Annotation of imach/src/imach.c, revision 1.119
1.119 ! brouard 1: /* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.119 ! brouard 4: Revision 1.118 2006/03/14 18:20:07 brouard
! 5: (Module): varevsij Comments added explaining the second
! 6: table of variances if popbased=1 .
! 7: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
! 8: (Module): Function pstamp added
! 9: (Module): Version 0.98d
! 10:
1.118 brouard 11: Revision 1.117 2006/03/14 17:16:22 brouard
12: (Module): varevsij Comments added explaining the second
13: table of variances if popbased=1 .
14: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
15: (Module): Function pstamp added
16: (Module): Version 0.98d
17:
1.117 brouard 18: Revision 1.116 2006/03/06 10:29:27 brouard
19: (Module): Variance-covariance wrong links and
20: varian-covariance of ej. is needed (Saito).
21:
1.116 brouard 22: Revision 1.115 2006/02/27 12:17:45 brouard
23: (Module): One freematrix added in mlikeli! 0.98c
24:
1.115 brouard 25: Revision 1.114 2006/02/26 12:57:58 brouard
26: (Module): Some improvements in processing parameter
27: filename with strsep.
28:
1.114 brouard 29: Revision 1.113 2006/02/24 14:20:24 brouard
30: (Module): Memory leaks checks with valgrind and:
31: datafile was not closed, some imatrix were not freed and on matrix
32: allocation too.
33:
1.113 brouard 34: Revision 1.112 2006/01/30 09:55:26 brouard
35: (Module): Back to gnuplot.exe instead of wgnuplot.exe
36:
1.112 brouard 37: Revision 1.111 2006/01/25 20:38:18 brouard
38: (Module): Lots of cleaning and bugs added (Gompertz)
39: (Module): Comments can be added in data file. Missing date values
40: can be a simple dot '.'.
41:
1.111 brouard 42: Revision 1.110 2006/01/25 00:51:50 brouard
43: (Module): Lots of cleaning and bugs added (Gompertz)
44:
1.110 brouard 45: Revision 1.109 2006/01/24 19:37:15 brouard
46: (Module): Comments (lines starting with a #) are allowed in data.
47:
1.109 brouard 48: Revision 1.108 2006/01/19 18:05:42 lievre
49: Gnuplot problem appeared...
50: To be fixed
51:
1.108 lievre 52: Revision 1.107 2006/01/19 16:20:37 brouard
53: Test existence of gnuplot in imach path
54:
1.107 brouard 55: Revision 1.106 2006/01/19 13:24:36 brouard
56: Some cleaning and links added in html output
57:
1.106 brouard 58: Revision 1.105 2006/01/05 20:23:19 lievre
59: *** empty log message ***
60:
1.105 lievre 61: Revision 1.104 2005/09/30 16:11:43 lievre
62: (Module): sump fixed, loop imx fixed, and simplifications.
63: (Module): If the status is missing at the last wave but we know
64: that the person is alive, then we can code his/her status as -2
65: (instead of missing=-1 in earlier versions) and his/her
66: contributions to the likelihood is 1 - Prob of dying from last
67: health status (= 1-p13= p11+p12 in the easiest case of somebody in
68: the healthy state at last known wave). Version is 0.98
69:
1.104 lievre 70: Revision 1.103 2005/09/30 15:54:49 lievre
71: (Module): sump fixed, loop imx fixed, and simplifications.
72:
1.103 lievre 73: Revision 1.102 2004/09/15 17:31:30 brouard
74: Add the possibility to read data file including tab characters.
75:
1.102 brouard 76: Revision 1.101 2004/09/15 10:38:38 brouard
77: Fix on curr_time
78:
1.101 brouard 79: Revision 1.100 2004/07/12 18:29:06 brouard
80: Add version for Mac OS X. Just define UNIX in Makefile
81:
1.100 brouard 82: Revision 1.99 2004/06/05 08:57:40 brouard
83: *** empty log message ***
84:
1.99 brouard 85: Revision 1.98 2004/05/16 15:05:56 brouard
86: New version 0.97 . First attempt to estimate force of mortality
87: directly from the data i.e. without the need of knowing the health
88: state at each age, but using a Gompertz model: log u =a + b*age .
89: This is the basic analysis of mortality and should be done before any
90: other analysis, in order to test if the mortality estimated from the
91: cross-longitudinal survey is different from the mortality estimated
92: from other sources like vital statistic data.
93:
94: The same imach parameter file can be used but the option for mle should be -3.
95:
96: Agnès, who wrote this part of the code, tried to keep most of the
97: former routines in order to include the new code within the former code.
98:
99: The output is very simple: only an estimate of the intercept and of
100: the slope with 95% confident intervals.
101:
102: Current limitations:
103: A) Even if you enter covariates, i.e. with the
104: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
105: B) There is no computation of Life Expectancy nor Life Table.
106:
1.98 brouard 107: Revision 1.97 2004/02/20 13:25:42 lievre
108: Version 0.96d. Population forecasting command line is (temporarily)
109: suppressed.
110:
1.97 lievre 111: Revision 1.96 2003/07/15 15:38:55 brouard
112: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
113: rewritten within the same printf. Workaround: many printfs.
114:
1.96 brouard 115: Revision 1.95 2003/07/08 07:54:34 brouard
116: * imach.c (Repository):
117: (Repository): Using imachwizard code to output a more meaningful covariance
118: matrix (cov(a12,c31) instead of numbers.
119:
1.95 brouard 120: Revision 1.94 2003/06/27 13:00:02 brouard
121: Just cleaning
122:
1.94 brouard 123: Revision 1.93 2003/06/25 16:33:55 brouard
124: (Module): On windows (cygwin) function asctime_r doesn't
125: exist so I changed back to asctime which exists.
126: (Module): Version 0.96b
127:
1.93 brouard 128: Revision 1.92 2003/06/25 16:30:45 brouard
129: (Module): On windows (cygwin) function asctime_r doesn't
130: exist so I changed back to asctime which exists.
131:
1.92 brouard 132: Revision 1.91 2003/06/25 15:30:29 brouard
133: * imach.c (Repository): Duplicated warning errors corrected.
134: (Repository): Elapsed time after each iteration is now output. It
135: helps to forecast when convergence will be reached. Elapsed time
136: is stamped in powell. We created a new html file for the graphs
137: concerning matrix of covariance. It has extension -cov.htm.
138:
1.91 brouard 139: Revision 1.90 2003/06/24 12:34:15 brouard
140: (Module): Some bugs corrected for windows. Also, when
141: mle=-1 a template is output in file "or"mypar.txt with the design
142: of the covariance matrix to be input.
143:
1.90 brouard 144: Revision 1.89 2003/06/24 12:30:52 brouard
145: (Module): Some bugs corrected for windows. Also, when
146: mle=-1 a template is output in file "or"mypar.txt with the design
147: of the covariance matrix to be input.
148:
1.89 brouard 149: Revision 1.88 2003/06/23 17:54:56 brouard
150: * 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.
151:
1.88 brouard 152: Revision 1.87 2003/06/18 12:26:01 brouard
153: Version 0.96
154:
1.87 brouard 155: Revision 1.86 2003/06/17 20:04:08 brouard
156: (Module): Change position of html and gnuplot routines and added
157: routine fileappend.
158:
1.86 brouard 159: Revision 1.85 2003/06/17 13:12:43 brouard
160: * imach.c (Repository): Check when date of death was earlier that
161: current date of interview. It may happen when the death was just
162: prior to the death. In this case, dh was negative and likelihood
163: was wrong (infinity). We still send an "Error" but patch by
164: assuming that the date of death was just one stepm after the
165: interview.
166: (Repository): Because some people have very long ID (first column)
167: we changed int to long in num[] and we added a new lvector for
168: memory allocation. But we also truncated to 8 characters (left
169: truncation)
170: (Repository): No more line truncation errors.
171:
1.85 brouard 172: Revision 1.84 2003/06/13 21:44:43 brouard
173: * imach.c (Repository): Replace "freqsummary" at a correct
174: place. It differs from routine "prevalence" which may be called
175: many times. Probs is memory consuming and must be used with
176: parcimony.
1.86 brouard 177: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 178:
1.84 brouard 179: Revision 1.83 2003/06/10 13:39:11 lievre
180: *** empty log message ***
181:
1.83 lievre 182: Revision 1.82 2003/06/05 15:57:20 brouard
183: Add log in imach.c and fullversion number is now printed.
184:
1.82 brouard 185: */
186: /*
1.53 brouard 187: Interpolated Markov Chain
188:
189: Short summary of the programme:
190:
191: This program computes Healthy Life Expectancies from
192: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
193: first survey ("cross") where individuals from different ages are
194: interviewed on their health status or degree of disability (in the
195: case of a health survey which is our main interest) -2- at least a
196: second wave of interviews ("longitudinal") which measure each change
197: (if any) in individual health status. Health expectancies are
198: computed from the time spent in each health state according to a
199: model. More health states you consider, more time is necessary to reach the
200: Maximum Likelihood of the parameters involved in the model. The
201: simplest model is the multinomial logistic model where pij is the
202: probability to be observed in state j at the second wave
203: conditional to be observed in state i at the first wave. Therefore
204: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
205: 'age' is age and 'sex' is a covariate. If you want to have a more
206: complex model than "constant and age", you should modify the program
207: where the markup *Covariates have to be included here again* invites
208: you to do it. More covariates you add, slower the
209: convergence.
210:
211: The advantage of this computer programme, compared to a simple
212: multinomial logistic model, is clear when the delay between waves is not
213: identical for each individual. Also, if a individual missed an
214: intermediate interview, the information is lost, but taken into
215: account using an interpolation or extrapolation.
216:
217: hPijx is the probability to be observed in state i at age x+h
218: conditional to the observed state i at age x. The delay 'h' can be
219: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 220: states. This elementary transition (by month, quarter,
221: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 222: matrix is simply the matrix product of nh*stepm elementary matrices
223: and the contribution of each individual to the likelihood is simply
224: hPijx.
225:
226: Also this programme outputs the covariance matrix of the parameters but also
1.117 brouard 227: of the life expectancies. It also computes the period (stable) prevalence.
1.53 brouard 228:
229: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
230: Institut national d'études démographiques, Paris.
231: This software have been partly granted by Euro-REVES, a concerted action
232: from the European Union.
233: It is copyrighted identically to a GNU software product, ie programme and
234: software can be distributed freely for non commercial use. Latest version
235: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 236:
237: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
238: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
239:
1.53 brouard 240: **********************************************************************/
1.74 brouard 241: /*
242: main
243: read parameterfile
244: read datafile
245: concatwav
1.84 brouard 246: freqsummary
1.74 brouard 247: if (mle >= 1)
248: mlikeli
249: print results files
250: if mle==1
251: computes hessian
252: read end of parameter file: agemin, agemax, bage, fage, estepm
253: begin-prev-date,...
254: open gnuplot file
255: open html file
1.117 brouard 256: period (stable) prevalence
1.74 brouard 257: for age prevalim()
258: h Pij x
259: variance of p varprob
260: forecasting if prevfcast==1 prevforecast call prevalence()
261: health expectancies
262: Variance-covariance of DFLE
263: prevalence()
264: movingaverage()
265: varevsij()
266: if popbased==1 varevsij(,popbased)
267: total life expectancies
1.117 brouard 268: Variance of period (stable) prevalence
1.74 brouard 269: end
270: */
271:
272:
273:
1.53 brouard 274:
275: #include <math.h>
276: #include <stdio.h>
277: #include <stdlib.h>
1.106 brouard 278: #include <string.h>
1.53 brouard 279: #include <unistd.h>
280:
1.109 brouard 281: #include <limits.h>
1.107 brouard 282: #include <sys/types.h>
283: #include <sys/stat.h>
284: #include <errno.h>
285: extern int errno;
286:
1.99 brouard 287: /* #include <sys/time.h> */
1.86 brouard 288: #include <time.h>
289: #include "timeval.h"
290:
1.95 brouard 291: /* #include <libintl.h> */
292: /* #define _(String) gettext (String) */
293:
1.53 brouard 294: #define MAXLINE 256
1.108 lievre 295:
1.53 brouard 296: #define GNUPLOTPROGRAM "gnuplot"
297: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 298: #define FILENAMELENGTH 132
1.108 lievre 299:
1.53 brouard 300: #define GLOCK_ERROR_NOPATH -1 /* empty path */
301: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
302:
303: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
304: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
305:
306: #define NINTERVMAX 8
307: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
308: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
309: #define NCOVMAX 8 /* Maximum number of covariates */
310: #define MAXN 20000
311: #define YEARM 12. /* Number of months per year */
312: #define AGESUP 130
313: #define AGEBASE 40
1.98 brouard 314: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.100 brouard 315: #ifdef UNIX
1.85 brouard 316: #define DIRSEPARATOR '/'
1.107 brouard 317: #define CHARSEPARATOR "/"
1.85 brouard 318: #define ODIRSEPARATOR '\\'
319: #else
1.53 brouard 320: #define DIRSEPARATOR '\\'
1.107 brouard 321: #define CHARSEPARATOR "\\"
1.53 brouard 322: #define ODIRSEPARATOR '/'
323: #endif
324:
1.119 ! brouard 325: /* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $ */
1.81 brouard 326: /* $State: Exp $ */
1.80 brouard 327:
1.119 ! brouard 328: char version[]="Imach version 0.98e, March 2006, INED-EUROREVES-Institut de longevite ";
! 329: char fullversion[]="$Revision: 1.118 $ $Date: 2006/03/14 18:20:07 $";
1.117 brouard 330: char strstart[80];
331: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.91 brouard 332: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 333: int nvar;
334: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
335: int npar=NPARMAX;
336: int nlstate=2; /* Number of live states */
337: int ndeath=1; /* Number of dead states */
338: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
339: int popbased=0;
340:
341: int *wav; /* Number of waves for this individuual 0 is possible */
342: int maxwav; /* Maxim number of waves */
343: int jmin, jmax; /* min, max spacing between 2 waves */
1.110 brouard 344: int ijmin, ijmax; /* Individuals having jmin and jmax */
1.87 brouard 345: int gipmx, gsw; /* Global variables on the number of contributions
346: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 347: int mle, weightopt;
348: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
349: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 350: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
351: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 352: double jmean; /* Mean space between 2 waves */
353: double **oldm, **newm, **savm; /* Working pointers to matrices */
354: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.117 brouard 355: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 356: FILE *ficlog, *ficrespow;
1.85 brouard 357: int globpr; /* Global variable for printing or not */
358: double fretone; /* Only one call to likelihood */
359: long ipmx; /* Number of contributions */
360: double sw; /* Sum of weights */
1.98 brouard 361: char filerespow[FILENAMELENGTH];
1.85 brouard 362: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
363: FILE *ficresilk;
1.53 brouard 364: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
365: FILE *ficresprobmorprev;
1.91 brouard 366: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 367: FILE *ficreseij;
368: char filerese[FILENAMELENGTH];
1.117 brouard 369: FILE *ficresstdeij;
370: char fileresstde[FILENAMELENGTH];
371: FILE *ficrescveij;
372: char filerescve[FILENAMELENGTH];
1.53 brouard 373: FILE *ficresvij;
374: char fileresv[FILENAMELENGTH];
375: FILE *ficresvpl;
376: char fileresvpl[FILENAMELENGTH];
377: char title[MAXLINE];
378: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
1.117 brouard 379: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1.96 brouard 380: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 381: char command[FILENAMELENGTH];
382: int outcmd=0;
1.53 brouard 383:
384: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 385:
1.53 brouard 386: char filelog[FILENAMELENGTH]; /* Log file */
387: char filerest[FILENAMELENGTH];
388: char fileregp[FILENAMELENGTH];
389: char popfile[FILENAMELENGTH];
390:
1.91 brouard 391: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
392:
393: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
394: struct timezone tzp;
395: extern int gettimeofday();
396: struct tm tmg, tm, tmf, *gmtime(), *localtime();
397: long time_value;
398: extern long time();
399: char strcurr[80], strfor[80];
1.53 brouard 400:
1.109 brouard 401: char *endptr;
402: long lval;
403:
1.53 brouard 404: #define NR_END 1
405: #define FREE_ARG char*
406: #define FTOL 1.0e-10
407:
408: #define NRANSI
409: #define ITMAX 200
410:
411: #define TOL 2.0e-4
412:
413: #define CGOLD 0.3819660
414: #define ZEPS 1.0e-10
415: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
416:
417: #define GOLD 1.618034
418: #define GLIMIT 100.0
419: #define TINY 1.0e-20
420:
421: static double maxarg1,maxarg2;
422: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
423: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
424:
425: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
426: #define rint(a) floor(a+0.5)
427:
428: static double sqrarg;
429: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
430: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 brouard 431: int agegomp= AGEGOMP;
1.53 brouard 432:
433: int imx;
1.98 brouard 434: int stepm=1;
1.53 brouard 435: /* Stepm, step in month: minimum step interpolation*/
436:
437: int estepm;
438: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
439:
440: int m,nb;
1.85 brouard 441: long *num;
1.98 brouard 442: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 443: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 444: double **pmmij, ***probs;
1.98 brouard 445: double *ageexmed,*agecens;
1.53 brouard 446: double dateintmean=0;
447:
448: double *weight;
449: int **s; /* Status */
450: double *agedc, **covar, idx;
451: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.105 lievre 452: double *lsurv, *lpop, *tpop;
1.53 brouard 453:
454: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
455: double ftolhess; /* Tolerance for computing hessian */
456:
457: /**************** split *************************/
458: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
459: {
1.107 brouard 460: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1.99 brouard 461: the name of the file (name), its extension only (ext) and its first part of the name (finame)
462: */
1.59 brouard 463: char *ss; /* pointer */
464: int l1, l2; /* length counters */
1.53 brouard 465:
1.59 brouard 466: l1 = strlen(path ); /* length of path */
467: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
468: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1.107 brouard 469: if ( ss == NULL ) { /* no directory, so determine current directory */
470: strcpy( name, path ); /* we got the fullname name because no directory */
1.59 brouard 471: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
472: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 473: /* get current working directory */
474: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 475: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
476: return( GLOCK_ERROR_GETCWD );
477: }
1.107 brouard 478: /* got dirc from getcwd*/
479: printf(" DIRC = %s \n",dirc);
1.59 brouard 480: } else { /* strip direcotry from path */
481: ss++; /* after this, the filename */
482: l2 = strlen( ss ); /* length of filename */
483: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
484: strcpy( name, ss ); /* save file name */
485: strncpy( dirc, path, l1 - l2 ); /* now the directory */
486: dirc[l1-l2] = 0; /* add zero */
1.107 brouard 487: printf(" DIRC2 = %s \n",dirc);
1.59 brouard 488: }
1.107 brouard 489: /* We add a separator at the end of dirc if not exists */
1.59 brouard 490: l1 = strlen( dirc ); /* length of directory */
1.107 brouard 491: if( dirc[l1-1] != DIRSEPARATOR ){
492: dirc[l1] = DIRSEPARATOR;
493: dirc[l1+1] = 0;
494: printf(" DIRC3 = %s \n",dirc);
495: }
1.59 brouard 496: ss = strrchr( name, '.' ); /* find last / */
1.99 brouard 497: if (ss >0){
498: ss++;
499: strcpy(ext,ss); /* save extension */
500: l1= strlen( name);
501: l2= strlen(ss)+1;
502: strncpy( finame, name, l1-l2);
503: finame[l1-l2]= 0;
504: }
1.107 brouard 505:
1.59 brouard 506: return( 0 ); /* we're done */
1.53 brouard 507: }
508:
509:
510: /******************************************/
511:
1.89 brouard 512: void replace_back_to_slash(char *s, char*t)
1.53 brouard 513: {
514: int i;
1.89 brouard 515: int lg=0;
1.53 brouard 516: i=0;
517: lg=strlen(t);
518: for(i=0; i<= lg; i++) {
519: (s[i] = t[i]);
520: if (t[i]== '\\') s[i]='/';
521: }
522: }
523:
524: int nbocc(char *s, char occ)
525: {
526: int i,j=0;
527: int lg=20;
528: i=0;
529: lg=strlen(s);
530: for(i=0; i<= lg; i++) {
531: if (s[i] == occ ) j++;
532: }
533: return j;
534: }
535:
536: void cutv(char *u,char *v, char*t, char occ)
537: {
1.102 brouard 538: /* cuts string t into u and v where u ends before first occurence of char 'occ'
539: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
1.53 brouard 540: gives u="abcedf" and v="ghi2j" */
541: int i,lg,j,p=0;
542: i=0;
543: for(j=0; j<=strlen(t)-1; j++) {
544: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
545: }
546:
547: lg=strlen(t);
548: for(j=0; j<p; j++) {
549: (u[j] = t[j]);
550: }
551: u[p]='\0';
552:
553: for(j=0; j<= lg; j++) {
554: if (j>=(p+1))(v[j-p-1] = t[j]);
555: }
556: }
557:
558: /********************** nrerror ********************/
559:
560: void nrerror(char error_text[])
561: {
562: fprintf(stderr,"ERREUR ...\n");
563: fprintf(stderr,"%s\n",error_text);
1.59 brouard 564: exit(EXIT_FAILURE);
1.53 brouard 565: }
566: /*********************** vector *******************/
567: double *vector(int nl, int nh)
568: {
569: double *v;
570: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
571: if (!v) nrerror("allocation failure in vector");
572: return v-nl+NR_END;
573: }
574:
575: /************************ free vector ******************/
576: void free_vector(double*v, int nl, int nh)
577: {
578: free((FREE_ARG)(v+nl-NR_END));
579: }
580:
581: /************************ivector *******************************/
1.85 brouard 582: int *ivector(long nl,long nh)
1.76 brouard 583: {
1.85 brouard 584: int *v;
585: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
586: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 587: return v-nl+NR_END;
588: }
589:
590: /******************free ivector **************************/
1.85 brouard 591: void free_ivector(int *v, long nl, long nh)
1.76 brouard 592: {
593: free((FREE_ARG)(v+nl-NR_END));
594: }
595:
1.85 brouard 596: /************************lvector *******************************/
597: long *lvector(long nl,long nh)
1.53 brouard 598: {
1.85 brouard 599: long *v;
600: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 601: if (!v) nrerror("allocation failure in ivector");
602: return v-nl+NR_END;
603: }
604:
1.85 brouard 605: /******************free lvector **************************/
606: void free_lvector(long *v, long nl, long nh)
1.53 brouard 607: {
608: free((FREE_ARG)(v+nl-NR_END));
609: }
610:
611: /******************* imatrix *******************************/
612: int **imatrix(long nrl, long nrh, long ncl, long nch)
613: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
614: {
615: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
616: int **m;
617:
618: /* allocate pointers to rows */
619: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
620: if (!m) nrerror("allocation failure 1 in matrix()");
621: m += NR_END;
622: m -= nrl;
623:
624:
625: /* allocate rows and set pointers to them */
626: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
627: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
628: m[nrl] += NR_END;
629: m[nrl] -= ncl;
630:
631: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
632:
633: /* return pointer to array of pointers to rows */
634: return m;
635: }
636:
637: /****************** free_imatrix *************************/
638: void free_imatrix(m,nrl,nrh,ncl,nch)
639: int **m;
640: long nch,ncl,nrh,nrl;
641: /* free an int matrix allocated by imatrix() */
642: {
643: free((FREE_ARG) (m[nrl]+ncl-NR_END));
644: free((FREE_ARG) (m+nrl-NR_END));
645: }
646:
647: /******************* matrix *******************************/
648: double **matrix(long nrl, long nrh, long ncl, long nch)
649: {
650: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
651: double **m;
652:
653: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
654: if (!m) nrerror("allocation failure 1 in matrix()");
655: m += NR_END;
656: m -= nrl;
657:
658: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
659: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
660: m[nrl] += NR_END;
661: m[nrl] -= ncl;
662:
663: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
664: return m;
1.85 brouard 665: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 666: */
1.53 brouard 667: }
668:
669: /*************************free matrix ************************/
670: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
671: {
672: free((FREE_ARG)(m[nrl]+ncl-NR_END));
673: free((FREE_ARG)(m+nrl-NR_END));
674: }
675:
676: /******************* ma3x *******************************/
677: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
678: {
679: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
680: double ***m;
681:
682: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
683: if (!m) nrerror("allocation failure 1 in matrix()");
684: m += NR_END;
685: m -= nrl;
686:
687: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
688: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
689: m[nrl] += NR_END;
690: m[nrl] -= ncl;
691:
692: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
693:
694: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
695: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
696: m[nrl][ncl] += NR_END;
697: m[nrl][ncl] -= nll;
698: for (j=ncl+1; j<=nch; j++)
699: m[nrl][j]=m[nrl][j-1]+nlay;
700:
701: for (i=nrl+1; i<=nrh; i++) {
702: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
703: for (j=ncl+1; j<=nch; j++)
704: m[i][j]=m[i][j-1]+nlay;
705: }
1.74 brouard 706: return m;
707: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
708: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
709: */
1.53 brouard 710: }
711:
712: /*************************free ma3x ************************/
713: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
714: {
715: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
716: free((FREE_ARG)(m[nrl]+ncl-NR_END));
717: free((FREE_ARG)(m+nrl-NR_END));
718: }
719:
1.94 brouard 720: /*************** function subdirf ***********/
721: char *subdirf(char fileres[])
722: {
723: /* Caution optionfilefiname is hidden */
724: strcpy(tmpout,optionfilefiname);
725: strcat(tmpout,"/"); /* Add to the right */
726: strcat(tmpout,fileres);
727: return tmpout;
728: }
729:
730: /*************** function subdirf2 ***********/
731: char *subdirf2(char fileres[], char *preop)
732: {
733:
734: /* Caution optionfilefiname is hidden */
735: strcpy(tmpout,optionfilefiname);
736: strcat(tmpout,"/");
737: strcat(tmpout,preop);
738: strcat(tmpout,fileres);
739: return tmpout;
740: }
741:
742: /*************** function subdirf3 ***********/
743: char *subdirf3(char fileres[], char *preop, char *preop2)
744: {
745:
746: /* Caution optionfilefiname is hidden */
747: strcpy(tmpout,optionfilefiname);
748: strcat(tmpout,"/");
749: strcat(tmpout,preop);
750: strcat(tmpout,preop2);
751: strcat(tmpout,fileres);
752: return tmpout;
753: }
754:
1.53 brouard 755: /***************** f1dim *************************/
756: extern int ncom;
757: extern double *pcom,*xicom;
758: extern double (*nrfunc)(double []);
759:
760: double f1dim(double x)
761: {
762: int j;
763: double f;
764: double *xt;
765:
766: xt=vector(1,ncom);
767: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
768: f=(*nrfunc)(xt);
769: free_vector(xt,1,ncom);
770: return f;
771: }
772:
773: /*****************brent *************************/
774: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
775: {
776: int iter;
777: double a,b,d,etemp;
778: double fu,fv,fw,fx;
779: double ftemp;
780: double p,q,r,tol1,tol2,u,v,w,x,xm;
781: double e=0.0;
782:
783: a=(ax < cx ? ax : cx);
784: b=(ax > cx ? ax : cx);
785: x=w=v=bx;
786: fw=fv=fx=(*f)(x);
787: for (iter=1;iter<=ITMAX;iter++) {
788: xm=0.5*(a+b);
789: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
790: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
791: printf(".");fflush(stdout);
792: fprintf(ficlog,".");fflush(ficlog);
793: #ifdef DEBUG
794: 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);
795: 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);
796: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
797: #endif
798: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
799: *xmin=x;
800: return fx;
801: }
802: ftemp=fu;
803: if (fabs(e) > tol1) {
804: r=(x-w)*(fx-fv);
805: q=(x-v)*(fx-fw);
806: p=(x-v)*q-(x-w)*r;
807: q=2.0*(q-r);
808: if (q > 0.0) p = -p;
809: q=fabs(q);
810: etemp=e;
811: e=d;
812: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
813: d=CGOLD*(e=(x >= xm ? a-x : b-x));
814: else {
815: d=p/q;
816: u=x+d;
817: if (u-a < tol2 || b-u < tol2)
818: d=SIGN(tol1,xm-x);
819: }
820: } else {
821: d=CGOLD*(e=(x >= xm ? a-x : b-x));
822: }
823: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
824: fu=(*f)(u);
825: if (fu <= fx) {
826: if (u >= x) a=x; else b=x;
827: SHFT(v,w,x,u)
828: SHFT(fv,fw,fx,fu)
829: } else {
830: if (u < x) a=u; else b=u;
831: if (fu <= fw || w == x) {
832: v=w;
833: w=u;
834: fv=fw;
835: fw=fu;
836: } else if (fu <= fv || v == x || v == w) {
837: v=u;
838: fv=fu;
839: }
840: }
841: }
842: nrerror("Too many iterations in brent");
843: *xmin=x;
844: return fx;
845: }
846:
847: /****************** mnbrak ***********************/
848:
849: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
850: double (*func)(double))
851: {
852: double ulim,u,r,q, dum;
853: double fu;
854:
855: *fa=(*func)(*ax);
856: *fb=(*func)(*bx);
857: if (*fb > *fa) {
858: SHFT(dum,*ax,*bx,dum)
859: SHFT(dum,*fb,*fa,dum)
860: }
861: *cx=(*bx)+GOLD*(*bx-*ax);
862: *fc=(*func)(*cx);
863: while (*fb > *fc) {
864: r=(*bx-*ax)*(*fb-*fc);
865: q=(*bx-*cx)*(*fb-*fa);
866: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
867: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
868: ulim=(*bx)+GLIMIT*(*cx-*bx);
869: if ((*bx-u)*(u-*cx) > 0.0) {
870: fu=(*func)(u);
871: } else if ((*cx-u)*(u-ulim) > 0.0) {
872: fu=(*func)(u);
873: if (fu < *fc) {
874: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
875: SHFT(*fb,*fc,fu,(*func)(u))
876: }
877: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
878: u=ulim;
879: fu=(*func)(u);
880: } else {
881: u=(*cx)+GOLD*(*cx-*bx);
882: fu=(*func)(u);
883: }
884: SHFT(*ax,*bx,*cx,u)
885: SHFT(*fa,*fb,*fc,fu)
886: }
887: }
888:
889: /*************** linmin ************************/
890:
891: int ncom;
892: double *pcom,*xicom;
893: double (*nrfunc)(double []);
894:
895: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
896: {
897: double brent(double ax, double bx, double cx,
898: double (*f)(double), double tol, double *xmin);
899: double f1dim(double x);
900: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
901: double *fc, double (*func)(double));
902: int j;
903: double xx,xmin,bx,ax;
904: double fx,fb,fa;
905:
906: ncom=n;
907: pcom=vector(1,n);
908: xicom=vector(1,n);
909: nrfunc=func;
910: for (j=1;j<=n;j++) {
911: pcom[j]=p[j];
912: xicom[j]=xi[j];
913: }
914: ax=0.0;
915: xx=1.0;
916: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
917: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
918: #ifdef DEBUG
919: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
920: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
921: #endif
922: for (j=1;j<=n;j++) {
923: xi[j] *= xmin;
924: p[j] += xi[j];
925: }
926: free_vector(xicom,1,n);
927: free_vector(pcom,1,n);
928: }
929:
1.91 brouard 930: char *asc_diff_time(long time_sec, char ascdiff[])
931: {
932: long sec_left, days, hours, minutes;
933: days = (time_sec) / (60*60*24);
934: sec_left = (time_sec) % (60*60*24);
935: hours = (sec_left) / (60*60) ;
936: sec_left = (sec_left) %(60*60);
937: minutes = (sec_left) /60;
938: sec_left = (sec_left) % (60);
939: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
940: return ascdiff;
941: }
942:
1.53 brouard 943: /*************** powell ************************/
944: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
945: double (*func)(double []))
946: {
947: void linmin(double p[], double xi[], int n, double *fret,
948: double (*func)(double []));
949: int i,ibig,j;
950: double del,t,*pt,*ptt,*xit;
951: double fp,fptt;
952: double *xits;
1.91 brouard 953: int niterf, itmp;
954:
1.53 brouard 955: pt=vector(1,n);
956: ptt=vector(1,n);
957: xit=vector(1,n);
958: xits=vector(1,n);
959: *fret=(*func)(p);
960: for (j=1;j<=n;j++) pt[j]=p[j];
961: for (*iter=1;;++(*iter)) {
962: fp=(*fret);
963: ibig=0;
964: del=0.0;
1.91 brouard 965: last_time=curr_time;
966: (void) gettimeofday(&curr_time,&tzp);
967: 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 968: /* 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 969: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.98 brouard 970: */
971: for (i=1;i<=n;i++) {
1.53 brouard 972: printf(" %d %.12f",i, p[i]);
1.76 brouard 973: fprintf(ficlog," %d %.12lf",i, p[i]);
974: fprintf(ficrespow," %.12lf", p[i]);
975: }
1.53 brouard 976: printf("\n");
977: fprintf(ficlog,"\n");
1.91 brouard 978: fprintf(ficrespow,"\n");fflush(ficrespow);
979: if(*iter <=3){
980: tm = *localtime(&curr_time.tv_sec);
1.101 brouard 981: strcpy(strcurr,asctime(&tm));
1.92 brouard 982: /* asctime_r(&tm,strcurr); */
1.101 brouard 983: forecast_time=curr_time;
1.91 brouard 984: itmp = strlen(strcurr);
1.101 brouard 985: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.91 brouard 986: strcurr[itmp-1]='\0';
987: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
988: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
989: for(niterf=10;niterf<=30;niterf+=10){
990: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
991: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 992: /* asctime_r(&tmf,strfor); */
993: strcpy(strfor,asctime(&tmf));
1.91 brouard 994: itmp = strlen(strfor);
995: if(strfor[itmp-1]=='\n')
996: strfor[itmp-1]='\0';
1.101 brouard 997: 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);
998: 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 999: }
1000: }
1.53 brouard 1001: for (i=1;i<=n;i++) {
1002: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1003: fptt=(*fret);
1004: #ifdef DEBUG
1005: printf("fret=%lf \n",*fret);
1006: fprintf(ficlog,"fret=%lf \n",*fret);
1007: #endif
1008: printf("%d",i);fflush(stdout);
1009: fprintf(ficlog,"%d",i);fflush(ficlog);
1010: linmin(p,xit,n,fret,func);
1011: if (fabs(fptt-(*fret)) > del) {
1012: del=fabs(fptt-(*fret));
1013: ibig=i;
1014: }
1015: #ifdef DEBUG
1016: printf("%d %.12e",i,(*fret));
1017: fprintf(ficlog,"%d %.12e",i,(*fret));
1018: for (j=1;j<=n;j++) {
1019: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1020: printf(" x(%d)=%.12e",j,xit[j]);
1021: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1022: }
1023: for(j=1;j<=n;j++) {
1024: printf(" p=%.12e",p[j]);
1025: fprintf(ficlog," p=%.12e",p[j]);
1026: }
1027: printf("\n");
1028: fprintf(ficlog,"\n");
1029: #endif
1030: }
1031: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1032: #ifdef DEBUG
1033: int k[2],l;
1034: k[0]=1;
1035: k[1]=-1;
1036: printf("Max: %.12e",(*func)(p));
1037: fprintf(ficlog,"Max: %.12e",(*func)(p));
1038: for (j=1;j<=n;j++) {
1039: printf(" %.12e",p[j]);
1040: fprintf(ficlog," %.12e",p[j]);
1041: }
1042: printf("\n");
1043: fprintf(ficlog,"\n");
1044: for(l=0;l<=1;l++) {
1045: for (j=1;j<=n;j++) {
1046: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1047: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1048: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1049: }
1050: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1051: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1052: }
1053: #endif
1054:
1055:
1056: free_vector(xit,1,n);
1057: free_vector(xits,1,n);
1058: free_vector(ptt,1,n);
1059: free_vector(pt,1,n);
1060: return;
1061: }
1062: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1063: for (j=1;j<=n;j++) {
1064: ptt[j]=2.0*p[j]-pt[j];
1065: xit[j]=p[j]-pt[j];
1066: pt[j]=p[j];
1067: }
1068: fptt=(*func)(ptt);
1069: if (fptt < fp) {
1070: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1071: if (t < 0.0) {
1072: linmin(p,xit,n,fret,func);
1073: for (j=1;j<=n;j++) {
1074: xi[j][ibig]=xi[j][n];
1075: xi[j][n]=xit[j];
1076: }
1077: #ifdef DEBUG
1078: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1079: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1080: for(j=1;j<=n;j++){
1081: printf(" %.12e",xit[j]);
1082: fprintf(ficlog," %.12e",xit[j]);
1083: }
1084: printf("\n");
1085: fprintf(ficlog,"\n");
1086: #endif
1.54 brouard 1087: }
1.53 brouard 1088: }
1089: }
1090: }
1091:
1.117 brouard 1092: /**** Prevalence limit (stable or period prevalence) ****************/
1.53 brouard 1093:
1094: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1095: {
1096: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1097: matrix by transitions matrix until convergence is reached */
1098:
1099: int i, ii,j,k;
1100: double min, max, maxmin, maxmax,sumnew=0.;
1101: double **matprod2();
1102: double **out, cov[NCOVMAX], **pmij();
1103: double **newm;
1104: double agefin, delaymax=50 ; /* Max number of years to converge */
1105:
1106: for (ii=1;ii<=nlstate+ndeath;ii++)
1107: for (j=1;j<=nlstate+ndeath;j++){
1108: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1109: }
1110:
1111: cov[1]=1.;
1112:
1113: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1114: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1115: newm=savm;
1116: /* Covariates have to be included here again */
1117: cov[2]=agefin;
1118:
1119: for (k=1; k<=cptcovn;k++) {
1120: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1121: /* 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]]);*/
1122: }
1123: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1124: for (k=1; k<=cptcovprod;k++)
1125: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1126:
1127: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1128: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1129: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1130: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1131:
1132: savm=oldm;
1133: oldm=newm;
1134: maxmax=0.;
1135: for(j=1;j<=nlstate;j++){
1136: min=1.;
1137: max=0.;
1138: for(i=1; i<=nlstate; i++) {
1139: sumnew=0;
1140: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1141: prlim[i][j]= newm[i][j]/(1-sumnew);
1142: max=FMAX(max,prlim[i][j]);
1143: min=FMIN(min,prlim[i][j]);
1144: }
1145: maxmin=max-min;
1146: maxmax=FMAX(maxmax,maxmin);
1147: }
1148: if(maxmax < ftolpl){
1149: return prlim;
1150: }
1151: }
1152: }
1153:
1154: /*************** transition probabilities ***************/
1155:
1156: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1157: {
1158: double s1, s2;
1159: /*double t34;*/
1160: int i,j,j1, nc, ii, jj;
1161:
1162: for(i=1; i<= nlstate; i++){
1.99 brouard 1163: for(j=1; j<i;j++){
1164: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1165: /*s2 += param[i][j][nc]*cov[nc];*/
1166: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1167: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1168: }
1169: ps[i][j]=s2;
1170: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1171: }
1172: for(j=i+1; j<=nlstate+ndeath;j++){
1173: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1174: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1175: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1176: }
1177: ps[i][j]=s2;
1.53 brouard 1178: }
1179: }
1180: /*ps[3][2]=1;*/
1.99 brouard 1181:
1182: for(i=1; i<= nlstate; i++){
1183: s1=0;
1184: for(j=1; j<i; j++)
1185: s1+=exp(ps[i][j]);
1186: for(j=i+1; j<=nlstate+ndeath; j++)
1187: s1+=exp(ps[i][j]);
1188: ps[i][i]=1./(s1+1.);
1189: for(j=1; j<i; j++)
1190: ps[i][j]= exp(ps[i][j])*ps[i][i];
1191: for(j=i+1; j<=nlstate+ndeath; j++)
1192: ps[i][j]= exp(ps[i][j])*ps[i][i];
1193: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1194: } /* end i */
1195:
1196: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1197: for(jj=1; jj<= nlstate+ndeath; jj++){
1198: ps[ii][jj]=0;
1199: ps[ii][ii]=1;
1200: }
1.53 brouard 1201: }
1.99 brouard 1202:
1.53 brouard 1203:
1.99 brouard 1204: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1205: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1206: /* printf("ddd %lf ",ps[ii][jj]); */
1207: /* } */
1208: /* printf("\n "); */
1209: /* } */
1210: /* printf("\n ");printf("%lf ",cov[2]); */
1211: /*
1212: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1213: goto end;*/
1.53 brouard 1214: return ps;
1215: }
1216:
1217: /**************** Product of 2 matrices ******************/
1218:
1219: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1220: {
1221: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1222: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1223: /* in, b, out are matrice of pointers which should have been initialized
1224: before: only the contents of out is modified. The function returns
1225: a pointer to pointers identical to out */
1226: long i, j, k;
1227: for(i=nrl; i<= nrh; i++)
1228: for(k=ncolol; k<=ncoloh; k++)
1229: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1230: out[i][k] +=in[i][j]*b[j][k];
1231:
1232: return out;
1233: }
1234:
1235:
1236: /************* Higher Matrix Product ***************/
1237:
1238: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1239: {
1.66 brouard 1240: /* Computes the transition matrix starting at age 'age' over
1241: 'nhstepm*hstepm*stepm' months (i.e. until
1242: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1243: nhstepm*hstepm matrices.
1.53 brouard 1244: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1245: (typically every 2 years instead of every month which is too big
1246: for the memory).
1.53 brouard 1247: Model is determined by parameters x and covariates have to be
1248: included manually here.
1249:
1250: */
1251:
1252: int i, j, d, h, k;
1253: double **out, cov[NCOVMAX];
1254: double **newm;
1255:
1256: /* Hstepm could be zero and should return the unit matrix */
1257: for (i=1;i<=nlstate+ndeath;i++)
1258: for (j=1;j<=nlstate+ndeath;j++){
1259: oldm[i][j]=(i==j ? 1.0 : 0.0);
1260: po[i][j][0]=(i==j ? 1.0 : 0.0);
1261: }
1262: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1263: for(h=1; h <=nhstepm; h++){
1264: for(d=1; d <=hstepm; d++){
1265: newm=savm;
1266: /* Covariates have to be included here again */
1267: cov[1]=1.;
1268: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1269: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1270: for (k=1; k<=cptcovage;k++)
1271: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1272: for (k=1; k<=cptcovprod;k++)
1273: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1274:
1275:
1276: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1277: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1278: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1279: pmij(pmmij,cov,ncovmodel,x,nlstate));
1280: savm=oldm;
1281: oldm=newm;
1282: }
1283: for(i=1; i<=nlstate+ndeath; i++)
1284: for(j=1;j<=nlstate+ndeath;j++) {
1285: po[i][j][h]=newm[i][j];
1286: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1287: */
1288: }
1289: } /* end h */
1290: return po;
1291: }
1292:
1293:
1294: /*************** log-likelihood *************/
1295: double func( double *x)
1296: {
1297: int i, ii, j, k, mi, d, kk;
1298: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1299: double **out;
1300: double sw; /* Sum of weights */
1301: double lli; /* Individual log likelihood */
1.59 brouard 1302: int s1, s2;
1.68 lievre 1303: double bbh, survp;
1.53 brouard 1304: long ipmx;
1305: /*extern weight */
1306: /* We are differentiating ll according to initial status */
1307: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1308: /*for(i=1;i<imx;i++)
1309: printf(" %d\n",s[4][i]);
1310: */
1311: cov[1]=1.;
1312:
1313: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1314:
1315: if(mle==1){
1316: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1317: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1318: for(mi=1; mi<= wav[i]-1; mi++){
1319: for (ii=1;ii<=nlstate+ndeath;ii++)
1320: for (j=1;j<=nlstate+ndeath;j++){
1321: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1322: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1323: }
1324: for(d=0; d<dh[mi][i]; d++){
1325: newm=savm;
1326: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1327: for (kk=1; kk<=cptcovage;kk++) {
1328: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1329: }
1330: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1331: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1332: savm=oldm;
1333: oldm=newm;
1334: } /* end mult */
1.53 brouard 1335:
1.61 brouard 1336: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1.101 brouard 1337: /* But now since version 0.9 we anticipate for bias at large stepm.
1.61 brouard 1338: * If stepm is larger than one month (smallest stepm) and if the exact delay
1339: * (in months) between two waves is not a multiple of stepm, we rounded to
1340: * the nearest (and in case of equal distance, to the lowest) interval but now
1341: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1.101 brouard 1342: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1.61 brouard 1343: * probability in order to take into account the bias as a fraction of the way
1.101 brouard 1344: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1.61 brouard 1345: * -stepm/2 to stepm/2 .
1346: * For stepm=1 the results are the same as for previous versions of Imach.
1347: * For stepm > 1 the results are less biased than in previous versions.
1348: */
1349: s1=s[mw[mi][i]][i];
1350: s2=s[mw[mi+1][i]][i];
1.64 lievre 1351: bbh=(double)bh[mi][i]/(double)stepm;
1.101 brouard 1352: /* bias bh is positive if real duration
1.64 lievre 1353: * is higher than the multiple of stepm and negative otherwise.
1354: */
1355: /* 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 1356: if( s2 > nlstate){
1.104 lievre 1357: /* i.e. if s2 is a death state and if the date of death is known
1358: then the contribution to the likelihood is the probability to
1359: die between last step unit time and current step unit time,
1360: which is also equal to probability to die before dh
1.101 brouard 1361: minus probability to die before dh-stepm .
1.71 brouard 1362: In version up to 0.92 likelihood was computed
1363: as if date of death was unknown. Death was treated as any other
1364: health state: the date of the interview describes the actual state
1365: and not the date of a change in health state. The former idea was
1366: to consider that at each interview the state was recorded
1367: (healthy, disable or death) and IMaCh was corrected; but when we
1368: introduced the exact date of death then we should have modified
1369: the contribution of an exact death to the likelihood. This new
1370: contribution is smaller and very dependent of the step unit
1371: stepm. It is no more the probability to die between last interview
1372: and month of death but the probability to survive from last
1373: interview up to one month before death multiplied by the
1374: probability to die within a month. Thanks to Chris
1375: Jackson for correcting this bug. Former versions increased
1376: mortality artificially. The bad side is that we add another loop
1377: which slows down the processing. The difference can be up to 10%
1378: lower mortality.
1379: */
1380: lli=log(out[s1][s2] - savm[s1][s2]);
1.104 lievre 1381:
1382:
1383: } else if (s2==-2) {
1384: for (j=1,survp=0. ; j<=nlstate; j++)
1385: survp += out[s1][j];
1.119 ! brouard 1386: lli= log(survp);
1.104 lievre 1387: }
1.105 lievre 1388:
1.119 ! brouard 1389: /* else if (s2==-4) { */
! 1390: /* for (j=3,survp=0. ; j<=nlstate; j++) */
! 1391: /* survp += out[s1][j]; */
! 1392: /* lli= survp; */
! 1393: /* } */
1.105 lievre 1394:
1.119 ! brouard 1395: /* else if (s2==-5) { */
! 1396: /* for (j=1,survp=0. ; j<=2; j++) */
! 1397: /* survp += out[s1][j]; */
! 1398: /* lli= survp; */
! 1399: /* } */
1.104 lievre 1400:
1401:
1402: else{
1.71 brouard 1403: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1404: /* 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 */
1405: }
1.64 lievre 1406: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1407: /*if(lli ==000.0)*/
1408: /*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 1409: ipmx +=1;
1.64 lievre 1410: sw += weight[i];
1411: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1412: } /* end of wave */
1413: } /* end of individual */
1414: } else if(mle==2){
1415: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1416: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1417: for(mi=1; mi<= wav[i]-1; mi++){
1418: for (ii=1;ii<=nlstate+ndeath;ii++)
1419: for (j=1;j<=nlstate+ndeath;j++){
1420: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1421: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1422: }
1423: for(d=0; d<=dh[mi][i]; d++){
1424: newm=savm;
1425: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1426: for (kk=1; kk<=cptcovage;kk++) {
1427: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1428: }
1429: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1430: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1431: savm=oldm;
1432: oldm=newm;
1433: } /* end mult */
1434:
1435: s1=s[mw[mi][i]][i];
1436: s2=s[mw[mi+1][i]][i];
1437: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1438: 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 1439: ipmx +=1;
1440: sw += weight[i];
1441: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1442: } /* end of wave */
1443: } /* end of individual */
1444: } else if(mle==3){ /* exponential inter-extrapolation */
1445: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1446: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1447: for(mi=1; mi<= wav[i]-1; mi++){
1448: for (ii=1;ii<=nlstate+ndeath;ii++)
1449: for (j=1;j<=nlstate+ndeath;j++){
1450: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1451: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1452: }
1453: for(d=0; d<dh[mi][i]; d++){
1454: newm=savm;
1455: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1456: for (kk=1; kk<=cptcovage;kk++) {
1457: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1458: }
1459: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1460: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1461: savm=oldm;
1462: oldm=newm;
1463: } /* end mult */
1464:
1465: s1=s[mw[mi][i]][i];
1466: s2=s[mw[mi+1][i]][i];
1467: bbh=(double)bh[mi][i]/(double)stepm;
1468: 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 1469: ipmx +=1;
1470: sw += weight[i];
1471: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1472: } /* end of wave */
1473: } /* end of individual */
1.84 brouard 1474: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1475: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1476: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1477: for(mi=1; mi<= wav[i]-1; mi++){
1478: for (ii=1;ii<=nlstate+ndeath;ii++)
1479: for (j=1;j<=nlstate+ndeath;j++){
1480: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1481: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1482: }
1483: for(d=0; d<dh[mi][i]; d++){
1484: newm=savm;
1485: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1486: for (kk=1; kk<=cptcovage;kk++) {
1487: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1488: }
1489:
1490: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1491: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1492: savm=oldm;
1493: oldm=newm;
1494: } /* end mult */
1495:
1.84 brouard 1496: s1=s[mw[mi][i]][i];
1497: s2=s[mw[mi+1][i]][i];
1498: if( s2 > nlstate){
1499: lli=log(out[s1][s2] - savm[s1][s2]);
1500: }else{
1501: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1502: }
1503: ipmx +=1;
1504: sw += weight[i];
1505: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1506: /* 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 1507: } /* end of wave */
1508: } /* end of individual */
1509: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1510: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1511: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1512: for(mi=1; mi<= wav[i]-1; mi++){
1513: for (ii=1;ii<=nlstate+ndeath;ii++)
1514: for (j=1;j<=nlstate+ndeath;j++){
1515: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1516: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1517: }
1518: for(d=0; d<dh[mi][i]; d++){
1519: newm=savm;
1520: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1521: for (kk=1; kk<=cptcovage;kk++) {
1522: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1523: }
1524:
1525: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1526: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1527: savm=oldm;
1528: oldm=newm;
1529: } /* end mult */
1530:
1531: s1=s[mw[mi][i]][i];
1532: s2=s[mw[mi+1][i]][i];
1.61 brouard 1533: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1534: ipmx +=1;
1535: sw += weight[i];
1536: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1537: /*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 1538: } /* end of wave */
1539: } /* end of individual */
1540: } /* End of if */
1.53 brouard 1541: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1542: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1543: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1544: return -l;
1545: }
1546:
1547: /*************** log-likelihood *************/
1548: double funcone( double *x)
1549: {
1.87 brouard 1550: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1551: int i, ii, j, k, mi, d, kk;
1552: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1553: double **out;
1554: double lli; /* Individual log likelihood */
1.87 brouard 1555: double llt;
1.85 brouard 1556: int s1, s2;
1557: double bbh, survp;
1558: /*extern weight */
1559: /* We are differentiating ll according to initial status */
1560: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1561: /*for(i=1;i<imx;i++)
1562: printf(" %d\n",s[4][i]);
1563: */
1564: cov[1]=1.;
1565:
1566: for(k=1; k<=nlstate; k++) ll[k]=0.;
1567:
1568: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1569: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1570: for(mi=1; mi<= wav[i]-1; mi++){
1571: for (ii=1;ii<=nlstate+ndeath;ii++)
1572: for (j=1;j<=nlstate+ndeath;j++){
1573: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1574: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1575: }
1576: for(d=0; d<dh[mi][i]; d++){
1577: newm=savm;
1578: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1579: for (kk=1; kk<=cptcovage;kk++) {
1580: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1581: }
1582: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1583: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1584: savm=oldm;
1585: oldm=newm;
1586: } /* end mult */
1587:
1588: s1=s[mw[mi][i]][i];
1589: s2=s[mw[mi+1][i]][i];
1590: bbh=(double)bh[mi][i]/(double)stepm;
1591: /* bias is positive if real duration
1592: * is higher than the multiple of stepm and negative otherwise.
1593: */
1594: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1595: lli=log(out[s1][s2] - savm[s1][s2]);
1.119 ! brouard 1596: } else if (s2==-2) {
! 1597: for (j=1,survp=0. ; j<=nlstate; j++)
! 1598: survp += out[s1][j];
! 1599: lli= log(survp);
! 1600: }else if (mle==1){
1.85 brouard 1601: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1602: } else if(mle==2){
1603: 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 */
1604: } else if(mle==3){ /* exponential inter-extrapolation */
1605: 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 */
1606: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1607: lli=log(out[s1][s2]); /* Original formula */
1608: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1609: lli=log(out[s1][s2]); /* Original formula */
1610: } /* End of if */
1611: ipmx +=1;
1612: sw += weight[i];
1613: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1614: /* 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]); */
1615: if(globpr){
1.119 ! brouard 1616: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
! 1617: %11.6f %11.6f %11.6f ", \
1.86 brouard 1618: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1619: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1620: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1621: llt +=ll[k]*gipmx/gsw;
1622: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1623: }
1624: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1625: }
1626: } /* end of wave */
1627: } /* end of individual */
1628: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1629: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1630: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1631: if(globpr==0){ /* First time we count the contributions and weights */
1632: gipmx=ipmx;
1633: gsw=sw;
1634: }
1.53 brouard 1635: return -l;
1636: }
1637:
1638:
1.94 brouard 1639: /*************** function likelione ***********/
1.87 brouard 1640: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1641: {
1.87 brouard 1642: /* This routine should help understanding what is done with
1643: the selection of individuals/waves and
1.85 brouard 1644: to check the exact contribution to the likelihood.
1645: Plotting could be done.
1646: */
1647: int k;
1.87 brouard 1648:
1.88 brouard 1649: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1650: strcpy(fileresilk,"ilk");
1651: strcat(fileresilk,fileres);
1652: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1653: printf("Problem with resultfile: %s\n", fileresilk);
1654: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1655: }
1.87 brouard 1656: 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 1657: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1658: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1659: for(k=1; k<=nlstate; k++)
1.87 brouard 1660: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1661: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1662: }
1663:
1664: *fretone=(*funcone)(p);
1.87 brouard 1665: if(*globpri !=0){
1.85 brouard 1666: fclose(ficresilk);
1.88 brouard 1667: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1668: fflush(fichtm);
1669: }
1.85 brouard 1670: return;
1671: }
1672:
1.88 brouard 1673:
1.53 brouard 1674: /*********** Maximum Likelihood Estimation ***************/
1675:
1676: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1677: {
1678: int i,j, iter;
1.74 brouard 1679: double **xi;
1.53 brouard 1680: double fret;
1.85 brouard 1681: double fretone; /* Only one call to likelihood */
1.98 brouard 1682: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1683: xi=matrix(1,npar,1,npar);
1684: for (i=1;i<=npar;i++)
1685: for (j=1;j<=npar;j++)
1686: xi[i][j]=(i==j ? 1.0 : 0.0);
1687: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1688: strcpy(filerespow,"pow");
1689: strcat(filerespow,fileres);
1690: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1691: printf("Problem with resultfile: %s\n", filerespow);
1692: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1693: }
1694: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1695: for (i=1;i<=nlstate;i++)
1696: for(j=1;j<=nlstate+ndeath;j++)
1697: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1698: fprintf(ficrespow,"\n");
1.85 brouard 1699:
1.53 brouard 1700: powell(p,xi,npar,ftol,&iter,&fret,func);
1701:
1.115 brouard 1702: free_matrix(xi,1,npar,1,npar);
1.76 brouard 1703: fclose(ficrespow);
1704: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1705: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1706: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1707:
1708: }
1709:
1710: /**** Computes Hessian and covariance matrix ***/
1711: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1712: {
1713: double **a,**y,*x,pd;
1714: double **hess;
1715: int i, j,jk;
1716: int *indx;
1717:
1.98 brouard 1718: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1719: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1720: void lubksb(double **a, int npar, int *indx, double b[]) ;
1721: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 brouard 1722: double gompertz(double p[]);
1.53 brouard 1723: hess=matrix(1,npar,1,npar);
1724:
1725: printf("\nCalculation of the hessian matrix. Wait...\n");
1726: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1727: for (i=1;i<=npar;i++){
1728: printf("%d",i);fflush(stdout);
1729: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 brouard 1730:
1731: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1732:
1733: /* printf(" %f ",p[i]);
1734: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1735: }
1736:
1737: for (i=1;i<=npar;i++) {
1738: for (j=1;j<=npar;j++) {
1739: if (j>i) {
1740: printf(".%d%d",i,j);fflush(stdout);
1741: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 brouard 1742: hess[i][j]=hessij(p,delti,i,j,func,npar);
1743:
1.53 brouard 1744: hess[j][i]=hess[i][j];
1745: /*printf(" %lf ",hess[i][j]);*/
1746: }
1747: }
1748: }
1749: printf("\n");
1750: fprintf(ficlog,"\n");
1751:
1752: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1753: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1754:
1755: a=matrix(1,npar,1,npar);
1756: y=matrix(1,npar,1,npar);
1757: x=vector(1,npar);
1758: indx=ivector(1,npar);
1759: for (i=1;i<=npar;i++)
1760: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1761: ludcmp(a,npar,indx,&pd);
1762:
1763: for (j=1;j<=npar;j++) {
1764: for (i=1;i<=npar;i++) x[i]=0;
1765: x[j]=1;
1766: lubksb(a,npar,indx,x);
1767: for (i=1;i<=npar;i++){
1768: matcov[i][j]=x[i];
1769: }
1770: }
1771:
1772: printf("\n#Hessian matrix#\n");
1773: fprintf(ficlog,"\n#Hessian matrix#\n");
1774: for (i=1;i<=npar;i++) {
1775: for (j=1;j<=npar;j++) {
1776: printf("%.3e ",hess[i][j]);
1777: fprintf(ficlog,"%.3e ",hess[i][j]);
1778: }
1779: printf("\n");
1780: fprintf(ficlog,"\n");
1781: }
1782:
1783: /* Recompute Inverse */
1784: for (i=1;i<=npar;i++)
1785: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1786: ludcmp(a,npar,indx,&pd);
1787:
1788: /* printf("\n#Hessian matrix recomputed#\n");
1789:
1790: for (j=1;j<=npar;j++) {
1791: for (i=1;i<=npar;i++) x[i]=0;
1792: x[j]=1;
1793: lubksb(a,npar,indx,x);
1794: for (i=1;i<=npar;i++){
1795: y[i][j]=x[i];
1796: printf("%.3e ",y[i][j]);
1797: fprintf(ficlog,"%.3e ",y[i][j]);
1798: }
1799: printf("\n");
1800: fprintf(ficlog,"\n");
1801: }
1802: */
1803:
1804: free_matrix(a,1,npar,1,npar);
1805: free_matrix(y,1,npar,1,npar);
1806: free_vector(x,1,npar);
1807: free_ivector(indx,1,npar);
1808: free_matrix(hess,1,npar,1,npar);
1809:
1810:
1811: }
1812:
1813: /*************** hessian matrix ****************/
1.98 brouard 1814: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1815: {
1816: int i;
1817: int l=1, lmax=20;
1818: double k1,k2;
1819: double p2[NPARMAX+1];
1820: double res;
1.98 brouard 1821: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1822: double fx;
1823: int k=0,kmax=10;
1824: double l1;
1825:
1826: fx=func(x);
1827: for (i=1;i<=npar;i++) p2[i]=x[i];
1828: for(l=0 ; l <=lmax; l++){
1829: l1=pow(10,l);
1830: delts=delt;
1831: for(k=1 ; k <kmax; k=k+1){
1832: delt = delta*(l1*k);
1833: p2[theta]=x[theta] +delt;
1834: k1=func(p2)-fx;
1835: p2[theta]=x[theta]-delt;
1836: k2=func(p2)-fx;
1837: /*res= (k1-2.0*fx+k2)/delt/delt; */
1838: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1839:
1840: #ifdef DEBUG
1841: 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);
1842: 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);
1843: #endif
1844: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1845: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1846: k=kmax;
1847: }
1848: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1849: k=kmax; l=lmax*10.;
1850: }
1851: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1852: delts=delt;
1853: }
1854: }
1855: }
1856: delti[theta]=delts;
1857: return res;
1858:
1859: }
1860:
1.98 brouard 1861: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1862: {
1863: int i;
1864: int l=1, l1, lmax=20;
1865: double k1,k2,k3,k4,res,fx;
1866: double p2[NPARMAX+1];
1867: int k;
1868:
1869: fx=func(x);
1870: for (k=1; k<=2; k++) {
1871: for (i=1;i<=npar;i++) p2[i]=x[i];
1872: p2[thetai]=x[thetai]+delti[thetai]/k;
1873: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1874: k1=func(p2)-fx;
1875:
1876: p2[thetai]=x[thetai]+delti[thetai]/k;
1877: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1878: k2=func(p2)-fx;
1879:
1880: p2[thetai]=x[thetai]-delti[thetai]/k;
1881: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1882: k3=func(p2)-fx;
1883:
1884: p2[thetai]=x[thetai]-delti[thetai]/k;
1885: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1886: k4=func(p2)-fx;
1887: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1888: #ifdef DEBUG
1889: 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);
1890: 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);
1891: #endif
1892: }
1893: return res;
1894: }
1895:
1896: /************** Inverse of matrix **************/
1897: void ludcmp(double **a, int n, int *indx, double *d)
1898: {
1899: int i,imax,j,k;
1900: double big,dum,sum,temp;
1901: double *vv;
1902:
1903: vv=vector(1,n);
1904: *d=1.0;
1905: for (i=1;i<=n;i++) {
1906: big=0.0;
1907: for (j=1;j<=n;j++)
1908: if ((temp=fabs(a[i][j])) > big) big=temp;
1909: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1910: vv[i]=1.0/big;
1911: }
1912: for (j=1;j<=n;j++) {
1913: for (i=1;i<j;i++) {
1914: sum=a[i][j];
1915: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1916: a[i][j]=sum;
1917: }
1918: big=0.0;
1919: for (i=j;i<=n;i++) {
1920: sum=a[i][j];
1921: for (k=1;k<j;k++)
1922: sum -= a[i][k]*a[k][j];
1923: a[i][j]=sum;
1924: if ( (dum=vv[i]*fabs(sum)) >= big) {
1925: big=dum;
1926: imax=i;
1927: }
1928: }
1929: if (j != imax) {
1930: for (k=1;k<=n;k++) {
1931: dum=a[imax][k];
1932: a[imax][k]=a[j][k];
1933: a[j][k]=dum;
1934: }
1935: *d = -(*d);
1936: vv[imax]=vv[j];
1937: }
1938: indx[j]=imax;
1939: if (a[j][j] == 0.0) a[j][j]=TINY;
1940: if (j != n) {
1941: dum=1.0/(a[j][j]);
1942: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1943: }
1944: }
1945: free_vector(vv,1,n); /* Doesn't work */
1946: ;
1947: }
1948:
1949: void lubksb(double **a, int n, int *indx, double b[])
1950: {
1951: int i,ii=0,ip,j;
1952: double sum;
1953:
1954: for (i=1;i<=n;i++) {
1955: ip=indx[i];
1956: sum=b[ip];
1957: b[ip]=b[i];
1958: if (ii)
1959: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1960: else if (sum) ii=i;
1961: b[i]=sum;
1962: }
1963: for (i=n;i>=1;i--) {
1964: sum=b[i];
1965: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1966: b[i]=sum/a[i][i];
1967: }
1968: }
1969:
1.117 brouard 1970: void pstamp(FILE *fichier)
1971: {
1972: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
1973: }
1974:
1.53 brouard 1975: /************ Frequencies ********************/
1.105 lievre 1976: 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 1977: { /* Some frequencies */
1978:
1979: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1980: int first;
1981: double ***freq; /* Frequencies */
1.73 lievre 1982: double *pp, **prop;
1983: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1984: char fileresp[FILENAMELENGTH];
1985:
1986: pp=vector(1,nlstate);
1.74 brouard 1987: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1988: strcpy(fileresp,"p");
1989: strcat(fileresp,fileres);
1990: if((ficresp=fopen(fileresp,"w"))==NULL) {
1991: printf("Problem with prevalence resultfile: %s\n", fileresp);
1992: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1993: exit(0);
1994: }
1.105 lievre 1995: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1996: j1=0;
1997:
1998: j=cptcoveff;
1999: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2000:
2001: first=1;
2002:
2003: for(k1=1; k1<=j;k1++){
2004: for(i1=1; i1<=ncodemax[k1];i1++){
2005: j1++;
2006: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2007: scanf("%d", i);*/
1.105 lievre 2008: for (i=-5; i<=nlstate+ndeath; i++)
2009: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.74 brouard 2010: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 2011: freq[i][jk][m]=0;
1.73 lievre 2012:
2013: for (i=1; i<=nlstate; i++)
1.74 brouard 2014: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 2015: prop[i][m]=0;
1.53 brouard 2016:
2017: dateintsum=0;
2018: k2cpt=0;
2019: for (i=1; i<=imx; i++) {
2020: bool=1;
2021: if (cptcovn>0) {
2022: for (z1=1; z1<=cptcoveff; z1++)
2023: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2024: bool=0;
2025: }
1.58 lievre 2026: if (bool==1){
1.53 brouard 2027: for(m=firstpass; m<=lastpass; m++){
2028: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 2029: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 2030: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2031: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 2032: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 2033: if (m<lastpass) {
2034: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 2035: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 2036: }
2037:
1.74 brouard 2038: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 2039: dateintsum=dateintsum+k2;
2040: k2cpt++;
2041: }
1.84 brouard 2042: /*}*/
1.53 brouard 2043: }
2044: }
2045: }
2046:
1.84 brouard 2047: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.117 brouard 2048: pstamp(ficresp);
1.53 brouard 2049: if (cptcovn>0) {
2050: fprintf(ficresp, "\n#********** Variable ");
2051: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2052: fprintf(ficresp, "**********\n#");
2053: }
2054: for(i=1; i<=nlstate;i++)
2055: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2056: fprintf(ficresp, "\n");
2057:
1.74 brouard 2058: for(i=iagemin; i <= iagemax+3; i++){
2059: if(i==iagemax+3){
1.53 brouard 2060: fprintf(ficlog,"Total");
2061: }else{
2062: if(first==1){
2063: first=0;
2064: printf("See log file for details...\n");
2065: }
2066: fprintf(ficlog,"Age %d", i);
2067: }
2068: for(jk=1; jk <=nlstate ; jk++){
2069: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2070: pp[jk] += freq[jk][m][i];
2071: }
2072: for(jk=1; jk <=nlstate ; jk++){
2073: for(m=-1, pos=0; m <=0 ; m++)
2074: pos += freq[jk][m][i];
2075: if(pp[jk]>=1.e-10){
2076: if(first==1){
2077: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2078: }
2079: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2080: }else{
2081: if(first==1)
2082: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2083: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2084: }
2085: }
2086:
2087: for(jk=1; jk <=nlstate ; jk++){
2088: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2089: pp[jk] += freq[jk][m][i];
1.73 lievre 2090: }
2091: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2092: pos += pp[jk];
2093: posprop += prop[jk][i];
1.53 brouard 2094: }
2095: for(jk=1; jk <=nlstate ; jk++){
2096: if(pos>=1.e-5){
2097: if(first==1)
2098: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2099: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2100: }else{
2101: if(first==1)
2102: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2103: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2104: }
1.74 brouard 2105: if( i <= iagemax){
1.53 brouard 2106: if(pos>=1.e-5){
1.73 lievre 2107: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 2108: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 2109: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2110: }
2111: else
1.73 lievre 2112: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 2113: }
2114: }
2115:
1.69 brouard 2116: for(jk=-1; jk <=nlstate+ndeath; jk++)
2117: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 2118: if(freq[jk][m][i] !=0 ) {
2119: if(first==1)
2120: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2121: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2122: }
1.74 brouard 2123: if(i <= iagemax)
1.53 brouard 2124: fprintf(ficresp,"\n");
2125: if(first==1)
2126: printf("Others in log...\n");
2127: fprintf(ficlog,"\n");
2128: }
2129: }
2130: }
2131: dateintmean=dateintsum/k2cpt;
2132:
2133: fclose(ficresp);
1.105 lievre 2134: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 2135: free_vector(pp,1,nlstate);
1.74 brouard 2136: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 2137: /* End of Freq */
2138: }
2139:
2140: /************ Prevalence ********************/
1.84 brouard 2141: 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 2142: {
2143: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2144: in each health status at the date of interview (if between dateprev1 and dateprev2).
2145: We still use firstpass and lastpass as another selection.
2146: */
1.53 brouard 2147:
2148: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2149: double ***freq; /* Frequencies */
1.73 lievre 2150: double *pp, **prop;
2151: double pos,posprop;
1.69 brouard 2152: double y2; /* in fractional years */
1.74 brouard 2153: int iagemin, iagemax;
1.53 brouard 2154:
1.74 brouard 2155: iagemin= (int) agemin;
2156: iagemax= (int) agemax;
2157: /*pp=vector(1,nlstate);*/
2158: prop=matrix(1,nlstate,iagemin,iagemax+3);
2159: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 2160: j1=0;
2161:
2162: j=cptcoveff;
2163: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2164:
2165: for(k1=1; k1<=j;k1++){
2166: for(i1=1; i1<=ncodemax[k1];i1++){
2167: j1++;
2168:
1.73 lievre 2169: for (i=1; i<=nlstate; i++)
1.74 brouard 2170: for(m=iagemin; m <= iagemax+3; m++)
2171: prop[i][m]=0.0;
1.53 brouard 2172:
1.69 brouard 2173: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2174: bool=1;
2175: if (cptcovn>0) {
2176: for (z1=1; z1<=cptcoveff; z1++)
2177: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2178: bool=0;
2179: }
2180: if (bool==1) {
1.69 brouard 2181: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2182: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2183: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2184: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2185: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2186: 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);
2187: if (s[m][i]>0 && s[m][i]<=nlstate) {
2188: /*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]]);*/
2189: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2190: prop[s[m][i]][iagemax+3] += weight[i];
2191: }
1.53 brouard 2192: }
1.69 brouard 2193: } /* end selection of waves */
1.53 brouard 2194: }
2195: }
1.74 brouard 2196: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2197:
1.74 brouard 2198: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2199: posprop += prop[jk][i];
2200: }
2201:
2202: for(jk=1; jk <=nlstate ; jk++){
2203: if( i <= iagemax){
2204: if(posprop>=1.e-5){
2205: probs[i][jk][j1]= prop[jk][i]/posprop;
2206: }
2207: }
2208: }/* end jk */
2209: }/* end i */
1.53 brouard 2210: } /* end i1 */
2211: } /* end k1 */
2212:
1.74 brouard 2213: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2214: /*free_vector(pp,1,nlstate);*/
2215: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2216: } /* End of prevalence */
1.53 brouard 2217:
2218: /************* Waves Concatenation ***************/
2219:
1.59 brouard 2220: 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 2221: {
2222: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2223: Death is a valid wave (if date is known).
2224: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2225: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2226: and mw[mi+1][i]. dh depends on stepm.
2227: */
2228:
2229: int i, mi, m;
2230: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2231: double sum=0., jmean=0.;*/
2232: int first;
2233: int j, k=0,jk, ju, jl;
2234: double sum=0.;
2235: first=0;
2236: jmin=1e+5;
2237: jmax=-1;
2238: jmean=0.;
2239: for(i=1; i<=imx; i++){
2240: mi=0;
2241: m=firstpass;
2242: while(s[m][i] <= nlstate){
1.105 lievre 2243: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
1.53 brouard 2244: mw[++mi][i]=m;
2245: if(m >=lastpass)
2246: break;
2247: else
2248: m++;
2249: }/* end while */
2250: if (s[m][i] > nlstate){
2251: mi++; /* Death is another wave */
2252: /* if(mi==0) never been interviewed correctly before death */
2253: /* Only death is a correct wave */
2254: mw[mi][i]=m;
2255: }
2256:
2257: wav[i]=mi;
2258: if(mi==0){
1.91 brouard 2259: nbwarn++;
1.53 brouard 2260: if(first==0){
1.111 brouard 2261: 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 2262: first=1;
2263: }
2264: if(first==1){
1.111 brouard 2265: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2266: }
2267: } /* end mi==0 */
1.77 brouard 2268: } /* End individuals */
1.53 brouard 2269:
2270: for(i=1; i<=imx; i++){
2271: for(mi=1; mi<wav[i];mi++){
2272: if (stepm <=0)
2273: dh[mi][i]=1;
2274: else{
1.77 brouard 2275: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2276: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2277: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2278: if(j==0) j=1; /* Survives at least one month after exam */
2279: else if(j<0){
1.91 brouard 2280: nberr++;
1.85 brouard 2281: 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 2282: j=1; /* Temporary Dangerous patch */
1.105 lievre 2283: 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 2284: 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 2285: 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 2286: }
2287: k=k+1;
1.110 brouard 2288: if (j >= jmax){
2289: jmax=j;
2290: ijmax=i;
2291: }
2292: if (j <= jmin){
2293: jmin=j;
2294: ijmin=i;
2295: }
1.85 brouard 2296: sum=sum+j;
2297: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2298: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2299: }
2300: }
2301: else{
2302: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.104 lievre 2303: /* 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]); */
2304:
1.53 brouard 2305: k=k+1;
1.110 brouard 2306: if (j >= jmax) {
2307: jmax=j;
2308: ijmax=i;
2309: }
2310: else if (j <= jmin){
2311: jmin=j;
2312: ijmin=i;
2313: }
1.53 brouard 2314: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2315: /*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 2316: if(j<0){
1.91 brouard 2317: nberr++;
1.85 brouard 2318: 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]);
2319: 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]);
2320: }
1.53 brouard 2321: sum=sum+j;
2322: }
2323: jk= j/stepm;
2324: jl= j -jk*stepm;
2325: ju= j -(jk+1)*stepm;
1.85 brouard 2326: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2327: if(jl==0){
2328: dh[mi][i]=jk;
2329: bh[mi][i]=0;
2330: }else{ /* We want a negative bias in order to only have interpolation ie
2331: * at the price of an extra matrix product in likelihood */
2332: dh[mi][i]=jk+1;
2333: bh[mi][i]=ju;
2334: }
2335: }else{
2336: if(jl <= -ju){
2337: dh[mi][i]=jk;
2338: bh[mi][i]=jl; /* bias is positive if real duration
2339: * is higher than the multiple of stepm and negative otherwise.
2340: */
2341: }
2342: else{
2343: dh[mi][i]=jk+1;
2344: bh[mi][i]=ju;
2345: }
2346: if(dh[mi][i]==0){
2347: dh[mi][i]=1; /* At least one step */
2348: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2349: /* 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 2350: }
1.85 brouard 2351: } /* end if mle */
2352: }
1.64 lievre 2353: } /* end wave */
1.53 brouard 2354: }
2355: jmean=sum/k;
1.110 brouard 2356: 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);
2357: 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 2358: }
2359:
2360: /*********** Tricode ****************************/
2361: void tricode(int *Tvar, int **nbcode, int imx)
2362: {
1.58 lievre 2363:
2364: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2365: int cptcode=0;
2366: cptcoveff=0;
2367:
1.58 lievre 2368: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2369: for (k=1; k<=7; k++) ncodemax[k]=0;
2370:
2371: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2372: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2373: modality*/
2374: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2375: Ndum[ij]++; /*store the modality */
1.53 brouard 2376: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2377: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2378: Tvar[j]. If V=sex and male is 0 and
2379: female is 1, then cptcode=1.*/
1.53 brouard 2380: }
2381:
2382: for (i=0; i<=cptcode; i++) {
1.58 lievre 2383: 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 2384: }
1.58 lievre 2385:
1.53 brouard 2386: ij=1;
2387: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2388: for (k=0; k<= maxncov; k++) {
1.53 brouard 2389: if (Ndum[k] != 0) {
2390: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2391: /* 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 2392:
2393: ij++;
2394: }
2395: if (ij > ncodemax[j]) break;
2396: }
2397: }
2398: }
2399:
1.58 lievre 2400: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2401:
1.58 lievre 2402: for (i=1; i<=ncovmodel-2; i++) {
1.104 lievre 2403: /* 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 2404: ij=Tvar[i];
1.58 lievre 2405: Ndum[ij]++;
1.53 brouard 2406: }
2407:
2408: ij=1;
1.58 lievre 2409: for (i=1; i<= maxncov; i++) {
1.53 brouard 2410: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2411: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2412: ij++;
2413: }
2414: }
2415:
1.58 lievre 2416: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2417: }
2418:
2419: /*********** Health Expectancies ****************/
2420:
1.117 brouard 2421: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.53 brouard 2422:
2423: {
1.117 brouard 2424: /* Health expectancies, no variances */
2425: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
1.53 brouard 2426: double age, agelim, hf;
1.117 brouard 2427: double ***p3mat;
2428: double eip;
2429:
2430: pstamp(ficreseij);
2431: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2432: fprintf(ficreseij,"# Age");
2433: for(i=1; i<=nlstate;i++){
2434: for(j=1; j<=nlstate;j++){
2435: fprintf(ficreseij," e%1d%1d ",i,j);
2436: }
2437: fprintf(ficreseij," e%1d. ",i);
2438: }
2439: fprintf(ficreseij,"\n");
2440:
2441:
2442: if(estepm < stepm){
2443: printf ("Problem %d lower than %d\n",estepm, stepm);
2444: }
2445: else hstepm=estepm;
2446: /* We compute the life expectancy from trapezoids spaced every estepm months
2447: * This is mainly to measure the difference between two models: for example
2448: * if stepm=24 months pijx are given only every 2 years and by summing them
2449: * we are calculating an estimate of the Life Expectancy assuming a linear
2450: * progression in between and thus overestimating or underestimating according
2451: * to the curvature of the survival function. If, for the same date, we
2452: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2453: * to compare the new estimate of Life expectancy with the same linear
2454: * hypothesis. A more precise result, taking into account a more precise
2455: * curvature will be obtained if estepm is as small as stepm. */
2456:
2457: /* For example we decided to compute the life expectancy with the smallest unit */
2458: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2459: nhstepm is the number of hstepm from age to agelim
2460: nstepm is the number of stepm from age to agelin.
2461: Look at hpijx to understand the reason of that which relies in memory size
2462: and note for a fixed period like estepm months */
2463: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2464: survival function given by stepm (the optimization length). Unfortunately it
2465: means that if the survival funtion is printed only each two years of age and if
2466: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2467: results. So we changed our mind and took the option of the best precision.
2468: */
2469: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2470:
2471: agelim=AGESUP;
2472: /* nhstepm age range expressed in number of stepm */
2473: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2474: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2475: /* if (stepm >= YEARM) hstepm=1;*/
2476: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2477: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2478:
2479: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2480: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2481: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1.119 ! brouard 2482:
1.117 brouard 2483: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
1.119 ! brouard 2484:
1.117 brouard 2485: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.119 ! brouard 2486:
! 2487: printf("%d|",(int)age);fflush(stdout);
! 2488: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
! 2489:
1.117 brouard 2490: /* Computing expectancies */
2491: for(i=1; i<=nlstate;i++)
2492: for(j=1; j<=nlstate;j++)
2493: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2494: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2495:
1.119 ! brouard 2496: /* 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]);*/
1.117 brouard 2497:
2498: }
2499:
2500: fprintf(ficreseij,"%3.0f",age );
2501: for(i=1; i<=nlstate;i++){
2502: eip=0;
2503: for(j=1; j<=nlstate;j++){
2504: eip +=eij[i][j][(int)age];
2505: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2506: }
2507: fprintf(ficreseij,"%9.4f", eip );
2508: }
2509: fprintf(ficreseij,"\n");
1.119 ! brouard 2510:
1.117 brouard 2511: }
2512: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2513: printf("\n");
2514: fprintf(ficlog,"\n");
1.119 ! brouard 2515:
1.117 brouard 2516: }
2517:
2518: void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
2519:
2520: {
2521: /* Covariances of health expectancies eij and of total life expectancies according
2522: to initial status i, ei. .
2523: */
2524: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2525: double age, agelim, hf;
2526: double ***p3matp, ***p3matm, ***varhe;
1.53 brouard 2527: double **dnewm,**doldm;
1.117 brouard 2528: double *xp, *xm;
1.53 brouard 2529: double **gp, **gm;
2530: double ***gradg, ***trgradg;
2531: int theta;
2532:
1.117 brouard 2533: double eip, vip;
2534:
1.74 brouard 2535: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2536: xp=vector(1,npar);
1.117 brouard 2537: xm=vector(1,npar);
1.74 brouard 2538: dnewm=matrix(1,nlstate*nlstate,1,npar);
2539: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2540:
1.117 brouard 2541: pstamp(ficresstdeij);
2542: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2543: fprintf(ficresstdeij,"# Age");
2544: for(i=1; i<=nlstate;i++){
1.53 brouard 2545: for(j=1; j<=nlstate;j++)
1.117 brouard 2546: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2547: fprintf(ficresstdeij," e%1d. ",i);
2548: }
2549: fprintf(ficresstdeij,"\n");
1.53 brouard 2550:
1.117 brouard 2551: pstamp(ficrescveij);
2552: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2553: fprintf(ficrescveij,"# Age");
2554: for(i=1; i<=nlstate;i++)
2555: for(j=1; j<=nlstate;j++){
2556: cptj= (j-1)*nlstate+i;
2557: for(i2=1; i2<=nlstate;i2++)
2558: for(j2=1; j2<=nlstate;j2++){
2559: cptj2= (j2-1)*nlstate+i2;
2560: if(cptj2 <= cptj)
2561: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2562: }
2563: }
2564: fprintf(ficrescveij,"\n");
2565:
1.53 brouard 2566: if(estepm < stepm){
2567: printf ("Problem %d lower than %d\n",estepm, stepm);
2568: }
2569: else hstepm=estepm;
2570: /* We compute the life expectancy from trapezoids spaced every estepm months
2571: * This is mainly to measure the difference between two models: for example
2572: * if stepm=24 months pijx are given only every 2 years and by summing them
2573: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2574: * progression in between and thus overestimating or underestimating according
1.53 brouard 2575: * to the curvature of the survival function. If, for the same date, we
2576: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2577: * to compare the new estimate of Life expectancy with the same linear
2578: * hypothesis. A more precise result, taking into account a more precise
2579: * curvature will be obtained if estepm is as small as stepm. */
2580:
2581: /* For example we decided to compute the life expectancy with the smallest unit */
2582: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2583: nhstepm is the number of hstepm from age to agelim
2584: nstepm is the number of stepm from age to agelin.
2585: Look at hpijx to understand the reason of that which relies in memory size
2586: and note for a fixed period like estepm months */
2587: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2588: survival function given by stepm (the optimization length). Unfortunately it
2589: means that if the survival funtion is printed only each two years of age and if
2590: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2591: results. So we changed our mind and took the option of the best precision.
2592: */
2593: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2594:
1.117 brouard 2595: /* If stepm=6 months */
2596: /* nhstepm age range expressed in number of stepm */
1.53 brouard 2597: agelim=AGESUP;
1.117 brouard 2598: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2599: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2600: /* if (stepm >= YEARM) hstepm=1;*/
2601: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2602:
2603: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2604: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2605: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2606: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2607: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2608: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2609:
2610: for (age=bage; age<=fage; age ++){
1.53 brouard 2611:
2612: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2613: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2614:
2615: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2616:
1.95 brouard 2617: /* Computing Variances of health expectancies */
1.117 brouard 2618: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2619: decrease memory allocation */
2620: for(theta=1; theta <=npar; theta++){
1.53 brouard 2621: for(i=1; i<=npar; i++){
2622: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1.117 brouard 2623: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.53 brouard 2624: }
1.117 brouard 2625: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2626: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.53 brouard 2627:
2628: for(j=1; j<= nlstate; j++){
2629: for(i=1; i<=nlstate; i++){
1.117 brouard 2630: for(h=0; h<=nhstepm-1; h++){
2631: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2632: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
1.53 brouard 2633: }
2634: }
2635: }
2636:
1.117 brouard 2637: for(ij=1; ij<= nlstate*nlstate; ij++)
1.53 brouard 2638: for(h=0; h<=nhstepm-1; h++){
1.117 brouard 2639: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
1.53 brouard 2640: }
1.117 brouard 2641: }/* End theta */
2642:
2643:
2644: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2645: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2646: for(theta=1; theta <=npar; theta++)
2647: trgradg[h][j][theta]=gradg[h][theta][j];
1.117 brouard 2648:
1.53 brouard 2649:
1.117 brouard 2650: for(ij=1;ij<=nlstate*nlstate;ij++)
2651: for(ji=1;ji<=nlstate*nlstate;ji++)
2652: varhe[ij][ji][(int)age] =0.;
1.53 brouard 2653:
2654: printf("%d|",(int)age);fflush(stdout);
2655: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2656: for(h=0;h<=nhstepm-1;h++){
2657: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2658: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2659: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
1.117 brouard 2660: for(ij=1;ij<=nlstate*nlstate;ij++)
2661: for(ji=1;ji<=nlstate*nlstate;ji++)
2662: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.53 brouard 2663: }
2664: }
2665: /* Computing expectancies */
1.117 brouard 2666: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
1.53 brouard 2667: for(i=1; i<=nlstate;i++)
2668: for(j=1; j<=nlstate;j++)
2669: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1.117 brouard 2670: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.53 brouard 2671:
1.117 brouard 2672: /* 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]);*/
1.53 brouard 2673:
2674: }
2675:
1.117 brouard 2676: fprintf(ficresstdeij,"%3.0f",age );
2677: for(i=1; i<=nlstate;i++){
2678: eip=0.;
2679: vip=0.;
2680: for(j=1; j<=nlstate;j++){
2681: eip += eij[i][j][(int)age];
2682: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2683: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2684: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2685: }
2686: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2687: }
2688: fprintf(ficresstdeij,"\n");
2689:
2690: fprintf(ficrescveij,"%3.0f",age );
1.53 brouard 2691: for(i=1; i<=nlstate;i++)
2692: for(j=1; j<=nlstate;j++){
1.117 brouard 2693: cptj= (j-1)*nlstate+i;
2694: for(i2=1; i2<=nlstate;i2++)
2695: for(j2=1; j2<=nlstate;j2++){
2696: cptj2= (j2-1)*nlstate+i2;
2697: if(cptj2 <= cptj)
2698: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2699: }
1.53 brouard 2700: }
1.117 brouard 2701: fprintf(ficrescveij,"\n");
1.53 brouard 2702:
2703: }
1.117 brouard 2704: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2705: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2706: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2707: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2708: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2709: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 2710: printf("\n");
2711: fprintf(ficlog,"\n");
2712:
1.117 brouard 2713: free_vector(xm,1,npar);
1.53 brouard 2714: free_vector(xp,1,npar);
1.74 brouard 2715: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2716: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2717: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2718: }
2719:
2720: /************ Variance ******************/
1.105 lievre 2721: 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 2722: {
2723: /* Variance of health expectancies */
2724: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2725: /* double **newm;*/
2726: double **dnewm,**doldm;
2727: double **dnewmp,**doldmp;
2728: int i, j, nhstepm, hstepm, h, nstepm ;
2729: int k, cptcode;
2730: double *xp;
2731: double **gp, **gm; /* for var eij */
2732: double ***gradg, ***trgradg; /*for var eij */
2733: double **gradgp, **trgradgp; /* for var p point j */
2734: double *gpp, *gmp; /* for var p point j */
2735: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2736: double ***p3mat;
2737: double age,agelim, hf;
2738: double ***mobaverage;
2739: int theta;
2740: char digit[4];
1.55 lievre 2741: char digitp[25];
1.53 brouard 2742:
2743: char fileresprobmorprev[FILENAMELENGTH];
2744:
1.55 lievre 2745: if(popbased==1){
1.58 lievre 2746: if(mobilav!=0)
1.55 lievre 2747: strcpy(digitp,"-populbased-mobilav-");
2748: else strcpy(digitp,"-populbased-nomobil-");
2749: }
2750: else
1.53 brouard 2751: strcpy(digitp,"-stablbased-");
1.56 lievre 2752:
1.54 brouard 2753: if (mobilav!=0) {
1.53 brouard 2754: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2755: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2756: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2757: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2758: }
1.53 brouard 2759: }
2760:
2761: strcpy(fileresprobmorprev,"prmorprev");
2762: sprintf(digit,"%-d",ij);
2763: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2764: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2765: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2766: strcat(fileresprobmorprev,fileres);
2767: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2768: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2769: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2770: }
2771: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2772:
1.53 brouard 2773: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.117 brouard 2774: pstamp(ficresprobmorprev);
1.66 brouard 2775: 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 2776: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2777: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2778: fprintf(ficresprobmorprev," p.%-d SE",j);
2779: for(i=1; i<=nlstate;i++)
2780: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2781: }
2782: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2783: fprintf(ficgp,"\n# Routine varevsij");
1.106 brouard 2784: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.87 brouard 2785: 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");
2786: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2787: /* } */
1.53 brouard 2788: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.117 brouard 2789: pstamp(ficresvij);
2790: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2791: if(popbased==1)
2792: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2793: else
2794: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
1.53 brouard 2795: fprintf(ficresvij,"# Age");
2796: for(i=1; i<=nlstate;i++)
2797: for(j=1; j<=nlstate;j++)
1.117 brouard 2798: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
1.53 brouard 2799: fprintf(ficresvij,"\n");
2800:
2801: xp=vector(1,npar);
2802: dnewm=matrix(1,nlstate,1,npar);
2803: doldm=matrix(1,nlstate,1,nlstate);
2804: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2805: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2806:
2807: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2808: gpp=vector(nlstate+1,nlstate+ndeath);
2809: gmp=vector(nlstate+1,nlstate+ndeath);
2810: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2811:
2812: if(estepm < stepm){
2813: printf ("Problem %d lower than %d\n",estepm, stepm);
2814: }
2815: else hstepm=estepm;
2816: /* For example we decided to compute the life expectancy with the smallest unit */
2817: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2818: nhstepm is the number of hstepm from age to agelim
2819: nstepm is the number of stepm from age to agelin.
2820: Look at hpijx to understand the reason of that which relies in memory size
2821: and note for a fixed period like k years */
2822: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2823: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2824: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2825: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2826: results. So we changed our mind and took the option of the best precision.
2827: */
2828: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2829: agelim = AGESUP;
2830: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2831: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2832: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2833: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2834: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2835: gp=matrix(0,nhstepm,1,nlstate);
2836: gm=matrix(0,nhstepm,1,nlstate);
2837:
2838:
2839: for(theta=1; theta <=npar; theta++){
1.66 brouard 2840: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2841: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2842: }
2843: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2844: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2845:
2846: if (popbased==1) {
1.54 brouard 2847: if(mobilav ==0){
1.53 brouard 2848: for(i=1; i<=nlstate;i++)
2849: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2850: }else{ /* mobilav */
1.53 brouard 2851: for(i=1; i<=nlstate;i++)
2852: prlim[i][i]=mobaverage[(int)age][i][ij];
2853: }
2854: }
2855:
2856: for(j=1; j<= nlstate; j++){
2857: for(h=0; h<=nhstepm; h++){
2858: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2859: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2860: }
2861: }
1.66 brouard 2862: /* This for computing probability of death (h=1 means
2863: computed over hstepm matrices product = hstepm*stepm months)
2864: as a weighted average of prlim.
2865: */
1.69 brouard 2866: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2867: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2868: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2869: }
1.66 brouard 2870: /* end probability of death */
1.53 brouard 2871:
1.66 brouard 2872: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2873: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2874: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2875: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2876:
2877: if (popbased==1) {
1.54 brouard 2878: if(mobilav ==0){
1.53 brouard 2879: for(i=1; i<=nlstate;i++)
2880: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2881: }else{ /* mobilav */
1.53 brouard 2882: for(i=1; i<=nlstate;i++)
2883: prlim[i][i]=mobaverage[(int)age][i][ij];
2884: }
2885: }
2886:
2887: for(j=1; j<= nlstate; j++){
2888: for(h=0; h<=nhstepm; h++){
2889: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2890: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2891: }
2892: }
1.66 brouard 2893: /* This for computing probability of death (h=1 means
2894: computed over hstepm matrices product = hstepm*stepm months)
2895: as a weighted average of prlim.
2896: */
1.69 brouard 2897: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2898: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2899: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2900: }
1.66 brouard 2901: /* end probability of death */
1.53 brouard 2902:
2903: for(j=1; j<= nlstate; j++) /* vareij */
2904: for(h=0; h<=nhstepm; h++){
2905: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2906: }
1.68 lievre 2907:
1.53 brouard 2908: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2909: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2910: }
2911:
2912: } /* End theta */
2913:
2914: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2915:
2916: for(h=0; h<=nhstepm; h++) /* veij */
2917: for(j=1; j<=nlstate;j++)
2918: for(theta=1; theta <=npar; theta++)
2919: trgradg[h][j][theta]=gradg[h][theta][j];
2920:
2921: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2922: for(theta=1; theta <=npar; theta++)
1.53 brouard 2923: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2924:
1.53 brouard 2925:
2926: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2927: for(i=1;i<=nlstate;i++)
2928: for(j=1;j<=nlstate;j++)
2929: vareij[i][j][(int)age] =0.;
2930:
2931: for(h=0;h<=nhstepm;h++){
2932: for(k=0;k<=nhstepm;k++){
2933: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2934: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2935: for(i=1;i<=nlstate;i++)
2936: for(j=1;j<=nlstate;j++)
2937: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2938: }
2939: }
1.70 brouard 2940:
1.53 brouard 2941: /* pptj */
2942: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2943: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2944: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2945: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2946: varppt[j][i]=doldmp[j][i];
2947: /* end ppptj */
1.66 brouard 2948: /* x centered again */
1.53 brouard 2949: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2950: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2951:
2952: if (popbased==1) {
1.54 brouard 2953: if(mobilav ==0){
1.53 brouard 2954: for(i=1; i<=nlstate;i++)
2955: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2956: }else{ /* mobilav */
1.53 brouard 2957: for(i=1; i<=nlstate;i++)
2958: prlim[i][i]=mobaverage[(int)age][i][ij];
2959: }
2960: }
1.70 brouard 2961:
1.66 brouard 2962: /* This for computing probability of death (h=1 means
2963: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2964: as a weighted average of prlim.
2965: */
1.68 lievre 2966: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2967: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2968: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2969: }
1.66 brouard 2970: /* end probability of death */
1.53 brouard 2971:
2972: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2973: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2974: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2975: for(i=1; i<=nlstate;i++){
2976: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2977: }
2978: }
2979: fprintf(ficresprobmorprev,"\n");
2980:
2981: fprintf(ficresvij,"%.0f ",age );
2982: for(i=1; i<=nlstate;i++)
2983: for(j=1; j<=nlstate;j++){
2984: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2985: }
2986: fprintf(ficresvij,"\n");
2987: free_matrix(gp,0,nhstepm,1,nlstate);
2988: free_matrix(gm,0,nhstepm,1,nlstate);
2989: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2990: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2991: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2992: } /* End age */
2993: free_vector(gpp,nlstate+1,nlstate+ndeath);
2994: free_vector(gmp,nlstate+1,nlstate+ndeath);
2995: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2996: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2997: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2998: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2999: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 3000: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3001: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3002: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 3003: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3004: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3005: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3006: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3007: 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 3008: /* 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);
3009: */
1.88 brouard 3010: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 3011: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 3012:
3013: free_vector(xp,1,npar);
3014: free_matrix(doldm,1,nlstate,1,nlstate);
3015: free_matrix(dnewm,1,nlstate,1,npar);
3016: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3017: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3018: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 3019: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3020: fclose(ficresprobmorprev);
1.88 brouard 3021: fflush(ficgp);
3022: fflush(fichtm);
1.84 brouard 3023: } /* end varevsij */
1.53 brouard 3024:
3025: /************ Variance of prevlim ******************/
1.105 lievre 3026: 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 3027: {
3028: /* Variance of prevalence limit */
1.59 brouard 3029: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 3030: double **newm;
3031: double **dnewm,**doldm;
3032: int i, j, nhstepm, hstepm;
3033: int k, cptcode;
3034: double *xp;
3035: double *gp, *gm;
3036: double **gradg, **trgradg;
3037: double age,agelim;
3038: int theta;
1.117 brouard 3039:
3040: pstamp(ficresvpl);
3041: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.53 brouard 3042: fprintf(ficresvpl,"# Age");
3043: for(i=1; i<=nlstate;i++)
3044: fprintf(ficresvpl," %1d-%1d",i,i);
3045: fprintf(ficresvpl,"\n");
3046:
3047: xp=vector(1,npar);
3048: dnewm=matrix(1,nlstate,1,npar);
3049: doldm=matrix(1,nlstate,1,nlstate);
3050:
3051: hstepm=1*YEARM; /* Every year of age */
3052: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3053: agelim = AGESUP;
3054: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3055: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3056: if (stepm >= YEARM) hstepm=1;
3057: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3058: gradg=matrix(1,npar,1,nlstate);
3059: gp=vector(1,nlstate);
3060: gm=vector(1,nlstate);
3061:
3062: for(theta=1; theta <=npar; theta++){
3063: for(i=1; i<=npar; i++){ /* Computes gradient */
3064: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3065: }
3066: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3067: for(i=1;i<=nlstate;i++)
3068: gp[i] = prlim[i][i];
3069:
3070: for(i=1; i<=npar; i++) /* Computes gradient */
3071: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3072: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3073: for(i=1;i<=nlstate;i++)
3074: gm[i] = prlim[i][i];
3075:
3076: for(i=1;i<=nlstate;i++)
3077: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3078: } /* End theta */
3079:
3080: trgradg =matrix(1,nlstate,1,npar);
3081:
3082: for(j=1; j<=nlstate;j++)
3083: for(theta=1; theta <=npar; theta++)
3084: trgradg[j][theta]=gradg[theta][j];
3085:
3086: for(i=1;i<=nlstate;i++)
3087: varpl[i][(int)age] =0.;
3088: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3089: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3090: for(i=1;i<=nlstate;i++)
3091: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3092:
3093: fprintf(ficresvpl,"%.0f ",age );
3094: for(i=1; i<=nlstate;i++)
3095: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3096: fprintf(ficresvpl,"\n");
3097: free_vector(gp,1,nlstate);
3098: free_vector(gm,1,nlstate);
3099: free_matrix(gradg,1,npar,1,nlstate);
3100: free_matrix(trgradg,1,nlstate,1,npar);
3101: } /* End age */
3102:
3103: free_vector(xp,1,npar);
3104: free_matrix(doldm,1,nlstate,1,npar);
3105: free_matrix(dnewm,1,nlstate,1,nlstate);
3106:
3107: }
3108:
3109: /************ Variance of one-step probabilities ******************/
1.105 lievre 3110: 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 3111: {
3112: int i, j=0, i1, k1, l1, t, tj;
3113: int k2, l2, j1, z1;
3114: int k=0,l, cptcode;
3115: int first=1, first1;
3116: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3117: double **dnewm,**doldm;
3118: double *xp;
3119: double *gp, *gm;
3120: double **gradg, **trgradg;
3121: double **mu;
3122: double age,agelim, cov[NCOVMAX];
3123: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3124: int theta;
3125: char fileresprob[FILENAMELENGTH];
3126: char fileresprobcov[FILENAMELENGTH];
3127: char fileresprobcor[FILENAMELENGTH];
3128:
3129: double ***varpij;
3130:
3131: strcpy(fileresprob,"prob");
3132: strcat(fileresprob,fileres);
3133: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3134: printf("Problem with resultfile: %s\n", fileresprob);
3135: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3136: }
3137: strcpy(fileresprobcov,"probcov");
3138: strcat(fileresprobcov,fileres);
3139: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3140: printf("Problem with resultfile: %s\n", fileresprobcov);
3141: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3142: }
3143: strcpy(fileresprobcor,"probcor");
3144: strcat(fileresprobcor,fileres);
3145: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3146: printf("Problem with resultfile: %s\n", fileresprobcor);
3147: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3148: }
3149: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3150: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3151: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3152: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3153: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3154: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.117 brouard 3155: pstamp(ficresprob);
1.53 brouard 3156: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3157: fprintf(ficresprob,"# Age");
1.117 brouard 3158: pstamp(ficresprobcov);
1.53 brouard 3159: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3160: fprintf(ficresprobcov,"# Age");
1.117 brouard 3161: pstamp(ficresprobcor);
1.53 brouard 3162: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
1.117 brouard 3163: fprintf(ficresprobcor,"# Age");
1.53 brouard 3164:
3165:
3166: for(i=1; i<=nlstate;i++)
3167: for(j=1; j<=(nlstate+ndeath);j++){
3168: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3169: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3170: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3171: }
1.69 brouard 3172: /* fprintf(ficresprob,"\n");
1.53 brouard 3173: fprintf(ficresprobcov,"\n");
3174: fprintf(ficresprobcor,"\n");
1.69 brouard 3175: */
3176: xp=vector(1,npar);
1.53 brouard 3177: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3178: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3179: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3180: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3181: first=1;
1.88 brouard 3182: fprintf(ficgp,"\n# Routine varprob");
3183: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3184: fprintf(fichtm,"\n");
3185:
1.95 brouard 3186: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3187: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 3188: file %s<br>\n",optionfilehtmcov);
3189: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3190: and drawn. It helps understanding how is the covariance between two incidences.\
3191: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3192: 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. \
3193: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3194: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3195: standard deviations wide on each axis. <br>\
3196: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3197: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3198: 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 3199:
3200: cov[1]=1;
3201: tj=cptcoveff;
3202: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3203: j1=0;
3204: for(t=1; t<=tj;t++){
3205: for(i1=1; i1<=ncodemax[t];i1++){
3206: j1++;
3207: if (cptcovn>0) {
3208: fprintf(ficresprob, "\n#********** Variable ");
3209: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3210: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 3211: fprintf(ficresprobcov, "\n#********** Variable ");
3212: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3213: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 3214:
3215: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 3216: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3217: fprintf(ficgp, "**********\n#\n");
1.53 brouard 3218:
3219:
1.96 brouard 3220: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 3221: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 3222: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 3223:
3224: fprintf(ficresprobcor, "\n#********** Variable ");
3225: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3226: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 3227: }
3228:
3229: for (age=bage; age<=fage; age ++){
3230: cov[2]=age;
3231: for (k=1; k<=cptcovn;k++) {
3232: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3233: }
3234: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3235: for (k=1; k<=cptcovprod;k++)
3236: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3237:
3238: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3239: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3240: gp=vector(1,(nlstate)*(nlstate+ndeath));
3241: gm=vector(1,(nlstate)*(nlstate+ndeath));
3242:
3243: for(theta=1; theta <=npar; theta++){
3244: for(i=1; i<=npar; i++)
1.74 brouard 3245: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 3246:
3247: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3248:
3249: k=0;
3250: for(i=1; i<= (nlstate); i++){
3251: for(j=1; j<=(nlstate+ndeath);j++){
3252: k=k+1;
3253: gp[k]=pmmij[i][j];
3254: }
3255: }
3256:
3257: for(i=1; i<=npar; i++)
1.74 brouard 3258: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 3259:
3260: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3261: k=0;
3262: for(i=1; i<=(nlstate); i++){
3263: for(j=1; j<=(nlstate+ndeath);j++){
3264: k=k+1;
3265: gm[k]=pmmij[i][j];
3266: }
3267: }
3268:
3269: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 3270: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 3271: }
3272:
3273: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3274: for(theta=1; theta <=npar; theta++)
3275: trgradg[j][theta]=gradg[theta][j];
3276:
3277: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3278: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 3279: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3280: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3281: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3282: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3283:
1.53 brouard 3284: pmij(pmmij,cov,ncovmodel,x,nlstate);
3285:
3286: k=0;
3287: for(i=1; i<=(nlstate); i++){
3288: for(j=1; j<=(nlstate+ndeath);j++){
3289: k=k+1;
3290: mu[k][(int) age]=pmmij[i][j];
3291: }
3292: }
3293: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3294: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3295: varpij[i][j][(int)age] = doldm[i][j];
3296:
3297: /*printf("\n%d ",(int)age);
1.59 brouard 3298: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3299: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3300: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3301: }*/
1.53 brouard 3302:
3303: fprintf(ficresprob,"\n%d ",(int)age);
3304: fprintf(ficresprobcov,"\n%d ",(int)age);
3305: fprintf(ficresprobcor,"\n%d ",(int)age);
3306:
3307: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3308: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3309: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3310: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3311: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3312: }
3313: i=0;
3314: for (k=1; k<=(nlstate);k++){
3315: for (l=1; l<=(nlstate+ndeath);l++){
3316: i=i++;
3317: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3318: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3319: for (j=1; j<=i;j++){
3320: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3321: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3322: }
3323: }
3324: }/* end of loop for state */
3325: } /* end of loop for age */
3326:
3327: /* Confidence intervalle of pij */
3328: /*
1.59 brouard 3329: fprintf(ficgp,"\nset noparametric;unset label");
3330: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3331: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3332: 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);
3333: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3334: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3335: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3336: */
3337:
3338: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3339: first1=1;
3340: for (k2=1; k2<=(nlstate);k2++){
3341: for (l2=1; l2<=(nlstate+ndeath);l2++){
3342: if(l2==k2) continue;
3343: j=(k2-1)*(nlstate+ndeath)+l2;
3344: for (k1=1; k1<=(nlstate);k1++){
3345: for (l1=1; l1<=(nlstate+ndeath);l1++){
3346: if(l1==k1) continue;
3347: i=(k1-1)*(nlstate+ndeath)+l1;
3348: if(i<=j) continue;
3349: for (age=bage; age<=fage; age ++){
3350: if ((int)age %5==0){
3351: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3352: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3353: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3354: mu1=mu[i][(int) age]/stepm*YEARM ;
3355: mu2=mu[j][(int) age]/stepm*YEARM;
3356: c12=cv12/sqrt(v1*v2);
3357: /* Computing eigen value of matrix of covariance */
3358: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3359: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3360: /* Eigen vectors */
3361: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3362: /*v21=sqrt(1.-v11*v11); *//* error */
3363: v21=(lc1-v1)/cv12*v11;
3364: v12=-v21;
3365: v22=v11;
3366: tnalp=v21/v11;
3367: if(first1==1){
3368: first1=0;
3369: 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);
3370: }
3371: 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);
3372: /*printf(fignu*/
3373: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3374: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3375: if(first==1){
3376: first=0;
3377: fprintf(ficgp,"\nset parametric;unset label");
3378: 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);
3379: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3380: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3381: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3382: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3383: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3384: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3385: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3386: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3387: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3388: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3389: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3390: 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",\
3391: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3392: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3393: }else{
3394: first=0;
1.91 brouard 3395: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3396: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3397: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3398: 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",\
3399: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3400: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3401: }/* if first */
3402: } /* age mod 5 */
3403: } /* end loop age */
1.88 brouard 3404: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3405: first=1;
3406: } /*l12 */
3407: } /* k12 */
3408: } /*l1 */
3409: }/* k1 */
3410: } /* loop covariates */
3411: }
1.59 brouard 3412: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3413: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.113 brouard 3414: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3415: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
1.53 brouard 3416: free_vector(xp,1,npar);
3417: fclose(ficresprob);
3418: fclose(ficresprobcov);
3419: fclose(ficresprobcor);
1.91 brouard 3420: fflush(ficgp);
3421: fflush(fichtmcov);
1.53 brouard 3422: }
3423:
3424:
3425: /******************* Printing html file ***********/
3426: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3427: int lastpass, int stepm, int weightopt, char model[],\
3428: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3429: int popforecast, int estepm ,\
3430: double jprev1, double mprev1,double anprev1, \
3431: double jprev2, double mprev2,double anprev2){
3432: int jj1, k1, i1, cpt;
3433:
1.107 brouard 3434: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3435: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
1.106 brouard 3436: </ul>");
1.107 brouard 3437: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
1.96 brouard 3438: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3439: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3440: fprintf(fichtm,"\
3441: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3442: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3443: fprintf(fichtm,"\
1.117 brouard 3444: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.96 brouard 3445: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3446: fprintf(fichtm,"\
1.117 brouard 3447: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (estepm=%2d months): \
1.96 brouard 3448: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3449: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.116 brouard 3450:
1.53 brouard 3451:
3452: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3453:
3454: m=cptcoveff;
3455: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3456:
3457: jj1=0;
3458: for(k1=1; k1<=m;k1++){
3459: for(i1=1; i1<=ncodemax[k1];i1++){
3460: jj1++;
3461: if (cptcovn > 0) {
3462: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3463: for (cpt=1; cpt<=cptcoveff;cpt++)
3464: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3465: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3466: }
3467: /* Pij */
1.117 brouard 3468: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
3469: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3470: /* Quasi-incidences */
1.85 brouard 3471: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.117 brouard 3472: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
3473: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3474: /* Period (stable) prevalence in each health state */
1.53 brouard 3475: for(cpt=1; cpt<nlstate;cpt++){
1.117 brouard 3476: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3477: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3478: }
3479: for(cpt=1; cpt<=nlstate;cpt++) {
1.117 brouard 3480: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3481: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3482: }
3483: } /* end i1 */
3484: }/* End k1 */
3485: fprintf(fichtm,"</ul>");
3486:
3487:
1.96 brouard 3488: fprintf(fichtm,"\
1.107 brouard 3489: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.96 brouard 3490: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3491:
3492: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3493: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3494: fprintf(fichtm,"\
3495: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3496: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3497:
3498: fprintf(fichtm,"\
3499: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3500: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3501: fprintf(fichtm,"\
1.117 brouard 3502: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
3503: <a href=\"%s\">%s</a> <br>\n</li>",
3504: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3505: fprintf(fichtm,"\
3506: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
3507: <a href=\"%s\">%s</a> <br>\n</li>",
3508: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3509: fprintf(fichtm,"\
3510: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.96 brouard 3511: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3512: fprintf(fichtm,"\
1.117 brouard 3513: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
1.96 brouard 3514: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3515: fprintf(fichtm,"\
1.117 brouard 3516: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.88 brouard 3517: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3518:
1.76 brouard 3519: /* if(popforecast==1) fprintf(fichtm,"\n */
3520: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3521: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3522: /* <br>",fileres,fileres,fileres,fileres); */
3523: /* else */
3524: /* 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 3525: fflush(fichtm);
3526: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3527:
3528: m=cptcoveff;
3529: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3530:
3531: jj1=0;
3532: for(k1=1; k1<=m;k1++){
3533: for(i1=1; i1<=ncodemax[k1];i1++){
3534: jj1++;
3535: if (cptcovn > 0) {
3536: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3537: for (cpt=1; cpt<=cptcoveff;cpt++)
3538: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3539: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3540: }
3541: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3542: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3543: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3544: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3545: }
1.96 brouard 3546: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3547: health expectancies in states (1) and (2): %s%d.png<br>\
3548: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3549: } /* end i1 */
3550: }/* End k1 */
3551: fprintf(fichtm,"</ul>");
1.87 brouard 3552: fflush(fichtm);
1.53 brouard 3553: }
3554:
3555: /******************* Gnuplot file **************/
1.89 brouard 3556: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3557:
1.88 brouard 3558: char dirfileres[132],optfileres[132];
1.53 brouard 3559: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3560: int ng;
1.88 brouard 3561: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3562: /* printf("Problem with file %s",optionfilegnuplot); */
3563: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3564: /* } */
1.53 brouard 3565:
1.54 brouard 3566: /*#ifdef windows */
1.89 brouard 3567: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3568: /*#endif */
1.88 brouard 3569: m=pow(2,cptcoveff);
3570:
3571: strcpy(dirfileres,optionfilefiname);
3572: strcpy(optfileres,"vpl");
1.53 brouard 3573: /* 1eme*/
3574: for (cpt=1; cpt<= nlstate ; cpt ++) {
3575: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3576: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3577: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3578: fprintf(ficgp,"set xlabel \"Age\" \n\
3579: set ylabel \"Probability\" \n\
3580: set ter png small\n\
3581: set size 0.65,0.65\n\
3582: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3583:
3584: for (i=1; i<= nlstate ; i ++) {
3585: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3586: else fprintf(ficgp," \%%*lf (\%%*lf)");
3587: }
1.117 brouard 3588: fprintf(ficgp,"\" t\"Period (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 3589: for (i=1; i<= nlstate ; i ++) {
3590: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3591: else fprintf(ficgp," \%%*lf (\%%*lf)");
3592: }
1.88 brouard 3593: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3594: for (i=1; i<= nlstate ; i ++) {
3595: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3596: else fprintf(ficgp," \%%*lf (\%%*lf)");
3597: }
1.88 brouard 3598: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3599: }
3600: }
3601: /*2 eme*/
3602:
3603: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3604: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3605: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3606:
3607: for (i=1; i<= nlstate+1 ; i ++) {
3608: k=2*i;
1.88 brouard 3609: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3610: for (j=1; j<= nlstate+1 ; j ++) {
3611: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3612: else fprintf(ficgp," \%%*lf (\%%*lf)");
3613: }
3614: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3615: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3616: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3617: for (j=1; j<= nlstate+1 ; j ++) {
3618: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3619: else fprintf(ficgp," \%%*lf (\%%*lf)");
3620: }
3621: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3622: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3623: for (j=1; j<= nlstate+1 ; j ++) {
3624: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3625: else fprintf(ficgp," \%%*lf (\%%*lf)");
3626: }
3627: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3628: else fprintf(ficgp,"\" t\"\" w l 0,");
3629: }
3630: }
3631:
3632: /*3eme*/
3633:
3634: for (k1=1; k1<= m ; k1 ++) {
3635: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.117 brouard 3636: /* k=2+nlstate*(2*cpt-2); */
3637: k=2+(nlstate+1)*(cpt-1);
1.88 brouard 3638: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3639: fprintf(ficgp,"set ter png small\n\
3640: set size 0.65,0.65\n\
3641: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3642: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3643: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3644: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3645: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3646: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3647: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3648:
3649: */
3650: for (i=1; i< nlstate ; i ++) {
1.117 brouard 3651: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
3652: /* 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 3653:
3654: }
1.117 brouard 3655: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
1.53 brouard 3656: }
3657: }
3658:
1.76 brouard 3659: /* CV preval stable (period) */
1.53 brouard 3660: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3661: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3662: k=3;
1.88 brouard 3663: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3664: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3665: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3666: unset log y\n\
1.88 brouard 3667: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3668:
1.83 lievre 3669: for (i=1; i< nlstate ; i ++)
1.53 brouard 3670: fprintf(ficgp,"+$%d",k+i+1);
3671: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3672:
3673: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3674: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3675: for (i=1; i< nlstate ; i ++) {
3676: l=3+(nlstate+ndeath)*cpt;
3677: fprintf(ficgp,"+$%d",l+i+1);
3678: }
3679: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3680: }
3681: }
3682:
3683: /* proba elementaires */
3684: for(i=1,jk=1; i <=nlstate; i++){
3685: for(k=1; k <=(nlstate+ndeath); k++){
3686: if (k != i) {
3687: for(j=1; j <=ncovmodel; j++){
3688: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3689: jk++;
3690: fprintf(ficgp,"\n");
3691: }
3692: }
3693: }
3694: }
3695:
3696: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3697: for(jk=1; jk <=m; jk++) {
1.88 brouard 3698: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3699: if (ng==2)
3700: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3701: else
3702: fprintf(ficgp,"\nset title \"Probability\"\n");
3703: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3704: i=1;
3705: for(k2=1; k2<=nlstate; k2++) {
3706: k3=i;
3707: for(k=1; k<=(nlstate+ndeath); k++) {
3708: if (k != k2){
3709: if(ng==2)
3710: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3711: else
3712: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3713: ij=1;
3714: for(j=3; j <=ncovmodel; j++) {
3715: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3716: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3717: ij++;
3718: }
3719: else
3720: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3721: }
3722: fprintf(ficgp,")/(1");
3723:
3724: for(k1=1; k1 <=nlstate; k1++){
3725: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3726: ij=1;
3727: for(j=3; j <=ncovmodel; j++){
3728: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3729: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3730: ij++;
3731: }
3732: else
3733: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3734: }
3735: fprintf(ficgp,")");
3736: }
3737: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3738: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3739: i=i+ncovmodel;
3740: }
3741: } /* end k */
3742: } /* end k2 */
3743: } /* end jk */
3744: } /* end ng */
1.88 brouard 3745: fflush(ficgp);
1.53 brouard 3746: } /* end gnuplot */
3747:
3748:
3749: /*************** Moving average **************/
1.54 brouard 3750: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3751:
3752: int i, cpt, cptcod;
1.58 lievre 3753: int modcovmax =1;
1.54 brouard 3754: int mobilavrange, mob;
1.53 brouard 3755: double age;
1.58 lievre 3756:
3757: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3758: a covariate has 2 modalities */
3759: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3760:
1.54 brouard 3761: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3762: if(mobilav==1) mobilavrange=5; /* default */
3763: else mobilavrange=mobilav;
3764: for (age=bage; age<=fage; age++)
3765: for (i=1; i<=nlstate;i++)
1.58 lievre 3766: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3767: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3768: /* We keep the original values on the extreme ages bage, fage and for
3769: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3770: we use a 5 terms etc. until the borders are no more concerned.
3771: */
3772: for (mob=3;mob <=mobilavrange;mob=mob+2){
3773: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3774: for (i=1; i<=nlstate;i++){
1.58 lievre 3775: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3776: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3777: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3778: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3779: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3780: }
3781: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3782: }
1.53 brouard 3783: }
1.54 brouard 3784: }/* end age */
3785: }/* end mob */
3786: }else return -1;
3787: return 0;
3788: }/* End movingaverage */
1.53 brouard 3789:
3790:
3791: /************** Forecasting ******************/
1.70 brouard 3792: 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 3793: /* proj1, year, month, day of starting projection
3794: agemin, agemax range of age
3795: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3796: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3797: */
1.73 lievre 3798: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3799: int *popage;
1.70 brouard 3800: double agec; /* generic age */
3801: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3802: double *popeffectif,*popcount;
3803: double ***p3mat;
1.55 lievre 3804: double ***mobaverage;
1.53 brouard 3805: char fileresf[FILENAMELENGTH];
3806:
1.69 brouard 3807: agelim=AGESUP;
1.84 brouard 3808: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3809:
3810: strcpy(fileresf,"f");
3811: strcat(fileresf,fileres);
3812: if((ficresf=fopen(fileresf,"w"))==NULL) {
3813: printf("Problem with forecast resultfile: %s\n", fileresf);
3814: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3815: }
3816: printf("Computing forecasting: result on file '%s' \n", fileresf);
3817: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3818:
3819: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3820:
1.54 brouard 3821: if (mobilav!=0) {
1.53 brouard 3822: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3823: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3824: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3825: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3826: }
1.53 brouard 3827: }
3828:
3829: stepsize=(int) (stepm+YEARM-1)/YEARM;
3830: if (stepm<=12) stepsize=1;
1.74 brouard 3831: if(estepm < stepm){
3832: printf ("Problem %d lower than %d\n",estepm, stepm);
3833: }
3834: else hstepm=estepm;
3835:
1.53 brouard 3836: hstepm=hstepm/stepm;
1.69 brouard 3837: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3838: fractional in yp1 */
1.53 brouard 3839: anprojmean=yp;
3840: yp2=modf((yp1*12),&yp);
3841: mprojmean=yp;
3842: yp1=modf((yp2*30.5),&yp);
3843: jprojmean=yp;
3844: if(jprojmean==0) jprojmean=1;
3845: if(mprojmean==0) jprojmean=1;
1.73 lievre 3846:
3847: i1=cptcoveff;
3848: if (cptcovn < 1){i1=1;}
1.53 brouard 3849:
1.70 brouard 3850: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3851:
1.70 brouard 3852: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3853:
1.75 brouard 3854: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3855: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3856: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3857: k=k+1;
3858: fprintf(ficresf,"\n#******");
3859: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3860: 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 3861: }
3862: fprintf(ficresf,"******\n");
1.70 brouard 3863: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3864: for(j=1; j<=nlstate+ndeath;j++){
3865: for(i=1; i<=nlstate;i++)
3866: fprintf(ficresf," p%d%d",i,j);
3867: fprintf(ficresf," p.%d",j);
3868: }
1.74 brouard 3869: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3870: fprintf(ficresf,"\n");
1.70 brouard 3871: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3872:
1.71 brouard 3873: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3874: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3875: nhstepm = nhstepm/hstepm;
3876: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3877: oldm=oldms;savm=savms;
1.70 brouard 3878: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3879:
3880: for (h=0; h<=nhstepm; h++){
1.75 brouard 3881: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3882: fprintf(ficresf,"\n");
3883: for(j=1;j<=cptcoveff;j++)
3884: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3885: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3886: }
3887: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3888: ppij=0.;
1.71 brouard 3889: for(i=1; i<=nlstate;i++) {
1.53 brouard 3890: if (mobilav==1)
1.71 brouard 3891: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3892: else {
1.71 brouard 3893: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3894: }
1.75 brouard 3895: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3896: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3897: }
3898: } /* end i */
3899: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3900: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3901: }
1.75 brouard 3902: }/* end j */
3903: } /* end h */
1.53 brouard 3904: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3905: } /* end agec */
3906: } /* end yearp */
3907: } /* end cptcod */
3908: } /* end cptcov */
1.53 brouard 3909:
1.54 brouard 3910: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3911:
3912: fclose(ficresf);
3913: }
1.70 brouard 3914:
3915: /************** Forecasting *****not tested NB*************/
1.53 brouard 3916: 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){
3917:
3918: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3919: int *popage;
1.69 brouard 3920: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3921: double *popeffectif,*popcount;
3922: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3923: double ***mobaverage;
1.53 brouard 3924: char filerespop[FILENAMELENGTH];
3925:
3926: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3927: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3928: agelim=AGESUP;
1.69 brouard 3929: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3930:
1.84 brouard 3931: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3932:
3933:
3934: strcpy(filerespop,"pop");
3935: strcat(filerespop,fileres);
3936: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3937: printf("Problem with forecast resultfile: %s\n", filerespop);
3938: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3939: }
3940: printf("Computing forecasting: result on file '%s' \n", filerespop);
3941: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3942:
3943: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3944:
1.54 brouard 3945: if (mobilav!=0) {
1.53 brouard 3946: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3947: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3948: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3949: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3950: }
1.53 brouard 3951: }
3952:
3953: stepsize=(int) (stepm+YEARM-1)/YEARM;
3954: if (stepm<=12) stepsize=1;
3955:
3956: agelim=AGESUP;
3957:
3958: hstepm=1;
3959: hstepm=hstepm/stepm;
3960:
3961: if (popforecast==1) {
3962: if((ficpop=fopen(popfile,"r"))==NULL) {
3963: printf("Problem with population file : %s\n",popfile);exit(0);
3964: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3965: }
3966: popage=ivector(0,AGESUP);
3967: popeffectif=vector(0,AGESUP);
3968: popcount=vector(0,AGESUP);
3969:
3970: i=1;
3971: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3972:
3973: imx=i;
3974: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3975: }
3976:
1.69 brouard 3977: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3978: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3979: k=k+1;
3980: fprintf(ficrespop,"\n#******");
3981: for(j=1;j<=cptcoveff;j++) {
3982: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3983: }
3984: fprintf(ficrespop,"******\n");
3985: fprintf(ficrespop,"# Age");
3986: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3987: if (popforecast==1) fprintf(ficrespop," [Population]");
3988:
3989: for (cpt=0; cpt<=0;cpt++) {
3990: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3991:
1.69 brouard 3992: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3993: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3994: nhstepm = nhstepm/hstepm;
3995:
3996: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3997: oldm=oldms;savm=savms;
3998: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3999:
4000: for (h=0; h<=nhstepm; h++){
1.69 brouard 4001: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 4002: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4003: }
4004: for(j=1; j<=nlstate+ndeath;j++) {
4005: kk1=0.;kk2=0;
4006: for(i=1; i<=nlstate;i++) {
4007: if (mobilav==1)
4008: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4009: else {
4010: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4011: }
4012: }
1.69 brouard 4013: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 4014: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4015: /*fprintf(ficrespop," %.3f", kk1);
4016: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4017: }
4018: }
4019: for(i=1; i<=nlstate;i++){
4020: kk1=0.;
4021: for(j=1; j<=nlstate;j++){
4022: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4023: }
1.69 brouard 4024: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 4025: }
4026:
1.69 brouard 4027: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 4028: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4029: }
4030: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4031: }
4032: }
4033:
4034: /******/
4035:
4036: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4037: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 4038: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 4039: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4040: nhstepm = nhstepm/hstepm;
4041:
4042: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4043: oldm=oldms;savm=savms;
4044: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4045: for (h=0; h<=nhstepm; h++){
1.69 brouard 4046: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 4047: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4048: }
4049: for(j=1; j<=nlstate+ndeath;j++) {
4050: kk1=0.;kk2=0;
4051: for(i=1; i<=nlstate;i++) {
4052: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4053: }
1.69 brouard 4054: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 4055: }
4056: }
4057: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4058: }
4059: }
4060: }
4061: }
4062:
1.54 brouard 4063: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4064:
4065: if (popforecast==1) {
4066: free_ivector(popage,0,AGESUP);
4067: free_vector(popeffectif,0,AGESUP);
4068: free_vector(popcount,0,AGESUP);
4069: }
4070: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4071: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4072: fclose(ficrespop);
1.84 brouard 4073: } /* End of popforecast */
1.53 brouard 4074:
1.87 brouard 4075: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 4076: {
1.87 brouard 4077: if((fichier=fopen(optionfich,"a"))==NULL) {
4078: printf("Problem with file: %s\n", optionfich);
4079: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4080: return (0);
1.86 brouard 4081: }
1.87 brouard 4082: fflush(fichier);
4083: return (1);
1.86 brouard 4084: }
1.94 brouard 4085:
4086:
4087: /**************** function prwizard **********************/
1.88 brouard 4088: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4089: {
4090:
1.94 brouard 4091: /* Wizard to print covariance matrix template */
4092:
1.88 brouard 4093: char ca[32], cb[32], cc[32];
4094: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4095: int numlinepar;
4096:
4097: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4098: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4099: for(i=1; i <=nlstate; i++){
4100: jj=0;
4101: for(j=1; j <=nlstate+ndeath; j++){
4102: if(j==i) continue;
4103: jj++;
4104: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4105: printf("%1d%1d",i,j);
4106: fprintf(ficparo,"%1d%1d",i,j);
4107: for(k=1; k<=ncovmodel;k++){
4108: /* printf(" %lf",param[i][j][k]); */
4109: /* fprintf(ficparo," %lf",param[i][j][k]); */
4110: printf(" 0.");
4111: fprintf(ficparo," 0.");
4112: }
4113: printf("\n");
4114: fprintf(ficparo,"\n");
4115: }
4116: }
4117: printf("# Scales (for hessian or gradient estimation)\n");
4118: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4119: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4120: for(i=1; i <=nlstate; i++){
4121: jj=0;
4122: for(j=1; j <=nlstate+ndeath; j++){
4123: if(j==i) continue;
4124: jj++;
4125: fprintf(ficparo,"%1d%1d",i,j);
4126: printf("%1d%1d",i,j);
4127: fflush(stdout);
4128: for(k=1; k<=ncovmodel;k++){
4129: /* printf(" %le",delti3[i][j][k]); */
4130: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4131: printf(" 0.");
4132: fprintf(ficparo," 0.");
4133: }
4134: numlinepar++;
4135: printf("\n");
4136: fprintf(ficparo,"\n");
4137: }
4138: }
4139: printf("# Covariance matrix\n");
4140: /* # 121 Var(a12)\n\ */
4141: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4142: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4143: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4144: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4145: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4146: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4147: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4148: fflush(stdout);
4149: fprintf(ficparo,"# Covariance matrix\n");
4150: /* # 121 Var(a12)\n\ */
4151: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4152: /* # ...\n\ */
4153: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4154:
4155: for(itimes=1;itimes<=2;itimes++){
4156: jj=0;
4157: for(i=1; i <=nlstate; i++){
4158: for(j=1; j <=nlstate+ndeath; j++){
4159: if(j==i) continue;
4160: for(k=1; k<=ncovmodel;k++){
4161: jj++;
4162: ca[0]= k+'a'-1;ca[1]='\0';
4163: if(itimes==1){
4164: printf("#%1d%1d%d",i,j,k);
4165: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4166: }else{
4167: printf("%1d%1d%d",i,j,k);
4168: fprintf(ficparo,"%1d%1d%d",i,j,k);
4169: /* printf(" %.5le",matcov[i][j]); */
4170: }
4171: ll=0;
4172: for(li=1;li <=nlstate; li++){
4173: for(lj=1;lj <=nlstate+ndeath; lj++){
4174: if(lj==li) continue;
4175: for(lk=1;lk<=ncovmodel;lk++){
4176: ll++;
4177: if(ll<=jj){
4178: cb[0]= lk +'a'-1;cb[1]='\0';
4179: if(ll<jj){
4180: if(itimes==1){
4181: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4182: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4183: }else{
4184: printf(" 0.");
4185: fprintf(ficparo," 0.");
4186: }
4187: }else{
4188: if(itimes==1){
4189: printf(" Var(%s%1d%1d)",ca,i,j);
4190: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4191: }else{
4192: printf(" 0.");
4193: fprintf(ficparo," 0.");
4194: }
4195: }
4196: }
4197: } /* end lk */
4198: } /* end lj */
4199: } /* end li */
4200: printf("\n");
4201: fprintf(ficparo,"\n");
4202: numlinepar++;
4203: } /* end k*/
4204: } /*end j */
4205: } /* end i */
1.95 brouard 4206: } /* end itimes */
1.88 brouard 4207:
4208: } /* end of prwizard */
1.98 brouard 4209: /******************* Gompertz Likelihood ******************************/
4210: double gompertz(double x[])
4211: {
4212: double A,B,L=0.0,sump=0.,num=0.;
4213: int i,n=0; /* n is the size of the sample */
1.110 brouard 4214:
1.98 brouard 4215: for (i=0;i<=imx-1 ; i++) {
4216: sump=sump+weight[i];
1.103 lievre 4217: /* sump=sump+1;*/
1.98 brouard 4218: num=num+1;
4219: }
4220:
4221:
1.103 lievre 4222: /* for (i=0; i<=imx; i++)
1.98 brouard 4223: 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]);*/
4224:
1.103 lievre 4225: for (i=1;i<=imx ; i++)
1.98 brouard 4226: {
1.110 brouard 4227: if (cens[i] == 1 && wav[i]>1)
1.103 lievre 4228: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
1.98 brouard 4229:
1.110 brouard 4230: if (cens[i] == 0 && wav[i]>1)
1.103 lievre 4231: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4232: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
1.98 brouard 4233:
1.110 brouard 4234: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4235: if (wav[i] > 1 ) { /* ??? */
1.98 brouard 4236: L=L+A*weight[i];
4237: /* 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]);*/
4238: }
4239: }
4240:
4241: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4242:
4243: return -2*L*num/sump;
4244: }
4245:
4246: /******************* Printing html file ***********/
4247: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4248: int lastpass, int stepm, int weightopt, char model[],\
1.105 lievre 4249: int imx, double p[],double **matcov,double agemortsup){
4250: int i,k;
1.98 brouard 4251:
4252: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4253: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4254: for (i=1;i<=2;i++)
4255: 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]));
4256: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4257: fprintf(fichtm,"</ul>");
1.105 lievre 4258:
4259: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4260:
1.106 brouard 4261: 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 4262:
4263: for (k=agegomp;k<(agemortsup-2);k++)
4264: 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]);
4265:
4266:
1.98 brouard 4267: fflush(fichtm);
4268: }
4269:
4270: /******************* Gnuplot file **************/
4271: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4272:
4273: char dirfileres[132],optfileres[132];
4274: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4275: int ng;
4276:
4277:
4278: /*#ifdef windows */
4279: fprintf(ficgp,"cd \"%s\" \n",pathc);
4280: /*#endif */
4281:
4282:
4283: strcpy(dirfileres,optionfilefiname);
4284: strcpy(optfileres,"vpl");
4285: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4286: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4287: fprintf(ficgp, "set ter png small\n set log y\n");
4288: fprintf(ficgp, "set size 0.65,0.65\n");
4289: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4290:
4291: }
4292:
4293:
1.88 brouard 4294:
1.91 brouard 4295:
1.117 brouard 4296:
1.53 brouard 4297: /***********************************************/
4298: /**************** Main Program *****************/
4299: /***********************************************/
4300:
4301: int main(int argc, char *argv[])
4302: {
1.61 brouard 4303: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 4304: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.110 brouard 4305: int linei, month, year,iout;
1.95 brouard 4306: int jj, ll, li, lj, lk, imk;
1.85 brouard 4307: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 4308: int itimes;
1.98 brouard 4309: int NDIM=2;
1.95 brouard 4310:
4311: char ca[32], cb[32], cc[32];
1.111 brouard 4312: char dummy[]=" ";
1.87 brouard 4313: /* FILE *fichtm; *//* Html File */
4314: /* FILE *ficgp;*/ /*Gnuplot File */
1.107 brouard 4315: struct stat info;
1.53 brouard 4316: double agedeb, agefin,hf;
4317: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4318:
4319: double fret;
4320: double **xi,tmp,delta;
4321:
4322: double dum; /* Dummy variable */
4323: double ***p3mat;
4324: double ***mobaverage;
4325: int *indx;
4326: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 4327: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.99 brouard 4328: char pathr[MAXLINE], pathimach[MAXLINE];
1.114 brouard 4329: char **bp, *tok, *val; /* pathtot */
1.53 brouard 4330: int firstobs=1, lastobs=10;
4331: int sdeb, sfin; /* Status at beginning and end */
4332: int c, h , cpt,l;
4333: int ju,jl, mi;
4334: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 4335: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 4336: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 4337: int mobilav=0,popforecast=0;
4338: int hstepm, nhstepm;
1.105 lievre 4339: int agemortsup;
4340: float sumlpop=0.;
1.74 brouard 4341: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4342: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 4343:
4344: double bage, fage, age, agelim, agebase;
4345: double ftolpl=FTOL;
4346: double **prlim;
4347: double *severity;
4348: double ***param; /* Matrix of parameters */
4349: double *p;
4350: double **matcov; /* Matrix of covariance */
4351: double ***delti3; /* Scale */
4352: double *delti; /* Scale */
4353: double ***eij, ***vareij;
4354: double **varpl; /* Variances of prevalence limits by age */
4355: double *epj, vepp;
4356: double kk1, kk2;
1.74 brouard 4357: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 brouard 4358: double **ximort;
1.53 brouard 4359: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 brouard 4360: int *dcwave;
1.53 brouard 4361:
4362: char z[1]="c", occ;
1.86 brouard 4363:
1.53 brouard 4364: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.117 brouard 4365: char *strt, strtend[80];
1.85 brouard 4366: char *stratrunc;
4367: int lstra;
4368:
4369: long total_usecs;
1.53 brouard 4370:
1.95 brouard 4371: /* setlocale (LC_ALL, ""); */
4372: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4373: /* textdomain (PACKAGE); */
4374: /* setlocale (LC_CTYPE, ""); */
4375: /* setlocale (LC_MESSAGES, ""); */
4376:
1.85 brouard 4377: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4378: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4379: curr_time=start_time;
1.85 brouard 4380: tm = *localtime(&start_time.tv_sec);
4381: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4382: strcpy(strstart,asctime(&tm));
1.86 brouard 4383:
1.88 brouard 4384: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4385: /* tp.tv_sec = tp.tv_sec +86400; */
4386: /* tm = *localtime(&start_time.tv_sec); */
4387: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4388: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4389: /* tmg.tm_hour=tmg.tm_hour + 1; */
4390: /* tp.tv_sec = mktime(&tmg); */
4391: /* strt=asctime(&tmg); */
1.88 brouard 4392: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4393: /* (void) time (&time_value);
4394: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4395: * tm = *localtime(&time_value);
1.88 brouard 4396: * strstart=asctime(&tm);
4397: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4398: */
4399:
1.91 brouard 4400: nberr=0; /* Number of errors and warnings */
4401: nbwarn=0;
1.53 brouard 4402: getcwd(pathcd, size);
4403:
1.81 brouard 4404: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4405: if(argc <=1){
4406: printf("\nEnter the parameter file name: ");
1.114 brouard 4407: fgets(pathr,FILENAMELENGTH,stdin);
4408: i=strlen(pathr);
4409: if(pathr[i-1]=='\n')
4410: pathr[i-1]='\0';
4411: for (tok = pathr; tok != NULL; ){
4412: printf("Pathr |%s|\n",pathr);
4413: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4414: printf("val= |%s| pathr=%s\n",val,pathr);
4415: strcpy (pathtot, val);
1.119 ! brouard 4416: if(pathr[0] == '\0') break; /* Dirty */
1.114 brouard 4417: }
1.53 brouard 4418: }
4419: else{
4420: strcpy(pathtot,argv[1]);
4421: }
1.88 brouard 4422: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4423: /*cygwin_split_path(pathtot,path,optionfile);
4424: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4425: /* cutv(path,optionfile,pathtot,'\\');*/
4426:
1.107 brouard 4427: /* Split argv[0], imach program to get pathimach */
4428: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
1.99 brouard 4429: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4430: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.99 brouard 4431: /* strcpy(pathimach,argv[0]); */
1.107 brouard 4432: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
1.53 brouard 4433: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4434: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.119 ! brouard 4435: chdir(path); /* Can be a relative path */
! 4436: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
! 4437: printf("Current directory %s!\n",pathcd);
1.88 brouard 4438: strcpy(command,"mkdir ");
4439: strcat(command,optionfilefiname);
4440: if((outcmd=system(command)) != 0){
4441: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4442: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4443: /* fclose(ficlog); */
4444: /* exit(1); */
4445: }
4446: /* if((imk=mkdir(optionfilefiname))<0){ */
4447: /* perror("mkdir"); */
4448: /* } */
1.53 brouard 4449:
1.59 brouard 4450: /*-------- arguments in the command line --------*/
1.53 brouard 4451:
4452: /* Log file */
4453: strcat(filelog, optionfilefiname);
4454: strcat(filelog,".log"); /* */
4455: if((ficlog=fopen(filelog,"w"))==NULL) {
4456: printf("Problem with logfile %s\n",filelog);
4457: goto end;
4458: }
4459: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4460: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.99 brouard 4461: fprintf(ficlog,"\nEnter the parameter file name: \n");
4462: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
1.88 brouard 4463: path=%s \n\
4464: optionfile=%s\n\
4465: optionfilext=%s\n\
1.99 brouard 4466: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4467:
1.94 brouard 4468: printf("Local time (at start):%s",strstart);
4469: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4470: fflush(ficlog);
1.91 brouard 4471: /* (void) gettimeofday(&curr_time,&tzp); */
4472: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4473:
4474: /* */
4475: strcpy(fileres,"r");
4476: strcat(fileres, optionfilefiname);
4477: strcat(fileres,".txt"); /* Other files have txt extension */
4478:
4479: /*---------arguments file --------*/
4480:
4481: if((ficpar=fopen(optionfile,"r"))==NULL) {
4482: printf("Problem with optionfile %s\n",optionfile);
4483: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4484: fflush(ficlog);
1.53 brouard 4485: goto end;
4486: }
4487:
1.88 brouard 4488:
4489:
1.53 brouard 4490: strcpy(filereso,"o");
4491: strcat(filereso,fileres);
1.88 brouard 4492: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4493: printf("Problem with Output resultfile: %s\n", filereso);
4494: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4495: fflush(ficlog);
1.53 brouard 4496: goto end;
4497: }
4498:
4499: /* Reads comments: lines beginning with '#' */
1.85 brouard 4500: numlinepar=0;
1.53 brouard 4501: while((c=getc(ficpar))=='#' && c!= EOF){
4502: ungetc(c,ficpar);
4503: fgets(line, MAXLINE, ficpar);
1.85 brouard 4504: numlinepar++;
1.53 brouard 4505: puts(line);
4506: fputs(line,ficparo);
1.85 brouard 4507: fputs(line,ficlog);
1.53 brouard 4508: }
4509: ungetc(c,ficpar);
4510:
4511: 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 4512: numlinepar++;
1.53 brouard 4513: 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);
4514: 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 4515: 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);
4516: fflush(ficlog);
1.59 brouard 4517: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4518: ungetc(c,ficpar);
4519: fgets(line, MAXLINE, ficpar);
1.85 brouard 4520: numlinepar++;
1.53 brouard 4521: puts(line);
4522: fputs(line,ficparo);
1.85 brouard 4523: fputs(line,ficlog);
1.53 brouard 4524: }
4525: ungetc(c,ficpar);
1.85 brouard 4526:
1.53 brouard 4527:
4528: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4529: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4530: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4531:
1.58 lievre 4532: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4533: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 brouard 4534: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4535:
4536: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4537: delti=delti3[1][1];
4538: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4539: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4540: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4541: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4542: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 brouard 4543: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4544: fclose (ficparo);
4545: fclose (ficlog);
4546: exit(0);
4547: }
1.98 brouard 4548: else if(mle==-3) {
4549: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4550: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4551: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4552: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4553: matcov=matrix(1,npar,1,npar);
1.53 brouard 4554: }
1.98 brouard 4555: else{
4556: /* Read guess parameters */
4557: /* Reads comments: lines beginning with '#' */
4558: while((c=getc(ficpar))=='#' && c!= EOF){
4559: ungetc(c,ficpar);
4560: fgets(line, MAXLINE, ficpar);
1.85 brouard 4561: numlinepar++;
1.98 brouard 4562: puts(line);
4563: fputs(line,ficparo);
4564: fputs(line,ficlog);
1.53 brouard 4565: }
1.98 brouard 4566: ungetc(c,ficpar);
4567:
4568: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4569: for(i=1; i <=nlstate; i++){
4570: j=0;
4571: for(jj=1; jj <=nlstate+ndeath; jj++){
4572: if(jj==i) continue;
4573: j++;
4574: fscanf(ficpar,"%1d%1d",&i1,&j1);
4575: if ((i1 != i) && (j1 != j)){
4576: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4577: exit(1);
4578: }
4579: fprintf(ficparo,"%1d%1d",i1,j1);
4580: if(mle==1)
4581: printf("%1d%1d",i,j);
4582: fprintf(ficlog,"%1d%1d",i,j);
4583: for(k=1; k<=ncovmodel;k++){
4584: fscanf(ficpar," %lf",¶m[i][j][k]);
4585: if(mle==1){
4586: printf(" %lf",param[i][j][k]);
4587: fprintf(ficlog," %lf",param[i][j][k]);
4588: }
4589: else
4590: fprintf(ficlog," %lf",param[i][j][k]);
4591: fprintf(ficparo," %lf",param[i][j][k]);
4592: }
4593: fscanf(ficpar,"\n");
4594: numlinepar++;
4595: if(mle==1)
4596: printf("\n");
4597: fprintf(ficlog,"\n");
4598: fprintf(ficparo,"\n");
4599: }
4600: }
4601: fflush(ficlog);
1.85 brouard 4602:
1.98 brouard 4603: p=param[1][1];
4604:
4605: /* Reads comments: lines beginning with '#' */
4606: while((c=getc(ficpar))=='#' && c!= EOF){
4607: ungetc(c,ficpar);
4608: fgets(line, MAXLINE, ficpar);
4609: numlinepar++;
4610: puts(line);
4611: fputs(line,ficparo);
4612: fputs(line,ficlog);
4613: }
1.53 brouard 4614: ungetc(c,ficpar);
4615:
1.98 brouard 4616: for(i=1; i <=nlstate; i++){
4617: for(j=1; j <=nlstate+ndeath-1; j++){
4618: fscanf(ficpar,"%1d%1d",&i1,&j1);
4619: if ((i1-i)*(j1-j)!=0){
4620: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4621: exit(1);
4622: }
4623: printf("%1d%1d",i,j);
4624: fprintf(ficparo,"%1d%1d",i1,j1);
4625: fprintf(ficlog,"%1d%1d",i1,j1);
4626: for(k=1; k<=ncovmodel;k++){
4627: fscanf(ficpar,"%le",&delti3[i][j][k]);
4628: printf(" %le",delti3[i][j][k]);
4629: fprintf(ficparo," %le",delti3[i][j][k]);
4630: fprintf(ficlog," %le",delti3[i][j][k]);
4631: }
4632: fscanf(ficpar,"\n");
4633: numlinepar++;
4634: printf("\n");
4635: fprintf(ficparo,"\n");
4636: fprintf(ficlog,"\n");
1.85 brouard 4637: }
1.53 brouard 4638: }
1.98 brouard 4639: fflush(ficlog);
1.85 brouard 4640:
1.98 brouard 4641: delti=delti3[1][1];
1.74 brouard 4642:
4643:
1.98 brouard 4644: /* 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 4645:
1.98 brouard 4646: /* Reads comments: lines beginning with '#' */
4647: while((c=getc(ficpar))=='#' && c!= EOF){
4648: ungetc(c,ficpar);
4649: fgets(line, MAXLINE, ficpar);
4650: numlinepar++;
4651: puts(line);
4652: fputs(line,ficparo);
4653: fputs(line,ficlog);
4654: }
1.53 brouard 4655: ungetc(c,ficpar);
4656:
1.98 brouard 4657: matcov=matrix(1,npar,1,npar);
4658: for(i=1; i <=npar; i++){
4659: fscanf(ficpar,"%s",&str);
4660: if(mle==1)
4661: printf("%s",str);
4662: fprintf(ficlog,"%s",str);
4663: fprintf(ficparo,"%s",str);
4664: for(j=1; j <=i; j++){
4665: fscanf(ficpar," %le",&matcov[i][j]);
4666: if(mle==1){
4667: printf(" %.5le",matcov[i][j]);
4668: }
4669: fprintf(ficlog," %.5le",matcov[i][j]);
4670: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4671: }
1.98 brouard 4672: fscanf(ficpar,"\n");
4673: numlinepar++;
4674: if(mle==1)
4675: printf("\n");
4676: fprintf(ficlog,"\n");
4677: fprintf(ficparo,"\n");
1.53 brouard 4678: }
1.98 brouard 4679: for(i=1; i <=npar; i++)
4680: for(j=i+1;j<=npar;j++)
4681: matcov[i][j]=matcov[j][i];
4682:
1.53 brouard 4683: if(mle==1)
4684: printf("\n");
4685: fprintf(ficlog,"\n");
1.98 brouard 4686:
4687: fflush(ficlog);
4688:
4689: /*-------- Rewriting parameter file ----------*/
4690: strcpy(rfileres,"r"); /* "Rparameterfile */
4691: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4692: strcat(rfileres,"."); /* */
4693: strcat(rfileres,optionfilext); /* Other files have txt extension */
4694: if((ficres =fopen(rfileres,"w"))==NULL) {
4695: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4696: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4697: }
4698: fprintf(ficres,"#%s\n",version);
4699: } /* End of mle != -3 */
1.53 brouard 4700:
1.59 brouard 4701: /*-------- data file ----------*/
4702: if((fic=fopen(datafile,"r"))==NULL) {
1.118 brouard 4703: printf("Problem while opening datafile: %s\n", datafile);goto end;
4704: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
1.59 brouard 4705: }
4706:
4707: n= lastobs;
4708: severity = vector(1,maxwav);
4709: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4710: num=lvector(1,n);
1.59 brouard 4711: moisnais=vector(1,n);
4712: annais=vector(1,n);
4713: moisdc=vector(1,n);
4714: andc=vector(1,n);
4715: agedc=vector(1,n);
4716: cod=ivector(1,n);
4717: weight=vector(1,n);
4718: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4719: mint=matrix(1,maxwav,1,n);
4720: anint=matrix(1,maxwav,1,n);
4721: s=imatrix(1,maxwav+1,1,n);
4722: tab=ivector(1,NCOVMAX);
4723: ncodemax=ivector(1,8);
4724:
4725: i=1;
1.109 brouard 4726: linei=0;
1.111 brouard 4727: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
1.109 brouard 4728: linei=linei+1;
4729: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
1.111 brouard 4730: if(line[j] == '\t')
4731: line[j] = ' ';
4732: }
4733: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4734: ;
4735: };
4736: line[j+1]=0; /* Trims blanks at end of line */
4737: if(line[0]=='#'){
4738: fprintf(ficlog,"Comment line\n%s\n",line);
4739: printf("Comment line\n%s\n",line);
4740: continue;
4741: }
1.109 brouard 4742:
1.111 brouard 4743: for (j=maxwav;j>=1;j--){
1.110 brouard 4744: cutv(stra, strb,line,' ');
1.111 brouard 4745: errno=0;
4746: lval=strtol(strb,&endptr,10);
4747: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4748: if( strb[0]=='\0' || (*endptr != '\0')){
4749: 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 4750: exit(1);
4751: }
1.111 brouard 4752: s[j][i]=lval;
4753:
1.109 brouard 4754: strcpy(line,stra);
1.111 brouard 4755: cutv(stra, strb,line,' ');
1.110 brouard 4756: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
1.109 brouard 4757: }
1.111 brouard 4758: else if(iout=sscanf(strb,"%s.") != 0){
1.110 brouard 4759: month=99;
4760: year=9999;
4761: }else{
1.111 brouard 4762: 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 4763: exit(1);
4764: }
1.111 brouard 4765: anint[j][i]= (double) year;
4766: mint[j][i]= (double)month;
1.109 brouard 4767: strcpy(line,stra);
1.111 brouard 4768: } /* ENd Waves */
4769:
4770: cutv(stra, strb,line,' ');
4771: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4772: }
4773: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4774: month=99;
4775: year=9999;
4776: }else{
4777: 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);
4778: exit(1);
4779: }
4780: andc[i]=(double) year;
4781: moisdc[i]=(double) month;
4782: strcpy(line,stra);
4783:
4784: cutv(stra, strb,line,' ');
4785: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4786: }
4787: else if(iout=sscanf(strb,"%s.") != 0){
4788: month=99;
4789: year=9999;
4790: }else{
4791: 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);
4792: exit(1);
4793: }
4794: annais[i]=(double)(year);
4795: moisnais[i]=(double)(month);
4796: strcpy(line,stra);
4797:
4798: cutv(stra, strb,line,' ');
4799: errno=0;
4800: lval=strtol(strb,&endptr,10);
4801: if( strb[0]=='\0' || (*endptr != '\0')){
4802: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4803: exit(1);
4804: }
4805: weight[i]=(double)(lval);
4806: strcpy(line,stra);
4807:
4808: for (j=ncovcol;j>=1;j--){
1.109 brouard 4809: cutv(stra, strb,line,' ');
4810: errno=0;
4811: lval=strtol(strb,&endptr,10);
4812: if( strb[0]=='\0' || (*endptr != '\0')){
1.111 brouard 4813: 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);
4814: exit(1);
4815: }
4816: if(lval <-1 || lval >1){
4817: 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 4818: exit(1);
4819: }
1.111 brouard 4820: covar[j][i]=(double)(lval);
1.109 brouard 4821: strcpy(line,stra);
1.111 brouard 4822: }
4823: lstra=strlen(stra);
4824:
4825: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4826: stratrunc = &(stra[lstra-9]);
4827: num[i]=atol(stratrunc);
4828: }
4829: else
4830: num[i]=atol(stra);
4831: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4832: 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;}*/
4833:
4834: i=i+1;
1.109 brouard 4835: } /* End loop reading data */
1.113 brouard 4836: fclose(fic);
1.59 brouard 4837: /* printf("ii=%d", ij);
4838: scanf("%d",i);*/
1.53 brouard 4839: imx=i-1; /* Number of individuals */
4840:
4841: /* for (i=1; i<=imx; i++){
4842: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4843: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4844: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4845: }*/
4846: /* for (i=1; i<=imx; i++){
4847: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4848: 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 4849:
1.106 brouard 4850: /* for (i=1; i<=imx; i++) */
1.53 brouard 4851:
1.71 brouard 4852: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4853: else weight[i]=1;*/
4854:
1.106 brouard 4855: /* Calculation of the number of parameters from char model */
1.53 brouard 4856: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4857: Tprod=ivector(1,15);
4858: Tvaraff=ivector(1,15);
4859: Tvard=imatrix(1,15,1,2);
4860: Tage=ivector(1,15);
4861:
1.58 lievre 4862: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4863: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4864: j=nbocc(model,'+'); /* j=Number of '+' */
4865: j1=nbocc(model,'*'); /* j1=Number of '*' */
4866: cptcovn=j+1;
4867: cptcovprod=j1; /*Number of products */
1.53 brouard 4868:
4869: strcpy(modelsav,model);
4870: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4871: printf("Error. Non available option model=%s ",model);
4872: fprintf(ficlog,"Error. Non available option model=%s ",model);
4873: goto end;
4874: }
4875:
1.59 brouard 4876: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4877:
1.53 brouard 4878: for(i=(j+1); i>=1;i--){
4879: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4880: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4881: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4882: /*scanf("%d",i);*/
4883: if (strchr(strb,'*')) { /* Model includes a product */
4884: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4885: if (strcmp(strc,"age")==0) { /* Vn*age */
4886: cptcovprod--;
4887: cutv(strb,stre,strd,'V');
4888: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4889: cptcovage++;
4890: Tage[cptcovage]=i;
4891: /*printf("stre=%s ", stre);*/
4892: }
4893: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4894: cptcovprod--;
4895: cutv(strb,stre,strc,'V');
4896: Tvar[i]=atoi(stre);
4897: cptcovage++;
4898: Tage[cptcovage]=i;
4899: }
4900: else { /* Age is not in the model */
4901: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4902: Tvar[i]=ncovcol+k1;
4903: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4904: Tprod[k1]=i;
4905: Tvard[k1][1]=atoi(strc); /* m*/
4906: Tvard[k1][2]=atoi(stre); /* n */
4907: Tvar[cptcovn+k2]=Tvard[k1][1];
4908: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4909: for (k=1; k<=lastobs;k++)
4910: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4911: k1++;
4912: k2=k2+2;
4913: }
4914: }
4915: else { /* no more sum */
4916: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4917: /* scanf("%d",i);*/
4918: cutv(strd,strc,strb,'V');
4919: Tvar[i]=atoi(strc);
4920: }
4921: strcpy(modelsav,stra);
4922: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4923: scanf("%d",i);*/
4924: } /* end of loop + */
4925: } /* end model */
4926:
1.58 lievre 4927: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4928: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4929:
1.53 brouard 4930: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4931: printf("cptcovprod=%d ", cptcovprod);
4932: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4933:
1.113 brouard 4934: scanf("%d ",i);*/
1.53 brouard 4935:
4936: /* if(mle==1){*/
1.59 brouard 4937: if (weightopt != 1) { /* Maximisation without weights*/
4938: for(i=1;i<=n;i++) weight[i]=1.0;
4939: }
1.53 brouard 4940: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4941: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4942:
1.59 brouard 4943: for (i=1; i<=imx; i++) {
4944: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4945: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4946: anint[m][i]=9999;
4947: s[m][i]=-1;
4948: }
1.76 brouard 4949: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4950: nberr++;
1.85 brouard 4951: 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);
4952: 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 4953: s[m][i]=-1;
4954: }
4955: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4956: nberr++;
1.85 brouard 4957: 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]);
4958: 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 4959: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4960: }
1.53 brouard 4961: }
1.59 brouard 4962: }
1.53 brouard 4963:
1.59 brouard 4964: for (i=1; i<=imx; i++) {
4965: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4966: for(m=firstpass; (m<= lastpass); m++){
1.105 lievre 4967: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
1.59 brouard 4968: if (s[m][i] >= nlstate+1) {
4969: if(agedc[i]>0)
1.76 brouard 4970: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4971: agev[m][i]=agedc[i];
1.59 brouard 4972: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4973: else {
1.76 brouard 4974: if ((int)andc[i]!=9999){
1.91 brouard 4975: nbwarn++;
1.85 brouard 4976: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4977: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4978: agev[m][i]=-1;
1.53 brouard 4979: }
4980: }
1.70 brouard 4981: }
1.69 brouard 4982: else if(s[m][i] !=9){ /* Standard case, age in fractional
1.108 lievre 4983: years but with the precision of a month */
1.59 brouard 4984: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4985: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4986: agev[m][i]=1;
4987: else if(agev[m][i] <agemin){
4988: agemin=agev[m][i];
4989: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4990: }
1.59 brouard 4991: else if(agev[m][i] >agemax){
4992: agemax=agev[m][i];
4993: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4994: }
1.59 brouard 4995: /*agev[m][i]=anint[m][i]-annais[i];*/
4996: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4997: }
1.59 brouard 4998: else { /* =9 */
1.53 brouard 4999: agev[m][i]=1;
1.59 brouard 5000: s[m][i]=-1;
5001: }
1.53 brouard 5002: }
1.59 brouard 5003: else /*= 0 Unknown */
5004: agev[m][i]=1;
5005: }
1.53 brouard 5006:
1.59 brouard 5007: }
5008: for (i=1; i<=imx; i++) {
1.71 brouard 5009: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 5010: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 5011: nberr++;
1.59 brouard 5012: 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);
5013: 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);
5014: goto end;
1.53 brouard 5015: }
5016: }
1.59 brouard 5017: }
1.53 brouard 5018:
1.71 brouard 5019: /*for (i=1; i<=imx; i++){
5020: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 5021: 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 5022: }
5023:
5024: }*/
5025:
1.97 lievre 5026:
1.59 brouard 5027: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5028: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5029:
1.98 brouard 5030: agegomp=(int)agemin;
1.59 brouard 5031: free_vector(severity,1,maxwav);
5032: free_imatrix(outcome,1,maxwav+1,1,n);
5033: free_vector(moisnais,1,n);
5034: free_vector(annais,1,n);
5035: /* free_matrix(mint,1,maxwav,1,n);
5036: free_matrix(anint,1,maxwav,1,n);*/
5037: free_vector(moisdc,1,n);
5038: free_vector(andc,1,n);
1.53 brouard 5039:
5040:
1.59 brouard 5041: wav=ivector(1,imx);
5042: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5043: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5044: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 5045:
1.59 brouard 5046: /* Concatenates waves */
5047: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 5048:
1.59 brouard 5049: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 5050:
1.59 brouard 5051: Tcode=ivector(1,100);
5052: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5053: ncodemax[1]=1;
5054: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 5055:
1.59 brouard 5056: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5057: the estimations*/
5058: h=0;
5059: m=pow(2,cptcoveff);
1.53 brouard 5060:
1.59 brouard 5061: for(k=1;k<=cptcoveff; k++){
5062: for(i=1; i <=(m/pow(2,k));i++){
5063: for(j=1; j <= ncodemax[k]; j++){
5064: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5065: h++;
5066: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5067: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5068: }
5069: }
5070: }
5071: }
5072: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5073: codtab[1][2]=1;codtab[2][2]=2; */
5074: /* for(i=1; i <=m ;i++){
5075: for(k=1; k <=cptcovn; k++){
5076: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5077: }
5078: printf("\n");
1.53 brouard 5079: }
1.59 brouard 5080: scanf("%d",i);*/
1.53 brouard 5081:
1.86 brouard 5082: /*------------ gnuplot -------------*/
5083: strcpy(optionfilegnuplot,optionfilefiname);
1.98 brouard 5084: if(mle==-3)
5085: strcat(optionfilegnuplot,"-mort");
1.86 brouard 5086: strcat(optionfilegnuplot,".gp");
1.98 brouard 5087:
1.86 brouard 5088: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5089: printf("Problem with file %s",optionfilegnuplot);
5090: }
5091: else{
5092: fprintf(ficgp,"\n# %s\n", version);
5093: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5094: fprintf(ficgp,"set missing 'NaNq'\n");
5095: }
1.88 brouard 5096: /* fclose(ficgp);*/
1.86 brouard 5097: /*--------- index.htm --------*/
5098:
1.91 brouard 5099: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 brouard 5100: if(mle==-3)
5101: strcat(optionfilehtm,"-mort");
1.86 brouard 5102: strcat(optionfilehtm,".htm");
5103: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5104: printf("Problem with %s \n",optionfilehtm), exit(0);
5105: }
5106:
1.91 brouard 5107: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5108: strcat(optionfilehtmcov,"-cov.htm");
5109: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5110: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5111: }
5112: else{
5113: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
5114: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5115: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5116: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5117: }
5118:
1.87 brouard 5119: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 5120: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5121: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5122: \n\
5123: <hr size=\"2\" color=\"#EC5E5E\">\
5124: <ul><li><h4>Parameter files</h4>\n\
1.117 brouard 5125: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
1.86 brouard 5126: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5127: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 5128: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 5129: - Date and time at start: %s</ul>\n",\
1.91 brouard 5130: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
1.117 brouard 5131: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
1.91 brouard 5132: fileres,fileres,\
1.88 brouard 5133: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 5134: fflush(fichtm);
1.86 brouard 5135:
1.88 brouard 5136: strcpy(pathr,path);
5137: strcat(pathr,optionfilefiname);
5138: chdir(optionfilefiname); /* Move to directory named optionfile */
5139:
1.59 brouard 5140: /* Calculates basic frequencies. Computes observed prevalence at single age
5141: and prints on file fileres'p'. */
1.105 lievre 5142: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
1.53 brouard 5143:
1.88 brouard 5144: fprintf(fichtm,"\n");
5145: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 5146: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5147: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 5148: imx,agemin,agemax,jmin,jmax,jmean);
5149: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 5150: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5151: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5152: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5153: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 5154:
5155:
1.59 brouard 5156: /* For Powell, parameters are in a vector p[] starting at p[1]
5157: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5158: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 5159:
1.86 brouard 5160: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.110 brouard 5161:
1.98 brouard 5162: if (mle==-3){
5163: ximort=matrix(1,NDIM,1,NDIM);
5164: cens=ivector(1,n);
5165: ageexmed=vector(1,n);
5166: agecens=vector(1,n);
5167: dcwave=ivector(1,n);
5168:
5169: for (i=1; i<=imx; i++){
5170: dcwave[i]=-1;
1.110 brouard 5171: for (m=firstpass; m<=lastpass; m++)
5172: if (s[m][i]>nlstate) {
5173: dcwave[i]=m;
1.98 brouard 5174: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5175: break;
5176: }
5177: }
5178:
5179: for (i=1; i<=imx; i++) {
5180: if (wav[i]>0){
5181: ageexmed[i]=agev[mw[1][i]][i];
1.110 brouard 5182: j=wav[i];
5183: agecens[i]=1.;
5184:
5185: if (ageexmed[i]> 1 && wav[i] > 0){
5186: agecens[i]=agev[mw[j][i]][i];
5187: cens[i]= 1;
5188: }else if (ageexmed[i]< 1)
5189: cens[i]= -1;
5190: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5191: cens[i]=0 ;
1.98 brouard 5192: }
5193: else cens[i]=-1;
5194: }
5195:
5196: for (i=1;i<=NDIM;i++) {
5197: for (j=1;j<=NDIM;j++)
5198: ximort[i][j]=(i == j ? 1.0 : 0.0);
5199: }
1.110 brouard 5200:
1.111 brouard 5201: p[1]=0.0268; p[NDIM]=0.083;
1.98 brouard 5202: /*printf("%lf %lf", p[1], p[2]);*/
5203:
5204:
1.110 brouard 5205: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5206: strcpy(filerespow,"pow-mort");
5207: strcat(filerespow,fileres);
5208: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5209: printf("Problem with resultfile: %s\n", filerespow);
5210: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5211: }
5212: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5213: /* for (i=1;i<=nlstate;i++)
5214: for(j=1;j<=nlstate+ndeath;j++)
5215: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5216: */
5217: fprintf(ficrespow,"\n");
5218:
1.98 brouard 5219: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5220: fclose(ficrespow);
1.53 brouard 5221:
1.110 brouard 5222: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
1.53 brouard 5223:
1.98 brouard 5224: for(i=1; i <=NDIM; i++)
5225: for(j=i+1;j<=NDIM;j++)
5226: matcov[i][j]=matcov[j][i];
5227:
5228: printf("\nCovariance matrix\n ");
5229: for(i=1; i <=NDIM; i++) {
5230: for(j=1;j<=NDIM;j++){
5231: printf("%f ",matcov[i][j]);
1.95 brouard 5232: }
1.98 brouard 5233: printf("\n ");
5234: }
5235:
5236: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5237: for (i=1;i<=NDIM;i++)
5238: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.105 lievre 5239:
1.110 brouard 5240: lsurv=vector(1,AGESUP);
1.105 lievre 5241: lpop=vector(1,AGESUP);
5242: tpop=vector(1,AGESUP);
5243: lsurv[agegomp]=100000;
1.110 brouard 5244:
5245: for (k=agegomp;k<=AGESUP;k++) {
1.105 lievre 5246: agemortsup=k;
5247: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5248: }
1.110 brouard 5249:
5250: for (k=agegomp;k<agemortsup;k++)
1.105 lievre 5251: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
1.110 brouard 5252:
1.105 lievre 5253: for (k=agegomp;k<agemortsup;k++){
5254: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5255: sumlpop=sumlpop+lpop[k];
5256: }
1.110 brouard 5257:
5258: tpop[agegomp]=sumlpop;
1.105 lievre 5259: for (k=agegomp;k<(agemortsup-3);k++){
5260: /* tpop[k+1]=2;*/
5261: tpop[k+1]=tpop[k]-lpop[k];
1.110 brouard 5262: }
5263:
5264:
5265: printf("\nAge lx qx dx Lx Tx e(x)\n");
1.105 lievre 5266: for (k=agegomp;k<(agemortsup-2);k++)
5267: 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 5268:
5269:
1.119 ! brouard 5270: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.98 brouard 5271: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5272:
5273: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5274: stepm, weightopt,\
1.105 lievre 5275: model,imx,p,matcov,agemortsup);
1.110 brouard 5276:
1.105 lievre 5277: free_vector(lsurv,1,AGESUP);
5278: free_vector(lpop,1,AGESUP);
5279: free_vector(tpop,1,AGESUP);
1.98 brouard 5280: } /* Endof if mle==-3 */
1.110 brouard 5281:
1.98 brouard 5282: else{ /* For mle >=1 */
5283:
5284: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5285: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5286: for (k=1; k<=npar;k++)
5287: printf(" %d %8.5f",k,p[k]);
5288: printf("\n");
5289: globpr=1; /* to print the contributions */
5290: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5291: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5292: for (k=1; k<=npar;k++)
5293: printf(" %d %8.5f",k,p[k]);
5294: printf("\n");
5295: if(mle>=1){ /* Could be 1 or 2 */
5296: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 5297: }
1.98 brouard 5298:
5299: /*--------- results files --------------*/
5300: 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);
5301:
5302:
5303: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5304: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5305: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5306: for(i=1,jk=1; i <=nlstate; i++){
5307: for(k=1; k <=(nlstate+ndeath); k++){
5308: if (k != i) {
5309: printf("%d%d ",i,k);
5310: fprintf(ficlog,"%d%d ",i,k);
5311: fprintf(ficres,"%1d%1d ",i,k);
5312: for(j=1; j <=ncovmodel; j++){
5313: printf("%f ",p[jk]);
5314: fprintf(ficlog,"%f ",p[jk]);
5315: fprintf(ficres,"%f ",p[jk]);
5316: jk++;
5317: }
5318: printf("\n");
5319: fprintf(ficlog,"\n");
5320: fprintf(ficres,"\n");
1.59 brouard 5321: }
5322: }
5323: }
1.98 brouard 5324: if(mle!=0){
5325: /* Computing hessian and covariance matrix */
5326: ftolhess=ftol; /* Usually correct */
5327: hesscov(matcov, p, npar, delti, ftolhess, func);
5328: }
5329: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5330: printf("# Scales (for hessian or gradient estimation)\n");
5331: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5332: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 5333: for(j=1; j <=nlstate+ndeath; j++){
1.98 brouard 5334: if (j!=i) {
5335: fprintf(ficres,"%1d%1d",i,j);
5336: printf("%1d%1d",i,j);
5337: fprintf(ficlog,"%1d%1d",i,j);
5338: for(k=1; k<=ncovmodel;k++){
5339: printf(" %.5e",delti[jk]);
5340: fprintf(ficlog," %.5e",delti[jk]);
5341: fprintf(ficres," %.5e",delti[jk]);
5342: jk++;
1.95 brouard 5343: }
1.98 brouard 5344: printf("\n");
5345: fprintf(ficlog,"\n");
5346: fprintf(ficres,"\n");
5347: }
5348: }
5349: }
5350:
5351: 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");
5352: if(mle>=1)
5353: 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");
5354: 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");
5355: /* # 121 Var(a12)\n\ */
5356: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5357: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5358: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5359: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5360: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5361: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5362: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5363:
5364:
5365: /* Just to have a covariance matrix which will be more understandable
5366: even is we still don't want to manage dictionary of variables
5367: */
5368: for(itimes=1;itimes<=2;itimes++){
5369: jj=0;
5370: for(i=1; i <=nlstate; i++){
5371: for(j=1; j <=nlstate+ndeath; j++){
5372: if(j==i) continue;
5373: for(k=1; k<=ncovmodel;k++){
5374: jj++;
5375: ca[0]= k+'a'-1;ca[1]='\0';
5376: if(itimes==1){
5377: if(mle>=1)
5378: printf("#%1d%1d%d",i,j,k);
5379: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5380: fprintf(ficres,"#%1d%1d%d",i,j,k);
5381: }else{
5382: if(mle>=1)
5383: printf("%1d%1d%d",i,j,k);
5384: fprintf(ficlog,"%1d%1d%d",i,j,k);
5385: fprintf(ficres,"%1d%1d%d",i,j,k);
5386: }
5387: ll=0;
5388: for(li=1;li <=nlstate; li++){
5389: for(lj=1;lj <=nlstate+ndeath; lj++){
5390: if(lj==li) continue;
5391: for(lk=1;lk<=ncovmodel;lk++){
5392: ll++;
5393: if(ll<=jj){
5394: cb[0]= lk +'a'-1;cb[1]='\0';
5395: if(ll<jj){
5396: if(itimes==1){
5397: if(mle>=1)
5398: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5399: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5400: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5401: }else{
5402: if(mle>=1)
5403: printf(" %.5e",matcov[jj][ll]);
5404: fprintf(ficlog," %.5e",matcov[jj][ll]);
5405: fprintf(ficres," %.5e",matcov[jj][ll]);
5406: }
1.95 brouard 5407: }else{
1.98 brouard 5408: if(itimes==1){
5409: if(mle>=1)
5410: printf(" Var(%s%1d%1d)",ca,i,j);
5411: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5412: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5413: }else{
5414: if(mle>=1)
5415: printf(" %.5e",matcov[jj][ll]);
5416: fprintf(ficlog," %.5e",matcov[jj][ll]);
5417: fprintf(ficres," %.5e",matcov[jj][ll]);
5418: }
1.95 brouard 5419: }
5420: }
1.98 brouard 5421: } /* end lk */
5422: } /* end lj */
5423: } /* end li */
5424: if(mle>=1)
5425: printf("\n");
5426: fprintf(ficlog,"\n");
5427: fprintf(ficres,"\n");
5428: numlinepar++;
5429: } /* end k*/
5430: } /*end j */
5431: } /* end i */
5432: } /* end itimes */
5433:
5434: fflush(ficlog);
5435: fflush(ficres);
5436:
5437: while((c=getc(ficpar))=='#' && c!= EOF){
5438: ungetc(c,ficpar);
5439: fgets(line, MAXLINE, ficpar);
5440: puts(line);
5441: fputs(line,ficparo);
5442: }
1.59 brouard 5443: ungetc(c,ficpar);
1.98 brouard 5444:
5445: estepm=0;
5446: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5447: if (estepm==0 || estepm < stepm) estepm=stepm;
5448: if (fage <= 2) {
5449: bage = ageminpar;
5450: fage = agemaxpar;
5451: }
5452:
5453: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5454: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5455: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5456:
5457: while((c=getc(ficpar))=='#' && c!= EOF){
5458: ungetc(c,ficpar);
5459: fgets(line, MAXLINE, ficpar);
5460: puts(line);
5461: fputs(line,ficparo);
5462: }
1.59 brouard 5463: ungetc(c,ficpar);
1.98 brouard 5464:
5465: 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);
5466: 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);
5467: 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);
5468: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5469: 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);
5470:
5471: while((c=getc(ficpar))=='#' && c!= EOF){
5472: ungetc(c,ficpar);
5473: fgets(line, MAXLINE, ficpar);
5474: puts(line);
5475: fputs(line,ficparo);
5476: }
1.59 brouard 5477: ungetc(c,ficpar);
1.98 brouard 5478:
5479:
5480: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5481: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5482:
5483: fscanf(ficpar,"pop_based=%d\n",&popbased);
5484: fprintf(ficparo,"pop_based=%d\n",popbased);
5485: fprintf(ficres,"pop_based=%d\n",popbased);
5486:
5487: while((c=getc(ficpar))=='#' && c!= EOF){
5488: ungetc(c,ficpar);
5489: fgets(line, MAXLINE, ficpar);
5490: puts(line);
5491: fputs(line,ficparo);
5492: }
1.53 brouard 5493: ungetc(c,ficpar);
1.98 brouard 5494:
5495: 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);
5496: 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);
5497: 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);
5498: 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);
5499: 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);
5500: /* day and month of proj2 are not used but only year anproj2.*/
5501:
5502:
5503:
5504: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5505: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5506:
1.119 ! brouard 5507: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.98 brouard 5508: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5509:
5510: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5511: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5512: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5513:
5514: /*------------ free_vector -------------*/
5515: /* chdir(path); */
1.53 brouard 5516:
1.98 brouard 5517: free_ivector(wav,1,imx);
5518: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5519: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5520: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5521: free_lvector(num,1,n);
5522: free_vector(agedc,1,n);
5523: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5524: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5525: fclose(ficparo);
5526: fclose(ficres);
5527:
5528:
1.117 brouard 5529: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.98 brouard 5530:
5531: strcpy(filerespl,"pl");
5532: strcat(filerespl,fileres);
5533: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.117 brouard 5534: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5535: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
1.98 brouard 5536: }
1.117 brouard 5537: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5538: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5539: pstamp(ficrespl);
5540: fprintf(ficrespl,"# Period (stable) prevalence \n");
1.98 brouard 5541: fprintf(ficrespl,"#Age ");
5542: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5543: fprintf(ficrespl,"\n");
5544:
5545: prlim=matrix(1,nlstate,1,nlstate);
5546:
5547: agebase=ageminpar;
5548: agelim=agemaxpar;
5549: ftolpl=1.e-10;
5550: i1=cptcoveff;
5551: if (cptcovn < 1){i1=1;}
5552:
5553: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5554: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5555: k=k+1;
5556: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5557: fprintf(ficrespl,"\n#******");
5558: printf("\n#******");
5559: fprintf(ficlog,"\n#******");
5560: for(j=1;j<=cptcoveff;j++) {
5561: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5562: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5563: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5564: }
5565: fprintf(ficrespl,"******\n");
5566: printf("******\n");
5567: fprintf(ficlog,"******\n");
1.53 brouard 5568:
1.98 brouard 5569: for (age=agebase; age<=agelim; age++){
5570: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5571: fprintf(ficrespl,"%.0f ",age );
5572: for(j=1;j<=cptcoveff;j++)
5573: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5574: for(i=1; i<=nlstate;i++)
5575: fprintf(ficrespl," %.5f", prlim[i][i]);
5576: fprintf(ficrespl,"\n");
5577: }
1.53 brouard 5578: }
5579: }
1.98 brouard 5580: fclose(ficrespl);
1.53 brouard 5581:
1.98 brouard 5582: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5583:
1.98 brouard 5584: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5585: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5586: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5587: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5588: }
5589: printf("Computing pij: result on file '%s' \n", filerespij);
5590: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5591:
1.98 brouard 5592: stepsize=(int) (stepm+YEARM-1)/YEARM;
5593: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5594:
1.98 brouard 5595: agelim=AGESUP;
5596: hstepm=stepsize*YEARM; /* Every year of age */
5597: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5598:
1.98 brouard 5599: /* hstepm=1; aff par mois*/
1.117 brouard 5600: pstamp(ficrespij);
1.98 brouard 5601: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5602: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5603: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5604: k=k+1;
5605: fprintf(ficrespij,"\n#****** ");
5606: for(j=1;j<=cptcoveff;j++)
5607: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5608: fprintf(ficrespij,"******\n");
1.53 brouard 5609:
1.98 brouard 5610: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5611: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5612: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5613:
1.98 brouard 5614: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5615:
1.98 brouard 5616: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5617: oldm=oldms;savm=savms;
5618: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5619: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5620: for(i=1; i<=nlstate;i++)
5621: for(j=1; j<=nlstate+ndeath;j++)
1.98 brouard 5622: fprintf(ficrespij," %1d-%1d",i,j);
5623: fprintf(ficrespij,"\n");
5624: for (h=0; h<=nhstepm; h++){
5625: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5626: for(i=1; i<=nlstate;i++)
5627: for(j=1; j<=nlstate+ndeath;j++)
5628: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5629: fprintf(ficrespij,"\n");
5630: }
5631: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5632: fprintf(ficrespij,"\n");
5633: }
1.59 brouard 5634: }
1.53 brouard 5635: }
5636:
1.105 lievre 5637: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.53 brouard 5638:
1.98 brouard 5639: fclose(ficrespij);
1.53 brouard 5640:
1.98 brouard 5641: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5642: for(i=1;i<=AGESUP;i++)
5643: for(j=1;j<=NCOVMAX;j++)
5644: for(k=1;k<=NCOVMAX;k++)
5645: probs[i][j][k]=0.;
5646:
5647: /*---------- Forecasting ------------------*/
5648: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5649: if(prevfcast==1){
5650: /* if(stepm ==1){*/
1.70 brouard 5651: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5652: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 brouard 5653: /* } */
5654: /* else{ */
5655: /* erreur=108; */
5656: /* 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); */
5657: /* 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); */
5658: /* } */
5659: }
1.53 brouard 5660:
5661:
1.98 brouard 5662: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5663:
1.98 brouard 5664: strcpy(filerest,"t");
5665: strcat(filerest,fileres);
5666: if((ficrest=fopen(filerest,"w"))==NULL) {
5667: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5668: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5669: }
1.117 brouard 5670: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5671: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
1.53 brouard 5672:
5673:
1.98 brouard 5674: strcpy(filerese,"e");
5675: strcat(filerese,fileres);
5676: if((ficreseij=fopen(filerese,"w"))==NULL) {
5677: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5678: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5679: }
5680: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5681: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5682:
1.117 brouard 5683: strcpy(fileresstde,"stde");
5684: strcat(fileresstde,fileres);
5685: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5686: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5687: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5688: }
5689: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5690: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5691:
5692: strcpy(filerescve,"cve");
5693: strcat(filerescve,fileres);
5694: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5695: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5696: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5697: }
5698: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5699: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5700:
1.98 brouard 5701: strcpy(fileresv,"v");
5702: strcat(fileresv,fileres);
5703: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5704: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5705: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5706: }
5707: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5708: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5709:
1.98 brouard 5710: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5711: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5712: /* 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",\
5713: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5714: */
1.58 lievre 5715:
1.98 brouard 5716: if (mobilav!=0) {
5717: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5718: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5719: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5720: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5721: }
1.54 brouard 5722: }
1.53 brouard 5723:
1.98 brouard 5724: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5725: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5726: k=k+1;
5727: fprintf(ficrest,"\n#****** ");
5728: for(j=1;j<=cptcoveff;j++)
5729: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5730: fprintf(ficrest,"******\n");
5731:
5732: fprintf(ficreseij,"\n#****** ");
1.117 brouard 5733: fprintf(ficresstdeij,"\n#****** ");
5734: fprintf(ficrescveij,"\n#****** ");
5735: for(j=1;j<=cptcoveff;j++) {
1.98 brouard 5736: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.117 brouard 5737: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5738: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5739: }
1.98 brouard 5740: fprintf(ficreseij,"******\n");
1.117 brouard 5741: fprintf(ficresstdeij,"******\n");
5742: fprintf(ficrescveij,"******\n");
1.98 brouard 5743:
5744: fprintf(ficresvij,"\n#****** ");
5745: for(j=1;j<=cptcoveff;j++)
5746: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5747: fprintf(ficresvij,"******\n");
5748:
5749: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5750: oldm=oldms;savm=savms;
1.117 brouard 5751: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5752: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.53 brouard 5753:
1.98 brouard 5754: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5755: oldm=oldms;savm=savms;
1.105 lievre 5756: 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 5757: if(popbased==1){
1.105 lievre 5758: 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 5759: }
1.53 brouard 5760:
1.117 brouard 5761: pstamp(ficrest);
1.118 brouard 5762: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
1.98 brouard 5763: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5764: fprintf(ficrest,"\n");
5765:
5766: epj=vector(1,nlstate+1);
5767: for(age=bage; age <=fage ;age++){
5768: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5769: if (popbased==1) {
5770: if(mobilav ==0){
5771: for(i=1; i<=nlstate;i++)
5772: prlim[i][i]=probs[(int)age][i][k];
5773: }else{ /* mobilav */
5774: for(i=1; i<=nlstate;i++)
5775: prlim[i][i]=mobaverage[(int)age][i][k];
5776: }
1.53 brouard 5777: }
5778:
1.98 brouard 5779: fprintf(ficrest," %4.0f",age);
5780: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5781: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5782: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5783: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5784: }
5785: epj[nlstate+1] +=epj[j];
1.53 brouard 5786: }
5787:
1.98 brouard 5788: for(i=1, vepp=0.;i <=nlstate;i++)
5789: for(j=1;j <=nlstate;j++)
5790: vepp += vareij[i][j][(int)age];
5791: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5792: for(j=1;j <=nlstate;j++){
5793: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5794: }
5795: fprintf(ficrest,"\n");
1.53 brouard 5796: }
1.98 brouard 5797: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5798: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5799: free_vector(epj,1,nlstate+1);
5800: }
5801: }
5802: free_vector(weight,1,n);
5803: free_imatrix(Tvard,1,15,1,2);
5804: free_imatrix(s,1,maxwav+1,1,n);
5805: free_matrix(anint,1,maxwav,1,n);
5806: free_matrix(mint,1,maxwav,1,n);
5807: free_ivector(cod,1,n);
5808: free_ivector(tab,1,NCOVMAX);
5809: fclose(ficreseij);
1.117 brouard 5810: fclose(ficresstdeij);
5811: fclose(ficrescveij);
1.98 brouard 5812: fclose(ficresvij);
5813: fclose(ficrest);
5814: fclose(ficpar);
5815:
1.117 brouard 5816: /*------- Variance of period (stable) prevalence------*/
1.98 brouard 5817:
5818: strcpy(fileresvpl,"vpl");
5819: strcat(fileresvpl,fileres);
5820: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.117 brouard 5821: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
1.98 brouard 5822: exit(0);
5823: }
1.117 brouard 5824: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
1.98 brouard 5825:
5826: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5827: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5828: k=k+1;
5829: fprintf(ficresvpl,"\n#****** ");
5830: for(j=1;j<=cptcoveff;j++)
5831: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5832: fprintf(ficresvpl,"******\n");
5833:
5834: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5835: oldm=oldms;savm=savms;
1.105 lievre 5836: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
1.98 brouard 5837: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5838: }
1.98 brouard 5839: }
1.53 brouard 5840:
1.98 brouard 5841: fclose(ficresvpl);
1.53 brouard 5842:
1.98 brouard 5843: /*---------- End : free ----------------*/
5844: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5845: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5846:
5847: } /* mle==-3 arrives here for freeing */
1.113 brouard 5848: free_matrix(prlim,1,nlstate,1,nlstate);
1.98 brouard 5849: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5850: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5851: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5852: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5853: free_matrix(covar,0,NCOVMAX,1,n);
5854: free_matrix(matcov,1,npar,1,npar);
5855: /*free_vector(delti,1,npar);*/
5856: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5857: free_matrix(agev,1,maxwav,1,imx);
5858: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5859:
5860: free_ivector(ncodemax,1,8);
5861: free_ivector(Tvar,1,15);
5862: free_ivector(Tprod,1,15);
5863: free_ivector(Tvaraff,1,15);
5864: free_ivector(Tage,1,15);
5865: free_ivector(Tcode,1,100);
1.74 brouard 5866:
1.113 brouard 5867: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5868: free_imatrix(codtab,1,100,1,10);
1.88 brouard 5869: fflush(fichtm);
5870: fflush(ficgp);
1.53 brouard 5871:
5872:
1.91 brouard 5873: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5874: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5875: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5876: }else{
1.91 brouard 5877: printf("End of Imach\n");
5878: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5879: }
5880: printf("See log file on %s\n",filelog);
5881: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5882: (void) gettimeofday(&end_time,&tzp);
5883: tm = *localtime(&end_time.tv_sec);
5884: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5885: strcpy(strtend,asctime(&tm));
1.105 lievre 5886: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
1.94 brouard 5887: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5888: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5889:
1.91 brouard 5890: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5891: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5892: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5893: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5894: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5895: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5896: fclose(fichtm);
1.91 brouard 5897: fclose(fichtmcov);
1.88 brouard 5898: fclose(ficgp);
1.91 brouard 5899: fclose(ficlog);
1.53 brouard 5900: /*------ End -----------*/
5901:
1.119 ! brouard 5902:
! 5903: printf("Before Current directory %s!\n",pathcd);
! 5904: if(chdir(pathcd) != 0)
! 5905: printf("Can't move to directory %s!\n",path);
! 5906: if(getcwd(pathcd,MAXLINE) > 0)
! 5907: printf("Current directory %s!\n",pathcd);
1.107 brouard 5908: /*strcat(plotcmd,CHARSEPARATOR);*/
1.111 brouard 5909: sprintf(plotcmd,"gnuplot");
1.107 brouard 5910: #ifndef UNIX
1.112 brouard 5911: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
1.107 brouard 5912: #endif
1.111 brouard 5913: if(!stat(plotcmd,&info)){
1.107 brouard 5914: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
1.111 brouard 5915: if(!stat(getenv("GNUPLOTBIN"),&info)){
5916: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5917: }else
5918: strcpy(pplotcmd,plotcmd);
5919: #ifdef UNIX
5920: strcpy(plotcmd,GNUPLOTPROGRAM);
5921: if(!stat(plotcmd,&info)){
5922: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5923: }else
5924: strcpy(pplotcmd,plotcmd);
1.108 lievre 5925: #endif
1.111 brouard 5926: }else
5927: strcpy(pplotcmd,plotcmd);
5928:
5929: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5930: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
1.107 brouard 5931:
1.91 brouard 5932: if((outcmd=system(plotcmd)) != 0){
1.108 lievre 5933: printf("\n Problem with gnuplot\n");
1.91 brouard 5934: }
1.75 brouard 5935: printf(" Wait...");
1.53 brouard 5936: while (z[0] != 'q') {
5937: /* chdir(path); */
1.91 brouard 5938: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5939: scanf("%s",z);
1.91 brouard 5940: /* if (z[0] == 'c') system("./imach"); */
1.99 brouard 5941: if (z[0] == 'e') {
5942: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5943: system(optionfilehtm);
5944: }
1.53 brouard 5945: else if (z[0] == 'g') system(plotcmd);
5946: else if (z[0] == 'q') exit(0);
5947: }
1.91 brouard 5948: end:
5949: while (z[0] != 'q') {
5950: printf("\nType q for exiting: ");
5951: scanf("%s",z);
5952: }
1.53 brouard 5953: }
1.88 brouard 5954:
1.53 brouard 5955:
5956:
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