<=nlstate+ndeath;j++){
1294: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1295: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1296: }
1297: for(d=0; d<dh[mi][i]; d++){
1298: newm=savm;
1299: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1300: for (kk=1; kk<=cptcovage;kk++) {
1301: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1302: }
1303: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1304: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1305: savm=oldm;
1306: oldm=newm;
1307: } /* end mult */
1.53 brouard 1308:
1.61 brouard 1309: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1.101 brouard 1310: /* But now since version 0.9 we anticipate for bias at large stepm.
1.61 brouard 1311: * If stepm is larger than one month (smallest stepm) and if the exact delay
1312: * (in months) between two waves is not a multiple of stepm, we rounded to
1313: * the nearest (and in case of equal distance, to the lowest) interval but now
1314: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1.101 brouard 1315: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1.61 brouard 1316: * probability in order to take into account the bias as a fraction of the way
1.101 brouard 1317: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1.61 brouard 1318: * -stepm/2 to stepm/2 .
1319: * For stepm=1 the results are the same as for previous versions of Imach.
1320: * For stepm > 1 the results are less biased than in previous versions.
1321: */
1322: s1=s[mw[mi][i]][i];
1323: s2=s[mw[mi+1][i]][i];
1.64 lievre 1324: bbh=(double)bh[mi][i]/(double)stepm;
1.101 brouard 1325: /* bias bh is positive if real duration
1.64 lievre 1326: * is higher than the multiple of stepm and negative otherwise.
1327: */
1328: /* 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 1329: if( s2 > nlstate){
1.104 lievre 1330: /* i.e. if s2 is a death state and if the date of death is known
1331: then the contribution to the likelihood is the probability to
1332: die between last step unit time and current step unit time,
1333: which is also equal to probability to die before dh
1.101 brouard 1334: minus probability to die before dh-stepm .
1.71 brouard 1335: In version up to 0.92 likelihood was computed
1336: as if date of death was unknown. Death was treated as any other
1337: health state: the date of the interview describes the actual state
1338: and not the date of a change in health state. The former idea was
1339: to consider that at each interview the state was recorded
1340: (healthy, disable or death) and IMaCh was corrected; but when we
1341: introduced the exact date of death then we should have modified
1342: the contribution of an exact death to the likelihood. This new
1343: contribution is smaller and very dependent of the step unit
1344: stepm. It is no more the probability to die between last interview
1345: and month of death but the probability to survive from last
1346: interview up to one month before death multiplied by the
1347: probability to die within a month. Thanks to Chris
1348: Jackson for correcting this bug. Former versions increased
1349: mortality artificially. The bad side is that we add another loop
1350: which slows down the processing. The difference can be up to 10%
1351: lower mortality.
1352: */
1353: lli=log(out[s1][s2] - savm[s1][s2]);
1.104 lievre 1354:
1355:
1356: } else if (s2==-2) {
1357: for (j=1,survp=0. ; j<=nlstate; j++)
1358: survp += out[s1][j];
1359: lli= survp;
1360: }
1.105 lievre 1361:
1362: else if (s2==-4) {
1363: for (j=3,survp=0. ; j<=nlstate; j++)
1364: survp += out[s1][j];
1365: lli= survp;
1366: }
1367:
1368: else if (s2==-5) {
1369: for (j=1,survp=0. ; j<=2; j++)
1370: survp += out[s1][j];
1371: lli= survp;
1372: }
1.104 lievre 1373:
1374:
1375: else{
1.71 brouard 1376: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1377: /* 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 */
1378: }
1.64 lievre 1379: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1380: /*if(lli ==000.0)*/
1381: /*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 1382: ipmx +=1;
1.64 lievre 1383: sw += weight[i];
1384: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1385: } /* end of wave */
1386: } /* end of individual */
1387: } else if(mle==2){
1388: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1389: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1390: for(mi=1; mi<= wav[i]-1; mi++){
1391: for (ii=1;ii<=nlstate+ndeath;ii++)
1392: for (j=1;j<=nlstate+ndeath;j++){
1393: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1394: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1395: }
1396: for(d=0; d<=dh[mi][i]; d++){
1397: newm=savm;
1398: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1399: for (kk=1; kk<=cptcovage;kk++) {
1400: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1401: }
1402: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1403: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1404: savm=oldm;
1405: oldm=newm;
1406: } /* end mult */
1407:
1408: s1=s[mw[mi][i]][i];
1409: s2=s[mw[mi+1][i]][i];
1410: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1411: 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 1412: ipmx +=1;
1413: sw += weight[i];
1414: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1415: } /* end of wave */
1416: } /* end of individual */
1417: } else if(mle==3){ /* exponential inter-extrapolation */
1418: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1419: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1420: for(mi=1; mi<= wav[i]-1; mi++){
1421: for (ii=1;ii<=nlstate+ndeath;ii++)
1422: for (j=1;j<=nlstate+ndeath;j++){
1423: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1424: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1425: }
1426: for(d=0; d<dh[mi][i]; d++){
1427: newm=savm;
1428: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1429: for (kk=1; kk<=cptcovage;kk++) {
1430: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1431: }
1432: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1433: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1434: savm=oldm;
1435: oldm=newm;
1436: } /* end mult */
1437:
1438: s1=s[mw[mi][i]][i];
1439: s2=s[mw[mi+1][i]][i];
1440: bbh=(double)bh[mi][i]/(double)stepm;
1441: 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 1442: ipmx +=1;
1443: sw += weight[i];
1444: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1445: } /* end of wave */
1446: } /* end of individual */
1.84 brouard 1447: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1448: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1449: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1450: for(mi=1; mi<= wav[i]-1; mi++){
1451: for (ii=1;ii<=nlstate+ndeath;ii++)
1452: for (j=1;j<=nlstate+ndeath;j++){
1453: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1454: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1455: }
1456: for(d=0; d<dh[mi][i]; d++){
1457: newm=savm;
1458: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1459: for (kk=1; kk<=cptcovage;kk++) {
1460: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1461: }
1462:
1463: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1464: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1465: savm=oldm;
1466: oldm=newm;
1467: } /* end mult */
1468:
1.84 brouard 1469: s1=s[mw[mi][i]][i];
1470: s2=s[mw[mi+1][i]][i];
1471: if( s2 > nlstate){
1472: lli=log(out[s1][s2] - savm[s1][s2]);
1473: }else{
1474: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1475: }
1476: ipmx +=1;
1477: sw += weight[i];
1478: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1479: /* 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 1480: } /* end of wave */
1481: } /* end of individual */
1482: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1483: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1484: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1485: for(mi=1; mi<= wav[i]-1; mi++){
1486: for (ii=1;ii<=nlstate+ndeath;ii++)
1487: for (j=1;j<=nlstate+ndeath;j++){
1488: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1489: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1490: }
1491: for(d=0; d<dh[mi][i]; d++){
1492: newm=savm;
1493: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1494: for (kk=1; kk<=cptcovage;kk++) {
1495: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1496: }
1497:
1498: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1499: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1500: savm=oldm;
1501: oldm=newm;
1502: } /* end mult */
1503:
1504: s1=s[mw[mi][i]][i];
1505: s2=s[mw[mi+1][i]][i];
1.61 brouard 1506: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1507: ipmx +=1;
1508: sw += weight[i];
1509: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1510: /*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 1511: } /* end of wave */
1512: } /* end of individual */
1513: } /* End of if */
1.53 brouard 1514: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1515: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1516: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1517: return -l;
1518: }
1519:
1520: /*************** log-likelihood *************/
1521: double funcone( double *x)
1522: {
1.87 brouard 1523: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1524: int i, ii, j, k, mi, d, kk;
1525: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1526: double **out;
1527: double lli; /* Individual log likelihood */
1.87 brouard 1528: double llt;
1.85 brouard 1529: int s1, s2;
1530: double bbh, survp;
1531: /*extern weight */
1532: /* We are differentiating ll according to initial status */
1533: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1534: /*for(i=1;i<imx;i++)
1535: printf(" %d\n",s[4][i]);
1536: */
1537: cov[1]=1.;
1538:
1539: for(k=1; k<=nlstate; k++) ll[k]=0.;
1540:
1541: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1542: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1543: for(mi=1; mi<= wav[i]-1; mi++){
1544: for (ii=1;ii<=nlstate+ndeath;ii++)
1545: for (j=1;j<=nlstate+ndeath;j++){
1546: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1547: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1548: }
1549: for(d=0; d<dh[mi][i]; d++){
1550: newm=savm;
1551: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1552: for (kk=1; kk<=cptcovage;kk++) {
1553: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1554: }
1555: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1556: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1557: savm=oldm;
1558: oldm=newm;
1559: } /* end mult */
1560:
1561: s1=s[mw[mi][i]][i];
1562: s2=s[mw[mi+1][i]][i];
1563: bbh=(double)bh[mi][i]/(double)stepm;
1564: /* bias is positive if real duration
1565: * is higher than the multiple of stepm and negative otherwise.
1566: */
1567: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1568: lli=log(out[s1][s2] - savm[s1][s2]);
1569: } else if (mle==1){
1570: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1571: } else if(mle==2){
1572: 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 */
1573: } else if(mle==3){ /* exponential inter-extrapolation */
1574: 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 */
1575: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1576: lli=log(out[s1][s2]); /* Original formula */
1577: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1578: lli=log(out[s1][s2]); /* Original formula */
1579: } /* End of if */
1580: ipmx +=1;
1581: sw += weight[i];
1582: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1583: /* 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]); */
1584: if(globpr){
1.88 brouard 1585: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1586: %10.6f %10.6f %10.6f ", \
1587: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1588: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1589: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1590: llt +=ll[k]*gipmx/gsw;
1591: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1592: }
1593: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1594: }
1595: } /* end of wave */
1596: } /* end of individual */
1597: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1598: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1599: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1600: if(globpr==0){ /* First time we count the contributions and weights */
1601: gipmx=ipmx;
1602: gsw=sw;
1603: }
1.53 brouard 1604: return -l;
1605: }
1606:
1607:
1.94 brouard 1608: /*************** function likelione ***********/
1.87 brouard 1609: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1610: {
1.87 brouard 1611: /* This routine should help understanding what is done with
1612: the selection of individuals/waves and
1.85 brouard 1613: to check the exact contribution to the likelihood.
1614: Plotting could be done.
1615: */
1616: int k;
1.87 brouard 1617:
1.88 brouard 1618: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1619: strcpy(fileresilk,"ilk");
1620: strcat(fileresilk,fileres);
1621: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1622: printf("Problem with resultfile: %s\n", fileresilk);
1623: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1624: }
1.87 brouard 1625: 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 1626: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1627: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1628: for(k=1; k<=nlstate; k++)
1.87 brouard 1629: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1630: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1631: }
1632:
1633: *fretone=(*funcone)(p);
1.87 brouard 1634: if(*globpri !=0){
1.85 brouard 1635: fclose(ficresilk);
1.88 brouard 1636: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1637: fflush(fichtm);
1638: }
1.85 brouard 1639: return;
1640: }
1641:
1.88 brouard 1642:
1.53 brouard 1643: /*********** Maximum Likelihood Estimation ***************/
1644:
1645: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1646: {
1647: int i,j, iter;
1.74 brouard 1648: double **xi;
1.53 brouard 1649: double fret;
1.85 brouard 1650: double fretone; /* Only one call to likelihood */
1.98 brouard 1651: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1652: xi=matrix(1,npar,1,npar);
1653: for (i=1;i<=npar;i++)
1654: for (j=1;j<=npar;j++)
1655: xi[i][j]=(i==j ? 1.0 : 0.0);
1656: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1657: strcpy(filerespow,"pow");
1658: strcat(filerespow,fileres);
1659: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1660: printf("Problem with resultfile: %s\n", filerespow);
1661: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1662: }
1663: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1664: for (i=1;i<=nlstate;i++)
1665: for(j=1;j<=nlstate+ndeath;j++)
1666: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1667: fprintf(ficrespow,"\n");
1.85 brouard 1668:
1.53 brouard 1669: powell(p,xi,npar,ftol,&iter,&fret,func);
1670:
1.115 ! brouard 1671: free_matrix(xi,1,npar,1,npar);
1.76 brouard 1672: fclose(ficrespow);
1673: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1674: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1675: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1676:
1677: }
1678:
1679: /**** Computes Hessian and covariance matrix ***/
1680: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1681: {
1682: double **a,**y,*x,pd;
1683: double **hess;
1684: int i, j,jk;
1685: int *indx;
1686:
1.98 brouard 1687: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1688: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1689: void lubksb(double **a, int npar, int *indx, double b[]) ;
1690: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 brouard 1691: double gompertz(double p[]);
1.53 brouard 1692: hess=matrix(1,npar,1,npar);
1693:
1694: printf("\nCalculation of the hessian matrix. Wait...\n");
1695: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1696: for (i=1;i<=npar;i++){
1697: printf("%d",i);fflush(stdout);
1698: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 brouard 1699:
1700: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1701:
1702: /* printf(" %f ",p[i]);
1703: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1704: }
1705:
1706: for (i=1;i<=npar;i++) {
1707: for (j=1;j<=npar;j++) {
1708: if (j>i) {
1709: printf(".%d%d",i,j);fflush(stdout);
1710: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 brouard 1711: hess[i][j]=hessij(p,delti,i,j,func,npar);
1712:
1.53 brouard 1713: hess[j][i]=hess[i][j];
1714: /*printf(" %lf ",hess[i][j]);*/
1715: }
1716: }
1717: }
1718: printf("\n");
1719: fprintf(ficlog,"\n");
1720:
1721: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1722: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1723:
1724: a=matrix(1,npar,1,npar);
1725: y=matrix(1,npar,1,npar);
1726: x=vector(1,npar);
1727: indx=ivector(1,npar);
1728: for (i=1;i<=npar;i++)
1729: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1730: ludcmp(a,npar,indx,&pd);
1731:
1732: for (j=1;j<=npar;j++) {
1733: for (i=1;i<=npar;i++) x[i]=0;
1734: x[j]=1;
1735: lubksb(a,npar,indx,x);
1736: for (i=1;i<=npar;i++){
1737: matcov[i][j]=x[i];
1738: }
1739: }
1740:
1741: printf("\n#Hessian matrix#\n");
1742: fprintf(ficlog,"\n#Hessian matrix#\n");
1743: for (i=1;i<=npar;i++) {
1744: for (j=1;j<=npar;j++) {
1745: printf("%.3e ",hess[i][j]);
1746: fprintf(ficlog,"%.3e ",hess[i][j]);
1747: }
1748: printf("\n");
1749: fprintf(ficlog,"\n");
1750: }
1751:
1752: /* Recompute Inverse */
1753: for (i=1;i<=npar;i++)
1754: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1755: ludcmp(a,npar,indx,&pd);
1756:
1757: /* printf("\n#Hessian matrix recomputed#\n");
1758:
1759: for (j=1;j<=npar;j++) {
1760: for (i=1;i<=npar;i++) x[i]=0;
1761: x[j]=1;
1762: lubksb(a,npar,indx,x);
1763: for (i=1;i<=npar;i++){
1764: y[i][j]=x[i];
1765: printf("%.3e ",y[i][j]);
1766: fprintf(ficlog,"%.3e ",y[i][j]);
1767: }
1768: printf("\n");
1769: fprintf(ficlog,"\n");
1770: }
1771: */
1772:
1773: free_matrix(a,1,npar,1,npar);
1774: free_matrix(y,1,npar,1,npar);
1775: free_vector(x,1,npar);
1776: free_ivector(indx,1,npar);
1777: free_matrix(hess,1,npar,1,npar);
1778:
1779:
1780: }
1781:
1782: /*************** hessian matrix ****************/
1.98 brouard 1783: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1784: {
1785: int i;
1786: int l=1, lmax=20;
1787: double k1,k2;
1788: double p2[NPARMAX+1];
1789: double res;
1.98 brouard 1790: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1791: double fx;
1792: int k=0,kmax=10;
1793: double l1;
1794:
1795: fx=func(x);
1796: for (i=1;i<=npar;i++) p2[i]=x[i];
1797: for(l=0 ; l <=lmax; l++){
1798: l1=pow(10,l);
1799: delts=delt;
1800: for(k=1 ; k <kmax; k=k+1){
1801: delt = delta*(l1*k);
1802: p2[theta]=x[theta] +delt;
1803: k1=func(p2)-fx;
1804: p2[theta]=x[theta]-delt;
1805: k2=func(p2)-fx;
1806: /*res= (k1-2.0*fx+k2)/delt/delt; */
1807: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1808:
1809: #ifdef DEBUG
1810: 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);
1811: 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);
1812: #endif
1813: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1814: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1815: k=kmax;
1816: }
1817: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1818: k=kmax; l=lmax*10.;
1819: }
1820: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1821: delts=delt;
1822: }
1823: }
1824: }
1825: delti[theta]=delts;
1826: return res;
1827:
1828: }
1829:
1.98 brouard 1830: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1831: {
1832: int i;
1833: int l=1, l1, lmax=20;
1834: double k1,k2,k3,k4,res,fx;
1835: double p2[NPARMAX+1];
1836: int k;
1837:
1838: fx=func(x);
1839: for (k=1; k<=2; k++) {
1840: for (i=1;i<=npar;i++) p2[i]=x[i];
1841: p2[thetai]=x[thetai]+delti[thetai]/k;
1842: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1843: k1=func(p2)-fx;
1844:
1845: p2[thetai]=x[thetai]+delti[thetai]/k;
1846: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1847: k2=func(p2)-fx;
1848:
1849: p2[thetai]=x[thetai]-delti[thetai]/k;
1850: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1851: k3=func(p2)-fx;
1852:
1853: p2[thetai]=x[thetai]-delti[thetai]/k;
1854: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1855: k4=func(p2)-fx;
1856: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1857: #ifdef DEBUG
1858: 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);
1859: 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);
1860: #endif
1861: }
1862: return res;
1863: }
1864:
1865: /************** Inverse of matrix **************/
1866: void ludcmp(double **a, int n, int *indx, double *d)
1867: {
1868: int i,imax,j,k;
1869: double big,dum,sum,temp;
1870: double *vv;
1871:
1872: vv=vector(1,n);
1873: *d=1.0;
1874: for (i=1;i<=n;i++) {
1875: big=0.0;
1876: for (j=1;j<=n;j++)
1877: if ((temp=fabs(a[i][j])) > big) big=temp;
1878: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1879: vv[i]=1.0/big;
1880: }
1881: for (j=1;j<=n;j++) {
1882: for (i=1;i<j;i++) {
1883: sum=a[i][j];
1884: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1885: a[i][j]=sum;
1886: }
1887: big=0.0;
1888: for (i=j;i<=n;i++) {
1889: sum=a[i][j];
1890: for (k=1;k<j;k++)
1891: sum -= a[i][k]*a[k][j];
1892: a[i][j]=sum;
1893: if ( (dum=vv[i]*fabs(sum)) >= big) {
1894: big=dum;
1895: imax=i;
1896: }
1897: }
1898: if (j != imax) {
1899: for (k=1;k<=n;k++) {
1900: dum=a[imax][k];
1901: a[imax][k]=a[j][k];
1902: a[j][k]=dum;
1903: }
1904: *d = -(*d);
1905: vv[imax]=vv[j];
1906: }
1907: indx[j]=imax;
1908: if (a[j][j] == 0.0) a[j][j]=TINY;
1909: if (j != n) {
1910: dum=1.0/(a[j][j]);
1911: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1912: }
1913: }
1914: free_vector(vv,1,n); /* Doesn't work */
1915: ;
1916: }
1917:
1918: void lubksb(double **a, int n, int *indx, double b[])
1919: {
1920: int i,ii=0,ip,j;
1921: double sum;
1922:
1923: for (i=1;i<=n;i++) {
1924: ip=indx[i];
1925: sum=b[ip];
1926: b[ip]=b[i];
1927: if (ii)
1928: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1929: else if (sum) ii=i;
1930: b[i]=sum;
1931: }
1932: for (i=n;i>=1;i--) {
1933: sum=b[i];
1934: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1935: b[i]=sum/a[i][i];
1936: }
1937: }
1938:
1939: /************ Frequencies ********************/
1.105 lievre 1940: 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 1941: { /* Some frequencies */
1942:
1943: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1944: int first;
1945: double ***freq; /* Frequencies */
1.73 lievre 1946: double *pp, **prop;
1947: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1948: FILE *ficresp;
1949: char fileresp[FILENAMELENGTH];
1950:
1951: pp=vector(1,nlstate);
1.74 brouard 1952: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1953: strcpy(fileresp,"p");
1954: strcat(fileresp,fileres);
1955: if((ficresp=fopen(fileresp,"w"))==NULL) {
1956: printf("Problem with prevalence resultfile: %s\n", fileresp);
1957: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1958: exit(0);
1959: }
1.105 lievre 1960: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1961: j1=0;
1962:
1963: j=cptcoveff;
1964: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1965:
1966: first=1;
1967:
1968: for(k1=1; k1<=j;k1++){
1969: for(i1=1; i1<=ncodemax[k1];i1++){
1970: j1++;
1971: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1972: scanf("%d", i);*/
1.105 lievre 1973: for (i=-5; i<=nlstate+ndeath; i++)
1974: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.74 brouard 1975: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1976: freq[i][jk][m]=0;
1.73 lievre 1977:
1978: for (i=1; i<=nlstate; i++)
1.74 brouard 1979: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1980: prop[i][m]=0;
1.53 brouard 1981:
1982: dateintsum=0;
1983: k2cpt=0;
1984: for (i=1; i<=imx; i++) {
1985: bool=1;
1986: if (cptcovn>0) {
1987: for (z1=1; z1<=cptcoveff; z1++)
1988: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1989: bool=0;
1990: }
1.58 lievre 1991: if (bool==1){
1.53 brouard 1992: for(m=firstpass; m<=lastpass; m++){
1993: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1994: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1995: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1996: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1997: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1998: if (m<lastpass) {
1999: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 2000: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 2001: }
2002:
1.74 brouard 2003: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 2004: dateintsum=dateintsum+k2;
2005: k2cpt++;
2006: }
1.84 brouard 2007: /*}*/
1.53 brouard 2008: }
2009: }
2010: }
2011:
1.84 brouard 2012: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.105 lievre 2013: fprintf(ficresp, "#Local time at start: %s", strstart);
1.53 brouard 2014: if (cptcovn>0) {
2015: fprintf(ficresp, "\n#********** Variable ");
2016: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2017: fprintf(ficresp, "**********\n#");
2018: }
2019: for(i=1; i<=nlstate;i++)
2020: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2021: fprintf(ficresp, "\n");
2022:
1.74 brouard 2023: for(i=iagemin; i <= iagemax+3; i++){
2024: if(i==iagemax+3){
1.53 brouard 2025: fprintf(ficlog,"Total");
2026: }else{
2027: if(first==1){
2028: first=0;
2029: printf("See log file for details...\n");
2030: }
2031: fprintf(ficlog,"Age %d", i);
2032: }
2033: for(jk=1; jk <=nlstate ; jk++){
2034: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2035: pp[jk] += freq[jk][m][i];
2036: }
2037: for(jk=1; jk <=nlstate ; jk++){
2038: for(m=-1, pos=0; m <=0 ; m++)
2039: pos += freq[jk][m][i];
2040: if(pp[jk]>=1.e-10){
2041: if(first==1){
2042: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2043: }
2044: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2045: }else{
2046: if(first==1)
2047: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2048: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2049: }
2050: }
2051:
2052: for(jk=1; jk <=nlstate ; jk++){
2053: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2054: pp[jk] += freq[jk][m][i];
1.73 lievre 2055: }
2056: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2057: pos += pp[jk];
2058: posprop += prop[jk][i];
1.53 brouard 2059: }
2060: for(jk=1; jk <=nlstate ; jk++){
2061: if(pos>=1.e-5){
2062: if(first==1)
2063: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2064: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2065: }else{
2066: if(first==1)
2067: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2068: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2069: }
1.74 brouard 2070: if( i <= iagemax){
1.53 brouard 2071: if(pos>=1.e-5){
1.73 lievre 2072: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 2073: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 2074: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2075: }
2076: else
1.73 lievre 2077: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 2078: }
2079: }
2080:
1.69 brouard 2081: for(jk=-1; jk <=nlstate+ndeath; jk++)
2082: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 2083: if(freq[jk][m][i] !=0 ) {
2084: if(first==1)
2085: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2086: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2087: }
1.74 brouard 2088: if(i <= iagemax)
1.53 brouard 2089: fprintf(ficresp,"\n");
2090: if(first==1)
2091: printf("Others in log...\n");
2092: fprintf(ficlog,"\n");
2093: }
2094: }
2095: }
2096: dateintmean=dateintsum/k2cpt;
2097:
2098: fclose(ficresp);
1.105 lievre 2099: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 2100: free_vector(pp,1,nlstate);
1.74 brouard 2101: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 2102: /* End of Freq */
2103: }
2104:
2105: /************ Prevalence ********************/
1.84 brouard 2106: 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 2107: {
2108: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2109: in each health status at the date of interview (if between dateprev1 and dateprev2).
2110: We still use firstpass and lastpass as another selection.
2111: */
1.53 brouard 2112:
2113: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2114: double ***freq; /* Frequencies */
1.73 lievre 2115: double *pp, **prop;
2116: double pos,posprop;
1.69 brouard 2117: double y2; /* in fractional years */
1.74 brouard 2118: int iagemin, iagemax;
1.53 brouard 2119:
1.74 brouard 2120: iagemin= (int) agemin;
2121: iagemax= (int) agemax;
2122: /*pp=vector(1,nlstate);*/
2123: prop=matrix(1,nlstate,iagemin,iagemax+3);
2124: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 2125: j1=0;
2126:
2127: j=cptcoveff;
2128: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2129:
2130: for(k1=1; k1<=j;k1++){
2131: for(i1=1; i1<=ncodemax[k1];i1++){
2132: j1++;
2133:
1.73 lievre 2134: for (i=1; i<=nlstate; i++)
1.74 brouard 2135: for(m=iagemin; m <= iagemax+3; m++)
2136: prop[i][m]=0.0;
1.53 brouard 2137:
1.69 brouard 2138: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2139: bool=1;
2140: if (cptcovn>0) {
2141: for (z1=1; z1<=cptcoveff; z1++)
2142: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2143: bool=0;
2144: }
2145: if (bool==1) {
1.69 brouard 2146: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2147: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2148: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2149: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2150: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2151: 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);
2152: if (s[m][i]>0 && s[m][i]<=nlstate) {
2153: /*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]]);*/
2154: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2155: prop[s[m][i]][iagemax+3] += weight[i];
2156: }
1.53 brouard 2157: }
1.69 brouard 2158: } /* end selection of waves */
1.53 brouard 2159: }
2160: }
1.74 brouard 2161: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2162:
1.74 brouard 2163: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2164: posprop += prop[jk][i];
2165: }
2166:
2167: for(jk=1; jk <=nlstate ; jk++){
2168: if( i <= iagemax){
2169: if(posprop>=1.e-5){
2170: probs[i][jk][j1]= prop[jk][i]/posprop;
2171: }
2172: }
2173: }/* end jk */
2174: }/* end i */
1.53 brouard 2175: } /* end i1 */
2176: } /* end k1 */
2177:
1.74 brouard 2178: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2179: /*free_vector(pp,1,nlstate);*/
2180: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2181: } /* End of prevalence */
1.53 brouard 2182:
2183: /************* Waves Concatenation ***************/
2184:
1.59 brouard 2185: 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 2186: {
2187: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2188: Death is a valid wave (if date is known).
2189: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2190: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2191: and mw[mi+1][i]. dh depends on stepm.
2192: */
2193:
2194: int i, mi, m;
2195: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2196: double sum=0., jmean=0.;*/
2197: int first;
2198: int j, k=0,jk, ju, jl;
2199: double sum=0.;
2200: first=0;
2201: jmin=1e+5;
2202: jmax=-1;
2203: jmean=0.;
2204: for(i=1; i<=imx; i++){
2205: mi=0;
2206: m=firstpass;
2207: while(s[m][i] <= nlstate){
1.105 lievre 2208: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
1.53 brouard 2209: mw[++mi][i]=m;
2210: if(m >=lastpass)
2211: break;
2212: else
2213: m++;
2214: }/* end while */
2215: if (s[m][i] > nlstate){
2216: mi++; /* Death is another wave */
2217: /* if(mi==0) never been interviewed correctly before death */
2218: /* Only death is a correct wave */
2219: mw[mi][i]=m;
2220: }
2221:
2222: wav[i]=mi;
2223: if(mi==0){
1.91 brouard 2224: nbwarn++;
1.53 brouard 2225: if(first==0){
1.111 brouard 2226: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2227: first=1;
2228: }
2229: if(first==1){
1.111 brouard 2230: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2231: }
2232: } /* end mi==0 */
1.77 brouard 2233: } /* End individuals */
1.53 brouard 2234:
2235: for(i=1; i<=imx; i++){
2236: for(mi=1; mi<wav[i];mi++){
2237: if (stepm <=0)
2238: dh[mi][i]=1;
2239: else{
1.77 brouard 2240: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2241: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2242: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2243: if(j==0) j=1; /* Survives at least one month after exam */
2244: else if(j<0){
1.91 brouard 2245: nberr++;
1.85 brouard 2246: 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 2247: j=1; /* Temporary Dangerous patch */
1.105 lievre 2248: 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 2249: 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 2250: 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 2251: }
2252: k=k+1;
1.110 brouard 2253: if (j >= jmax){
2254: jmax=j;
2255: ijmax=i;
2256: }
2257: if (j <= jmin){
2258: jmin=j;
2259: ijmin=i;
2260: }
1.85 brouard 2261: sum=sum+j;
2262: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2263: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2264: }
2265: }
2266: else{
2267: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.104 lievre 2268: /* 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]); */
2269:
1.53 brouard 2270: k=k+1;
1.110 brouard 2271: if (j >= jmax) {
2272: jmax=j;
2273: ijmax=i;
2274: }
2275: else if (j <= jmin){
2276: jmin=j;
2277: ijmin=i;
2278: }
1.53 brouard 2279: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2280: /*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 2281: if(j<0){
1.91 brouard 2282: nberr++;
1.85 brouard 2283: 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]);
2284: 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]);
2285: }
1.53 brouard 2286: sum=sum+j;
2287: }
2288: jk= j/stepm;
2289: jl= j -jk*stepm;
2290: ju= j -(jk+1)*stepm;
1.85 brouard 2291: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2292: if(jl==0){
2293: dh[mi][i]=jk;
2294: bh[mi][i]=0;
2295: }else{ /* We want a negative bias in order to only have interpolation ie
2296: * at the price of an extra matrix product in likelihood */
2297: dh[mi][i]=jk+1;
2298: bh[mi][i]=ju;
2299: }
2300: }else{
2301: if(jl <= -ju){
2302: dh[mi][i]=jk;
2303: bh[mi][i]=jl; /* bias is positive if real duration
2304: * is higher than the multiple of stepm and negative otherwise.
2305: */
2306: }
2307: else{
2308: dh[mi][i]=jk+1;
2309: bh[mi][i]=ju;
2310: }
2311: if(dh[mi][i]==0){
2312: dh[mi][i]=1; /* At least one step */
2313: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2314: /* 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 2315: }
1.85 brouard 2316: } /* end if mle */
2317: }
1.64 lievre 2318: } /* end wave */
1.53 brouard 2319: }
2320: jmean=sum/k;
1.110 brouard 2321: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
2322: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.53 brouard 2323: }
2324:
2325: /*********** Tricode ****************************/
2326: void tricode(int *Tvar, int **nbcode, int imx)
2327: {
1.58 lievre 2328:
2329: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2330: int cptcode=0;
2331: cptcoveff=0;
2332:
1.58 lievre 2333: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2334: for (k=1; k<=7; k++) ncodemax[k]=0;
2335:
2336: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2337: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2338: modality*/
2339: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2340: Ndum[ij]++; /*store the modality */
1.53 brouard 2341: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2342: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2343: Tvar[j]. If V=sex and male is 0 and
2344: female is 1, then cptcode=1.*/
1.53 brouard 2345: }
2346:
2347: for (i=0; i<=cptcode; i++) {
1.58 lievre 2348: 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 2349: }
1.58 lievre 2350:
1.53 brouard 2351: ij=1;
2352: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2353: for (k=0; k<= maxncov; k++) {
1.53 brouard 2354: if (Ndum[k] != 0) {
2355: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2356: /* 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 2357:
2358: ij++;
2359: }
2360: if (ij > ncodemax[j]) break;
2361: }
2362: }
2363: }
2364:
1.58 lievre 2365: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2366:
1.58 lievre 2367: for (i=1; i<=ncovmodel-2; i++) {
1.104 lievre 2368: /* 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 2369: ij=Tvar[i];
1.58 lievre 2370: Ndum[ij]++;
1.53 brouard 2371: }
2372:
2373: ij=1;
1.58 lievre 2374: for (i=1; i<= maxncov; i++) {
1.53 brouard 2375: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2376: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2377: ij++;
2378: }
2379: }
2380:
1.58 lievre 2381: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2382: }
2383:
2384: /*********** Health Expectancies ****************/
2385:
1.105 lievre 2386: 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 2387:
2388: {
2389: /* Health expectancies */
2390: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2391: double age, agelim, hf;
2392: double ***p3mat,***varhe;
2393: double **dnewm,**doldm;
2394: double *xp;
2395: double **gp, **gm;
2396: double ***gradg, ***trgradg;
2397: int theta;
2398:
1.74 brouard 2399: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2400: xp=vector(1,npar);
1.74 brouard 2401: dnewm=matrix(1,nlstate*nlstate,1,npar);
2402: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2403:
1.105 lievre 2404: fprintf(ficreseij,"# Local time at start: %s", strstart);
1.53 brouard 2405: fprintf(ficreseij,"# Health expectancies\n");
2406: fprintf(ficreseij,"# Age");
2407: for(i=1; i<=nlstate;i++)
2408: for(j=1; j<=nlstate;j++)
2409: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2410: fprintf(ficreseij,"\n");
2411:
2412: if(estepm < stepm){
2413: printf ("Problem %d lower than %d\n",estepm, stepm);
2414: }
2415: else hstepm=estepm;
2416: /* We compute the life expectancy from trapezoids spaced every estepm months
2417: * This is mainly to measure the difference between two models: for example
2418: * if stepm=24 months pijx are given only every 2 years and by summing them
2419: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2420: * progression in between and thus overestimating or underestimating according
1.53 brouard 2421: * to the curvature of the survival function. If, for the same date, we
2422: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2423: * to compare the new estimate of Life expectancy with the same linear
2424: * hypothesis. A more precise result, taking into account a more precise
2425: * curvature will be obtained if estepm is as small as stepm. */
2426:
2427: /* For example we decided to compute the life expectancy with the smallest unit */
2428: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2429: nhstepm is the number of hstepm from age to agelim
2430: nstepm is the number of stepm from age to agelin.
2431: Look at hpijx to understand the reason of that which relies in memory size
2432: and note for a fixed period like estepm months */
2433: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2434: survival function given by stepm (the optimization length). Unfortunately it
2435: means that if the survival funtion is printed only each two years of age and if
2436: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2437: results. So we changed our mind and took the option of the best precision.
2438: */
2439: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2440:
2441: agelim=AGESUP;
2442: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2443: /* nhstepm age range expressed in number of stepm */
2444: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2445: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2446: /* if (stepm >= YEARM) hstepm=1;*/
2447: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2448: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2449: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2450: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2451: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2452:
2453: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2454: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2455: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2456:
2457:
2458: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2459:
1.95 brouard 2460: /* Computing Variances of health expectancies */
1.53 brouard 2461:
2462: for(theta=1; theta <=npar; theta++){
2463: for(i=1; i<=npar; i++){
2464: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2465: }
2466: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2467:
2468: cptj=0;
2469: for(j=1; j<= nlstate; j++){
2470: for(i=1; i<=nlstate; i++){
2471: cptj=cptj+1;
2472: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2473: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2474: }
2475: }
2476: }
2477:
2478:
2479: for(i=1; i<=npar; i++)
2480: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2481: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2482:
2483: cptj=0;
2484: for(j=1; j<= nlstate; j++){
2485: for(i=1;i<=nlstate;i++){
2486: cptj=cptj+1;
2487: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2488:
1.53 brouard 2489: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2490: }
2491: }
2492: }
1.74 brouard 2493: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2494: for(h=0; h<=nhstepm-1; h++){
2495: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2496: }
2497: }
2498:
2499: /* End theta */
2500:
1.74 brouard 2501: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2502:
2503: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2504: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2505: for(theta=1; theta <=npar; theta++)
2506: trgradg[h][j][theta]=gradg[h][theta][j];
2507:
2508:
1.74 brouard 2509: for(i=1;i<=nlstate*nlstate;i++)
2510: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2511: varhe[i][j][(int)age] =0.;
2512:
2513: printf("%d|",(int)age);fflush(stdout);
2514: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2515: for(h=0;h<=nhstepm-1;h++){
2516: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2517: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2518: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2519: for(i=1;i<=nlstate*nlstate;i++)
2520: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2521: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2522: }
2523: }
2524: /* Computing expectancies */
2525: for(i=1; i<=nlstate;i++)
2526: for(j=1; j<=nlstate;j++)
2527: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2528: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2529:
2530: /* 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]);*/
2531:
2532: }
2533:
2534: fprintf(ficreseij,"%3.0f",age );
2535: cptj=0;
2536: for(i=1; i<=nlstate;i++)
2537: for(j=1; j<=nlstate;j++){
2538: cptj++;
2539: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2540: }
2541: fprintf(ficreseij,"\n");
2542:
1.74 brouard 2543: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2544: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2545: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2546: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2547: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2548: }
2549: printf("\n");
2550: fprintf(ficlog,"\n");
2551:
2552: free_vector(xp,1,npar);
1.74 brouard 2553: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2554: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2555: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2556: }
2557:
2558: /************ Variance ******************/
1.105 lievre 2559: 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 2560: {
2561: /* Variance of health expectancies */
2562: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2563: /* double **newm;*/
2564: double **dnewm,**doldm;
2565: double **dnewmp,**doldmp;
2566: int i, j, nhstepm, hstepm, h, nstepm ;
2567: int k, cptcode;
2568: double *xp;
2569: double **gp, **gm; /* for var eij */
2570: double ***gradg, ***trgradg; /*for var eij */
2571: double **gradgp, **trgradgp; /* for var p point j */
2572: double *gpp, *gmp; /* for var p point j */
2573: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2574: double ***p3mat;
2575: double age,agelim, hf;
2576: double ***mobaverage;
2577: int theta;
2578: char digit[4];
1.55 lievre 2579: char digitp[25];
1.53 brouard 2580:
2581: char fileresprobmorprev[FILENAMELENGTH];
2582:
1.55 lievre 2583: if(popbased==1){
1.58 lievre 2584: if(mobilav!=0)
1.55 lievre 2585: strcpy(digitp,"-populbased-mobilav-");
2586: else strcpy(digitp,"-populbased-nomobil-");
2587: }
2588: else
1.53 brouard 2589: strcpy(digitp,"-stablbased-");
1.56 lievre 2590:
1.54 brouard 2591: if (mobilav!=0) {
1.53 brouard 2592: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2593: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2594: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2595: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2596: }
1.53 brouard 2597: }
2598:
2599: strcpy(fileresprobmorprev,"prmorprev");
2600: sprintf(digit,"%-d",ij);
2601: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2602: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2603: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2604: strcat(fileresprobmorprev,fileres);
2605: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2606: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2607: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2608: }
2609: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2610:
1.53 brouard 2611: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2612: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
1.66 brouard 2613: 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 2614: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2615: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2616: fprintf(ficresprobmorprev," p.%-d SE",j);
2617: for(i=1; i<=nlstate;i++)
2618: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2619: }
2620: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2621: fprintf(ficgp,"\n# Routine varevsij");
1.106 brouard 2622: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.87 brouard 2623: 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");
2624: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2625: /* } */
1.53 brouard 2626: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.105 lievre 2627: fprintf(ficresvij, "#Local time at start: %s", strstart);
1.53 brouard 2628: 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");
2629: fprintf(ficresvij,"# Age");
2630: for(i=1; i<=nlstate;i++)
2631: for(j=1; j<=nlstate;j++)
2632: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2633: fprintf(ficresvij,"\n");
2634:
2635: xp=vector(1,npar);
2636: dnewm=matrix(1,nlstate,1,npar);
2637: doldm=matrix(1,nlstate,1,nlstate);
2638: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2639: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2640:
2641: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2642: gpp=vector(nlstate+1,nlstate+ndeath);
2643: gmp=vector(nlstate+1,nlstate+ndeath);
2644: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2645:
2646: if(estepm < stepm){
2647: printf ("Problem %d lower than %d\n",estepm, stepm);
2648: }
2649: else hstepm=estepm;
2650: /* For example we decided to compute the life expectancy with the smallest unit */
2651: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2652: nhstepm is the number of hstepm from age to agelim
2653: nstepm is the number of stepm from age to agelin.
2654: Look at hpijx to understand the reason of that which relies in memory size
2655: and note for a fixed period like k years */
2656: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2657: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2658: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2659: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2660: results. So we changed our mind and took the option of the best precision.
2661: */
2662: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2663: agelim = AGESUP;
2664: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2665: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2666: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2667: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2668: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2669: gp=matrix(0,nhstepm,1,nlstate);
2670: gm=matrix(0,nhstepm,1,nlstate);
2671:
2672:
2673: for(theta=1; theta <=npar; theta++){
1.66 brouard 2674: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2675: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2676: }
2677: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2678: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2679:
2680: if (popbased==1) {
1.54 brouard 2681: if(mobilav ==0){
1.53 brouard 2682: for(i=1; i<=nlstate;i++)
2683: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2684: }else{ /* mobilav */
1.53 brouard 2685: for(i=1; i<=nlstate;i++)
2686: prlim[i][i]=mobaverage[(int)age][i][ij];
2687: }
2688: }
2689:
2690: for(j=1; j<= nlstate; j++){
2691: for(h=0; h<=nhstepm; h++){
2692: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2693: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2694: }
2695: }
1.66 brouard 2696: /* This for computing probability of death (h=1 means
2697: computed over hstepm matrices product = hstepm*stepm months)
2698: as a weighted average of prlim.
2699: */
1.69 brouard 2700: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2701: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2702: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2703: }
1.66 brouard 2704: /* end probability of death */
1.53 brouard 2705:
1.66 brouard 2706: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2707: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2708: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2709: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2710:
2711: if (popbased==1) {
1.54 brouard 2712: if(mobilav ==0){
1.53 brouard 2713: for(i=1; i<=nlstate;i++)
2714: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2715: }else{ /* mobilav */
1.53 brouard 2716: for(i=1; i<=nlstate;i++)
2717: prlim[i][i]=mobaverage[(int)age][i][ij];
2718: }
2719: }
2720:
2721: for(j=1; j<= nlstate; j++){
2722: for(h=0; h<=nhstepm; h++){
2723: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2724: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2725: }
2726: }
1.66 brouard 2727: /* This for computing probability of death (h=1 means
2728: computed over hstepm matrices product = hstepm*stepm months)
2729: as a weighted average of prlim.
2730: */
1.69 brouard 2731: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2732: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2733: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2734: }
1.66 brouard 2735: /* end probability of death */
1.53 brouard 2736:
2737: for(j=1; j<= nlstate; j++) /* vareij */
2738: for(h=0; h<=nhstepm; h++){
2739: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2740: }
1.68 lievre 2741:
1.53 brouard 2742: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2743: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2744: }
2745:
2746: } /* End theta */
2747:
2748: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2749:
2750: for(h=0; h<=nhstepm; h++) /* veij */
2751: for(j=1; j<=nlstate;j++)
2752: for(theta=1; theta <=npar; theta++)
2753: trgradg[h][j][theta]=gradg[h][theta][j];
2754:
2755: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2756: for(theta=1; theta <=npar; theta++)
1.53 brouard 2757: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2758:
1.53 brouard 2759:
2760: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2761: for(i=1;i<=nlstate;i++)
2762: for(j=1;j<=nlstate;j++)
2763: vareij[i][j][(int)age] =0.;
2764:
2765: for(h=0;h<=nhstepm;h++){
2766: for(k=0;k<=nhstepm;k++){
2767: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2768: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2769: for(i=1;i<=nlstate;i++)
2770: for(j=1;j<=nlstate;j++)
2771: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2772: }
2773: }
1.70 brouard 2774:
1.53 brouard 2775: /* pptj */
2776: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2777: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2778: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2779: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2780: varppt[j][i]=doldmp[j][i];
2781: /* end ppptj */
1.66 brouard 2782: /* x centered again */
1.53 brouard 2783: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2784: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2785:
2786: if (popbased==1) {
1.54 brouard 2787: if(mobilav ==0){
1.53 brouard 2788: for(i=1; i<=nlstate;i++)
2789: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2790: }else{ /* mobilav */
1.53 brouard 2791: for(i=1; i<=nlstate;i++)
2792: prlim[i][i]=mobaverage[(int)age][i][ij];
2793: }
2794: }
1.70 brouard 2795:
1.66 brouard 2796: /* This for computing probability of death (h=1 means
2797: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2798: as a weighted average of prlim.
2799: */
1.68 lievre 2800: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2801: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2802: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2803: }
1.66 brouard 2804: /* end probability of death */
1.53 brouard 2805:
2806: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2807: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2808: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2809: for(i=1; i<=nlstate;i++){
2810: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2811: }
2812: }
2813: fprintf(ficresprobmorprev,"\n");
2814:
2815: fprintf(ficresvij,"%.0f ",age );
2816: for(i=1; i<=nlstate;i++)
2817: for(j=1; j<=nlstate;j++){
2818: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2819: }
2820: fprintf(ficresvij,"\n");
2821: free_matrix(gp,0,nhstepm,1,nlstate);
2822: free_matrix(gm,0,nhstepm,1,nlstate);
2823: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2824: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2825: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2826: } /* End age */
2827: free_vector(gpp,nlstate+1,nlstate+ndeath);
2828: free_vector(gmp,nlstate+1,nlstate+ndeath);
2829: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2830: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2831: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2832: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2833: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2834: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2835: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2836: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2837: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2838: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2839: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2840: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2841: 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 2842: /* 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);
2843: */
1.88 brouard 2844: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2845: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2846:
2847: free_vector(xp,1,npar);
2848: free_matrix(doldm,1,nlstate,1,nlstate);
2849: free_matrix(dnewm,1,nlstate,1,npar);
2850: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2851: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2852: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2853: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2854: fclose(ficresprobmorprev);
1.88 brouard 2855: fflush(ficgp);
2856: fflush(fichtm);
1.84 brouard 2857: } /* end varevsij */
1.53 brouard 2858:
2859: /************ Variance of prevlim ******************/
1.105 lievre 2860: 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 2861: {
2862: /* Variance of prevalence limit */
1.59 brouard 2863: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2864: double **newm;
2865: double **dnewm,**doldm;
2866: int i, j, nhstepm, hstepm;
2867: int k, cptcode;
2868: double *xp;
2869: double *gp, *gm;
2870: double **gradg, **trgradg;
2871: double age,agelim;
2872: int theta;
1.105 lievre 2873: fprintf(ficresvpl, "#Local time at start: %s", strstart);
1.54 brouard 2874: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2875: fprintf(ficresvpl,"# Age");
2876: for(i=1; i<=nlstate;i++)
2877: fprintf(ficresvpl," %1d-%1d",i,i);
2878: fprintf(ficresvpl,"\n");
2879:
2880: xp=vector(1,npar);
2881: dnewm=matrix(1,nlstate,1,npar);
2882: doldm=matrix(1,nlstate,1,nlstate);
2883:
2884: hstepm=1*YEARM; /* Every year of age */
2885: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2886: agelim = AGESUP;
2887: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2888: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2889: if (stepm >= YEARM) hstepm=1;
2890: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2891: gradg=matrix(1,npar,1,nlstate);
2892: gp=vector(1,nlstate);
2893: gm=vector(1,nlstate);
2894:
2895: for(theta=1; theta <=npar; theta++){
2896: for(i=1; i<=npar; i++){ /* Computes gradient */
2897: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2898: }
2899: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2900: for(i=1;i<=nlstate;i++)
2901: gp[i] = prlim[i][i];
2902:
2903: for(i=1; i<=npar; i++) /* Computes gradient */
2904: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2905: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2906: for(i=1;i<=nlstate;i++)
2907: gm[i] = prlim[i][i];
2908:
2909: for(i=1;i<=nlstate;i++)
2910: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2911: } /* End theta */
2912:
2913: trgradg =matrix(1,nlstate,1,npar);
2914:
2915: for(j=1; j<=nlstate;j++)
2916: for(theta=1; theta <=npar; theta++)
2917: trgradg[j][theta]=gradg[theta][j];
2918:
2919: for(i=1;i<=nlstate;i++)
2920: varpl[i][(int)age] =0.;
2921: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2922: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2923: for(i=1;i<=nlstate;i++)
2924: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2925:
2926: fprintf(ficresvpl,"%.0f ",age );
2927: for(i=1; i<=nlstate;i++)
2928: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2929: fprintf(ficresvpl,"\n");
2930: free_vector(gp,1,nlstate);
2931: free_vector(gm,1,nlstate);
2932: free_matrix(gradg,1,npar,1,nlstate);
2933: free_matrix(trgradg,1,nlstate,1,npar);
2934: } /* End age */
2935:
2936: free_vector(xp,1,npar);
2937: free_matrix(doldm,1,nlstate,1,npar);
2938: free_matrix(dnewm,1,nlstate,1,nlstate);
2939:
2940: }
2941:
2942: /************ Variance of one-step probabilities ******************/
1.105 lievre 2943: 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 2944: {
2945: int i, j=0, i1, k1, l1, t, tj;
2946: int k2, l2, j1, z1;
2947: int k=0,l, cptcode;
2948: int first=1, first1;
2949: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2950: double **dnewm,**doldm;
2951: double *xp;
2952: double *gp, *gm;
2953: double **gradg, **trgradg;
2954: double **mu;
2955: double age,agelim, cov[NCOVMAX];
2956: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2957: int theta;
2958: char fileresprob[FILENAMELENGTH];
2959: char fileresprobcov[FILENAMELENGTH];
2960: char fileresprobcor[FILENAMELENGTH];
2961:
2962: double ***varpij;
2963:
2964: strcpy(fileresprob,"prob");
2965: strcat(fileresprob,fileres);
2966: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2967: printf("Problem with resultfile: %s\n", fileresprob);
2968: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2969: }
2970: strcpy(fileresprobcov,"probcov");
2971: strcat(fileresprobcov,fileres);
2972: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2973: printf("Problem with resultfile: %s\n", fileresprobcov);
2974: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2975: }
2976: strcpy(fileresprobcor,"probcor");
2977: strcat(fileresprobcor,fileres);
2978: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2979: printf("Problem with resultfile: %s\n", fileresprobcor);
2980: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2981: }
2982: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2983: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2984: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2985: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2986: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2987: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.105 lievre 2988: fprintf(ficresprob, "#Local time at start: %s", strstart);
1.53 brouard 2989: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2990: fprintf(ficresprob,"# Age");
1.105 lievre 2991: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
1.53 brouard 2992: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2993: fprintf(ficresprobcov,"# Age");
1.105 lievre 2994: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
1.53 brouard 2995: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2996: fprintf(ficresprobcov,"# Age");
2997:
2998:
2999: for(i=1; i<=nlstate;i++)
3000: for(j=1; j<=(nlstate+ndeath);j++){
3001: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3002: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3003: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3004: }
1.69 brouard 3005: /* fprintf(ficresprob,"\n");
1.53 brouard 3006: fprintf(ficresprobcov,"\n");
3007: fprintf(ficresprobcor,"\n");
1.69 brouard 3008: */
3009: xp=vector(1,npar);
1.53 brouard 3010: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3011: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3012: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3013: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3014: first=1;
1.88 brouard 3015: fprintf(ficgp,"\n# Routine varprob");
3016: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3017: fprintf(fichtm,"\n");
3018:
1.95 brouard 3019: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3020: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 3021: file %s<br>\n",optionfilehtmcov);
3022: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3023: and drawn. It helps understanding how is the covariance between two incidences.\
3024: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3025: 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. \
3026: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3027: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3028: standard deviations wide on each axis. <br>\
3029: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3030: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3031: 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 3032:
3033: cov[1]=1;
3034: tj=cptcoveff;
3035: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3036: j1=0;
3037: for(t=1; t<=tj;t++){
3038: for(i1=1; i1<=ncodemax[t];i1++){
3039: j1++;
3040: if (cptcovn>0) {
3041: fprintf(ficresprob, "\n#********** Variable ");
3042: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3043: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 3044: fprintf(ficresprobcov, "\n#********** Variable ");
3045: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3046: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 3047:
3048: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 3049: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3050: fprintf(ficgp, "**********\n#\n");
1.53 brouard 3051:
3052:
1.96 brouard 3053: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 3054: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 3055: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 3056:
3057: fprintf(ficresprobcor, "\n#********** Variable ");
3058: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3059: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 3060: }
3061:
3062: for (age=bage; age<=fage; age ++){
3063: cov[2]=age;
3064: for (k=1; k<=cptcovn;k++) {
3065: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3066: }
3067: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3068: for (k=1; k<=cptcovprod;k++)
3069: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3070:
3071: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3072: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3073: gp=vector(1,(nlstate)*(nlstate+ndeath));
3074: gm=vector(1,(nlstate)*(nlstate+ndeath));
3075:
3076: for(theta=1; theta <=npar; theta++){
3077: for(i=1; i<=npar; i++)
1.74 brouard 3078: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 3079:
3080: pmij(pmmij,cov,ncovmodel,xp,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: gp[k]=pmmij[i][j];
3087: }
3088: }
3089:
3090: for(i=1; i<=npar; i++)
1.74 brouard 3091: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 3092:
3093: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3094: k=0;
3095: for(i=1; i<=(nlstate); i++){
3096: for(j=1; j<=(nlstate+ndeath);j++){
3097: k=k+1;
3098: gm[k]=pmmij[i][j];
3099: }
3100: }
3101:
3102: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 3103: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 3104: }
3105:
3106: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3107: for(theta=1; theta <=npar; theta++)
3108: trgradg[j][theta]=gradg[theta][j];
3109:
3110: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3111: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 3112: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3113: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3114: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3115: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3116:
1.53 brouard 3117: pmij(pmmij,cov,ncovmodel,x,nlstate);
3118:
3119: k=0;
3120: for(i=1; i<=(nlstate); i++){
3121: for(j=1; j<=(nlstate+ndeath);j++){
3122: k=k+1;
3123: mu[k][(int) age]=pmmij[i][j];
3124: }
3125: }
3126: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3127: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3128: varpij[i][j][(int)age] = doldm[i][j];
3129:
3130: /*printf("\n%d ",(int)age);
1.59 brouard 3131: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3132: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3133: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3134: }*/
1.53 brouard 3135:
3136: fprintf(ficresprob,"\n%d ",(int)age);
3137: fprintf(ficresprobcov,"\n%d ",(int)age);
3138: fprintf(ficresprobcor,"\n%d ",(int)age);
3139:
3140: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3141: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3142: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3143: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3144: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3145: }
3146: i=0;
3147: for (k=1; k<=(nlstate);k++){
3148: for (l=1; l<=(nlstate+ndeath);l++){
3149: i=i++;
3150: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3151: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3152: for (j=1; j<=i;j++){
3153: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3154: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3155: }
3156: }
3157: }/* end of loop for state */
3158: } /* end of loop for age */
3159:
3160: /* Confidence intervalle of pij */
3161: /*
1.59 brouard 3162: fprintf(ficgp,"\nset noparametric;unset label");
3163: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3164: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3165: 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);
3166: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3167: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3168: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3169: */
3170:
3171: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3172: first1=1;
3173: for (k2=1; k2<=(nlstate);k2++){
3174: for (l2=1; l2<=(nlstate+ndeath);l2++){
3175: if(l2==k2) continue;
3176: j=(k2-1)*(nlstate+ndeath)+l2;
3177: for (k1=1; k1<=(nlstate);k1++){
3178: for (l1=1; l1<=(nlstate+ndeath);l1++){
3179: if(l1==k1) continue;
3180: i=(k1-1)*(nlstate+ndeath)+l1;
3181: if(i<=j) continue;
3182: for (age=bage; age<=fage; age ++){
3183: if ((int)age %5==0){
3184: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3185: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3186: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3187: mu1=mu[i][(int) age]/stepm*YEARM ;
3188: mu2=mu[j][(int) age]/stepm*YEARM;
3189: c12=cv12/sqrt(v1*v2);
3190: /* Computing eigen value of matrix of covariance */
3191: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3192: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3193: /* Eigen vectors */
3194: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3195: /*v21=sqrt(1.-v11*v11); *//* error */
3196: v21=(lc1-v1)/cv12*v11;
3197: v12=-v21;
3198: v22=v11;
3199: tnalp=v21/v11;
3200: if(first1==1){
3201: first1=0;
3202: 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);
3203: }
3204: 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);
3205: /*printf(fignu*/
3206: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3207: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3208: if(first==1){
3209: first=0;
3210: fprintf(ficgp,"\nset parametric;unset label");
3211: 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);
3212: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3213: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3214: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3215: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3216: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3217: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3218: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3219: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3220: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3221: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3222: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3223: 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",\
3224: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3225: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3226: }else{
3227: first=0;
1.91 brouard 3228: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3229: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3230: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3231: 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",\
3232: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3233: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3234: }/* if first */
3235: } /* age mod 5 */
3236: } /* end loop age */
1.88 brouard 3237: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3238: first=1;
3239: } /*l12 */
3240: } /* k12 */
3241: } /*l1 */
3242: }/* k1 */
3243: } /* loop covariates */
3244: }
1.59 brouard 3245: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3246: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.113 brouard 3247: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3248: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
1.53 brouard 3249: free_vector(xp,1,npar);
3250: fclose(ficresprob);
3251: fclose(ficresprobcov);
3252: fclose(ficresprobcor);
1.91 brouard 3253: fflush(ficgp);
3254: fflush(fichtmcov);
1.53 brouard 3255: }
3256:
3257:
3258: /******************* Printing html file ***********/
3259: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3260: int lastpass, int stepm, int weightopt, char model[],\
3261: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3262: int popforecast, int estepm ,\
3263: double jprev1, double mprev1,double anprev1, \
3264: double jprev2, double mprev2,double anprev2){
3265: int jj1, k1, i1, cpt;
3266:
1.107 brouard 3267: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3268: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
1.106 brouard 3269: </ul>");
1.107 brouard 3270: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
1.96 brouard 3271: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3272: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3273: fprintf(fichtm,"\
3274: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3275: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3276: fprintf(fichtm,"\
3277: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3278: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3279: fprintf(fichtm,"\
1.85 brouard 3280: - Life expectancies by age and initial health status (estepm=%2d months): \
1.96 brouard 3281: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3282: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3283:
3284: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3285:
3286: m=cptcoveff;
3287: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3288:
3289: jj1=0;
3290: for(k1=1; k1<=m;k1++){
3291: for(i1=1; i1<=ncodemax[k1];i1++){
3292: jj1++;
3293: if (cptcovn > 0) {
3294: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3295: for (cpt=1; cpt<=cptcoveff;cpt++)
3296: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3297: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3298: }
3299: /* Pij */
1.88 brouard 3300: 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> \
3301: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3302: /* Quasi-incidences */
1.85 brouard 3303: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3304: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3305: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3306: /* Stable prevalence in each health state */
3307: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3308: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3309: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3310: }
3311: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3312: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3313: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3314: }
3315: } /* end i1 */
3316: }/* End k1 */
3317: fprintf(fichtm,"</ul>");
3318:
3319:
1.96 brouard 3320: fprintf(fichtm,"\
1.107 brouard 3321: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.96 brouard 3322: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3323:
3324: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3325: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3326: fprintf(fichtm,"\
3327: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3328: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3329:
3330: fprintf(fichtm,"\
3331: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3332: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3333: fprintf(fichtm,"\
3334: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3335: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3336: fprintf(fichtm,"\
3337: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3338: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3339: fprintf(fichtm,"\
1.88 brouard 3340: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3341: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3342:
1.76 brouard 3343: /* if(popforecast==1) fprintf(fichtm,"\n */
3344: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3345: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3346: /* <br>",fileres,fileres,fileres,fileres); */
3347: /* else */
3348: /* 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 3349: fflush(fichtm);
3350: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3351:
3352: m=cptcoveff;
3353: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3354:
3355: jj1=0;
3356: for(k1=1; k1<=m;k1++){
3357: for(i1=1; i1<=ncodemax[k1];i1++){
3358: jj1++;
3359: if (cptcovn > 0) {
3360: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3361: for (cpt=1; cpt<=cptcoveff;cpt++)
3362: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3363: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3364: }
3365: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3366: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3367: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3368: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3369: }
1.96 brouard 3370: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3371: health expectancies in states (1) and (2): %s%d.png<br>\
3372: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3373: } /* end i1 */
3374: }/* End k1 */
3375: fprintf(fichtm,"</ul>");
1.87 brouard 3376: fflush(fichtm);
1.53 brouard 3377: }
3378:
3379: /******************* Gnuplot file **************/
1.89 brouard 3380: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3381:
1.88 brouard 3382: char dirfileres[132],optfileres[132];
1.53 brouard 3383: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3384: int ng;
1.88 brouard 3385: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3386: /* printf("Problem with file %s",optionfilegnuplot); */
3387: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3388: /* } */
1.53 brouard 3389:
1.54 brouard 3390: /*#ifdef windows */
1.89 brouard 3391: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3392: /*#endif */
1.88 brouard 3393: m=pow(2,cptcoveff);
3394:
3395: strcpy(dirfileres,optionfilefiname);
3396: strcpy(optfileres,"vpl");
1.53 brouard 3397: /* 1eme*/
3398: for (cpt=1; cpt<= nlstate ; cpt ++) {
3399: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3400: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3401: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3402: fprintf(ficgp,"set xlabel \"Age\" \n\
3403: set ylabel \"Probability\" \n\
3404: set ter png small\n\
3405: set size 0.65,0.65\n\
3406: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3407:
3408: for (i=1; i<= nlstate ; i ++) {
3409: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3410: else fprintf(ficgp," \%%*lf (\%%*lf)");
3411: }
1.88 brouard 3412: 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 3413: for (i=1; i<= nlstate ; i ++) {
3414: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3415: else fprintf(ficgp," \%%*lf (\%%*lf)");
3416: }
1.88 brouard 3417: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3418: for (i=1; i<= nlstate ; i ++) {
3419: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3420: else fprintf(ficgp," \%%*lf (\%%*lf)");
3421: }
1.88 brouard 3422: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3423: }
3424: }
3425: /*2 eme*/
3426:
3427: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3428: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3429: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3430:
3431: for (i=1; i<= nlstate+1 ; i ++) {
3432: k=2*i;
1.88 brouard 3433: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3434: for (j=1; j<= nlstate+1 ; j ++) {
3435: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3436: else fprintf(ficgp," \%%*lf (\%%*lf)");
3437: }
3438: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3439: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3440: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3441: for (j=1; j<= nlstate+1 ; j ++) {
3442: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3443: else fprintf(ficgp," \%%*lf (\%%*lf)");
3444: }
3445: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3446: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3447: for (j=1; j<= nlstate+1 ; j ++) {
3448: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3449: else fprintf(ficgp," \%%*lf (\%%*lf)");
3450: }
3451: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3452: else fprintf(ficgp,"\" t\"\" w l 0,");
3453: }
3454: }
3455:
3456: /*3eme*/
3457:
3458: for (k1=1; k1<= m ; k1 ++) {
3459: for (cpt=1; cpt<= nlstate ; cpt ++) {
3460: k=2+nlstate*(2*cpt-2);
1.88 brouard 3461: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3462: fprintf(ficgp,"set ter png small\n\
3463: set size 0.65,0.65\n\
3464: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3465: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3466: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3467: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3468: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3469: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3470: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3471:
3472: */
3473: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3474: 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 3475:
3476: }
3477: }
3478: }
3479:
1.76 brouard 3480: /* CV preval stable (period) */
1.53 brouard 3481: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3482: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3483: k=3;
1.88 brouard 3484: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3485: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3486: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3487: unset log y\n\
1.88 brouard 3488: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3489:
1.83 lievre 3490: for (i=1; i< nlstate ; i ++)
1.53 brouard 3491: fprintf(ficgp,"+$%d",k+i+1);
3492: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3493:
3494: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3495: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3496: for (i=1; i< nlstate ; i ++) {
3497: l=3+(nlstate+ndeath)*cpt;
3498: fprintf(ficgp,"+$%d",l+i+1);
3499: }
3500: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3501: }
3502: }
3503:
3504: /* proba elementaires */
3505: for(i=1,jk=1; i <=nlstate; i++){
3506: for(k=1; k <=(nlstate+ndeath); k++){
3507: if (k != i) {
3508: for(j=1; j <=ncovmodel; j++){
3509: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3510: jk++;
3511: fprintf(ficgp,"\n");
3512: }
3513: }
3514: }
3515: }
3516:
3517: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3518: for(jk=1; jk <=m; jk++) {
1.88 brouard 3519: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3520: if (ng==2)
3521: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3522: else
3523: fprintf(ficgp,"\nset title \"Probability\"\n");
3524: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3525: i=1;
3526: for(k2=1; k2<=nlstate; k2++) {
3527: k3=i;
3528: for(k=1; k<=(nlstate+ndeath); k++) {
3529: if (k != k2){
3530: if(ng==2)
3531: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3532: else
3533: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3534: ij=1;
3535: for(j=3; j <=ncovmodel; j++) {
3536: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3537: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3538: ij++;
3539: }
3540: else
3541: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3542: }
3543: fprintf(ficgp,")/(1");
3544:
3545: for(k1=1; k1 <=nlstate; k1++){
3546: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3547: ij=1;
3548: for(j=3; j <=ncovmodel; j++){
3549: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3550: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3551: ij++;
3552: }
3553: else
3554: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3555: }
3556: fprintf(ficgp,")");
3557: }
3558: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3559: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3560: i=i+ncovmodel;
3561: }
3562: } /* end k */
3563: } /* end k2 */
3564: } /* end jk */
3565: } /* end ng */
1.88 brouard 3566: fflush(ficgp);
1.53 brouard 3567: } /* end gnuplot */
3568:
3569:
3570: /*************** Moving average **************/
1.54 brouard 3571: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3572:
3573: int i, cpt, cptcod;
1.58 lievre 3574: int modcovmax =1;
1.54 brouard 3575: int mobilavrange, mob;
1.53 brouard 3576: double age;
1.58 lievre 3577:
3578: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3579: a covariate has 2 modalities */
3580: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3581:
1.54 brouard 3582: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3583: if(mobilav==1) mobilavrange=5; /* default */
3584: else mobilavrange=mobilav;
3585: for (age=bage; age<=fage; age++)
3586: for (i=1; i<=nlstate;i++)
1.58 lievre 3587: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3588: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3589: /* We keep the original values on the extreme ages bage, fage and for
3590: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3591: we use a 5 terms etc. until the borders are no more concerned.
3592: */
3593: for (mob=3;mob <=mobilavrange;mob=mob+2){
3594: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3595: for (i=1; i<=nlstate;i++){
1.58 lievre 3596: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3597: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3598: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3599: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3600: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3601: }
3602: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3603: }
1.53 brouard 3604: }
1.54 brouard 3605: }/* end age */
3606: }/* end mob */
3607: }else return -1;
3608: return 0;
3609: }/* End movingaverage */
1.53 brouard 3610:
3611:
3612: /************** Forecasting ******************/
1.70 brouard 3613: 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 3614: /* proj1, year, month, day of starting projection
3615: agemin, agemax range of age
3616: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3617: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3618: */
1.73 lievre 3619: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3620: int *popage;
1.70 brouard 3621: double agec; /* generic age */
3622: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3623: double *popeffectif,*popcount;
3624: double ***p3mat;
1.55 lievre 3625: double ***mobaverage;
1.53 brouard 3626: char fileresf[FILENAMELENGTH];
3627:
1.69 brouard 3628: agelim=AGESUP;
1.84 brouard 3629: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3630:
3631: strcpy(fileresf,"f");
3632: strcat(fileresf,fileres);
3633: if((ficresf=fopen(fileresf,"w"))==NULL) {
3634: printf("Problem with forecast resultfile: %s\n", fileresf);
3635: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3636: }
3637: printf("Computing forecasting: result on file '%s' \n", fileresf);
3638: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3639:
3640: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3641:
1.54 brouard 3642: if (mobilav!=0) {
1.53 brouard 3643: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3644: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3645: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3646: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3647: }
1.53 brouard 3648: }
3649:
3650: stepsize=(int) (stepm+YEARM-1)/YEARM;
3651: if (stepm<=12) stepsize=1;
1.74 brouard 3652: if(estepm < stepm){
3653: printf ("Problem %d lower than %d\n",estepm, stepm);
3654: }
3655: else hstepm=estepm;
3656:
1.53 brouard 3657: hstepm=hstepm/stepm;
1.69 brouard 3658: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3659: fractional in yp1 */
1.53 brouard 3660: anprojmean=yp;
3661: yp2=modf((yp1*12),&yp);
3662: mprojmean=yp;
3663: yp1=modf((yp2*30.5),&yp);
3664: jprojmean=yp;
3665: if(jprojmean==0) jprojmean=1;
3666: if(mprojmean==0) jprojmean=1;
1.73 lievre 3667:
3668: i1=cptcoveff;
3669: if (cptcovn < 1){i1=1;}
1.53 brouard 3670:
1.70 brouard 3671: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3672:
1.70 brouard 3673: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3674:
1.75 brouard 3675: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3676: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3677: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3678: k=k+1;
3679: fprintf(ficresf,"\n#******");
3680: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3681: 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 3682: }
3683: fprintf(ficresf,"******\n");
1.70 brouard 3684: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3685: for(j=1; j<=nlstate+ndeath;j++){
3686: for(i=1; i<=nlstate;i++)
3687: fprintf(ficresf," p%d%d",i,j);
3688: fprintf(ficresf," p.%d",j);
3689: }
1.74 brouard 3690: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3691: fprintf(ficresf,"\n");
1.70 brouard 3692: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3693:
1.71 brouard 3694: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3695: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3696: nhstepm = nhstepm/hstepm;
3697: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3698: oldm=oldms;savm=savms;
1.70 brouard 3699: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3700:
3701: for (h=0; h<=nhstepm; h++){
1.75 brouard 3702: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3703: fprintf(ficresf,"\n");
3704: for(j=1;j<=cptcoveff;j++)
3705: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3706: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3707: }
3708: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3709: ppij=0.;
1.71 brouard 3710: for(i=1; i<=nlstate;i++) {
1.53 brouard 3711: if (mobilav==1)
1.71 brouard 3712: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3713: else {
1.71 brouard 3714: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3715: }
1.75 brouard 3716: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3717: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3718: }
3719: } /* end i */
3720: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3721: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3722: }
1.75 brouard 3723: }/* end j */
3724: } /* end h */
1.53 brouard 3725: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3726: } /* end agec */
3727: } /* end yearp */
3728: } /* end cptcod */
3729: } /* end cptcov */
1.53 brouard 3730:
1.54 brouard 3731: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3732:
3733: fclose(ficresf);
3734: }
1.70 brouard 3735:
3736: /************** Forecasting *****not tested NB*************/
1.53 brouard 3737: 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){
3738:
3739: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3740: int *popage;
1.69 brouard 3741: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3742: double *popeffectif,*popcount;
3743: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3744: double ***mobaverage;
1.53 brouard 3745: char filerespop[FILENAMELENGTH];
3746:
3747: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3748: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3749: agelim=AGESUP;
1.69 brouard 3750: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3751:
1.84 brouard 3752: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3753:
3754:
3755: strcpy(filerespop,"pop");
3756: strcat(filerespop,fileres);
3757: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3758: printf("Problem with forecast resultfile: %s\n", filerespop);
3759: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3760: }
3761: printf("Computing forecasting: result on file '%s' \n", filerespop);
3762: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3763:
3764: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3765:
1.54 brouard 3766: if (mobilav!=0) {
1.53 brouard 3767: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3768: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3769: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3770: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3771: }
1.53 brouard 3772: }
3773:
3774: stepsize=(int) (stepm+YEARM-1)/YEARM;
3775: if (stepm<=12) stepsize=1;
3776:
3777: agelim=AGESUP;
3778:
3779: hstepm=1;
3780: hstepm=hstepm/stepm;
3781:
3782: if (popforecast==1) {
3783: if((ficpop=fopen(popfile,"r"))==NULL) {
3784: printf("Problem with population file : %s\n",popfile);exit(0);
3785: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3786: }
3787: popage=ivector(0,AGESUP);
3788: popeffectif=vector(0,AGESUP);
3789: popcount=vector(0,AGESUP);
3790:
3791: i=1;
3792: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3793:
3794: imx=i;
3795: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3796: }
3797:
1.69 brouard 3798: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3799: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3800: k=k+1;
3801: fprintf(ficrespop,"\n#******");
3802: for(j=1;j<=cptcoveff;j++) {
3803: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3804: }
3805: fprintf(ficrespop,"******\n");
3806: fprintf(ficrespop,"# Age");
3807: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3808: if (popforecast==1) fprintf(ficrespop," [Population]");
3809:
3810: for (cpt=0; cpt<=0;cpt++) {
3811: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3812:
1.69 brouard 3813: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3814: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3815: nhstepm = nhstepm/hstepm;
3816:
3817: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3818: oldm=oldms;savm=savms;
3819: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3820:
3821: for (h=0; h<=nhstepm; h++){
1.69 brouard 3822: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3823: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3824: }
3825: for(j=1; j<=nlstate+ndeath;j++) {
3826: kk1=0.;kk2=0;
3827: for(i=1; i<=nlstate;i++) {
3828: if (mobilav==1)
3829: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3830: else {
3831: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3832: }
3833: }
1.69 brouard 3834: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3835: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3836: /*fprintf(ficrespop," %.3f", kk1);
3837: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3838: }
3839: }
3840: for(i=1; i<=nlstate;i++){
3841: kk1=0.;
3842: for(j=1; j<=nlstate;j++){
3843: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3844: }
1.69 brouard 3845: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3846: }
3847:
1.69 brouard 3848: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3849: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3850: }
3851: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3852: }
3853: }
3854:
3855: /******/
3856:
3857: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3858: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3859: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3860: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3861: nhstepm = nhstepm/hstepm;
3862:
3863: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3864: oldm=oldms;savm=savms;
3865: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3866: for (h=0; h<=nhstepm; h++){
1.69 brouard 3867: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3868: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3869: }
3870: for(j=1; j<=nlstate+ndeath;j++) {
3871: kk1=0.;kk2=0;
3872: for(i=1; i<=nlstate;i++) {
3873: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3874: }
1.69 brouard 3875: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3876: }
3877: }
3878: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3879: }
3880: }
3881: }
3882: }
3883:
1.54 brouard 3884: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3885:
3886: if (popforecast==1) {
3887: free_ivector(popage,0,AGESUP);
3888: free_vector(popeffectif,0,AGESUP);
3889: free_vector(popcount,0,AGESUP);
3890: }
3891: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3892: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3893: fclose(ficrespop);
1.84 brouard 3894: } /* End of popforecast */
1.53 brouard 3895:
1.87 brouard 3896: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3897: {
1.87 brouard 3898: if((fichier=fopen(optionfich,"a"))==NULL) {
3899: printf("Problem with file: %s\n", optionfich);
3900: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3901: return (0);
1.86 brouard 3902: }
1.87 brouard 3903: fflush(fichier);
3904: return (1);
1.86 brouard 3905: }
1.94 brouard 3906:
3907:
3908: /**************** function prwizard **********************/
1.88 brouard 3909: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3910: {
3911:
1.94 brouard 3912: /* Wizard to print covariance matrix template */
3913:
1.88 brouard 3914: char ca[32], cb[32], cc[32];
3915: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3916: int numlinepar;
3917:
3918: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3919: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3920: for(i=1; i <=nlstate; i++){
3921: jj=0;
3922: for(j=1; j <=nlstate+ndeath; j++){
3923: if(j==i) continue;
3924: jj++;
3925: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3926: printf("%1d%1d",i,j);
3927: fprintf(ficparo,"%1d%1d",i,j);
3928: for(k=1; k<=ncovmodel;k++){
3929: /* printf(" %lf",param[i][j][k]); */
3930: /* fprintf(ficparo," %lf",param[i][j][k]); */
3931: printf(" 0.");
3932: fprintf(ficparo," 0.");
3933: }
3934: printf("\n");
3935: fprintf(ficparo,"\n");
3936: }
3937: }
3938: printf("# Scales (for hessian or gradient estimation)\n");
3939: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3940: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3941: for(i=1; i <=nlstate; i++){
3942: jj=0;
3943: for(j=1; j <=nlstate+ndeath; j++){
3944: if(j==i) continue;
3945: jj++;
3946: fprintf(ficparo,"%1d%1d",i,j);
3947: printf("%1d%1d",i,j);
3948: fflush(stdout);
3949: for(k=1; k<=ncovmodel;k++){
3950: /* printf(" %le",delti3[i][j][k]); */
3951: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3952: printf(" 0.");
3953: fprintf(ficparo," 0.");
3954: }
3955: numlinepar++;
3956: printf("\n");
3957: fprintf(ficparo,"\n");
3958: }
3959: }
3960: printf("# Covariance matrix\n");
3961: /* # 121 Var(a12)\n\ */
3962: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3963: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3964: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3965: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3966: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3967: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3968: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3969: fflush(stdout);
3970: fprintf(ficparo,"# Covariance matrix\n");
3971: /* # 121 Var(a12)\n\ */
3972: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3973: /* # ...\n\ */
3974: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3975:
3976: for(itimes=1;itimes<=2;itimes++){
3977: jj=0;
3978: for(i=1; i <=nlstate; i++){
3979: for(j=1; j <=nlstate+ndeath; j++){
3980: if(j==i) continue;
3981: for(k=1; k<=ncovmodel;k++){
3982: jj++;
3983: ca[0]= k+'a'-1;ca[1]='\0';
3984: if(itimes==1){
3985: printf("#%1d%1d%d",i,j,k);
3986: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3987: }else{
3988: printf("%1d%1d%d",i,j,k);
3989: fprintf(ficparo,"%1d%1d%d",i,j,k);
3990: /* printf(" %.5le",matcov[i][j]); */
3991: }
3992: ll=0;
3993: for(li=1;li <=nlstate; li++){
3994: for(lj=1;lj <=nlstate+ndeath; lj++){
3995: if(lj==li) continue;
3996: for(lk=1;lk<=ncovmodel;lk++){
3997: ll++;
3998: if(ll<=jj){
3999: cb[0]= lk +'a'-1;cb[1]='\0';
4000: if(ll<jj){
4001: if(itimes==1){
4002: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4003: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4004: }else{
4005: printf(" 0.");
4006: fprintf(ficparo," 0.");
4007: }
4008: }else{
4009: if(itimes==1){
4010: printf(" Var(%s%1d%1d)",ca,i,j);
4011: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4012: }else{
4013: printf(" 0.");
4014: fprintf(ficparo," 0.");
4015: }
4016: }
4017: }
4018: } /* end lk */
4019: } /* end lj */
4020: } /* end li */
4021: printf("\n");
4022: fprintf(ficparo,"\n");
4023: numlinepar++;
4024: } /* end k*/
4025: } /*end j */
4026: } /* end i */
1.95 brouard 4027: } /* end itimes */
1.88 brouard 4028:
4029: } /* end of prwizard */
1.98 brouard 4030: /******************* Gompertz Likelihood ******************************/
4031: double gompertz(double x[])
4032: {
4033: double A,B,L=0.0,sump=0.,num=0.;
4034: int i,n=0; /* n is the size of the sample */
1.110 brouard 4035:
1.98 brouard 4036: for (i=0;i<=imx-1 ; i++) {
4037: sump=sump+weight[i];
1.103 lievre 4038: /* sump=sump+1;*/
1.98 brouard 4039: num=num+1;
4040: }
4041:
4042:
1.103 lievre 4043: /* for (i=0; i<=imx; i++)
1.98 brouard 4044: 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]);*/
4045:
1.103 lievre 4046: for (i=1;i<=imx ; i++)
1.98 brouard 4047: {
1.110 brouard 4048: if (cens[i] == 1 && wav[i]>1)
1.103 lievre 4049: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
1.98 brouard 4050:
1.110 brouard 4051: if (cens[i] == 0 && wav[i]>1)
1.103 lievre 4052: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4053: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
1.98 brouard 4054:
1.110 brouard 4055: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4056: if (wav[i] > 1 ) { /* ??? */
1.98 brouard 4057: L=L+A*weight[i];
4058: /* 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]);*/
4059: }
4060: }
4061:
4062: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4063:
4064: return -2*L*num/sump;
4065: }
4066:
4067: /******************* Printing html file ***********/
4068: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4069: int lastpass, int stepm, int weightopt, char model[],\
1.105 lievre 4070: int imx, double p[],double **matcov,double agemortsup){
4071: int i,k;
1.98 brouard 4072:
4073: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4074: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4075: for (i=1;i<=2;i++)
4076: 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]));
4077: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4078: fprintf(fichtm,"</ul>");
1.105 lievre 4079:
4080: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4081:
1.106 brouard 4082: 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 4083:
4084: for (k=agegomp;k<(agemortsup-2);k++)
4085: 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]);
4086:
4087:
1.98 brouard 4088: fflush(fichtm);
4089: }
4090:
4091: /******************* Gnuplot file **************/
4092: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4093:
4094: char dirfileres[132],optfileres[132];
4095: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4096: int ng;
4097:
4098:
4099: /*#ifdef windows */
4100: fprintf(ficgp,"cd \"%s\" \n",pathc);
4101: /*#endif */
4102:
4103:
4104: strcpy(dirfileres,optionfilefiname);
4105: strcpy(optfileres,"vpl");
4106: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4107: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4108: fprintf(ficgp, "set ter png small\n set log y\n");
4109: fprintf(ficgp, "set size 0.65,0.65\n");
4110: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4111:
4112: }
4113:
4114:
1.88 brouard 4115:
1.91 brouard 4116:
1.53 brouard 4117: /***********************************************/
4118: /**************** Main Program *****************/
4119: /***********************************************/
4120:
4121: int main(int argc, char *argv[])
4122: {
1.61 brouard 4123: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 4124: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.110 brouard 4125: int linei, month, year,iout;
1.95 brouard 4126: int jj, ll, li, lj, lk, imk;
1.85 brouard 4127: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 4128: int itimes;
1.98 brouard 4129: int NDIM=2;
1.95 brouard 4130:
4131: char ca[32], cb[32], cc[32];
1.111 brouard 4132: char dummy[]=" ";
1.87 brouard 4133: /* FILE *fichtm; *//* Html File */
4134: /* FILE *ficgp;*/ /*Gnuplot File */
1.107 brouard 4135: struct stat info;
1.53 brouard 4136: double agedeb, agefin,hf;
4137: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4138:
4139: double fret;
4140: double **xi,tmp,delta;
4141:
4142: double dum; /* Dummy variable */
4143: double ***p3mat;
4144: double ***mobaverage;
4145: int *indx;
4146: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 4147: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.99 brouard 4148: char pathr[MAXLINE], pathimach[MAXLINE];
1.114 brouard 4149: char **bp, *tok, *val; /* pathtot */
1.53 brouard 4150: int firstobs=1, lastobs=10;
4151: int sdeb, sfin; /* Status at beginning and end */
4152: int c, h , cpt,l;
4153: int ju,jl, mi;
4154: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 4155: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 4156: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 4157: int mobilav=0,popforecast=0;
4158: int hstepm, nhstepm;
1.105 lievre 4159: int agemortsup;
4160: float sumlpop=0.;
1.74 brouard 4161: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4162: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 4163:
4164: double bage, fage, age, agelim, agebase;
4165: double ftolpl=FTOL;
4166: double **prlim;
4167: double *severity;
4168: double ***param; /* Matrix of parameters */
4169: double *p;
4170: double **matcov; /* Matrix of covariance */
4171: double ***delti3; /* Scale */
4172: double *delti; /* Scale */
4173: double ***eij, ***vareij;
4174: double **varpl; /* Variances of prevalence limits by age */
4175: double *epj, vepp;
4176: double kk1, kk2;
1.74 brouard 4177: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 brouard 4178: double **ximort;
1.53 brouard 4179: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 brouard 4180: int *dcwave;
1.53 brouard 4181:
4182: char z[1]="c", occ;
1.86 brouard 4183:
1.53 brouard 4184: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 4185: char strstart[80], *strt, strtend[80];
1.85 brouard 4186: char *stratrunc;
4187: int lstra;
4188:
4189: long total_usecs;
1.53 brouard 4190:
1.95 brouard 4191: /* setlocale (LC_ALL, ""); */
4192: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4193: /* textdomain (PACKAGE); */
4194: /* setlocale (LC_CTYPE, ""); */
4195: /* setlocale (LC_MESSAGES, ""); */
4196:
1.85 brouard 4197: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4198: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4199: curr_time=start_time;
1.85 brouard 4200: tm = *localtime(&start_time.tv_sec);
4201: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4202: strcpy(strstart,asctime(&tm));
1.86 brouard 4203:
1.88 brouard 4204: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4205: /* tp.tv_sec = tp.tv_sec +86400; */
4206: /* tm = *localtime(&start_time.tv_sec); */
4207: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4208: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4209: /* tmg.tm_hour=tmg.tm_hour + 1; */
4210: /* tp.tv_sec = mktime(&tmg); */
4211: /* strt=asctime(&tmg); */
1.88 brouard 4212: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4213: /* (void) time (&time_value);
4214: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4215: * tm = *localtime(&time_value);
1.88 brouard 4216: * strstart=asctime(&tm);
4217: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4218: */
4219:
1.91 brouard 4220: nberr=0; /* Number of errors and warnings */
4221: nbwarn=0;
1.53 brouard 4222: getcwd(pathcd, size);
4223:
1.81 brouard 4224: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4225: if(argc <=1){
4226: printf("\nEnter the parameter file name: ");
1.114 brouard 4227: fgets(pathr,FILENAMELENGTH,stdin);
4228: i=strlen(pathr);
4229: if(pathr[i-1]=='\n')
4230: pathr[i-1]='\0';
4231: for (tok = pathr; tok != NULL; ){
4232: printf("Pathr |%s|\n",pathr);
4233: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4234: printf("val= |%s| pathr=%s\n",val,pathr);
4235: strcpy (pathtot, val);
4236: if(pathr[0] == '\0') break; /* Un peu sale */
4237: }
1.53 brouard 4238: }
4239: else{
4240: strcpy(pathtot,argv[1]);
4241: }
1.88 brouard 4242: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4243: /*cygwin_split_path(pathtot,path,optionfile);
4244: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4245: /* cutv(path,optionfile,pathtot,'\\');*/
4246:
1.107 brouard 4247: /* Split argv[0], imach program to get pathimach */
4248: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
1.99 brouard 4249: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4250: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.99 brouard 4251: /* strcpy(pathimach,argv[0]); */
1.107 brouard 4252: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
1.53 brouard 4253: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4254: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 4255: chdir(path);
1.88 brouard 4256: strcpy(command,"mkdir ");
4257: strcat(command,optionfilefiname);
4258: if((outcmd=system(command)) != 0){
4259: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4260: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4261: /* fclose(ficlog); */
4262: /* exit(1); */
4263: }
4264: /* if((imk=mkdir(optionfilefiname))<0){ */
4265: /* perror("mkdir"); */
4266: /* } */
1.53 brouard 4267:
1.59 brouard 4268: /*-------- arguments in the command line --------*/
1.53 brouard 4269:
4270: /* Log file */
4271: strcat(filelog, optionfilefiname);
4272: strcat(filelog,".log"); /* */
4273: if((ficlog=fopen(filelog,"w"))==NULL) {
4274: printf("Problem with logfile %s\n",filelog);
4275: goto end;
4276: }
4277: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4278: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.99 brouard 4279: fprintf(ficlog,"\nEnter the parameter file name: \n");
4280: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
1.88 brouard 4281: path=%s \n\
4282: optionfile=%s\n\
4283: optionfilext=%s\n\
1.99 brouard 4284: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4285:
1.94 brouard 4286: printf("Local time (at start):%s",strstart);
4287: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4288: fflush(ficlog);
1.91 brouard 4289: /* (void) gettimeofday(&curr_time,&tzp); */
4290: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4291:
4292: /* */
4293: strcpy(fileres,"r");
4294: strcat(fileres, optionfilefiname);
4295: strcat(fileres,".txt"); /* Other files have txt extension */
4296:
4297: /*---------arguments file --------*/
4298:
4299: if((ficpar=fopen(optionfile,"r"))==NULL) {
4300: printf("Problem with optionfile %s\n",optionfile);
4301: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4302: fflush(ficlog);
1.53 brouard 4303: goto end;
4304: }
4305:
1.88 brouard 4306:
4307:
1.53 brouard 4308: strcpy(filereso,"o");
4309: strcat(filereso,fileres);
1.88 brouard 4310: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4311: printf("Problem with Output resultfile: %s\n", filereso);
4312: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4313: fflush(ficlog);
1.53 brouard 4314: goto end;
4315: }
4316:
4317: /* Reads comments: lines beginning with '#' */
1.85 brouard 4318: numlinepar=0;
1.53 brouard 4319: while((c=getc(ficpar))=='#' && c!= EOF){
4320: ungetc(c,ficpar);
4321: fgets(line, MAXLINE, ficpar);
1.85 brouard 4322: numlinepar++;
1.53 brouard 4323: puts(line);
4324: fputs(line,ficparo);
1.85 brouard 4325: fputs(line,ficlog);
1.53 brouard 4326: }
4327: ungetc(c,ficpar);
4328:
4329: 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 4330: numlinepar++;
1.53 brouard 4331: 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);
4332: 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 4333: 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);
4334: fflush(ficlog);
1.59 brouard 4335: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4336: ungetc(c,ficpar);
4337: fgets(line, MAXLINE, ficpar);
1.85 brouard 4338: numlinepar++;
1.53 brouard 4339: puts(line);
4340: fputs(line,ficparo);
1.85 brouard 4341: fputs(line,ficlog);
1.53 brouard 4342: }
4343: ungetc(c,ficpar);
1.85 brouard 4344:
1.53 brouard 4345:
4346: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4347: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4348: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4349:
1.58 lievre 4350: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4351: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 brouard 4352: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4353:
4354: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4355: delti=delti3[1][1];
4356: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4357: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4358: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4359: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4360: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 brouard 4361: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4362: fclose (ficparo);
4363: fclose (ficlog);
4364: exit(0);
4365: }
1.98 brouard 4366: else if(mle==-3) {
4367: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4368: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4369: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4370: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4371: matcov=matrix(1,npar,1,npar);
1.53 brouard 4372: }
1.98 brouard 4373: else{
4374: /* Read guess parameters */
4375: /* Reads comments: lines beginning with '#' */
4376: while((c=getc(ficpar))=='#' && c!= EOF){
4377: ungetc(c,ficpar);
4378: fgets(line, MAXLINE, ficpar);
1.85 brouard 4379: numlinepar++;
1.98 brouard 4380: puts(line);
4381: fputs(line,ficparo);
4382: fputs(line,ficlog);
1.53 brouard 4383: }
1.98 brouard 4384: ungetc(c,ficpar);
4385:
4386: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4387: for(i=1; i <=nlstate; i++){
4388: j=0;
4389: for(jj=1; jj <=nlstate+ndeath; jj++){
4390: if(jj==i) continue;
4391: j++;
4392: fscanf(ficpar,"%1d%1d",&i1,&j1);
4393: if ((i1 != i) && (j1 != j)){
4394: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4395: exit(1);
4396: }
4397: fprintf(ficparo,"%1d%1d",i1,j1);
4398: if(mle==1)
4399: printf("%1d%1d",i,j);
4400: fprintf(ficlog,"%1d%1d",i,j);
4401: for(k=1; k<=ncovmodel;k++){
4402: fscanf(ficpar," %lf",¶m[i][j][k]);
4403: if(mle==1){
4404: printf(" %lf",param[i][j][k]);
4405: fprintf(ficlog," %lf",param[i][j][k]);
4406: }
4407: else
4408: fprintf(ficlog," %lf",param[i][j][k]);
4409: fprintf(ficparo," %lf",param[i][j][k]);
4410: }
4411: fscanf(ficpar,"\n");
4412: numlinepar++;
4413: if(mle==1)
4414: printf("\n");
4415: fprintf(ficlog,"\n");
4416: fprintf(ficparo,"\n");
4417: }
4418: }
4419: fflush(ficlog);
1.85 brouard 4420:
1.98 brouard 4421: p=param[1][1];
4422:
4423: /* Reads comments: lines beginning with '#' */
4424: while((c=getc(ficpar))=='#' && c!= EOF){
4425: ungetc(c,ficpar);
4426: fgets(line, MAXLINE, ficpar);
4427: numlinepar++;
4428: puts(line);
4429: fputs(line,ficparo);
4430: fputs(line,ficlog);
4431: }
1.53 brouard 4432: ungetc(c,ficpar);
4433:
1.98 brouard 4434: for(i=1; i <=nlstate; i++){
4435: for(j=1; j <=nlstate+ndeath-1; j++){
4436: fscanf(ficpar,"%1d%1d",&i1,&j1);
4437: if ((i1-i)*(j1-j)!=0){
4438: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4439: exit(1);
4440: }
4441: printf("%1d%1d",i,j);
4442: fprintf(ficparo,"%1d%1d",i1,j1);
4443: fprintf(ficlog,"%1d%1d",i1,j1);
4444: for(k=1; k<=ncovmodel;k++){
4445: fscanf(ficpar,"%le",&delti3[i][j][k]);
4446: printf(" %le",delti3[i][j][k]);
4447: fprintf(ficparo," %le",delti3[i][j][k]);
4448: fprintf(ficlog," %le",delti3[i][j][k]);
4449: }
4450: fscanf(ficpar,"\n");
4451: numlinepar++;
4452: printf("\n");
4453: fprintf(ficparo,"\n");
4454: fprintf(ficlog,"\n");
1.85 brouard 4455: }
1.53 brouard 4456: }
1.98 brouard 4457: fflush(ficlog);
1.85 brouard 4458:
1.98 brouard 4459: delti=delti3[1][1];
1.74 brouard 4460:
4461:
1.98 brouard 4462: /* 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 4463:
1.98 brouard 4464: /* Reads comments: lines beginning with '#' */
4465: while((c=getc(ficpar))=='#' && c!= EOF){
4466: ungetc(c,ficpar);
4467: fgets(line, MAXLINE, ficpar);
4468: numlinepar++;
4469: puts(line);
4470: fputs(line,ficparo);
4471: fputs(line,ficlog);
4472: }
1.53 brouard 4473: ungetc(c,ficpar);
4474:
1.98 brouard 4475: matcov=matrix(1,npar,1,npar);
4476: for(i=1; i <=npar; i++){
4477: fscanf(ficpar,"%s",&str);
4478: if(mle==1)
4479: printf("%s",str);
4480: fprintf(ficlog,"%s",str);
4481: fprintf(ficparo,"%s",str);
4482: for(j=1; j <=i; j++){
4483: fscanf(ficpar," %le",&matcov[i][j]);
4484: if(mle==1){
4485: printf(" %.5le",matcov[i][j]);
4486: }
4487: fprintf(ficlog," %.5le",matcov[i][j]);
4488: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4489: }
1.98 brouard 4490: fscanf(ficpar,"\n");
4491: numlinepar++;
4492: if(mle==1)
4493: printf("\n");
4494: fprintf(ficlog,"\n");
4495: fprintf(ficparo,"\n");
1.53 brouard 4496: }
1.98 brouard 4497: for(i=1; i <=npar; i++)
4498: for(j=i+1;j<=npar;j++)
4499: matcov[i][j]=matcov[j][i];
4500:
1.53 brouard 4501: if(mle==1)
4502: printf("\n");
4503: fprintf(ficlog,"\n");
1.98 brouard 4504:
4505: fflush(ficlog);
4506:
4507: /*-------- Rewriting parameter file ----------*/
4508: strcpy(rfileres,"r"); /* "Rparameterfile */
4509: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4510: strcat(rfileres,"."); /* */
4511: strcat(rfileres,optionfilext); /* Other files have txt extension */
4512: if((ficres =fopen(rfileres,"w"))==NULL) {
4513: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4514: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4515: }
4516: fprintf(ficres,"#%s\n",version);
4517: } /* End of mle != -3 */
1.53 brouard 4518:
1.59 brouard 4519: /*-------- data file ----------*/
4520: if((fic=fopen(datafile,"r"))==NULL) {
4521: printf("Problem with datafile: %s\n", datafile);goto end;
4522: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4523: }
4524:
4525: n= lastobs;
4526: severity = vector(1,maxwav);
4527: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4528: num=lvector(1,n);
1.59 brouard 4529: moisnais=vector(1,n);
4530: annais=vector(1,n);
4531: moisdc=vector(1,n);
4532: andc=vector(1,n);
4533: agedc=vector(1,n);
4534: cod=ivector(1,n);
4535: weight=vector(1,n);
4536: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4537: mint=matrix(1,maxwav,1,n);
4538: anint=matrix(1,maxwav,1,n);
4539: s=imatrix(1,maxwav+1,1,n);
4540: tab=ivector(1,NCOVMAX);
4541: ncodemax=ivector(1,8);
4542:
4543: i=1;
1.109 brouard 4544: linei=0;
1.111 brouard 4545: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
1.109 brouard 4546: linei=linei+1;
4547: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
1.111 brouard 4548: if(line[j] == '\t')
4549: line[j] = ' ';
4550: }
4551: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4552: ;
4553: };
4554: line[j+1]=0; /* Trims blanks at end of line */
4555: if(line[0]=='#'){
4556: fprintf(ficlog,"Comment line\n%s\n",line);
4557: printf("Comment line\n%s\n",line);
4558: continue;
4559: }
1.109 brouard 4560:
1.111 brouard 4561: for (j=maxwav;j>=1;j--){
1.110 brouard 4562: cutv(stra, strb,line,' ');
1.111 brouard 4563: errno=0;
4564: lval=strtol(strb,&endptr,10);
4565: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4566: if( strb[0]=='\0' || (*endptr != '\0')){
4567: printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
1.109 brouard 4568: exit(1);
4569: }
1.111 brouard 4570: s[j][i]=lval;
4571:
1.109 brouard 4572: strcpy(line,stra);
1.111 brouard 4573: cutv(stra, strb,line,' ');
1.110 brouard 4574: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
1.109 brouard 4575: }
1.111 brouard 4576: else if(iout=sscanf(strb,"%s.") != 0){
1.110 brouard 4577: month=99;
4578: year=9999;
4579: }else{
1.111 brouard 4580: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
1.109 brouard 4581: exit(1);
4582: }
1.111 brouard 4583: anint[j][i]= (double) year;
4584: mint[j][i]= (double)month;
1.109 brouard 4585: strcpy(line,stra);
1.111 brouard 4586: } /* ENd Waves */
4587:
4588: cutv(stra, strb,line,' ');
4589: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4590: }
4591: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4592: month=99;
4593: year=9999;
4594: }else{
4595: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4596: exit(1);
4597: }
4598: andc[i]=(double) year;
4599: moisdc[i]=(double) month;
4600: strcpy(line,stra);
4601:
4602: cutv(stra, strb,line,' ');
4603: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4604: }
4605: else if(iout=sscanf(strb,"%s.") != 0){
4606: month=99;
4607: year=9999;
4608: }else{
4609: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
4610: exit(1);
4611: }
4612: annais[i]=(double)(year);
4613: moisnais[i]=(double)(month);
4614: strcpy(line,stra);
4615:
4616: cutv(stra, strb,line,' ');
4617: errno=0;
4618: lval=strtol(strb,&endptr,10);
4619: if( strb[0]=='\0' || (*endptr != '\0')){
4620: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4621: exit(1);
4622: }
4623: weight[i]=(double)(lval);
4624: strcpy(line,stra);
4625:
4626: for (j=ncovcol;j>=1;j--){
1.109 brouard 4627: cutv(stra, strb,line,' ');
4628: errno=0;
4629: lval=strtol(strb,&endptr,10);
4630: if( strb[0]=='\0' || (*endptr != '\0')){
1.111 brouard 4631: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
4632: exit(1);
4633: }
4634: if(lval <-1 || lval >1){
4635: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\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,linei, i,line,j);
1.109 brouard 4636: exit(1);
4637: }
1.111 brouard 4638: covar[j][i]=(double)(lval);
1.109 brouard 4639: strcpy(line,stra);
1.111 brouard 4640: }
4641: lstra=strlen(stra);
4642:
4643: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4644: stratrunc = &(stra[lstra-9]);
4645: num[i]=atol(stratrunc);
4646: }
4647: else
4648: num[i]=atol(stra);
4649: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4650: 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;}*/
4651:
4652: i=i+1;
1.109 brouard 4653: } /* End loop reading data */
1.113 brouard 4654: fclose(fic);
1.59 brouard 4655: /* printf("ii=%d", ij);
4656: scanf("%d",i);*/
1.53 brouard 4657: imx=i-1; /* Number of individuals */
4658:
4659: /* for (i=1; i<=imx; i++){
4660: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4661: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4662: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4663: }*/
4664: /* for (i=1; i<=imx; i++){
4665: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4666: 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 4667:
1.106 brouard 4668: /* for (i=1; i<=imx; i++) */
1.53 brouard 4669:
1.71 brouard 4670: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4671: else weight[i]=1;*/
4672:
1.106 brouard 4673: /* Calculation of the number of parameters from char model */
1.53 brouard 4674: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4675: Tprod=ivector(1,15);
4676: Tvaraff=ivector(1,15);
4677: Tvard=imatrix(1,15,1,2);
4678: Tage=ivector(1,15);
4679:
1.58 lievre 4680: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4681: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4682: j=nbocc(model,'+'); /* j=Number of '+' */
4683: j1=nbocc(model,'*'); /* j1=Number of '*' */
4684: cptcovn=j+1;
4685: cptcovprod=j1; /*Number of products */
1.53 brouard 4686:
4687: strcpy(modelsav,model);
4688: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4689: printf("Error. Non available option model=%s ",model);
4690: fprintf(ficlog,"Error. Non available option model=%s ",model);
4691: goto end;
4692: }
4693:
1.59 brouard 4694: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4695:
1.53 brouard 4696: for(i=(j+1); i>=1;i--){
4697: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4698: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4699: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4700: /*scanf("%d",i);*/
4701: if (strchr(strb,'*')) { /* Model includes a product */
4702: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4703: if (strcmp(strc,"age")==0) { /* Vn*age */
4704: cptcovprod--;
4705: cutv(strb,stre,strd,'V');
4706: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4707: cptcovage++;
4708: Tage[cptcovage]=i;
4709: /*printf("stre=%s ", stre);*/
4710: }
4711: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4712: cptcovprod--;
4713: cutv(strb,stre,strc,'V');
4714: Tvar[i]=atoi(stre);
4715: cptcovage++;
4716: Tage[cptcovage]=i;
4717: }
4718: else { /* Age is not in the model */
4719: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4720: Tvar[i]=ncovcol+k1;
4721: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4722: Tprod[k1]=i;
4723: Tvard[k1][1]=atoi(strc); /* m*/
4724: Tvard[k1][2]=atoi(stre); /* n */
4725: Tvar[cptcovn+k2]=Tvard[k1][1];
4726: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4727: for (k=1; k<=lastobs;k++)
4728: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4729: k1++;
4730: k2=k2+2;
4731: }
4732: }
4733: else { /* no more sum */
4734: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4735: /* scanf("%d",i);*/
4736: cutv(strd,strc,strb,'V');
4737: Tvar[i]=atoi(strc);
4738: }
4739: strcpy(modelsav,stra);
4740: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4741: scanf("%d",i);*/
4742: } /* end of loop + */
4743: } /* end model */
4744:
1.58 lievre 4745: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4746: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4747:
1.53 brouard 4748: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4749: printf("cptcovprod=%d ", cptcovprod);
4750: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4751:
1.113 brouard 4752: scanf("%d ",i);*/
1.53 brouard 4753:
4754: /* if(mle==1){*/
1.59 brouard 4755: if (weightopt != 1) { /* Maximisation without weights*/
4756: for(i=1;i<=n;i++) weight[i]=1.0;
4757: }
1.53 brouard 4758: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4759: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4760:
1.59 brouard 4761: for (i=1; i<=imx; i++) {
4762: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4763: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4764: anint[m][i]=9999;
4765: s[m][i]=-1;
4766: }
1.76 brouard 4767: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4768: nberr++;
1.85 brouard 4769: 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);
4770: 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 4771: s[m][i]=-1;
4772: }
4773: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4774: nberr++;
1.85 brouard 4775: 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]);
4776: 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 4777: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4778: }
1.53 brouard 4779: }
1.59 brouard 4780: }
1.53 brouard 4781:
1.59 brouard 4782: for (i=1; i<=imx; i++) {
4783: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4784: for(m=firstpass; (m<= lastpass); m++){
1.105 lievre 4785: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
1.59 brouard 4786: if (s[m][i] >= nlstate+1) {
4787: if(agedc[i]>0)
1.76 brouard 4788: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4789: agev[m][i]=agedc[i];
1.59 brouard 4790: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4791: else {
1.76 brouard 4792: if ((int)andc[i]!=9999){
1.91 brouard 4793: nbwarn++;
1.85 brouard 4794: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4795: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4796: agev[m][i]=-1;
1.53 brouard 4797: }
4798: }
1.70 brouard 4799: }
1.69 brouard 4800: else if(s[m][i] !=9){ /* Standard case, age in fractional
1.108 lievre 4801: years but with the precision of a month */
1.59 brouard 4802: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4803: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4804: agev[m][i]=1;
4805: else if(agev[m][i] <agemin){
4806: agemin=agev[m][i];
4807: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4808: }
1.59 brouard 4809: else if(agev[m][i] >agemax){
4810: agemax=agev[m][i];
4811: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4812: }
1.59 brouard 4813: /*agev[m][i]=anint[m][i]-annais[i];*/
4814: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4815: }
1.59 brouard 4816: else { /* =9 */
1.53 brouard 4817: agev[m][i]=1;
1.59 brouard 4818: s[m][i]=-1;
4819: }
1.53 brouard 4820: }
1.59 brouard 4821: else /*= 0 Unknown */
4822: agev[m][i]=1;
4823: }
1.53 brouard 4824:
1.59 brouard 4825: }
4826: for (i=1; i<=imx; i++) {
1.71 brouard 4827: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4828: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4829: nberr++;
1.59 brouard 4830: 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);
4831: 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);
4832: goto end;
1.53 brouard 4833: }
4834: }
1.59 brouard 4835: }
1.53 brouard 4836:
1.71 brouard 4837: /*for (i=1; i<=imx; i++){
4838: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4839: 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 4840: }
4841:
4842: }*/
4843:
1.97 lievre 4844:
1.59 brouard 4845: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4846: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4847:
1.98 brouard 4848: agegomp=(int)agemin;
1.59 brouard 4849: free_vector(severity,1,maxwav);
4850: free_imatrix(outcome,1,maxwav+1,1,n);
4851: free_vector(moisnais,1,n);
4852: free_vector(annais,1,n);
4853: /* free_matrix(mint,1,maxwav,1,n);
4854: free_matrix(anint,1,maxwav,1,n);*/
4855: free_vector(moisdc,1,n);
4856: free_vector(andc,1,n);
1.53 brouard 4857:
4858:
1.59 brouard 4859: wav=ivector(1,imx);
4860: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4861: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4862: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4863:
1.59 brouard 4864: /* Concatenates waves */
4865: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4866:
1.59 brouard 4867: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4868:
1.59 brouard 4869: Tcode=ivector(1,100);
4870: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4871: ncodemax[1]=1;
4872: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4873:
1.59 brouard 4874: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4875: the estimations*/
4876: h=0;
4877: m=pow(2,cptcoveff);
1.53 brouard 4878:
1.59 brouard 4879: for(k=1;k<=cptcoveff; k++){
4880: for(i=1; i <=(m/pow(2,k));i++){
4881: for(j=1; j <= ncodemax[k]; j++){
4882: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4883: h++;
4884: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4885: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4886: }
4887: }
4888: }
4889: }
4890: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4891: codtab[1][2]=1;codtab[2][2]=2; */
4892: /* for(i=1; i <=m ;i++){
4893: for(k=1; k <=cptcovn; k++){
4894: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4895: }
4896: printf("\n");
1.53 brouard 4897: }
1.59 brouard 4898: scanf("%d",i);*/
1.53 brouard 4899:
1.86 brouard 4900: /*------------ gnuplot -------------*/
4901: strcpy(optionfilegnuplot,optionfilefiname);
1.98 brouard 4902: if(mle==-3)
4903: strcat(optionfilegnuplot,"-mort");
1.86 brouard 4904: strcat(optionfilegnuplot,".gp");
1.98 brouard 4905:
1.86 brouard 4906: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4907: printf("Problem with file %s",optionfilegnuplot);
4908: }
4909: else{
4910: fprintf(ficgp,"\n# %s\n", version);
4911: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4912: fprintf(ficgp,"set missing 'NaNq'\n");
4913: }
1.88 brouard 4914: /* fclose(ficgp);*/
1.86 brouard 4915: /*--------- index.htm --------*/
4916:
1.91 brouard 4917: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 brouard 4918: if(mle==-3)
4919: strcat(optionfilehtm,"-mort");
1.86 brouard 4920: strcat(optionfilehtm,".htm");
4921: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4922: printf("Problem with %s \n",optionfilehtm), exit(0);
4923: }
4924:
1.91 brouard 4925: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4926: strcat(optionfilehtmcov,"-cov.htm");
4927: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4928: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4929: }
4930: else{
4931: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4932: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4933: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4934: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4935: }
4936:
1.87 brouard 4937: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4938: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4939: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4940: \n\
4941: <hr size=\"2\" color=\"#EC5E5E\">\
4942: <ul><li><h4>Parameter files</h4>\n\
4943: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4944: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4945: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4946: - Date and time at start: %s</ul>\n",\
1.91 brouard 4947: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4948: fileres,fileres,\
1.88 brouard 4949: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4950: fflush(fichtm);
1.86 brouard 4951:
1.88 brouard 4952: strcpy(pathr,path);
4953: strcat(pathr,optionfilefiname);
4954: chdir(optionfilefiname); /* Move to directory named optionfile */
4955:
1.59 brouard 4956: /* Calculates basic frequencies. Computes observed prevalence at single age
4957: and prints on file fileres'p'. */
1.105 lievre 4958: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
1.53 brouard 4959:
1.88 brouard 4960: fprintf(fichtm,"\n");
4961: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4962: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4963: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4964: imx,agemin,agemax,jmin,jmax,jmean);
4965: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4966: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4967: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4968: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4969: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4970:
4971:
1.59 brouard 4972: /* For Powell, parameters are in a vector p[] starting at p[1]
4973: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4974: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4975:
1.86 brouard 4976: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.110 brouard 4977:
1.98 brouard 4978: if (mle==-3){
4979: ximort=matrix(1,NDIM,1,NDIM);
4980: cens=ivector(1,n);
4981: ageexmed=vector(1,n);
4982: agecens=vector(1,n);
4983: dcwave=ivector(1,n);
4984:
4985: for (i=1; i<=imx; i++){
4986: dcwave[i]=-1;
1.110 brouard 4987: for (m=firstpass; m<=lastpass; m++)
4988: if (s[m][i]>nlstate) {
4989: dcwave[i]=m;
1.98 brouard 4990: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4991: break;
4992: }
4993: }
4994:
4995: for (i=1; i<=imx; i++) {
4996: if (wav[i]>0){
4997: ageexmed[i]=agev[mw[1][i]][i];
1.110 brouard 4998: j=wav[i];
4999: agecens[i]=1.;
5000:
5001: if (ageexmed[i]> 1 && wav[i] > 0){
5002: agecens[i]=agev[mw[j][i]][i];
5003: cens[i]= 1;
5004: }else if (ageexmed[i]< 1)
5005: cens[i]= -1;
5006: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5007: cens[i]=0 ;
1.98 brouard 5008: }
5009: else cens[i]=-1;
5010: }
5011:
5012: for (i=1;i<=NDIM;i++) {
5013: for (j=1;j<=NDIM;j++)
5014: ximort[i][j]=(i == j ? 1.0 : 0.0);
5015: }
1.110 brouard 5016:
1.111 brouard 5017: p[1]=0.0268; p[NDIM]=0.083;
1.98 brouard 5018: /*printf("%lf %lf", p[1], p[2]);*/
5019:
5020:
1.110 brouard 5021: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5022: strcpy(filerespow,"pow-mort");
5023: strcat(filerespow,fileres);
5024: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5025: printf("Problem with resultfile: %s\n", filerespow);
5026: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5027: }
5028: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5029: /* for (i=1;i<=nlstate;i++)
5030: for(j=1;j<=nlstate+ndeath;j++)
5031: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5032: */
5033: fprintf(ficrespow,"\n");
5034:
1.98 brouard 5035: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5036: fclose(ficrespow);
1.53 brouard 5037:
1.110 brouard 5038: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
1.53 brouard 5039:
1.98 brouard 5040: for(i=1; i <=NDIM; i++)
5041: for(j=i+1;j<=NDIM;j++)
5042: matcov[i][j]=matcov[j][i];
5043:
5044: printf("\nCovariance matrix\n ");
5045: for(i=1; i <=NDIM; i++) {
5046: for(j=1;j<=NDIM;j++){
5047: printf("%f ",matcov[i][j]);
1.95 brouard 5048: }
1.98 brouard 5049: printf("\n ");
5050: }
5051:
5052: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5053: for (i=1;i<=NDIM;i++)
5054: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.105 lievre 5055:
1.110 brouard 5056: lsurv=vector(1,AGESUP);
1.105 lievre 5057: lpop=vector(1,AGESUP);
5058: tpop=vector(1,AGESUP);
5059: lsurv[agegomp]=100000;
1.110 brouard 5060:
5061: for (k=agegomp;k<=AGESUP;k++) {
1.105 lievre 5062: agemortsup=k;
5063: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5064: }
1.110 brouard 5065:
5066: for (k=agegomp;k<agemortsup;k++)
1.105 lievre 5067: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
1.110 brouard 5068:
1.105 lievre 5069: for (k=agegomp;k<agemortsup;k++){
5070: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5071: sumlpop=sumlpop+lpop[k];
5072: }
1.110 brouard 5073:
5074: tpop[agegomp]=sumlpop;
1.105 lievre 5075: for (k=agegomp;k<(agemortsup-3);k++){
5076: /* tpop[k+1]=2;*/
5077: tpop[k+1]=tpop[k]-lpop[k];
1.110 brouard 5078: }
5079:
5080:
5081: printf("\nAge lx qx dx Lx Tx e(x)\n");
1.105 lievre 5082: for (k=agegomp;k<(agemortsup-2);k++)
5083: 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]);
1.110 brouard 5084:
5085:
1.98 brouard 5086: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5087: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5088:
5089: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5090: stepm, weightopt,\
1.105 lievre 5091: model,imx,p,matcov,agemortsup);
1.110 brouard 5092:
1.105 lievre 5093: free_vector(lsurv,1,AGESUP);
5094: free_vector(lpop,1,AGESUP);
5095: free_vector(tpop,1,AGESUP);
1.98 brouard 5096: } /* Endof if mle==-3 */
1.110 brouard 5097:
1.98 brouard 5098: else{ /* For mle >=1 */
5099:
5100: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5101: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5102: for (k=1; k<=npar;k++)
5103: printf(" %d %8.5f",k,p[k]);
5104: printf("\n");
5105: globpr=1; /* to print the contributions */
5106: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5107: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5108: for (k=1; k<=npar;k++)
5109: printf(" %d %8.5f",k,p[k]);
5110: printf("\n");
5111: if(mle>=1){ /* Could be 1 or 2 */
5112: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 5113: }
1.98 brouard 5114:
5115: /*--------- results files --------------*/
5116: 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);
5117:
5118:
5119: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5120: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5121: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5122: for(i=1,jk=1; i <=nlstate; i++){
5123: for(k=1; k <=(nlstate+ndeath); k++){
5124: if (k != i) {
5125: printf("%d%d ",i,k);
5126: fprintf(ficlog,"%d%d ",i,k);
5127: fprintf(ficres,"%1d%1d ",i,k);
5128: for(j=1; j <=ncovmodel; j++){
5129: printf("%f ",p[jk]);
5130: fprintf(ficlog,"%f ",p[jk]);
5131: fprintf(ficres,"%f ",p[jk]);
5132: jk++;
5133: }
5134: printf("\n");
5135: fprintf(ficlog,"\n");
5136: fprintf(ficres,"\n");
1.59 brouard 5137: }
5138: }
5139: }
1.98 brouard 5140: if(mle!=0){
5141: /* Computing hessian and covariance matrix */
5142: ftolhess=ftol; /* Usually correct */
5143: hesscov(matcov, p, npar, delti, ftolhess, func);
5144: }
5145: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5146: printf("# Scales (for hessian or gradient estimation)\n");
5147: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5148: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 5149: for(j=1; j <=nlstate+ndeath; j++){
1.98 brouard 5150: if (j!=i) {
5151: fprintf(ficres,"%1d%1d",i,j);
5152: printf("%1d%1d",i,j);
5153: fprintf(ficlog,"%1d%1d",i,j);
5154: for(k=1; k<=ncovmodel;k++){
5155: printf(" %.5e",delti[jk]);
5156: fprintf(ficlog," %.5e",delti[jk]);
5157: fprintf(ficres," %.5e",delti[jk]);
5158: jk++;
1.95 brouard 5159: }
1.98 brouard 5160: printf("\n");
5161: fprintf(ficlog,"\n");
5162: fprintf(ficres,"\n");
5163: }
5164: }
5165: }
5166:
5167: 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");
5168: if(mle>=1)
5169: 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");
5170: 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");
5171: /* # 121 Var(a12)\n\ */
5172: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5173: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5174: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5175: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5176: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5177: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5178: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5179:
5180:
5181: /* Just to have a covariance matrix which will be more understandable
5182: even is we still don't want to manage dictionary of variables
5183: */
5184: for(itimes=1;itimes<=2;itimes++){
5185: jj=0;
5186: for(i=1; i <=nlstate; i++){
5187: for(j=1; j <=nlstate+ndeath; j++){
5188: if(j==i) continue;
5189: for(k=1; k<=ncovmodel;k++){
5190: jj++;
5191: ca[0]= k+'a'-1;ca[1]='\0';
5192: if(itimes==1){
5193: if(mle>=1)
5194: printf("#%1d%1d%d",i,j,k);
5195: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5196: fprintf(ficres,"#%1d%1d%d",i,j,k);
5197: }else{
5198: if(mle>=1)
5199: printf("%1d%1d%d",i,j,k);
5200: fprintf(ficlog,"%1d%1d%d",i,j,k);
5201: fprintf(ficres,"%1d%1d%d",i,j,k);
5202: }
5203: ll=0;
5204: for(li=1;li <=nlstate; li++){
5205: for(lj=1;lj <=nlstate+ndeath; lj++){
5206: if(lj==li) continue;
5207: for(lk=1;lk<=ncovmodel;lk++){
5208: ll++;
5209: if(ll<=jj){
5210: cb[0]= lk +'a'-1;cb[1]='\0';
5211: if(ll<jj){
5212: if(itimes==1){
5213: if(mle>=1)
5214: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5215: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5216: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5217: }else{
5218: if(mle>=1)
5219: printf(" %.5e",matcov[jj][ll]);
5220: fprintf(ficlog," %.5e",matcov[jj][ll]);
5221: fprintf(ficres," %.5e",matcov[jj][ll]);
5222: }
1.95 brouard 5223: }else{
1.98 brouard 5224: if(itimes==1){
5225: if(mle>=1)
5226: printf(" Var(%s%1d%1d)",ca,i,j);
5227: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5228: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5229: }else{
5230: if(mle>=1)
5231: printf(" %.5e",matcov[jj][ll]);
5232: fprintf(ficlog," %.5e",matcov[jj][ll]);
5233: fprintf(ficres," %.5e",matcov[jj][ll]);
5234: }
1.95 brouard 5235: }
5236: }
1.98 brouard 5237: } /* end lk */
5238: } /* end lj */
5239: } /* end li */
5240: if(mle>=1)
5241: printf("\n");
5242: fprintf(ficlog,"\n");
5243: fprintf(ficres,"\n");
5244: numlinepar++;
5245: } /* end k*/
5246: } /*end j */
5247: } /* end i */
5248: } /* end itimes */
5249:
5250: fflush(ficlog);
5251: fflush(ficres);
5252:
5253: while((c=getc(ficpar))=='#' && c!= EOF){
5254: ungetc(c,ficpar);
5255: fgets(line, MAXLINE, ficpar);
5256: puts(line);
5257: fputs(line,ficparo);
5258: }
1.59 brouard 5259: ungetc(c,ficpar);
1.98 brouard 5260:
5261: estepm=0;
5262: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5263: if (estepm==0 || estepm < stepm) estepm=stepm;
5264: if (fage <= 2) {
5265: bage = ageminpar;
5266: fage = agemaxpar;
5267: }
5268:
5269: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5270: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5271: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5272:
5273: while((c=getc(ficpar))=='#' && c!= EOF){
5274: ungetc(c,ficpar);
5275: fgets(line, MAXLINE, ficpar);
5276: puts(line);
5277: fputs(line,ficparo);
5278: }
1.59 brouard 5279: ungetc(c,ficpar);
1.98 brouard 5280:
5281: 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);
5282: 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);
5283: 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);
5284: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5285: 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);
5286:
5287: while((c=getc(ficpar))=='#' && c!= EOF){
5288: ungetc(c,ficpar);
5289: fgets(line, MAXLINE, ficpar);
5290: puts(line);
5291: fputs(line,ficparo);
5292: }
1.59 brouard 5293: ungetc(c,ficpar);
1.98 brouard 5294:
5295:
5296: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5297: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5298:
5299: fscanf(ficpar,"pop_based=%d\n",&popbased);
5300: fprintf(ficparo,"pop_based=%d\n",popbased);
5301: fprintf(ficres,"pop_based=%d\n",popbased);
5302:
5303: while((c=getc(ficpar))=='#' && c!= EOF){
5304: ungetc(c,ficpar);
5305: fgets(line, MAXLINE, ficpar);
5306: puts(line);
5307: fputs(line,ficparo);
5308: }
1.53 brouard 5309: ungetc(c,ficpar);
1.98 brouard 5310:
5311: 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);
5312: 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);
5313: 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);
5314: 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);
5315: 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);
5316: /* day and month of proj2 are not used but only year anproj2.*/
5317:
5318:
5319:
5320: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5321: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5322:
5323: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5324: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5325:
5326: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5327: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5328: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5329:
5330: /*------------ free_vector -------------*/
5331: /* chdir(path); */
1.53 brouard 5332:
1.98 brouard 5333: free_ivector(wav,1,imx);
5334: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5335: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5336: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5337: free_lvector(num,1,n);
5338: free_vector(agedc,1,n);
5339: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5340: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5341: fclose(ficparo);
5342: fclose(ficres);
5343:
5344:
5345: /*--------------- Prevalence limit (stable prevalence) --------------*/
5346:
5347: strcpy(filerespl,"pl");
5348: strcat(filerespl,fileres);
5349: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5350: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5351: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5352: }
5353: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5354: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
1.105 lievre 5355: fprintf(ficrespl, "#Local time at start: %s", strstart);
1.98 brouard 5356: fprintf(ficrespl,"#Stable prevalence \n");
5357: fprintf(ficrespl,"#Age ");
5358: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5359: fprintf(ficrespl,"\n");
5360:
5361: prlim=matrix(1,nlstate,1,nlstate);
5362:
5363: agebase=ageminpar;
5364: agelim=agemaxpar;
5365: ftolpl=1.e-10;
5366: i1=cptcoveff;
5367: if (cptcovn < 1){i1=1;}
5368:
5369: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5370: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5371: k=k+1;
5372: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5373: fprintf(ficrespl,"\n#******");
5374: printf("\n#******");
5375: fprintf(ficlog,"\n#******");
5376: for(j=1;j<=cptcoveff;j++) {
5377: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5378: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5379: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5380: }
5381: fprintf(ficrespl,"******\n");
5382: printf("******\n");
5383: fprintf(ficlog,"******\n");
1.53 brouard 5384:
1.98 brouard 5385: for (age=agebase; age<=agelim; age++){
5386: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5387: fprintf(ficrespl,"%.0f ",age );
5388: for(j=1;j<=cptcoveff;j++)
5389: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5390: for(i=1; i<=nlstate;i++)
5391: fprintf(ficrespl," %.5f", prlim[i][i]);
5392: fprintf(ficrespl,"\n");
5393: }
1.53 brouard 5394: }
5395: }
1.98 brouard 5396: fclose(ficrespl);
1.53 brouard 5397:
1.98 brouard 5398: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5399:
1.98 brouard 5400: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5401: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5402: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5403: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5404: }
5405: printf("Computing pij: result on file '%s' \n", filerespij);
5406: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5407:
1.98 brouard 5408: stepsize=(int) (stepm+YEARM-1)/YEARM;
5409: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5410:
1.98 brouard 5411: agelim=AGESUP;
5412: hstepm=stepsize*YEARM; /* Every year of age */
5413: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5414:
1.98 brouard 5415: /* hstepm=1; aff par mois*/
1.105 lievre 5416: fprintf(ficrespij, "#Local time at start: %s", strstart);
1.98 brouard 5417: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5418: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5419: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5420: k=k+1;
5421: fprintf(ficrespij,"\n#****** ");
5422: for(j=1;j<=cptcoveff;j++)
5423: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5424: fprintf(ficrespij,"******\n");
1.53 brouard 5425:
1.98 brouard 5426: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5427: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5428: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5429:
1.98 brouard 5430: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5431:
1.98 brouard 5432: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5433: oldm=oldms;savm=savms;
5434: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5435: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5436: for(i=1; i<=nlstate;i++)
5437: for(j=1; j<=nlstate+ndeath;j++)
1.98 brouard 5438: fprintf(ficrespij," %1d-%1d",i,j);
5439: fprintf(ficrespij,"\n");
5440: for (h=0; h<=nhstepm; h++){
5441: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5442: for(i=1; i<=nlstate;i++)
5443: for(j=1; j<=nlstate+ndeath;j++)
5444: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5445: fprintf(ficrespij,"\n");
5446: }
5447: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5448: fprintf(ficrespij,"\n");
5449: }
1.59 brouard 5450: }
1.53 brouard 5451: }
5452:
1.105 lievre 5453: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.53 brouard 5454:
1.98 brouard 5455: fclose(ficrespij);
1.53 brouard 5456:
1.98 brouard 5457: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5458: for(i=1;i<=AGESUP;i++)
5459: for(j=1;j<=NCOVMAX;j++)
5460: for(k=1;k<=NCOVMAX;k++)
5461: probs[i][j][k]=0.;
5462:
5463: /*---------- Forecasting ------------------*/
5464: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5465: if(prevfcast==1){
5466: /* if(stepm ==1){*/
1.70 brouard 5467: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5468: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 brouard 5469: /* } */
5470: /* else{ */
5471: /* erreur=108; */
5472: /* 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); */
5473: /* 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); */
5474: /* } */
5475: }
1.53 brouard 5476:
5477:
1.98 brouard 5478: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5479:
1.98 brouard 5480: strcpy(filerest,"t");
5481: strcat(filerest,fileres);
5482: if((ficrest=fopen(filerest,"w"))==NULL) {
5483: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5484: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5485: }
5486: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5487: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
1.53 brouard 5488:
5489:
1.98 brouard 5490: strcpy(filerese,"e");
5491: strcat(filerese,fileres);
5492: if((ficreseij=fopen(filerese,"w"))==NULL) {
5493: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5494: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5495: }
5496: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5497: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5498:
1.98 brouard 5499: strcpy(fileresv,"v");
5500: strcat(fileresv,fileres);
5501: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5502: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5503: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5504: }
5505: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5506: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5507:
1.98 brouard 5508: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5509: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5510: /* 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",\
5511: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5512: */
1.58 lievre 5513:
1.98 brouard 5514: if (mobilav!=0) {
5515: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5516: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5517: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5518: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5519: }
1.54 brouard 5520: }
1.53 brouard 5521:
1.98 brouard 5522: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5523: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5524: k=k+1;
5525: fprintf(ficrest,"\n#****** ");
5526: for(j=1;j<=cptcoveff;j++)
5527: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5528: fprintf(ficrest,"******\n");
5529:
5530: fprintf(ficreseij,"\n#****** ");
5531: for(j=1;j<=cptcoveff;j++)
5532: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5533: fprintf(ficreseij,"******\n");
5534:
5535: fprintf(ficresvij,"\n#****** ");
5536: for(j=1;j<=cptcoveff;j++)
5537: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5538: fprintf(ficresvij,"******\n");
5539:
5540: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5541: oldm=oldms;savm=savms;
1.105 lievre 5542: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.53 brouard 5543:
1.98 brouard 5544: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5545: oldm=oldms;savm=savms;
1.105 lievre 5546: 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 5547: if(popbased==1){
1.105 lievre 5548: 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 5549: }
1.53 brouard 5550:
1.105 lievre 5551: fprintf(ficrest, "#Local time at start: %s", strstart);
1.98 brouard 5552: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5553: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5554: fprintf(ficrest,"\n");
5555:
5556: epj=vector(1,nlstate+1);
5557: for(age=bage; age <=fage ;age++){
5558: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5559: if (popbased==1) {
5560: if(mobilav ==0){
5561: for(i=1; i<=nlstate;i++)
5562: prlim[i][i]=probs[(int)age][i][k];
5563: }else{ /* mobilav */
5564: for(i=1; i<=nlstate;i++)
5565: prlim[i][i]=mobaverage[(int)age][i][k];
5566: }
1.53 brouard 5567: }
5568:
1.98 brouard 5569: fprintf(ficrest," %4.0f",age);
5570: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5571: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5572: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5573: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5574: }
5575: epj[nlstate+1] +=epj[j];
1.53 brouard 5576: }
5577:
1.98 brouard 5578: for(i=1, vepp=0.;i <=nlstate;i++)
5579: for(j=1;j <=nlstate;j++)
5580: vepp += vareij[i][j][(int)age];
5581: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5582: for(j=1;j <=nlstate;j++){
5583: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5584: }
5585: fprintf(ficrest,"\n");
1.53 brouard 5586: }
1.98 brouard 5587: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5588: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5589: free_vector(epj,1,nlstate+1);
5590: }
5591: }
5592: free_vector(weight,1,n);
5593: free_imatrix(Tvard,1,15,1,2);
5594: free_imatrix(s,1,maxwav+1,1,n);
5595: free_matrix(anint,1,maxwav,1,n);
5596: free_matrix(mint,1,maxwav,1,n);
5597: free_ivector(cod,1,n);
5598: free_ivector(tab,1,NCOVMAX);
5599: fclose(ficreseij);
5600: fclose(ficresvij);
5601: fclose(ficrest);
5602: fclose(ficpar);
5603:
5604: /*------- Variance of stable prevalence------*/
5605:
5606: strcpy(fileresvpl,"vpl");
5607: strcat(fileresvpl,fileres);
5608: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5609: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5610: exit(0);
5611: }
5612: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5613:
5614: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5615: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5616: k=k+1;
5617: fprintf(ficresvpl,"\n#****** ");
5618: for(j=1;j<=cptcoveff;j++)
5619: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5620: fprintf(ficresvpl,"******\n");
5621:
5622: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5623: oldm=oldms;savm=savms;
1.105 lievre 5624: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
1.98 brouard 5625: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5626: }
1.98 brouard 5627: }
1.53 brouard 5628:
1.98 brouard 5629: fclose(ficresvpl);
1.53 brouard 5630:
1.98 brouard 5631: /*---------- End : free ----------------*/
5632: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5633: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5634:
5635: } /* mle==-3 arrives here for freeing */
1.113 brouard 5636: free_matrix(prlim,1,nlstate,1,nlstate);
1.98 brouard 5637: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5638: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5639: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5640: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5641: free_matrix(covar,0,NCOVMAX,1,n);
5642: free_matrix(matcov,1,npar,1,npar);
5643: /*free_vector(delti,1,npar);*/
5644: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5645: free_matrix(agev,1,maxwav,1,imx);
5646: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5647:
5648: free_ivector(ncodemax,1,8);
5649: free_ivector(Tvar,1,15);
5650: free_ivector(Tprod,1,15);
5651: free_ivector(Tvaraff,1,15);
5652: free_ivector(Tage,1,15);
5653: free_ivector(Tcode,1,100);
1.74 brouard 5654:
1.113 brouard 5655: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5656: free_imatrix(codtab,1,100,1,10);
1.88 brouard 5657: fflush(fichtm);
5658: fflush(ficgp);
1.53 brouard 5659:
5660:
1.91 brouard 5661: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5662: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5663: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5664: }else{
1.91 brouard 5665: printf("End of Imach\n");
5666: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5667: }
5668: printf("See log file on %s\n",filelog);
5669: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5670: (void) gettimeofday(&end_time,&tzp);
5671: tm = *localtime(&end_time.tv_sec);
5672: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5673: strcpy(strtend,asctime(&tm));
1.105 lievre 5674: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
1.94 brouard 5675: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5676: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5677:
1.91 brouard 5678: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5679: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5680: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5681: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5682: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5683: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5684: fclose(fichtm);
1.91 brouard 5685: fclose(fichtmcov);
1.88 brouard 5686: fclose(ficgp);
1.91 brouard 5687: fclose(ficlog);
1.53 brouard 5688: /*------ End -----------*/
5689:
1.88 brouard 5690: chdir(path);
1.107 brouard 5691: /*strcat(plotcmd,CHARSEPARATOR);*/
1.111 brouard 5692: sprintf(plotcmd,"gnuplot");
1.107 brouard 5693: #ifndef UNIX
1.112 brouard 5694: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
1.107 brouard 5695: #endif
1.111 brouard 5696: if(!stat(plotcmd,&info)){
1.107 brouard 5697: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
1.111 brouard 5698: if(!stat(getenv("GNUPLOTBIN"),&info)){
5699: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5700: }else
5701: strcpy(pplotcmd,plotcmd);
5702: #ifdef UNIX
5703: strcpy(plotcmd,GNUPLOTPROGRAM);
5704: if(!stat(plotcmd,&info)){
5705: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5706: }else
5707: strcpy(pplotcmd,plotcmd);
1.108 lievre 5708: #endif
1.111 brouard 5709: }else
5710: strcpy(pplotcmd,plotcmd);
5711:
5712: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5713: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
1.107 brouard 5714:
1.91 brouard 5715: if((outcmd=system(plotcmd)) != 0){
1.108 lievre 5716: printf("\n Problem with gnuplot\n");
1.91 brouard 5717: }
1.75 brouard 5718: printf(" Wait...");
1.53 brouard 5719: while (z[0] != 'q') {
5720: /* chdir(path); */
1.91 brouard 5721: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5722: scanf("%s",z);
1.91 brouard 5723: /* if (z[0] == 'c') system("./imach"); */
1.99 brouard 5724: if (z[0] == 'e') {
5725: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5726: system(optionfilehtm);
5727: }
1.53 brouard 5728: else if (z[0] == 'g') system(plotcmd);
5729: else if (z[0] == 'q') exit(0);
5730: }
1.91 brouard 5731: end:
5732: while (z[0] != 'q') {
5733: printf("\nType q for exiting: ");
5734: scanf("%s",z);
5735: }
1.53 brouard 5736: }
1.88 brouard 5737:
1.53 brouard 5738:
5739:
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