Annotation of imach/src/imach.c, revision 1.124
1.124 ! lievre 1: /* $Id: imach.c,v 1.123 2006/03/20 10:52:43 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.124 ! lievre 4: Revision 1.123 2006/03/20 10:52:43 brouard
! 5: * imach.c (Module): <title> changed, corresponds to .htm file
! 6: name. <head> headers where missing.
! 7:
! 8: * imach.c (Module): Weights can have a decimal point as for
! 9: English (a comma might work with a correct LC_NUMERIC environment,
! 10: otherwise the weight is truncated).
! 11: Modification of warning when the covariates values are not 0 or
! 12: 1.
! 13: Version 0.98g
! 14:
1.123 brouard 15: Revision 1.122 2006/03/20 09:45:41 brouard
16: (Module): Weights can have a decimal point as for
17: English (a comma might work with a correct LC_NUMERIC environment,
18: otherwise the weight is truncated).
19: Modification of warning when the covariates values are not 0 or
20: 1.
21: Version 0.98g
22:
1.122 brouard 23: Revision 1.121 2006/03/16 17:45:01 lievre
24: * imach.c (Module): Comments concerning covariates added
25:
26: * imach.c (Module): refinements in the computation of lli if
27: status=-2 in order to have more reliable computation if stepm is
28: not 1 month. Version 0.98f
29:
1.121 lievre 30: Revision 1.120 2006/03/16 15:10:38 lievre
31: (Module): refinements in the computation of lli if
32: status=-2 in order to have more reliable computation if stepm is
33: not 1 month. Version 0.98f
34:
1.120 lievre 35: Revision 1.119 2006/03/15 17:42:26 brouard
36: (Module): Bug if status = -2, the loglikelihood was
37: computed as likelihood omitting the logarithm. Version O.98e
38:
1.119 brouard 39: Revision 1.118 2006/03/14 18:20:07 brouard
40: (Module): varevsij Comments added explaining the second
41: table of variances if popbased=1 .
42: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
43: (Module): Function pstamp added
44: (Module): Version 0.98d
45:
1.118 brouard 46: Revision 1.117 2006/03/14 17:16:22 brouard
47: (Module): varevsij Comments added explaining the second
48: table of variances if popbased=1 .
49: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
50: (Module): Function pstamp added
51: (Module): Version 0.98d
52:
1.117 brouard 53: Revision 1.116 2006/03/06 10:29:27 brouard
54: (Module): Variance-covariance wrong links and
55: varian-covariance of ej. is needed (Saito).
56:
1.116 brouard 57: Revision 1.115 2006/02/27 12:17:45 brouard
58: (Module): One freematrix added in mlikeli! 0.98c
59:
1.115 brouard 60: Revision 1.114 2006/02/26 12:57:58 brouard
61: (Module): Some improvements in processing parameter
62: filename with strsep.
63:
1.114 brouard 64: Revision 1.113 2006/02/24 14:20:24 brouard
65: (Module): Memory leaks checks with valgrind and:
66: datafile was not closed, some imatrix were not freed and on matrix
67: allocation too.
68:
1.113 brouard 69: Revision 1.112 2006/01/30 09:55:26 brouard
70: (Module): Back to gnuplot.exe instead of wgnuplot.exe
71:
1.112 brouard 72: Revision 1.111 2006/01/25 20:38:18 brouard
73: (Module): Lots of cleaning and bugs added (Gompertz)
74: (Module): Comments can be added in data file. Missing date values
75: can be a simple dot '.'.
76:
1.111 brouard 77: Revision 1.110 2006/01/25 00:51:50 brouard
78: (Module): Lots of cleaning and bugs added (Gompertz)
79:
1.110 brouard 80: Revision 1.109 2006/01/24 19:37:15 brouard
81: (Module): Comments (lines starting with a #) are allowed in data.
82:
1.109 brouard 83: Revision 1.108 2006/01/19 18:05:42 lievre
84: Gnuplot problem appeared...
85: To be fixed
86:
1.108 lievre 87: Revision 1.107 2006/01/19 16:20:37 brouard
88: Test existence of gnuplot in imach path
89:
1.107 brouard 90: Revision 1.106 2006/01/19 13:24:36 brouard
91: Some cleaning and links added in html output
92:
1.106 brouard 93: Revision 1.105 2006/01/05 20:23:19 lievre
94: *** empty log message ***
95:
1.105 lievre 96: Revision 1.104 2005/09/30 16:11:43 lievre
97: (Module): sump fixed, loop imx fixed, and simplifications.
98: (Module): If the status is missing at the last wave but we know
99: that the person is alive, then we can code his/her status as -2
100: (instead of missing=-1 in earlier versions) and his/her
101: contributions to the likelihood is 1 - Prob of dying from last
102: health status (= 1-p13= p11+p12 in the easiest case of somebody in
103: the healthy state at last known wave). Version is 0.98
104:
1.104 lievre 105: Revision 1.103 2005/09/30 15:54:49 lievre
106: (Module): sump fixed, loop imx fixed, and simplifications.
107:
1.103 lievre 108: Revision 1.102 2004/09/15 17:31:30 brouard
109: Add the possibility to read data file including tab characters.
110:
1.102 brouard 111: Revision 1.101 2004/09/15 10:38:38 brouard
112: Fix on curr_time
113:
1.101 brouard 114: Revision 1.100 2004/07/12 18:29:06 brouard
115: Add version for Mac OS X. Just define UNIX in Makefile
116:
1.100 brouard 117: Revision 1.99 2004/06/05 08:57:40 brouard
118: *** empty log message ***
119:
1.99 brouard 120: Revision 1.98 2004/05/16 15:05:56 brouard
121: New version 0.97 . First attempt to estimate force of mortality
122: directly from the data i.e. without the need of knowing the health
123: state at each age, but using a Gompertz model: log u =a + b*age .
124: This is the basic analysis of mortality and should be done before any
125: other analysis, in order to test if the mortality estimated from the
126: cross-longitudinal survey is different from the mortality estimated
127: from other sources like vital statistic data.
128:
129: The same imach parameter file can be used but the option for mle should be -3.
130:
131: Agnès, who wrote this part of the code, tried to keep most of the
132: former routines in order to include the new code within the former code.
133:
134: The output is very simple: only an estimate of the intercept and of
135: the slope with 95% confident intervals.
136:
137: Current limitations:
138: A) Even if you enter covariates, i.e. with the
139: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
140: B) There is no computation of Life Expectancy nor Life Table.
141:
1.98 brouard 142: Revision 1.97 2004/02/20 13:25:42 lievre
143: Version 0.96d. Population forecasting command line is (temporarily)
144: suppressed.
145:
1.97 lievre 146: Revision 1.96 2003/07/15 15:38:55 brouard
147: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
148: rewritten within the same printf. Workaround: many printfs.
149:
1.96 brouard 150: Revision 1.95 2003/07/08 07:54:34 brouard
151: * imach.c (Repository):
152: (Repository): Using imachwizard code to output a more meaningful covariance
153: matrix (cov(a12,c31) instead of numbers.
154:
1.95 brouard 155: Revision 1.94 2003/06/27 13:00:02 brouard
156: Just cleaning
157:
1.94 brouard 158: Revision 1.93 2003/06/25 16:33:55 brouard
159: (Module): On windows (cygwin) function asctime_r doesn't
160: exist so I changed back to asctime which exists.
161: (Module): Version 0.96b
162:
1.93 brouard 163: Revision 1.92 2003/06/25 16:30:45 brouard
164: (Module): On windows (cygwin) function asctime_r doesn't
165: exist so I changed back to asctime which exists.
166:
1.92 brouard 167: Revision 1.91 2003/06/25 15:30:29 brouard
168: * imach.c (Repository): Duplicated warning errors corrected.
169: (Repository): Elapsed time after each iteration is now output. It
170: helps to forecast when convergence will be reached. Elapsed time
171: is stamped in powell. We created a new html file for the graphs
172: concerning matrix of covariance. It has extension -cov.htm.
173:
1.91 brouard 174: Revision 1.90 2003/06/24 12:34:15 brouard
175: (Module): Some bugs corrected for windows. Also, when
176: mle=-1 a template is output in file "or"mypar.txt with the design
177: of the covariance matrix to be input.
178:
1.90 brouard 179: Revision 1.89 2003/06/24 12:30:52 brouard
180: (Module): Some bugs corrected for windows. Also, when
181: mle=-1 a template is output in file "or"mypar.txt with the design
182: of the covariance matrix to be input.
183:
1.89 brouard 184: Revision 1.88 2003/06/23 17:54:56 brouard
185: * 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.
186:
1.88 brouard 187: Revision 1.87 2003/06/18 12:26:01 brouard
188: Version 0.96
189:
1.87 brouard 190: Revision 1.86 2003/06/17 20:04:08 brouard
191: (Module): Change position of html and gnuplot routines and added
192: routine fileappend.
193:
1.86 brouard 194: Revision 1.85 2003/06/17 13:12:43 brouard
195: * imach.c (Repository): Check when date of death was earlier that
196: current date of interview. It may happen when the death was just
197: prior to the death. In this case, dh was negative and likelihood
198: was wrong (infinity). We still send an "Error" but patch by
199: assuming that the date of death was just one stepm after the
200: interview.
201: (Repository): Because some people have very long ID (first column)
202: we changed int to long in num[] and we added a new lvector for
203: memory allocation. But we also truncated to 8 characters (left
204: truncation)
205: (Repository): No more line truncation errors.
206:
1.85 brouard 207: Revision 1.84 2003/06/13 21:44:43 brouard
208: * imach.c (Repository): Replace "freqsummary" at a correct
209: place. It differs from routine "prevalence" which may be called
210: many times. Probs is memory consuming and must be used with
211: parcimony.
1.86 brouard 212: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 213:
1.84 brouard 214: Revision 1.83 2003/06/10 13:39:11 lievre
215: *** empty log message ***
216:
1.83 lievre 217: Revision 1.82 2003/06/05 15:57:20 brouard
218: Add log in imach.c and fullversion number is now printed.
219:
1.82 brouard 220: */
221: /*
1.53 brouard 222: Interpolated Markov Chain
223:
224: Short summary of the programme:
225:
226: This program computes Healthy Life Expectancies from
227: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
228: first survey ("cross") where individuals from different ages are
229: interviewed on their health status or degree of disability (in the
230: case of a health survey which is our main interest) -2- at least a
231: second wave of interviews ("longitudinal") which measure each change
232: (if any) in individual health status. Health expectancies are
233: computed from the time spent in each health state according to a
234: model. More health states you consider, more time is necessary to reach the
235: Maximum Likelihood of the parameters involved in the model. The
236: simplest model is the multinomial logistic model where pij is the
237: probability to be observed in state j at the second wave
238: conditional to be observed in state i at the first wave. Therefore
239: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
240: 'age' is age and 'sex' is a covariate. If you want to have a more
241: complex model than "constant and age", you should modify the program
242: where the markup *Covariates have to be included here again* invites
243: you to do it. More covariates you add, slower the
244: convergence.
245:
246: The advantage of this computer programme, compared to a simple
247: multinomial logistic model, is clear when the delay between waves is not
248: identical for each individual. Also, if a individual missed an
249: intermediate interview, the information is lost, but taken into
250: account using an interpolation or extrapolation.
251:
252: hPijx is the probability to be observed in state i at age x+h
253: conditional to the observed state i at age x. The delay 'h' can be
254: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 255: states. This elementary transition (by month, quarter,
256: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 257: matrix is simply the matrix product of nh*stepm elementary matrices
258: and the contribution of each individual to the likelihood is simply
259: hPijx.
260:
261: Also this programme outputs the covariance matrix of the parameters but also
1.117 brouard 262: of the life expectancies. It also computes the period (stable) prevalence.
1.53 brouard 263:
264: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
265: Institut national d'études démographiques, Paris.
266: This software have been partly granted by Euro-REVES, a concerted action
267: from the European Union.
268: It is copyrighted identically to a GNU software product, ie programme and
269: software can be distributed freely for non commercial use. Latest version
270: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 271:
272: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
273: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
274:
1.53 brouard 275: **********************************************************************/
1.74 brouard 276: /*
277: main
278: read parameterfile
279: read datafile
280: concatwav
1.84 brouard 281: freqsummary
1.74 brouard 282: if (mle >= 1)
283: mlikeli
284: print results files
285: if mle==1
286: computes hessian
287: read end of parameter file: agemin, agemax, bage, fage, estepm
288: begin-prev-date,...
289: open gnuplot file
290: open html file
1.117 brouard 291: period (stable) prevalence
1.74 brouard 292: for age prevalim()
293: h Pij x
294: variance of p varprob
295: forecasting if prevfcast==1 prevforecast call prevalence()
296: health expectancies
297: Variance-covariance of DFLE
298: prevalence()
299: movingaverage()
300: varevsij()
301: if popbased==1 varevsij(,popbased)
302: total life expectancies
1.117 brouard 303: Variance of period (stable) prevalence
1.74 brouard 304: end
305: */
306:
307:
308:
1.53 brouard 309:
310: #include <math.h>
311: #include <stdio.h>
312: #include <stdlib.h>
1.106 brouard 313: #include <string.h>
1.53 brouard 314: #include <unistd.h>
315:
1.109 brouard 316: #include <limits.h>
1.107 brouard 317: #include <sys/types.h>
318: #include <sys/stat.h>
319: #include <errno.h>
320: extern int errno;
321:
1.99 brouard 322: /* #include <sys/time.h> */
1.86 brouard 323: #include <time.h>
324: #include "timeval.h"
325:
1.95 brouard 326: /* #include <libintl.h> */
327: /* #define _(String) gettext (String) */
328:
1.53 brouard 329: #define MAXLINE 256
1.108 lievre 330:
1.53 brouard 331: #define GNUPLOTPROGRAM "gnuplot"
332: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 333: #define FILENAMELENGTH 132
1.108 lievre 334:
1.53 brouard 335: #define GLOCK_ERROR_NOPATH -1 /* empty path */
336: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
337:
338: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
339: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
340:
341: #define NINTERVMAX 8
342: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
343: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
344: #define NCOVMAX 8 /* Maximum number of covariates */
345: #define MAXN 20000
346: #define YEARM 12. /* Number of months per year */
347: #define AGESUP 130
348: #define AGEBASE 40
1.98 brouard 349: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.100 brouard 350: #ifdef UNIX
1.85 brouard 351: #define DIRSEPARATOR '/'
1.107 brouard 352: #define CHARSEPARATOR "/"
1.85 brouard 353: #define ODIRSEPARATOR '\\'
354: #else
1.53 brouard 355: #define DIRSEPARATOR '\\'
1.107 brouard 356: #define CHARSEPARATOR "\\"
1.53 brouard 357: #define ODIRSEPARATOR '/'
358: #endif
359:
1.124 ! lievre 360: /* $Id: imach.c,v 1.123 2006/03/20 10:52:43 brouard Exp $ */
1.81 brouard 361: /* $State: Exp $ */
1.80 brouard 362:
1.122 brouard 363: char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
1.124 ! lievre 364: char fullversion[]="$Revision: 1.123 $ $Date: 2006/03/20 10:52:43 $";
1.117 brouard 365: char strstart[80];
366: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.91 brouard 367: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 368: int nvar;
369: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
370: int npar=NPARMAX;
371: int nlstate=2; /* Number of live states */
372: int ndeath=1; /* Number of dead states */
373: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
374: int popbased=0;
375:
376: int *wav; /* Number of waves for this individuual 0 is possible */
377: int maxwav; /* Maxim number of waves */
378: int jmin, jmax; /* min, max spacing between 2 waves */
1.110 brouard 379: int ijmin, ijmax; /* Individuals having jmin and jmax */
1.87 brouard 380: int gipmx, gsw; /* Global variables on the number of contributions
381: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 382: int mle, weightopt;
383: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
384: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 385: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
386: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 387: double jmean; /* Mean space between 2 waves */
388: double **oldm, **newm, **savm; /* Working pointers to matrices */
389: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.117 brouard 390: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 391: FILE *ficlog, *ficrespow;
1.85 brouard 392: int globpr; /* Global variable for printing or not */
393: double fretone; /* Only one call to likelihood */
394: long ipmx; /* Number of contributions */
395: double sw; /* Sum of weights */
1.98 brouard 396: char filerespow[FILENAMELENGTH];
1.85 brouard 397: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
398: FILE *ficresilk;
1.53 brouard 399: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
400: FILE *ficresprobmorprev;
1.91 brouard 401: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 402: FILE *ficreseij;
403: char filerese[FILENAMELENGTH];
1.117 brouard 404: FILE *ficresstdeij;
405: char fileresstde[FILENAMELENGTH];
406: FILE *ficrescveij;
407: char filerescve[FILENAMELENGTH];
1.53 brouard 408: FILE *ficresvij;
409: char fileresv[FILENAMELENGTH];
410: FILE *ficresvpl;
411: char fileresvpl[FILENAMELENGTH];
412: char title[MAXLINE];
413: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
1.117 brouard 414: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1.96 brouard 415: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 416: char command[FILENAMELENGTH];
417: int outcmd=0;
1.53 brouard 418:
419: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 420:
1.53 brouard 421: char filelog[FILENAMELENGTH]; /* Log file */
422: char filerest[FILENAMELENGTH];
423: char fileregp[FILENAMELENGTH];
424: char popfile[FILENAMELENGTH];
425:
1.91 brouard 426: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
427:
428: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
429: struct timezone tzp;
430: extern int gettimeofday();
431: struct tm tmg, tm, tmf, *gmtime(), *localtime();
432: long time_value;
433: extern long time();
434: char strcurr[80], strfor[80];
1.53 brouard 435:
1.109 brouard 436: char *endptr;
437: long lval;
1.122 brouard 438: double dval;
1.109 brouard 439:
1.53 brouard 440: #define NR_END 1
441: #define FREE_ARG char*
442: #define FTOL 1.0e-10
443:
444: #define NRANSI
445: #define ITMAX 200
446:
447: #define TOL 2.0e-4
448:
449: #define CGOLD 0.3819660
450: #define ZEPS 1.0e-10
451: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
452:
453: #define GOLD 1.618034
454: #define GLIMIT 100.0
455: #define TINY 1.0e-20
456:
457: static double maxarg1,maxarg2;
458: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
459: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
460:
461: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
462: #define rint(a) floor(a+0.5)
463:
464: static double sqrarg;
465: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
466: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 brouard 467: int agegomp= AGEGOMP;
1.53 brouard 468:
469: int imx;
1.98 brouard 470: int stepm=1;
1.53 brouard 471: /* Stepm, step in month: minimum step interpolation*/
472:
473: int estepm;
474: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
475:
476: int m,nb;
1.85 brouard 477: long *num;
1.98 brouard 478: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 479: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 480: double **pmmij, ***probs;
1.98 brouard 481: double *ageexmed,*agecens;
1.53 brouard 482: double dateintmean=0;
483:
484: double *weight;
485: int **s; /* Status */
486: double *agedc, **covar, idx;
487: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.105 lievre 488: double *lsurv, *lpop, *tpop;
1.53 brouard 489:
490: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
491: double ftolhess; /* Tolerance for computing hessian */
492:
493: /**************** split *************************/
494: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
495: {
1.107 brouard 496: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1.99 brouard 497: the name of the file (name), its extension only (ext) and its first part of the name (finame)
498: */
1.59 brouard 499: char *ss; /* pointer */
500: int l1, l2; /* length counters */
1.53 brouard 501:
1.59 brouard 502: l1 = strlen(path ); /* length of path */
503: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
504: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1.107 brouard 505: if ( ss == NULL ) { /* no directory, so determine current directory */
506: strcpy( name, path ); /* we got the fullname name because no directory */
1.59 brouard 507: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
508: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 509: /* get current working directory */
510: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 511: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
512: return( GLOCK_ERROR_GETCWD );
513: }
1.107 brouard 514: /* got dirc from getcwd*/
515: printf(" DIRC = %s \n",dirc);
1.59 brouard 516: } else { /* strip direcotry from path */
517: ss++; /* after this, the filename */
518: l2 = strlen( ss ); /* length of filename */
519: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
520: strcpy( name, ss ); /* save file name */
521: strncpy( dirc, path, l1 - l2 ); /* now the directory */
522: dirc[l1-l2] = 0; /* add zero */
1.107 brouard 523: printf(" DIRC2 = %s \n",dirc);
1.59 brouard 524: }
1.107 brouard 525: /* We add a separator at the end of dirc if not exists */
1.59 brouard 526: l1 = strlen( dirc ); /* length of directory */
1.107 brouard 527: if( dirc[l1-1] != DIRSEPARATOR ){
528: dirc[l1] = DIRSEPARATOR;
529: dirc[l1+1] = 0;
530: printf(" DIRC3 = %s \n",dirc);
531: }
1.59 brouard 532: ss = strrchr( name, '.' ); /* find last / */
1.99 brouard 533: if (ss >0){
534: ss++;
535: strcpy(ext,ss); /* save extension */
536: l1= strlen( name);
537: l2= strlen(ss)+1;
538: strncpy( finame, name, l1-l2);
539: finame[l1-l2]= 0;
540: }
1.107 brouard 541:
1.59 brouard 542: return( 0 ); /* we're done */
1.53 brouard 543: }
544:
545:
546: /******************************************/
547:
1.89 brouard 548: void replace_back_to_slash(char *s, char*t)
1.53 brouard 549: {
550: int i;
1.89 brouard 551: int lg=0;
1.53 brouard 552: i=0;
553: lg=strlen(t);
554: for(i=0; i<= lg; i++) {
555: (s[i] = t[i]);
556: if (t[i]== '\\') s[i]='/';
557: }
558: }
559:
560: int nbocc(char *s, char occ)
561: {
562: int i,j=0;
563: int lg=20;
564: i=0;
565: lg=strlen(s);
566: for(i=0; i<= lg; i++) {
567: if (s[i] == occ ) j++;
568: }
569: return j;
570: }
571:
572: void cutv(char *u,char *v, char*t, char occ)
573: {
1.102 brouard 574: /* cuts string t into u and v where u ends before first occurence of char 'occ'
575: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
1.53 brouard 576: gives u="abcedf" and v="ghi2j" */
577: int i,lg,j,p=0;
578: i=0;
579: for(j=0; j<=strlen(t)-1; j++) {
580: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
581: }
582:
583: lg=strlen(t);
584: for(j=0; j<p; j++) {
585: (u[j] = t[j]);
586: }
587: u[p]='\0';
588:
589: for(j=0; j<= lg; j++) {
590: if (j>=(p+1))(v[j-p-1] = t[j]);
591: }
592: }
593:
594: /********************** nrerror ********************/
595:
596: void nrerror(char error_text[])
597: {
598: fprintf(stderr,"ERREUR ...\n");
599: fprintf(stderr,"%s\n",error_text);
1.59 brouard 600: exit(EXIT_FAILURE);
1.53 brouard 601: }
602: /*********************** vector *******************/
603: double *vector(int nl, int nh)
604: {
605: double *v;
606: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
607: if (!v) nrerror("allocation failure in vector");
608: return v-nl+NR_END;
609: }
610:
611: /************************ free vector ******************/
612: void free_vector(double*v, int nl, int nh)
613: {
614: free((FREE_ARG)(v+nl-NR_END));
615: }
616:
617: /************************ivector *******************************/
1.85 brouard 618: int *ivector(long nl,long nh)
1.76 brouard 619: {
1.85 brouard 620: int *v;
621: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
622: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 623: return v-nl+NR_END;
624: }
625:
626: /******************free ivector **************************/
1.85 brouard 627: void free_ivector(int *v, long nl, long nh)
1.76 brouard 628: {
629: free((FREE_ARG)(v+nl-NR_END));
630: }
631:
1.85 brouard 632: /************************lvector *******************************/
633: long *lvector(long nl,long nh)
1.53 brouard 634: {
1.85 brouard 635: long *v;
636: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 637: if (!v) nrerror("allocation failure in ivector");
638: return v-nl+NR_END;
639: }
640:
1.85 brouard 641: /******************free lvector **************************/
642: void free_lvector(long *v, long nl, long nh)
1.53 brouard 643: {
644: free((FREE_ARG)(v+nl-NR_END));
645: }
646:
647: /******************* imatrix *******************************/
648: int **imatrix(long nrl, long nrh, long ncl, long nch)
649: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
650: {
651: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
652: int **m;
653:
654: /* allocate pointers to rows */
655: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
656: if (!m) nrerror("allocation failure 1 in matrix()");
657: m += NR_END;
658: m -= nrl;
659:
660:
661: /* allocate rows and set pointers to them */
662: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
663: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
664: m[nrl] += NR_END;
665: m[nrl] -= ncl;
666:
667: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
668:
669: /* return pointer to array of pointers to rows */
670: return m;
671: }
672:
673: /****************** free_imatrix *************************/
674: void free_imatrix(m,nrl,nrh,ncl,nch)
675: int **m;
676: long nch,ncl,nrh,nrl;
677: /* free an int matrix allocated by imatrix() */
678: {
679: free((FREE_ARG) (m[nrl]+ncl-NR_END));
680: free((FREE_ARG) (m+nrl-NR_END));
681: }
682:
683: /******************* matrix *******************************/
684: double **matrix(long nrl, long nrh, long ncl, long nch)
685: {
686: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
687: double **m;
688:
689: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
690: if (!m) nrerror("allocation failure 1 in matrix()");
691: m += NR_END;
692: m -= nrl;
693:
694: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
695: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
696: m[nrl] += NR_END;
697: m[nrl] -= ncl;
698:
699: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
700: return m;
1.85 brouard 701: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 702: */
1.53 brouard 703: }
704:
705: /*************************free matrix ************************/
706: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
707: {
708: free((FREE_ARG)(m[nrl]+ncl-NR_END));
709: free((FREE_ARG)(m+nrl-NR_END));
710: }
711:
712: /******************* ma3x *******************************/
713: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
714: {
715: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
716: double ***m;
717:
718: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
719: if (!m) nrerror("allocation failure 1 in matrix()");
720: m += NR_END;
721: m -= nrl;
722:
723: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
724: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
725: m[nrl] += NR_END;
726: m[nrl] -= ncl;
727:
728: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
729:
730: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
731: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
732: m[nrl][ncl] += NR_END;
733: m[nrl][ncl] -= nll;
734: for (j=ncl+1; j<=nch; j++)
735: m[nrl][j]=m[nrl][j-1]+nlay;
736:
737: for (i=nrl+1; i<=nrh; i++) {
738: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
739: for (j=ncl+1; j<=nch; j++)
740: m[i][j]=m[i][j-1]+nlay;
741: }
1.74 brouard 742: return m;
743: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
744: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
745: */
1.53 brouard 746: }
747:
748: /*************************free ma3x ************************/
749: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
750: {
751: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
752: free((FREE_ARG)(m[nrl]+ncl-NR_END));
753: free((FREE_ARG)(m+nrl-NR_END));
754: }
755:
1.94 brouard 756: /*************** function subdirf ***********/
757: char *subdirf(char fileres[])
758: {
759: /* Caution optionfilefiname is hidden */
760: strcpy(tmpout,optionfilefiname);
761: strcat(tmpout,"/"); /* Add to the right */
762: strcat(tmpout,fileres);
763: return tmpout;
764: }
765:
766: /*************** function subdirf2 ***********/
767: char *subdirf2(char fileres[], char *preop)
768: {
769:
770: /* Caution optionfilefiname is hidden */
771: strcpy(tmpout,optionfilefiname);
772: strcat(tmpout,"/");
773: strcat(tmpout,preop);
774: strcat(tmpout,fileres);
775: return tmpout;
776: }
777:
778: /*************** function subdirf3 ***********/
779: char *subdirf3(char fileres[], char *preop, char *preop2)
780: {
781:
782: /* Caution optionfilefiname is hidden */
783: strcpy(tmpout,optionfilefiname);
784: strcat(tmpout,"/");
785: strcat(tmpout,preop);
786: strcat(tmpout,preop2);
787: strcat(tmpout,fileres);
788: return tmpout;
789: }
790:
1.53 brouard 791: /***************** f1dim *************************/
792: extern int ncom;
793: extern double *pcom,*xicom;
794: extern double (*nrfunc)(double []);
795:
796: double f1dim(double x)
797: {
798: int j;
799: double f;
800: double *xt;
801:
802: xt=vector(1,ncom);
803: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
804: f=(*nrfunc)(xt);
805: free_vector(xt,1,ncom);
806: return f;
807: }
808:
809: /*****************brent *************************/
810: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
811: {
812: int iter;
813: double a,b,d,etemp;
814: double fu,fv,fw,fx;
815: double ftemp;
816: double p,q,r,tol1,tol2,u,v,w,x,xm;
817: double e=0.0;
818:
819: a=(ax < cx ? ax : cx);
820: b=(ax > cx ? ax : cx);
821: x=w=v=bx;
822: fw=fv=fx=(*f)(x);
823: for (iter=1;iter<=ITMAX;iter++) {
824: xm=0.5*(a+b);
825: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
826: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
827: printf(".");fflush(stdout);
828: fprintf(ficlog,".");fflush(ficlog);
829: #ifdef DEBUG
830: 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);
831: 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);
832: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
833: #endif
834: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
835: *xmin=x;
836: return fx;
837: }
838: ftemp=fu;
839: if (fabs(e) > tol1) {
840: r=(x-w)*(fx-fv);
841: q=(x-v)*(fx-fw);
842: p=(x-v)*q-(x-w)*r;
843: q=2.0*(q-r);
844: if (q > 0.0) p = -p;
845: q=fabs(q);
846: etemp=e;
847: e=d;
848: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
849: d=CGOLD*(e=(x >= xm ? a-x : b-x));
850: else {
851: d=p/q;
852: u=x+d;
853: if (u-a < tol2 || b-u < tol2)
854: d=SIGN(tol1,xm-x);
855: }
856: } else {
857: d=CGOLD*(e=(x >= xm ? a-x : b-x));
858: }
859: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
860: fu=(*f)(u);
861: if (fu <= fx) {
862: if (u >= x) a=x; else b=x;
863: SHFT(v,w,x,u)
864: SHFT(fv,fw,fx,fu)
865: } else {
866: if (u < x) a=u; else b=u;
867: if (fu <= fw || w == x) {
868: v=w;
869: w=u;
870: fv=fw;
871: fw=fu;
872: } else if (fu <= fv || v == x || v == w) {
873: v=u;
874: fv=fu;
875: }
876: }
877: }
878: nrerror("Too many iterations in brent");
879: *xmin=x;
880: return fx;
881: }
882:
883: /****************** mnbrak ***********************/
884:
885: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
886: double (*func)(double))
887: {
888: double ulim,u,r,q, dum;
889: double fu;
890:
891: *fa=(*func)(*ax);
892: *fb=(*func)(*bx);
893: if (*fb > *fa) {
894: SHFT(dum,*ax,*bx,dum)
895: SHFT(dum,*fb,*fa,dum)
896: }
897: *cx=(*bx)+GOLD*(*bx-*ax);
898: *fc=(*func)(*cx);
899: while (*fb > *fc) {
900: r=(*bx-*ax)*(*fb-*fc);
901: q=(*bx-*cx)*(*fb-*fa);
902: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
903: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
904: ulim=(*bx)+GLIMIT*(*cx-*bx);
905: if ((*bx-u)*(u-*cx) > 0.0) {
906: fu=(*func)(u);
907: } else if ((*cx-u)*(u-ulim) > 0.0) {
908: fu=(*func)(u);
909: if (fu < *fc) {
910: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
911: SHFT(*fb,*fc,fu,(*func)(u))
912: }
913: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
914: u=ulim;
915: fu=(*func)(u);
916: } else {
917: u=(*cx)+GOLD*(*cx-*bx);
918: fu=(*func)(u);
919: }
920: SHFT(*ax,*bx,*cx,u)
921: SHFT(*fa,*fb,*fc,fu)
922: }
923: }
924:
925: /*************** linmin ************************/
926:
927: int ncom;
928: double *pcom,*xicom;
929: double (*nrfunc)(double []);
930:
931: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
932: {
933: double brent(double ax, double bx, double cx,
934: double (*f)(double), double tol, double *xmin);
935: double f1dim(double x);
936: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
937: double *fc, double (*func)(double));
938: int j;
939: double xx,xmin,bx,ax;
940: double fx,fb,fa;
941:
942: ncom=n;
943: pcom=vector(1,n);
944: xicom=vector(1,n);
945: nrfunc=func;
946: for (j=1;j<=n;j++) {
947: pcom[j]=p[j];
948: xicom[j]=xi[j];
949: }
950: ax=0.0;
951: xx=1.0;
952: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
953: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
954: #ifdef DEBUG
955: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
956: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
957: #endif
958: for (j=1;j<=n;j++) {
959: xi[j] *= xmin;
960: p[j] += xi[j];
961: }
962: free_vector(xicom,1,n);
963: free_vector(pcom,1,n);
964: }
965:
1.91 brouard 966: char *asc_diff_time(long time_sec, char ascdiff[])
967: {
968: long sec_left, days, hours, minutes;
969: days = (time_sec) / (60*60*24);
970: sec_left = (time_sec) % (60*60*24);
971: hours = (sec_left) / (60*60) ;
972: sec_left = (sec_left) %(60*60);
973: minutes = (sec_left) /60;
974: sec_left = (sec_left) % (60);
975: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
976: return ascdiff;
977: }
978:
1.53 brouard 979: /*************** powell ************************/
980: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
981: double (*func)(double []))
982: {
983: void linmin(double p[], double xi[], int n, double *fret,
984: double (*func)(double []));
985: int i,ibig,j;
986: double del,t,*pt,*ptt,*xit;
987: double fp,fptt;
988: double *xits;
1.91 brouard 989: int niterf, itmp;
990:
1.53 brouard 991: pt=vector(1,n);
992: ptt=vector(1,n);
993: xit=vector(1,n);
994: xits=vector(1,n);
995: *fret=(*func)(p);
996: for (j=1;j<=n;j++) pt[j]=p[j];
997: for (*iter=1;;++(*iter)) {
998: fp=(*fret);
999: ibig=0;
1000: del=0.0;
1.91 brouard 1001: last_time=curr_time;
1002: (void) gettimeofday(&curr_time,&tzp);
1003: 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);
1.124 ! lievre 1004: 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); fflush(ficlog);
! 1005: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1.98 brouard 1006: for (i=1;i<=n;i++) {
1.53 brouard 1007: printf(" %d %.12f",i, p[i]);
1.76 brouard 1008: fprintf(ficlog," %d %.12lf",i, p[i]);
1009: fprintf(ficrespow," %.12lf", p[i]);
1010: }
1.53 brouard 1011: printf("\n");
1012: fprintf(ficlog,"\n");
1.91 brouard 1013: fprintf(ficrespow,"\n");fflush(ficrespow);
1014: if(*iter <=3){
1015: tm = *localtime(&curr_time.tv_sec);
1.101 brouard 1016: strcpy(strcurr,asctime(&tm));
1.92 brouard 1017: /* asctime_r(&tm,strcurr); */
1.101 brouard 1018: forecast_time=curr_time;
1.91 brouard 1019: itmp = strlen(strcurr);
1.101 brouard 1020: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.91 brouard 1021: strcurr[itmp-1]='\0';
1022: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1023: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1024: for(niterf=10;niterf<=30;niterf+=10){
1025: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1026: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 1027: /* asctime_r(&tmf,strfor); */
1028: strcpy(strfor,asctime(&tmf));
1.91 brouard 1029: itmp = strlen(strfor);
1030: if(strfor[itmp-1]=='\n')
1031: strfor[itmp-1]='\0';
1.101 brouard 1032: 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);
1033: 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 1034: }
1035: }
1.53 brouard 1036: for (i=1;i<=n;i++) {
1037: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1038: fptt=(*fret);
1039: #ifdef DEBUG
1040: printf("fret=%lf \n",*fret);
1041: fprintf(ficlog,"fret=%lf \n",*fret);
1042: #endif
1043: printf("%d",i);fflush(stdout);
1044: fprintf(ficlog,"%d",i);fflush(ficlog);
1045: linmin(p,xit,n,fret,func);
1046: if (fabs(fptt-(*fret)) > del) {
1047: del=fabs(fptt-(*fret));
1048: ibig=i;
1049: }
1050: #ifdef DEBUG
1051: printf("%d %.12e",i,(*fret));
1052: fprintf(ficlog,"%d %.12e",i,(*fret));
1053: for (j=1;j<=n;j++) {
1054: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1055: printf(" x(%d)=%.12e",j,xit[j]);
1056: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1057: }
1058: for(j=1;j<=n;j++) {
1059: printf(" p=%.12e",p[j]);
1060: fprintf(ficlog," p=%.12e",p[j]);
1061: }
1062: printf("\n");
1063: fprintf(ficlog,"\n");
1064: #endif
1065: }
1066: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1067: #ifdef DEBUG
1068: int k[2],l;
1069: k[0]=1;
1070: k[1]=-1;
1071: printf("Max: %.12e",(*func)(p));
1072: fprintf(ficlog,"Max: %.12e",(*func)(p));
1073: for (j=1;j<=n;j++) {
1074: printf(" %.12e",p[j]);
1075: fprintf(ficlog," %.12e",p[j]);
1076: }
1077: printf("\n");
1078: fprintf(ficlog,"\n");
1079: for(l=0;l<=1;l++) {
1080: for (j=1;j<=n;j++) {
1081: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1082: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1083: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1084: }
1085: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1086: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1087: }
1088: #endif
1089:
1090:
1091: free_vector(xit,1,n);
1092: free_vector(xits,1,n);
1093: free_vector(ptt,1,n);
1094: free_vector(pt,1,n);
1095: return;
1096: }
1097: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1098: for (j=1;j<=n;j++) {
1099: ptt[j]=2.0*p[j]-pt[j];
1100: xit[j]=p[j]-pt[j];
1101: pt[j]=p[j];
1102: }
1103: fptt=(*func)(ptt);
1104: if (fptt < fp) {
1105: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1106: if (t < 0.0) {
1107: linmin(p,xit,n,fret,func);
1108: for (j=1;j<=n;j++) {
1109: xi[j][ibig]=xi[j][n];
1110: xi[j][n]=xit[j];
1111: }
1112: #ifdef DEBUG
1113: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1114: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1115: for(j=1;j<=n;j++){
1116: printf(" %.12e",xit[j]);
1117: fprintf(ficlog," %.12e",xit[j]);
1118: }
1119: printf("\n");
1120: fprintf(ficlog,"\n");
1121: #endif
1.54 brouard 1122: }
1.53 brouard 1123: }
1124: }
1125: }
1126:
1.117 brouard 1127: /**** Prevalence limit (stable or period prevalence) ****************/
1.53 brouard 1128:
1129: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1130: {
1131: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1132: matrix by transitions matrix until convergence is reached */
1133:
1134: int i, ii,j,k;
1135: double min, max, maxmin, maxmax,sumnew=0.;
1136: double **matprod2();
1137: double **out, cov[NCOVMAX], **pmij();
1138: double **newm;
1139: double agefin, delaymax=50 ; /* Max number of years to converge */
1140:
1141: for (ii=1;ii<=nlstate+ndeath;ii++)
1142: for (j=1;j<=nlstate+ndeath;j++){
1143: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1144: }
1145:
1146: cov[1]=1.;
1147:
1148: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1149: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1150: newm=savm;
1151: /* Covariates have to be included here again */
1152: cov[2]=agefin;
1153:
1154: for (k=1; k<=cptcovn;k++) {
1155: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1156: /* 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]]);*/
1157: }
1158: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1159: for (k=1; k<=cptcovprod;k++)
1160: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1161:
1162: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1163: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1164: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1165: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1166:
1167: savm=oldm;
1168: oldm=newm;
1169: maxmax=0.;
1170: for(j=1;j<=nlstate;j++){
1171: min=1.;
1172: max=0.;
1173: for(i=1; i<=nlstate; i++) {
1174: sumnew=0;
1175: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1176: prlim[i][j]= newm[i][j]/(1-sumnew);
1177: max=FMAX(max,prlim[i][j]);
1178: min=FMIN(min,prlim[i][j]);
1179: }
1180: maxmin=max-min;
1181: maxmax=FMAX(maxmax,maxmin);
1182: }
1183: if(maxmax < ftolpl){
1184: return prlim;
1185: }
1186: }
1187: }
1188:
1189: /*************** transition probabilities ***************/
1190:
1191: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1192: {
1193: double s1, s2;
1194: /*double t34;*/
1195: int i,j,j1, nc, ii, jj;
1196:
1197: for(i=1; i<= nlstate; i++){
1.99 brouard 1198: for(j=1; j<i;j++){
1199: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1200: /*s2 += param[i][j][nc]*cov[nc];*/
1201: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1202: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1203: }
1204: ps[i][j]=s2;
1205: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1206: }
1207: for(j=i+1; j<=nlstate+ndeath;j++){
1208: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1209: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1210: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1211: }
1212: ps[i][j]=s2;
1.53 brouard 1213: }
1214: }
1215: /*ps[3][2]=1;*/
1.99 brouard 1216:
1217: for(i=1; i<= nlstate; i++){
1218: s1=0;
1219: for(j=1; j<i; j++)
1220: s1+=exp(ps[i][j]);
1221: for(j=i+1; j<=nlstate+ndeath; j++)
1222: s1+=exp(ps[i][j]);
1223: ps[i][i]=1./(s1+1.);
1224: for(j=1; j<i; j++)
1225: ps[i][j]= exp(ps[i][j])*ps[i][i];
1226: for(j=i+1; j<=nlstate+ndeath; j++)
1227: ps[i][j]= exp(ps[i][j])*ps[i][i];
1228: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1229: } /* end i */
1230:
1231: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1232: for(jj=1; jj<= nlstate+ndeath; jj++){
1233: ps[ii][jj]=0;
1234: ps[ii][ii]=1;
1235: }
1.53 brouard 1236: }
1.99 brouard 1237:
1.53 brouard 1238:
1.99 brouard 1239: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1240: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1241: /* printf("ddd %lf ",ps[ii][jj]); */
1242: /* } */
1243: /* printf("\n "); */
1244: /* } */
1245: /* printf("\n ");printf("%lf ",cov[2]); */
1246: /*
1247: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1248: goto end;*/
1.53 brouard 1249: return ps;
1250: }
1251:
1252: /**************** Product of 2 matrices ******************/
1253:
1254: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1255: {
1256: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1257: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1258: /* in, b, out are matrice of pointers which should have been initialized
1259: before: only the contents of out is modified. The function returns
1260: a pointer to pointers identical to out */
1261: long i, j, k;
1262: for(i=nrl; i<= nrh; i++)
1263: for(k=ncolol; k<=ncoloh; k++)
1264: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1265: out[i][k] +=in[i][j]*b[j][k];
1266:
1267: return out;
1268: }
1269:
1270:
1271: /************* Higher Matrix Product ***************/
1272:
1273: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1274: {
1.66 brouard 1275: /* Computes the transition matrix starting at age 'age' over
1276: 'nhstepm*hstepm*stepm' months (i.e. until
1277: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1278: nhstepm*hstepm matrices.
1.53 brouard 1279: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1280: (typically every 2 years instead of every month which is too big
1281: for the memory).
1.53 brouard 1282: Model is determined by parameters x and covariates have to be
1283: included manually here.
1284:
1285: */
1286:
1287: int i, j, d, h, k;
1288: double **out, cov[NCOVMAX];
1289: double **newm;
1290:
1291: /* Hstepm could be zero and should return the unit matrix */
1292: for (i=1;i<=nlstate+ndeath;i++)
1293: for (j=1;j<=nlstate+ndeath;j++){
1294: oldm[i][j]=(i==j ? 1.0 : 0.0);
1295: po[i][j][0]=(i==j ? 1.0 : 0.0);
1296: }
1297: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1298: for(h=1; h <=nhstepm; h++){
1299: for(d=1; d <=hstepm; d++){
1300: newm=savm;
1301: /* Covariates have to be included here again */
1302: cov[1]=1.;
1303: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1304: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1305: for (k=1; k<=cptcovage;k++)
1306: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1307: for (k=1; k<=cptcovprod;k++)
1308: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1309:
1310:
1311: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1312: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1313: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1314: pmij(pmmij,cov,ncovmodel,x,nlstate));
1315: savm=oldm;
1316: oldm=newm;
1317: }
1318: for(i=1; i<=nlstate+ndeath; i++)
1319: for(j=1;j<=nlstate+ndeath;j++) {
1320: po[i][j][h]=newm[i][j];
1321: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1322: */
1323: }
1324: } /* end h */
1325: return po;
1326: }
1327:
1328:
1329: /*************** log-likelihood *************/
1330: double func( double *x)
1331: {
1332: int i, ii, j, k, mi, d, kk;
1333: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1334: double **out;
1335: double sw; /* Sum of weights */
1336: double lli; /* Individual log likelihood */
1.59 brouard 1337: int s1, s2;
1.68 lievre 1338: double bbh, survp;
1.53 brouard 1339: long ipmx;
1340: /*extern weight */
1341: /* We are differentiating ll according to initial status */
1342: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1343: /*for(i=1;i<imx;i++)
1344: printf(" %d\n",s[4][i]);
1345: */
1346: cov[1]=1.;
1347:
1348: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1349:
1350: if(mle==1){
1351: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1352: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1353: for(mi=1; mi<= wav[i]-1; mi++){
1354: for (ii=1;ii<=nlstate+ndeath;ii++)
1355: for (j=1;j<=nlstate+ndeath;j++){
1356: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1357: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1358: }
1359: for(d=0; d<dh[mi][i]; d++){
1360: newm=savm;
1361: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1362: for (kk=1; kk<=cptcovage;kk++) {
1363: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1364: }
1365: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1366: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1367: savm=oldm;
1368: oldm=newm;
1369: } /* end mult */
1.53 brouard 1370:
1.61 brouard 1371: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1.101 brouard 1372: /* But now since version 0.9 we anticipate for bias at large stepm.
1.61 brouard 1373: * If stepm is larger than one month (smallest stepm) and if the exact delay
1374: * (in months) between two waves is not a multiple of stepm, we rounded to
1375: * the nearest (and in case of equal distance, to the lowest) interval but now
1376: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1.101 brouard 1377: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1.61 brouard 1378: * probability in order to take into account the bias as a fraction of the way
1.101 brouard 1379: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1.61 brouard 1380: * -stepm/2 to stepm/2 .
1381: * For stepm=1 the results are the same as for previous versions of Imach.
1382: * For stepm > 1 the results are less biased than in previous versions.
1383: */
1384: s1=s[mw[mi][i]][i];
1385: s2=s[mw[mi+1][i]][i];
1.64 lievre 1386: bbh=(double)bh[mi][i]/(double)stepm;
1.101 brouard 1387: /* bias bh is positive if real duration
1.64 lievre 1388: * is higher than the multiple of stepm and negative otherwise.
1389: */
1390: /* 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 1391: if( s2 > nlstate){
1.104 lievre 1392: /* i.e. if s2 is a death state and if the date of death is known
1393: then the contribution to the likelihood is the probability to
1394: die between last step unit time and current step unit time,
1395: which is also equal to probability to die before dh
1.101 brouard 1396: minus probability to die before dh-stepm .
1.71 brouard 1397: In version up to 0.92 likelihood was computed
1398: as if date of death was unknown. Death was treated as any other
1399: health state: the date of the interview describes the actual state
1400: and not the date of a change in health state. The former idea was
1401: to consider that at each interview the state was recorded
1402: (healthy, disable or death) and IMaCh was corrected; but when we
1403: introduced the exact date of death then we should have modified
1404: the contribution of an exact death to the likelihood. This new
1405: contribution is smaller and very dependent of the step unit
1406: stepm. It is no more the probability to die between last interview
1407: and month of death but the probability to survive from last
1408: interview up to one month before death multiplied by the
1409: probability to die within a month. Thanks to Chris
1410: Jackson for correcting this bug. Former versions increased
1411: mortality artificially. The bad side is that we add another loop
1412: which slows down the processing. The difference can be up to 10%
1413: lower mortality.
1414: */
1415: lli=log(out[s1][s2] - savm[s1][s2]);
1.104 lievre 1416:
1417:
1418: } else if (s2==-2) {
1419: for (j=1,survp=0. ; j<=nlstate; j++)
1.120 lievre 1420: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1421: /*survp += out[s1][j]; */
1.119 brouard 1422: lli= log(survp);
1.104 lievre 1423: }
1.105 lievre 1424:
1.120 lievre 1425: else if (s2==-4) {
1426: for (j=3,survp=0. ; j<=nlstate; j++)
1427: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1428: lli= log(survp);
1429: }
1430:
1431: else if (s2==-5) {
1432: for (j=1,survp=0. ; j<=2; j++)
1433: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1434: lli= log(survp);
1435: }
1.105 lievre 1436:
1.104 lievre 1437: else{
1.71 brouard 1438: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1439: /* 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 */
1440: }
1.64 lievre 1441: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1442: /*if(lli ==000.0)*/
1443: /*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 1444: ipmx +=1;
1.64 lievre 1445: sw += weight[i];
1446: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1447: } /* end of wave */
1448: } /* end of individual */
1449: } else if(mle==2){
1450: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1451: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1452: for(mi=1; mi<= wav[i]-1; mi++){
1453: for (ii=1;ii<=nlstate+ndeath;ii++)
1454: for (j=1;j<=nlstate+ndeath;j++){
1455: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1456: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1457: }
1458: for(d=0; d<=dh[mi][i]; d++){
1459: newm=savm;
1460: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1461: for (kk=1; kk<=cptcovage;kk++) {
1462: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1463: }
1464: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1465: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1466: savm=oldm;
1467: oldm=newm;
1468: } /* end mult */
1469:
1470: s1=s[mw[mi][i]][i];
1471: s2=s[mw[mi+1][i]][i];
1472: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1473: 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 1474: ipmx +=1;
1475: sw += weight[i];
1476: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1477: } /* end of wave */
1478: } /* end of individual */
1479: } else if(mle==3){ /* exponential inter-extrapolation */
1480: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1481: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1482: for(mi=1; mi<= wav[i]-1; mi++){
1483: for (ii=1;ii<=nlstate+ndeath;ii++)
1484: for (j=1;j<=nlstate+ndeath;j++){
1485: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1486: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1487: }
1488: for(d=0; d<dh[mi][i]; d++){
1489: newm=savm;
1490: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1491: for (kk=1; kk<=cptcovage;kk++) {
1492: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1493: }
1494: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1495: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1496: savm=oldm;
1497: oldm=newm;
1498: } /* end mult */
1499:
1500: s1=s[mw[mi][i]][i];
1501: s2=s[mw[mi+1][i]][i];
1502: bbh=(double)bh[mi][i]/(double)stepm;
1503: 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 1504: ipmx +=1;
1505: sw += weight[i];
1506: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1507: } /* end of wave */
1508: } /* end of individual */
1.84 brouard 1509: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 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:
1.84 brouard 1531: s1=s[mw[mi][i]][i];
1532: s2=s[mw[mi+1][i]][i];
1533: if( s2 > nlstate){
1534: lli=log(out[s1][s2] - savm[s1][s2]);
1535: }else{
1536: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1537: }
1538: ipmx +=1;
1539: sw += weight[i];
1540: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1541: /* 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 1542: } /* end of wave */
1543: } /* end of individual */
1544: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1545: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1546: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1547: for(mi=1; mi<= wav[i]-1; mi++){
1548: for (ii=1;ii<=nlstate+ndeath;ii++)
1549: for (j=1;j<=nlstate+ndeath;j++){
1550: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1551: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1552: }
1553: for(d=0; d<dh[mi][i]; d++){
1554: newm=savm;
1555: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1556: for (kk=1; kk<=cptcovage;kk++) {
1557: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1558: }
1559:
1560: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1561: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1562: savm=oldm;
1563: oldm=newm;
1564: } /* end mult */
1565:
1566: s1=s[mw[mi][i]][i];
1567: s2=s[mw[mi+1][i]][i];
1.61 brouard 1568: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1569: ipmx +=1;
1570: sw += weight[i];
1571: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1572: /*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 1573: } /* end of wave */
1574: } /* end of individual */
1575: } /* End of if */
1.53 brouard 1576: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1577: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1578: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1579: return -l;
1580: }
1581:
1582: /*************** log-likelihood *************/
1583: double funcone( double *x)
1584: {
1.87 brouard 1585: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1586: int i, ii, j, k, mi, d, kk;
1587: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1588: double **out;
1589: double lli; /* Individual log likelihood */
1.87 brouard 1590: double llt;
1.85 brouard 1591: int s1, s2;
1592: double bbh, survp;
1593: /*extern weight */
1594: /* We are differentiating ll according to initial status */
1595: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1596: /*for(i=1;i<imx;i++)
1597: printf(" %d\n",s[4][i]);
1598: */
1599: cov[1]=1.;
1600:
1601: for(k=1; k<=nlstate; k++) ll[k]=0.;
1602:
1603: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1604: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1605: for(mi=1; mi<= wav[i]-1; mi++){
1606: for (ii=1;ii<=nlstate+ndeath;ii++)
1607: for (j=1;j<=nlstate+ndeath;j++){
1608: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1609: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1610: }
1611: for(d=0; d<dh[mi][i]; d++){
1612: newm=savm;
1613: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1614: for (kk=1; kk<=cptcovage;kk++) {
1615: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1616: }
1617: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1618: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1619: savm=oldm;
1620: oldm=newm;
1621: } /* end mult */
1622:
1623: s1=s[mw[mi][i]][i];
1624: s2=s[mw[mi+1][i]][i];
1625: bbh=(double)bh[mi][i]/(double)stepm;
1626: /* bias is positive if real duration
1627: * is higher than the multiple of stepm and negative otherwise.
1628: */
1629: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1630: lli=log(out[s1][s2] - savm[s1][s2]);
1.119 brouard 1631: } else if (s2==-2) {
1632: for (j=1,survp=0. ; j<=nlstate; j++)
1.120 lievre 1633: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1.119 brouard 1634: lli= log(survp);
1635: }else if (mle==1){
1.85 brouard 1636: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1637: } else if(mle==2){
1638: 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 */
1639: } else if(mle==3){ /* exponential inter-extrapolation */
1640: 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 */
1641: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1642: lli=log(out[s1][s2]); /* Original formula */
1643: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1644: lli=log(out[s1][s2]); /* Original formula */
1645: } /* End of if */
1646: ipmx +=1;
1647: sw += weight[i];
1648: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1649: /* 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]); */
1650: if(globpr){
1.119 brouard 1651: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1652: %11.6f %11.6f %11.6f ", \
1.86 brouard 1653: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1654: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1655: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1656: llt +=ll[k]*gipmx/gsw;
1657: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1658: }
1659: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1660: }
1661: } /* end of wave */
1662: } /* end of individual */
1663: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1664: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1665: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1666: if(globpr==0){ /* First time we count the contributions and weights */
1667: gipmx=ipmx;
1668: gsw=sw;
1669: }
1.53 brouard 1670: return -l;
1671: }
1672:
1673:
1.94 brouard 1674: /*************** function likelione ***********/
1.87 brouard 1675: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1676: {
1.87 brouard 1677: /* This routine should help understanding what is done with
1678: the selection of individuals/waves and
1.85 brouard 1679: to check the exact contribution to the likelihood.
1680: Plotting could be done.
1681: */
1682: int k;
1.87 brouard 1683:
1.88 brouard 1684: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1685: strcpy(fileresilk,"ilk");
1686: strcat(fileresilk,fileres);
1687: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1688: printf("Problem with resultfile: %s\n", fileresilk);
1689: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1690: }
1.87 brouard 1691: 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 1692: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1693: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1694: for(k=1; k<=nlstate; k++)
1.87 brouard 1695: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1696: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1697: }
1698:
1699: *fretone=(*funcone)(p);
1.87 brouard 1700: if(*globpri !=0){
1.85 brouard 1701: fclose(ficresilk);
1.88 brouard 1702: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1703: fflush(fichtm);
1704: }
1.85 brouard 1705: return;
1706: }
1707:
1.88 brouard 1708:
1.53 brouard 1709: /*********** Maximum Likelihood Estimation ***************/
1710:
1711: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1712: {
1713: int i,j, iter;
1.74 brouard 1714: double **xi;
1.53 brouard 1715: double fret;
1.85 brouard 1716: double fretone; /* Only one call to likelihood */
1.98 brouard 1717: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1718: xi=matrix(1,npar,1,npar);
1719: for (i=1;i<=npar;i++)
1720: for (j=1;j<=npar;j++)
1721: xi[i][j]=(i==j ? 1.0 : 0.0);
1722: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1723: strcpy(filerespow,"pow");
1724: strcat(filerespow,fileres);
1725: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1726: printf("Problem with resultfile: %s\n", filerespow);
1727: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1728: }
1729: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1730: for (i=1;i<=nlstate;i++)
1731: for(j=1;j<=nlstate+ndeath;j++)
1732: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1733: fprintf(ficrespow,"\n");
1.85 brouard 1734:
1.53 brouard 1735: powell(p,xi,npar,ftol,&iter,&fret,func);
1736:
1.115 brouard 1737: free_matrix(xi,1,npar,1,npar);
1.76 brouard 1738: fclose(ficrespow);
1739: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1740: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1741: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1742:
1743: }
1744:
1745: /**** Computes Hessian and covariance matrix ***/
1746: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1747: {
1748: double **a,**y,*x,pd;
1749: double **hess;
1750: int i, j,jk;
1751: int *indx;
1752:
1.98 brouard 1753: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1754: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1755: void lubksb(double **a, int npar, int *indx, double b[]) ;
1756: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 brouard 1757: double gompertz(double p[]);
1.53 brouard 1758: hess=matrix(1,npar,1,npar);
1759:
1760: printf("\nCalculation of the hessian matrix. Wait...\n");
1761: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1762: for (i=1;i<=npar;i++){
1763: printf("%d",i);fflush(stdout);
1764: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 brouard 1765:
1766: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1767:
1768: /* printf(" %f ",p[i]);
1769: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1770: }
1771:
1772: for (i=1;i<=npar;i++) {
1773: for (j=1;j<=npar;j++) {
1774: if (j>i) {
1775: printf(".%d%d",i,j);fflush(stdout);
1776: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 brouard 1777: hess[i][j]=hessij(p,delti,i,j,func,npar);
1778:
1.53 brouard 1779: hess[j][i]=hess[i][j];
1780: /*printf(" %lf ",hess[i][j]);*/
1781: }
1782: }
1783: }
1784: printf("\n");
1785: fprintf(ficlog,"\n");
1786:
1787: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1788: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1789:
1790: a=matrix(1,npar,1,npar);
1791: y=matrix(1,npar,1,npar);
1792: x=vector(1,npar);
1793: indx=ivector(1,npar);
1794: for (i=1;i<=npar;i++)
1795: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1796: ludcmp(a,npar,indx,&pd);
1797:
1798: for (j=1;j<=npar;j++) {
1799: for (i=1;i<=npar;i++) x[i]=0;
1800: x[j]=1;
1801: lubksb(a,npar,indx,x);
1802: for (i=1;i<=npar;i++){
1803: matcov[i][j]=x[i];
1804: }
1805: }
1806:
1807: printf("\n#Hessian matrix#\n");
1808: fprintf(ficlog,"\n#Hessian matrix#\n");
1809: for (i=1;i<=npar;i++) {
1810: for (j=1;j<=npar;j++) {
1811: printf("%.3e ",hess[i][j]);
1812: fprintf(ficlog,"%.3e ",hess[i][j]);
1813: }
1814: printf("\n");
1815: fprintf(ficlog,"\n");
1816: }
1817:
1818: /* Recompute Inverse */
1819: for (i=1;i<=npar;i++)
1820: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1821: ludcmp(a,npar,indx,&pd);
1822:
1823: /* printf("\n#Hessian matrix recomputed#\n");
1824:
1825: for (j=1;j<=npar;j++) {
1826: for (i=1;i<=npar;i++) x[i]=0;
1827: x[j]=1;
1828: lubksb(a,npar,indx,x);
1829: for (i=1;i<=npar;i++){
1830: y[i][j]=x[i];
1831: printf("%.3e ",y[i][j]);
1832: fprintf(ficlog,"%.3e ",y[i][j]);
1833: }
1834: printf("\n");
1835: fprintf(ficlog,"\n");
1836: }
1837: */
1838:
1839: free_matrix(a,1,npar,1,npar);
1840: free_matrix(y,1,npar,1,npar);
1841: free_vector(x,1,npar);
1842: free_ivector(indx,1,npar);
1843: free_matrix(hess,1,npar,1,npar);
1844:
1845:
1846: }
1847:
1848: /*************** hessian matrix ****************/
1.98 brouard 1849: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1850: {
1851: int i;
1852: int l=1, lmax=20;
1853: double k1,k2;
1854: double p2[NPARMAX+1];
1855: double res;
1.98 brouard 1856: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1857: double fx;
1858: int k=0,kmax=10;
1859: double l1;
1860:
1861: fx=func(x);
1862: for (i=1;i<=npar;i++) p2[i]=x[i];
1863: for(l=0 ; l <=lmax; l++){
1864: l1=pow(10,l);
1865: delts=delt;
1866: for(k=1 ; k <kmax; k=k+1){
1867: delt = delta*(l1*k);
1868: p2[theta]=x[theta] +delt;
1869: k1=func(p2)-fx;
1870: p2[theta]=x[theta]-delt;
1871: k2=func(p2)-fx;
1872: /*res= (k1-2.0*fx+k2)/delt/delt; */
1873: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1874:
1875: #ifdef DEBUG
1876: 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);
1877: 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);
1878: #endif
1879: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1880: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1881: k=kmax;
1882: }
1883: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1884: k=kmax; l=lmax*10.;
1885: }
1886: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1887: delts=delt;
1888: }
1889: }
1890: }
1891: delti[theta]=delts;
1892: return res;
1893:
1894: }
1895:
1.98 brouard 1896: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1897: {
1898: int i;
1899: int l=1, l1, lmax=20;
1900: double k1,k2,k3,k4,res,fx;
1901: double p2[NPARMAX+1];
1902: int k;
1903:
1904: fx=func(x);
1905: for (k=1; k<=2; k++) {
1906: for (i=1;i<=npar;i++) p2[i]=x[i];
1907: p2[thetai]=x[thetai]+delti[thetai]/k;
1908: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1909: k1=func(p2)-fx;
1910:
1911: p2[thetai]=x[thetai]+delti[thetai]/k;
1912: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1913: k2=func(p2)-fx;
1914:
1915: p2[thetai]=x[thetai]-delti[thetai]/k;
1916: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1917: k3=func(p2)-fx;
1918:
1919: p2[thetai]=x[thetai]-delti[thetai]/k;
1920: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1921: k4=func(p2)-fx;
1922: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1923: #ifdef DEBUG
1924: 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);
1925: 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);
1926: #endif
1927: }
1928: return res;
1929: }
1930:
1931: /************** Inverse of matrix **************/
1932: void ludcmp(double **a, int n, int *indx, double *d)
1933: {
1934: int i,imax,j,k;
1935: double big,dum,sum,temp;
1936: double *vv;
1937:
1938: vv=vector(1,n);
1939: *d=1.0;
1940: for (i=1;i<=n;i++) {
1941: big=0.0;
1942: for (j=1;j<=n;j++)
1943: if ((temp=fabs(a[i][j])) > big) big=temp;
1944: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1945: vv[i]=1.0/big;
1946: }
1947: for (j=1;j<=n;j++) {
1948: for (i=1;i<j;i++) {
1949: sum=a[i][j];
1950: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1951: a[i][j]=sum;
1952: }
1953: big=0.0;
1954: for (i=j;i<=n;i++) {
1955: sum=a[i][j];
1956: for (k=1;k<j;k++)
1957: sum -= a[i][k]*a[k][j];
1958: a[i][j]=sum;
1959: if ( (dum=vv[i]*fabs(sum)) >= big) {
1960: big=dum;
1961: imax=i;
1962: }
1963: }
1964: if (j != imax) {
1965: for (k=1;k<=n;k++) {
1966: dum=a[imax][k];
1967: a[imax][k]=a[j][k];
1968: a[j][k]=dum;
1969: }
1970: *d = -(*d);
1971: vv[imax]=vv[j];
1972: }
1973: indx[j]=imax;
1974: if (a[j][j] == 0.0) a[j][j]=TINY;
1975: if (j != n) {
1976: dum=1.0/(a[j][j]);
1977: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1978: }
1979: }
1980: free_vector(vv,1,n); /* Doesn't work */
1981: ;
1982: }
1983:
1984: void lubksb(double **a, int n, int *indx, double b[])
1985: {
1986: int i,ii=0,ip,j;
1987: double sum;
1988:
1989: for (i=1;i<=n;i++) {
1990: ip=indx[i];
1991: sum=b[ip];
1992: b[ip]=b[i];
1993: if (ii)
1994: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1995: else if (sum) ii=i;
1996: b[i]=sum;
1997: }
1998: for (i=n;i>=1;i--) {
1999: sum=b[i];
2000: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2001: b[i]=sum/a[i][i];
2002: }
2003: }
2004:
1.117 brouard 2005: void pstamp(FILE *fichier)
2006: {
2007: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2008: }
2009:
1.53 brouard 2010: /************ Frequencies ********************/
1.105 lievre 2011: 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 2012: { /* Some frequencies */
2013:
2014: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
2015: int first;
2016: double ***freq; /* Frequencies */
1.73 lievre 2017: double *pp, **prop;
2018: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 2019: char fileresp[FILENAMELENGTH];
2020:
2021: pp=vector(1,nlstate);
1.74 brouard 2022: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 2023: strcpy(fileresp,"p");
2024: strcat(fileresp,fileres);
2025: if((ficresp=fopen(fileresp,"w"))==NULL) {
2026: printf("Problem with prevalence resultfile: %s\n", fileresp);
2027: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2028: exit(0);
2029: }
1.105 lievre 2030: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 2031: j1=0;
2032:
2033: j=cptcoveff;
2034: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2035:
2036: first=1;
2037:
2038: for(k1=1; k1<=j;k1++){
2039: for(i1=1; i1<=ncodemax[k1];i1++){
2040: j1++;
2041: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2042: scanf("%d", i);*/
1.105 lievre 2043: for (i=-5; i<=nlstate+ndeath; i++)
2044: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.74 brouard 2045: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 2046: freq[i][jk][m]=0;
1.73 lievre 2047:
2048: for (i=1; i<=nlstate; i++)
1.74 brouard 2049: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 2050: prop[i][m]=0;
1.53 brouard 2051:
2052: dateintsum=0;
2053: k2cpt=0;
2054: for (i=1; i<=imx; i++) {
2055: bool=1;
2056: if (cptcovn>0) {
2057: for (z1=1; z1<=cptcoveff; z1++)
2058: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2059: bool=0;
2060: }
1.58 lievre 2061: if (bool==1){
1.53 brouard 2062: for(m=firstpass; m<=lastpass; m++){
2063: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 2064: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 2065: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2066: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 2067: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 2068: if (m<lastpass) {
2069: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 2070: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 2071: }
2072:
1.74 brouard 2073: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 2074: dateintsum=dateintsum+k2;
2075: k2cpt++;
2076: }
1.84 brouard 2077: /*}*/
1.53 brouard 2078: }
2079: }
2080: }
2081:
1.84 brouard 2082: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.117 brouard 2083: pstamp(ficresp);
1.53 brouard 2084: if (cptcovn>0) {
2085: fprintf(ficresp, "\n#********** Variable ");
2086: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2087: fprintf(ficresp, "**********\n#");
2088: }
2089: for(i=1; i<=nlstate;i++)
2090: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2091: fprintf(ficresp, "\n");
2092:
1.74 brouard 2093: for(i=iagemin; i <= iagemax+3; i++){
2094: if(i==iagemax+3){
1.53 brouard 2095: fprintf(ficlog,"Total");
1.124 ! lievre 2096: fprintf(fichtm,"<br>Total<br>");
1.53 brouard 2097: }else{
2098: if(first==1){
2099: first=0;
2100: printf("See log file for details...\n");
2101: }
2102: fprintf(ficlog,"Age %d", i);
2103: }
2104: for(jk=1; jk <=nlstate ; jk++){
2105: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2106: pp[jk] += freq[jk][m][i];
2107: }
2108: for(jk=1; jk <=nlstate ; jk++){
2109: for(m=-1, pos=0; m <=0 ; m++)
2110: pos += freq[jk][m][i];
2111: if(pp[jk]>=1.e-10){
2112: if(first==1){
2113: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2114: }
2115: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2116: }else{
2117: if(first==1)
2118: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2119: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2120: }
2121: }
2122:
2123: for(jk=1; jk <=nlstate ; jk++){
2124: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2125: pp[jk] += freq[jk][m][i];
1.73 lievre 2126: }
2127: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2128: pos += pp[jk];
2129: posprop += prop[jk][i];
1.53 brouard 2130: }
2131: for(jk=1; jk <=nlstate ; jk++){
2132: if(pos>=1.e-5){
2133: if(first==1)
2134: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2135: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2136: }else{
2137: if(first==1)
2138: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2139: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2140: }
1.74 brouard 2141: if( i <= iagemax){
1.53 brouard 2142: if(pos>=1.e-5){
1.73 lievre 2143: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 2144: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 2145: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2146: }
2147: else
1.73 lievre 2148: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 2149: }
2150: }
2151:
1.69 brouard 2152: for(jk=-1; jk <=nlstate+ndeath; jk++)
2153: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 2154: if(freq[jk][m][i] !=0 ) {
2155: if(first==1)
2156: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2157: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2158: }
1.74 brouard 2159: if(i <= iagemax)
1.53 brouard 2160: fprintf(ficresp,"\n");
2161: if(first==1)
2162: printf("Others in log...\n");
2163: fprintf(ficlog,"\n");
2164: }
2165: }
2166: }
2167: dateintmean=dateintsum/k2cpt;
2168:
2169: fclose(ficresp);
1.105 lievre 2170: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 2171: free_vector(pp,1,nlstate);
1.74 brouard 2172: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 2173: /* End of Freq */
2174: }
2175:
2176: /************ Prevalence ********************/
1.84 brouard 2177: 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 2178: {
2179: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2180: in each health status at the date of interview (if between dateprev1 and dateprev2).
2181: We still use firstpass and lastpass as another selection.
2182: */
1.53 brouard 2183:
2184: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2185: double ***freq; /* Frequencies */
1.73 lievre 2186: double *pp, **prop;
2187: double pos,posprop;
1.69 brouard 2188: double y2; /* in fractional years */
1.74 brouard 2189: int iagemin, iagemax;
1.53 brouard 2190:
1.74 brouard 2191: iagemin= (int) agemin;
2192: iagemax= (int) agemax;
2193: /*pp=vector(1,nlstate);*/
2194: prop=matrix(1,nlstate,iagemin,iagemax+3);
2195: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 2196: j1=0;
2197:
2198: j=cptcoveff;
2199: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2200:
2201: for(k1=1; k1<=j;k1++){
2202: for(i1=1; i1<=ncodemax[k1];i1++){
2203: j1++;
2204:
1.73 lievre 2205: for (i=1; i<=nlstate; i++)
1.74 brouard 2206: for(m=iagemin; m <= iagemax+3; m++)
2207: prop[i][m]=0.0;
1.53 brouard 2208:
1.69 brouard 2209: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2210: bool=1;
2211: if (cptcovn>0) {
2212: for (z1=1; z1<=cptcoveff; z1++)
2213: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2214: bool=0;
2215: }
2216: if (bool==1) {
1.69 brouard 2217: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2218: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2219: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2220: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2221: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2222: 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);
2223: if (s[m][i]>0 && s[m][i]<=nlstate) {
2224: /*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]]);*/
2225: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2226: prop[s[m][i]][iagemax+3] += weight[i];
2227: }
1.53 brouard 2228: }
1.69 brouard 2229: } /* end selection of waves */
1.53 brouard 2230: }
2231: }
1.74 brouard 2232: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2233:
1.74 brouard 2234: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2235: posprop += prop[jk][i];
2236: }
2237:
2238: for(jk=1; jk <=nlstate ; jk++){
2239: if( i <= iagemax){
2240: if(posprop>=1.e-5){
2241: probs[i][jk][j1]= prop[jk][i]/posprop;
2242: }
2243: }
2244: }/* end jk */
2245: }/* end i */
1.53 brouard 2246: } /* end i1 */
2247: } /* end k1 */
2248:
1.74 brouard 2249: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2250: /*free_vector(pp,1,nlstate);*/
2251: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2252: } /* End of prevalence */
1.53 brouard 2253:
2254: /************* Waves Concatenation ***************/
2255:
1.59 brouard 2256: 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 2257: {
2258: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2259: Death is a valid wave (if date is known).
2260: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2261: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2262: and mw[mi+1][i]. dh depends on stepm.
2263: */
2264:
2265: int i, mi, m;
2266: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2267: double sum=0., jmean=0.;*/
2268: int first;
2269: int j, k=0,jk, ju, jl;
2270: double sum=0.;
2271: first=0;
2272: jmin=1e+5;
2273: jmax=-1;
2274: jmean=0.;
2275: for(i=1; i<=imx; i++){
2276: mi=0;
2277: m=firstpass;
2278: while(s[m][i] <= nlstate){
1.105 lievre 2279: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
1.53 brouard 2280: mw[++mi][i]=m;
2281: if(m >=lastpass)
2282: break;
2283: else
2284: m++;
2285: }/* end while */
2286: if (s[m][i] > nlstate){
2287: mi++; /* Death is another wave */
2288: /* if(mi==0) never been interviewed correctly before death */
2289: /* Only death is a correct wave */
2290: mw[mi][i]=m;
2291: }
2292:
2293: wav[i]=mi;
2294: if(mi==0){
1.91 brouard 2295: nbwarn++;
1.53 brouard 2296: if(first==0){
1.111 brouard 2297: 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 2298: first=1;
2299: }
2300: if(first==1){
1.111 brouard 2301: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2302: }
2303: } /* end mi==0 */
1.77 brouard 2304: } /* End individuals */
1.53 brouard 2305:
2306: for(i=1; i<=imx; i++){
2307: for(mi=1; mi<wav[i];mi++){
2308: if (stepm <=0)
2309: dh[mi][i]=1;
2310: else{
1.77 brouard 2311: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2312: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2313: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2314: if(j==0) j=1; /* Survives at least one month after exam */
2315: else if(j<0){
1.91 brouard 2316: nberr++;
1.85 brouard 2317: 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 2318: j=1; /* Temporary Dangerous patch */
1.105 lievre 2319: 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 2320: 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 2321: 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 2322: }
2323: k=k+1;
1.110 brouard 2324: if (j >= jmax){
2325: jmax=j;
2326: ijmax=i;
2327: }
2328: if (j <= jmin){
2329: jmin=j;
2330: ijmin=i;
2331: }
1.85 brouard 2332: sum=sum+j;
2333: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2334: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2335: }
2336: }
2337: else{
2338: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.104 lievre 2339: /* 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]); */
2340:
1.53 brouard 2341: k=k+1;
1.110 brouard 2342: if (j >= jmax) {
2343: jmax=j;
2344: ijmax=i;
2345: }
2346: else if (j <= jmin){
2347: jmin=j;
2348: ijmin=i;
2349: }
1.53 brouard 2350: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2351: /*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 2352: if(j<0){
1.91 brouard 2353: nberr++;
1.85 brouard 2354: 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]);
2355: 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]);
2356: }
1.53 brouard 2357: sum=sum+j;
2358: }
2359: jk= j/stepm;
2360: jl= j -jk*stepm;
2361: ju= j -(jk+1)*stepm;
1.85 brouard 2362: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2363: if(jl==0){
2364: dh[mi][i]=jk;
2365: bh[mi][i]=0;
2366: }else{ /* We want a negative bias in order to only have interpolation ie
2367: * at the price of an extra matrix product in likelihood */
2368: dh[mi][i]=jk+1;
2369: bh[mi][i]=ju;
2370: }
2371: }else{
2372: if(jl <= -ju){
2373: dh[mi][i]=jk;
2374: bh[mi][i]=jl; /* bias is positive if real duration
2375: * is higher than the multiple of stepm and negative otherwise.
2376: */
2377: }
2378: else{
2379: dh[mi][i]=jk+1;
2380: bh[mi][i]=ju;
2381: }
2382: if(dh[mi][i]==0){
2383: dh[mi][i]=1; /* At least one step */
2384: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2385: /* 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 2386: }
1.85 brouard 2387: } /* end if mle */
2388: }
1.64 lievre 2389: } /* end wave */
1.53 brouard 2390: }
2391: jmean=sum/k;
1.110 brouard 2392: 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);
2393: 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 2394: }
2395:
2396: /*********** Tricode ****************************/
2397: void tricode(int *Tvar, int **nbcode, int imx)
2398: {
1.58 lievre 2399:
2400: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2401: int cptcode=0;
2402: cptcoveff=0;
2403:
1.58 lievre 2404: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2405: for (k=1; k<=7; k++) ncodemax[k]=0;
2406:
2407: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2408: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2409: modality*/
2410: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2411: Ndum[ij]++; /*store the modality */
1.53 brouard 2412: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2413: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2414: Tvar[j]. If V=sex and male is 0 and
2415: female is 1, then cptcode=1.*/
1.53 brouard 2416: }
2417:
2418: for (i=0; i<=cptcode; i++) {
1.58 lievre 2419: 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 2420: }
1.58 lievre 2421:
1.53 brouard 2422: ij=1;
2423: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2424: for (k=0; k<= maxncov; k++) {
1.53 brouard 2425: if (Ndum[k] != 0) {
2426: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2427: /* 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 2428:
2429: ij++;
2430: }
2431: if (ij > ncodemax[j]) break;
2432: }
2433: }
2434: }
2435:
1.58 lievre 2436: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2437:
1.58 lievre 2438: for (i=1; i<=ncovmodel-2; i++) {
1.104 lievre 2439: /* 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 2440: ij=Tvar[i];
1.58 lievre 2441: Ndum[ij]++;
1.53 brouard 2442: }
2443:
2444: ij=1;
1.58 lievre 2445: for (i=1; i<= maxncov; i++) {
1.53 brouard 2446: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2447: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2448: ij++;
2449: }
2450: }
2451:
1.58 lievre 2452: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2453: }
2454:
2455: /*********** Health Expectancies ****************/
2456:
1.117 brouard 2457: 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 2458:
2459: {
1.117 brouard 2460: /* Health expectancies, no variances */
2461: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
1.53 brouard 2462: double age, agelim, hf;
1.117 brouard 2463: double ***p3mat;
2464: double eip;
2465:
2466: pstamp(ficreseij);
2467: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2468: fprintf(ficreseij,"# Age");
2469: for(i=1; i<=nlstate;i++){
2470: for(j=1; j<=nlstate;j++){
2471: fprintf(ficreseij," e%1d%1d ",i,j);
2472: }
2473: fprintf(ficreseij," e%1d. ",i);
2474: }
2475: fprintf(ficreseij,"\n");
2476:
2477:
2478: if(estepm < stepm){
2479: printf ("Problem %d lower than %d\n",estepm, stepm);
2480: }
2481: else hstepm=estepm;
2482: /* We compute the life expectancy from trapezoids spaced every estepm months
2483: * This is mainly to measure the difference between two models: for example
2484: * if stepm=24 months pijx are given only every 2 years and by summing them
2485: * we are calculating an estimate of the Life Expectancy assuming a linear
2486: * progression in between and thus overestimating or underestimating according
2487: * to the curvature of the survival function. If, for the same date, we
2488: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2489: * to compare the new estimate of Life expectancy with the same linear
2490: * hypothesis. A more precise result, taking into account a more precise
2491: * curvature will be obtained if estepm is as small as stepm. */
2492:
2493: /* For example we decided to compute the life expectancy with the smallest unit */
2494: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2495: nhstepm is the number of hstepm from age to agelim
2496: nstepm is the number of stepm from age to agelin.
2497: Look at hpijx to understand the reason of that which relies in memory size
2498: and note for a fixed period like estepm months */
2499: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2500: survival function given by stepm (the optimization length). Unfortunately it
2501: means that if the survival funtion is printed only each two years of age and if
2502: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2503: results. So we changed our mind and took the option of the best precision.
2504: */
2505: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2506:
2507: agelim=AGESUP;
2508: /* nhstepm age range expressed in number of stepm */
2509: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2510: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2511: /* if (stepm >= YEARM) hstepm=1;*/
2512: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2513: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2514:
2515: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2516: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2517: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1.119 brouard 2518:
1.117 brouard 2519: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
1.119 brouard 2520:
1.117 brouard 2521: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.119 brouard 2522:
2523: printf("%d|",(int)age);fflush(stdout);
2524: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2525:
1.117 brouard 2526: /* Computing expectancies */
2527: for(i=1; i<=nlstate;i++)
2528: for(j=1; j<=nlstate;j++)
2529: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2530: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2531:
1.119 brouard 2532: /* 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 2533:
2534: }
2535:
2536: fprintf(ficreseij,"%3.0f",age );
2537: for(i=1; i<=nlstate;i++){
2538: eip=0;
2539: for(j=1; j<=nlstate;j++){
2540: eip +=eij[i][j][(int)age];
2541: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2542: }
2543: fprintf(ficreseij,"%9.4f", eip );
2544: }
2545: fprintf(ficreseij,"\n");
1.119 brouard 2546:
1.117 brouard 2547: }
2548: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2549: printf("\n");
2550: fprintf(ficlog,"\n");
1.119 brouard 2551:
1.117 brouard 2552: }
2553:
2554: 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[] )
2555:
2556: {
2557: /* Covariances of health expectancies eij and of total life expectancies according
2558: to initial status i, ei. .
2559: */
2560: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2561: double age, agelim, hf;
2562: double ***p3matp, ***p3matm, ***varhe;
1.53 brouard 2563: double **dnewm,**doldm;
1.117 brouard 2564: double *xp, *xm;
1.53 brouard 2565: double **gp, **gm;
2566: double ***gradg, ***trgradg;
2567: int theta;
2568:
1.117 brouard 2569: double eip, vip;
2570:
1.74 brouard 2571: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2572: xp=vector(1,npar);
1.117 brouard 2573: xm=vector(1,npar);
1.74 brouard 2574: dnewm=matrix(1,nlstate*nlstate,1,npar);
2575: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2576:
1.117 brouard 2577: pstamp(ficresstdeij);
2578: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2579: fprintf(ficresstdeij,"# Age");
2580: for(i=1; i<=nlstate;i++){
1.53 brouard 2581: for(j=1; j<=nlstate;j++)
1.117 brouard 2582: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2583: fprintf(ficresstdeij," e%1d. ",i);
2584: }
2585: fprintf(ficresstdeij,"\n");
1.53 brouard 2586:
1.117 brouard 2587: pstamp(ficrescveij);
2588: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2589: fprintf(ficrescveij,"# Age");
2590: for(i=1; i<=nlstate;i++)
2591: for(j=1; j<=nlstate;j++){
2592: cptj= (j-1)*nlstate+i;
2593: for(i2=1; i2<=nlstate;i2++)
2594: for(j2=1; j2<=nlstate;j2++){
2595: cptj2= (j2-1)*nlstate+i2;
2596: if(cptj2 <= cptj)
2597: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2598: }
2599: }
2600: fprintf(ficrescveij,"\n");
2601:
1.53 brouard 2602: if(estepm < stepm){
2603: printf ("Problem %d lower than %d\n",estepm, stepm);
2604: }
2605: else hstepm=estepm;
2606: /* We compute the life expectancy from trapezoids spaced every estepm months
2607: * This is mainly to measure the difference between two models: for example
2608: * if stepm=24 months pijx are given only every 2 years and by summing them
2609: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2610: * progression in between and thus overestimating or underestimating according
1.53 brouard 2611: * to the curvature of the survival function. If, for the same date, we
2612: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2613: * to compare the new estimate of Life expectancy with the same linear
2614: * hypothesis. A more precise result, taking into account a more precise
2615: * curvature will be obtained if estepm is as small as stepm. */
2616:
2617: /* For example we decided to compute the life expectancy with the smallest unit */
2618: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2619: nhstepm is the number of hstepm from age to agelim
2620: nstepm is the number of stepm from age to agelin.
2621: Look at hpijx to understand the reason of that which relies in memory size
2622: and note for a fixed period like estepm months */
2623: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2624: survival function given by stepm (the optimization length). Unfortunately it
2625: means that if the survival funtion is printed only each two years of age and if
2626: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2627: results. So we changed our mind and took the option of the best precision.
2628: */
2629: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2630:
1.117 brouard 2631: /* If stepm=6 months */
2632: /* nhstepm age range expressed in number of stepm */
1.53 brouard 2633: agelim=AGESUP;
1.117 brouard 2634: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2635: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2636: /* if (stepm >= YEARM) hstepm=1;*/
2637: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2638:
2639: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2640: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2641: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2642: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2643: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2644: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2645:
2646: for (age=bage; age<=fage; age ++){
1.53 brouard 2647:
2648: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2649: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2650:
2651: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2652:
1.95 brouard 2653: /* Computing Variances of health expectancies */
1.117 brouard 2654: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2655: decrease memory allocation */
2656: for(theta=1; theta <=npar; theta++){
1.53 brouard 2657: for(i=1; i<=npar; i++){
2658: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1.117 brouard 2659: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.53 brouard 2660: }
1.117 brouard 2661: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2662: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.53 brouard 2663:
2664: for(j=1; j<= nlstate; j++){
2665: for(i=1; i<=nlstate; i++){
1.117 brouard 2666: for(h=0; h<=nhstepm-1; h++){
2667: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2668: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
1.53 brouard 2669: }
2670: }
2671: }
2672:
1.117 brouard 2673: for(ij=1; ij<= nlstate*nlstate; ij++)
1.53 brouard 2674: for(h=0; h<=nhstepm-1; h++){
1.117 brouard 2675: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
1.53 brouard 2676: }
1.117 brouard 2677: }/* End theta */
2678:
2679:
2680: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2681: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2682: for(theta=1; theta <=npar; theta++)
2683: trgradg[h][j][theta]=gradg[h][theta][j];
1.117 brouard 2684:
1.53 brouard 2685:
1.117 brouard 2686: for(ij=1;ij<=nlstate*nlstate;ij++)
2687: for(ji=1;ji<=nlstate*nlstate;ji++)
2688: varhe[ij][ji][(int)age] =0.;
1.53 brouard 2689:
2690: printf("%d|",(int)age);fflush(stdout);
2691: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2692: for(h=0;h<=nhstepm-1;h++){
2693: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2694: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2695: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
1.117 brouard 2696: for(ij=1;ij<=nlstate*nlstate;ij++)
2697: for(ji=1;ji<=nlstate*nlstate;ji++)
2698: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.53 brouard 2699: }
2700: }
2701: /* Computing expectancies */
1.117 brouard 2702: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
1.53 brouard 2703: for(i=1; i<=nlstate;i++)
2704: for(j=1; j<=nlstate;j++)
2705: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
1.117 brouard 2706: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.53 brouard 2707:
1.117 brouard 2708: /* 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 2709:
2710: }
2711:
1.117 brouard 2712: fprintf(ficresstdeij,"%3.0f",age );
2713: for(i=1; i<=nlstate;i++){
2714: eip=0.;
2715: vip=0.;
2716: for(j=1; j<=nlstate;j++){
2717: eip += eij[i][j][(int)age];
2718: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2719: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2720: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2721: }
2722: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2723: }
2724: fprintf(ficresstdeij,"\n");
2725:
2726: fprintf(ficrescveij,"%3.0f",age );
1.53 brouard 2727: for(i=1; i<=nlstate;i++)
2728: for(j=1; j<=nlstate;j++){
1.117 brouard 2729: cptj= (j-1)*nlstate+i;
2730: for(i2=1; i2<=nlstate;i2++)
2731: for(j2=1; j2<=nlstate;j2++){
2732: cptj2= (j2-1)*nlstate+i2;
2733: if(cptj2 <= cptj)
2734: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2735: }
1.53 brouard 2736: }
1.117 brouard 2737: fprintf(ficrescveij,"\n");
1.53 brouard 2738:
2739: }
1.117 brouard 2740: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2741: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2742: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2743: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2744: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2745: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 2746: printf("\n");
2747: fprintf(ficlog,"\n");
2748:
1.117 brouard 2749: free_vector(xm,1,npar);
1.53 brouard 2750: free_vector(xp,1,npar);
1.74 brouard 2751: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2752: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2753: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2754: }
2755:
2756: /************ Variance ******************/
1.105 lievre 2757: 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 2758: {
2759: /* Variance of health expectancies */
2760: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2761: /* double **newm;*/
2762: double **dnewm,**doldm;
2763: double **dnewmp,**doldmp;
2764: int i, j, nhstepm, hstepm, h, nstepm ;
2765: int k, cptcode;
2766: double *xp;
2767: double **gp, **gm; /* for var eij */
2768: double ***gradg, ***trgradg; /*for var eij */
2769: double **gradgp, **trgradgp; /* for var p point j */
2770: double *gpp, *gmp; /* for var p point j */
2771: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2772: double ***p3mat;
2773: double age,agelim, hf;
2774: double ***mobaverage;
2775: int theta;
2776: char digit[4];
1.55 lievre 2777: char digitp[25];
1.53 brouard 2778:
2779: char fileresprobmorprev[FILENAMELENGTH];
2780:
1.55 lievre 2781: if(popbased==1){
1.58 lievre 2782: if(mobilav!=0)
1.55 lievre 2783: strcpy(digitp,"-populbased-mobilav-");
2784: else strcpy(digitp,"-populbased-nomobil-");
2785: }
2786: else
1.53 brouard 2787: strcpy(digitp,"-stablbased-");
1.56 lievre 2788:
1.54 brouard 2789: if (mobilav!=0) {
1.53 brouard 2790: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2791: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2792: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2793: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2794: }
1.53 brouard 2795: }
2796:
2797: strcpy(fileresprobmorprev,"prmorprev");
2798: sprintf(digit,"%-d",ij);
2799: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2800: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2801: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2802: strcat(fileresprobmorprev,fileres);
2803: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2804: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2805: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2806: }
2807: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2808:
1.53 brouard 2809: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.117 brouard 2810: pstamp(ficresprobmorprev);
1.66 brouard 2811: 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 2812: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2813: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2814: fprintf(ficresprobmorprev," p.%-d SE",j);
2815: for(i=1; i<=nlstate;i++)
2816: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2817: }
2818: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2819: fprintf(ficgp,"\n# Routine varevsij");
1.106 brouard 2820: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.87 brouard 2821: 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");
2822: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2823: /* } */
1.53 brouard 2824: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.117 brouard 2825: pstamp(ficresvij);
2826: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2827: if(popbased==1)
2828: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2829: else
2830: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
1.53 brouard 2831: fprintf(ficresvij,"# Age");
2832: for(i=1; i<=nlstate;i++)
2833: for(j=1; j<=nlstate;j++)
1.117 brouard 2834: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
1.53 brouard 2835: fprintf(ficresvij,"\n");
2836:
2837: xp=vector(1,npar);
2838: dnewm=matrix(1,nlstate,1,npar);
2839: doldm=matrix(1,nlstate,1,nlstate);
2840: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2841: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2842:
2843: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2844: gpp=vector(nlstate+1,nlstate+ndeath);
2845: gmp=vector(nlstate+1,nlstate+ndeath);
2846: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2847:
2848: if(estepm < stepm){
2849: printf ("Problem %d lower than %d\n",estepm, stepm);
2850: }
2851: else hstepm=estepm;
2852: /* For example we decided to compute the life expectancy with the smallest unit */
2853: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2854: nhstepm is the number of hstepm from age to agelim
2855: nstepm is the number of stepm from age to agelin.
2856: Look at hpijx to understand the reason of that which relies in memory size
2857: and note for a fixed period like k years */
2858: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2859: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2860: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2861: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2862: results. So we changed our mind and took the option of the best precision.
2863: */
2864: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2865: agelim = AGESUP;
2866: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2867: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2868: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2869: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2870: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2871: gp=matrix(0,nhstepm,1,nlstate);
2872: gm=matrix(0,nhstepm,1,nlstate);
2873:
2874:
2875: for(theta=1; theta <=npar; theta++){
1.66 brouard 2876: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2877: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2878: }
2879: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2880: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2881:
2882: if (popbased==1) {
1.54 brouard 2883: if(mobilav ==0){
1.53 brouard 2884: for(i=1; i<=nlstate;i++)
2885: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2886: }else{ /* mobilav */
1.53 brouard 2887: for(i=1; i<=nlstate;i++)
2888: prlim[i][i]=mobaverage[(int)age][i][ij];
2889: }
2890: }
2891:
2892: for(j=1; j<= nlstate; j++){
2893: for(h=0; h<=nhstepm; h++){
2894: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2895: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2896: }
2897: }
1.66 brouard 2898: /* This for computing probability of death (h=1 means
2899: computed over hstepm matrices product = hstepm*stepm months)
2900: as a weighted average of prlim.
2901: */
1.69 brouard 2902: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2903: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2904: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2905: }
1.66 brouard 2906: /* end probability of death */
1.53 brouard 2907:
1.66 brouard 2908: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2909: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2910: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2911: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2912:
2913: if (popbased==1) {
1.54 brouard 2914: if(mobilav ==0){
1.53 brouard 2915: for(i=1; i<=nlstate;i++)
2916: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2917: }else{ /* mobilav */
1.53 brouard 2918: for(i=1; i<=nlstate;i++)
2919: prlim[i][i]=mobaverage[(int)age][i][ij];
2920: }
2921: }
2922:
2923: for(j=1; j<= nlstate; j++){
2924: for(h=0; h<=nhstepm; h++){
2925: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2926: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2927: }
2928: }
1.66 brouard 2929: /* This for computing probability of death (h=1 means
2930: computed over hstepm matrices product = hstepm*stepm months)
2931: as a weighted average of prlim.
2932: */
1.69 brouard 2933: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2934: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2935: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2936: }
1.66 brouard 2937: /* end probability of death */
1.53 brouard 2938:
2939: for(j=1; j<= nlstate; j++) /* vareij */
2940: for(h=0; h<=nhstepm; h++){
2941: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2942: }
1.68 lievre 2943:
1.53 brouard 2944: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2945: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2946: }
2947:
2948: } /* End theta */
2949:
2950: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2951:
2952: for(h=0; h<=nhstepm; h++) /* veij */
2953: for(j=1; j<=nlstate;j++)
2954: for(theta=1; theta <=npar; theta++)
2955: trgradg[h][j][theta]=gradg[h][theta][j];
2956:
2957: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2958: for(theta=1; theta <=npar; theta++)
1.53 brouard 2959: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2960:
1.53 brouard 2961:
2962: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2963: for(i=1;i<=nlstate;i++)
2964: for(j=1;j<=nlstate;j++)
2965: vareij[i][j][(int)age] =0.;
2966:
2967: for(h=0;h<=nhstepm;h++){
2968: for(k=0;k<=nhstepm;k++){
2969: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2970: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2971: for(i=1;i<=nlstate;i++)
2972: for(j=1;j<=nlstate;j++)
2973: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2974: }
2975: }
1.70 brouard 2976:
1.53 brouard 2977: /* pptj */
2978: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2979: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2980: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2981: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2982: varppt[j][i]=doldmp[j][i];
2983: /* end ppptj */
1.66 brouard 2984: /* x centered again */
1.53 brouard 2985: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2986: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2987:
2988: if (popbased==1) {
1.54 brouard 2989: if(mobilav ==0){
1.53 brouard 2990: for(i=1; i<=nlstate;i++)
2991: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2992: }else{ /* mobilav */
1.53 brouard 2993: for(i=1; i<=nlstate;i++)
2994: prlim[i][i]=mobaverage[(int)age][i][ij];
2995: }
2996: }
1.70 brouard 2997:
1.66 brouard 2998: /* This for computing probability of death (h=1 means
2999: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3000: as a weighted average of prlim.
3001: */
1.68 lievre 3002: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3003: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 3004: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3005: }
1.66 brouard 3006: /* end probability of death */
1.53 brouard 3007:
3008: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3009: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3010: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3011: for(i=1; i<=nlstate;i++){
3012: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3013: }
3014: }
3015: fprintf(ficresprobmorprev,"\n");
3016:
3017: fprintf(ficresvij,"%.0f ",age );
3018: for(i=1; i<=nlstate;i++)
3019: for(j=1; j<=nlstate;j++){
3020: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3021: }
3022: fprintf(ficresvij,"\n");
3023: free_matrix(gp,0,nhstepm,1,nlstate);
3024: free_matrix(gm,0,nhstepm,1,nlstate);
3025: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3026: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3027: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3028: } /* End age */
3029: free_vector(gpp,nlstate+1,nlstate+ndeath);
3030: free_vector(gmp,nlstate+1,nlstate+ndeath);
3031: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3032: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3033: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
3034: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3035: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 3036: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3037: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3038: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 3039: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3040: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3041: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3042: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3043: 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 3044: /* 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);
3045: */
1.88 brouard 3046: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 3047: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 3048:
3049: free_vector(xp,1,npar);
3050: free_matrix(doldm,1,nlstate,1,nlstate);
3051: free_matrix(dnewm,1,nlstate,1,npar);
3052: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3053: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3054: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 3055: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3056: fclose(ficresprobmorprev);
1.88 brouard 3057: fflush(ficgp);
3058: fflush(fichtm);
1.84 brouard 3059: } /* end varevsij */
1.53 brouard 3060:
3061: /************ Variance of prevlim ******************/
1.105 lievre 3062: 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 3063: {
3064: /* Variance of prevalence limit */
1.59 brouard 3065: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 3066: double **newm;
3067: double **dnewm,**doldm;
3068: int i, j, nhstepm, hstepm;
3069: int k, cptcode;
3070: double *xp;
3071: double *gp, *gm;
3072: double **gradg, **trgradg;
3073: double age,agelim;
3074: int theta;
1.117 brouard 3075:
3076: pstamp(ficresvpl);
3077: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.53 brouard 3078: fprintf(ficresvpl,"# Age");
3079: for(i=1; i<=nlstate;i++)
3080: fprintf(ficresvpl," %1d-%1d",i,i);
3081: fprintf(ficresvpl,"\n");
3082:
3083: xp=vector(1,npar);
3084: dnewm=matrix(1,nlstate,1,npar);
3085: doldm=matrix(1,nlstate,1,nlstate);
3086:
3087: hstepm=1*YEARM; /* Every year of age */
3088: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3089: agelim = AGESUP;
3090: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3091: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3092: if (stepm >= YEARM) hstepm=1;
3093: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3094: gradg=matrix(1,npar,1,nlstate);
3095: gp=vector(1,nlstate);
3096: gm=vector(1,nlstate);
3097:
3098: for(theta=1; theta <=npar; theta++){
3099: for(i=1; i<=npar; i++){ /* Computes gradient */
3100: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3101: }
3102: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3103: for(i=1;i<=nlstate;i++)
3104: gp[i] = prlim[i][i];
3105:
3106: for(i=1; i<=npar; i++) /* Computes gradient */
3107: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3108: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3109: for(i=1;i<=nlstate;i++)
3110: gm[i] = prlim[i][i];
3111:
3112: for(i=1;i<=nlstate;i++)
3113: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3114: } /* End theta */
3115:
3116: trgradg =matrix(1,nlstate,1,npar);
3117:
3118: for(j=1; j<=nlstate;j++)
3119: for(theta=1; theta <=npar; theta++)
3120: trgradg[j][theta]=gradg[theta][j];
3121:
3122: for(i=1;i<=nlstate;i++)
3123: varpl[i][(int)age] =0.;
3124: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3125: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3126: for(i=1;i<=nlstate;i++)
3127: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3128:
3129: fprintf(ficresvpl,"%.0f ",age );
3130: for(i=1; i<=nlstate;i++)
3131: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3132: fprintf(ficresvpl,"\n");
3133: free_vector(gp,1,nlstate);
3134: free_vector(gm,1,nlstate);
3135: free_matrix(gradg,1,npar,1,nlstate);
3136: free_matrix(trgradg,1,nlstate,1,npar);
3137: } /* End age */
3138:
3139: free_vector(xp,1,npar);
3140: free_matrix(doldm,1,nlstate,1,npar);
3141: free_matrix(dnewm,1,nlstate,1,nlstate);
3142:
3143: }
3144:
3145: /************ Variance of one-step probabilities ******************/
1.105 lievre 3146: 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 3147: {
3148: int i, j=0, i1, k1, l1, t, tj;
3149: int k2, l2, j1, z1;
3150: int k=0,l, cptcode;
3151: int first=1, first1;
3152: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3153: double **dnewm,**doldm;
3154: double *xp;
3155: double *gp, *gm;
3156: double **gradg, **trgradg;
3157: double **mu;
3158: double age,agelim, cov[NCOVMAX];
3159: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3160: int theta;
3161: char fileresprob[FILENAMELENGTH];
3162: char fileresprobcov[FILENAMELENGTH];
3163: char fileresprobcor[FILENAMELENGTH];
3164:
3165: double ***varpij;
3166:
3167: strcpy(fileresprob,"prob");
3168: strcat(fileresprob,fileres);
3169: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3170: printf("Problem with resultfile: %s\n", fileresprob);
3171: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3172: }
3173: strcpy(fileresprobcov,"probcov");
3174: strcat(fileresprobcov,fileres);
3175: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3176: printf("Problem with resultfile: %s\n", fileresprobcov);
3177: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3178: }
3179: strcpy(fileresprobcor,"probcor");
3180: strcat(fileresprobcor,fileres);
3181: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3182: printf("Problem with resultfile: %s\n", fileresprobcor);
3183: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3184: }
3185: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3186: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3187: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3188: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3189: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3190: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.117 brouard 3191: pstamp(ficresprob);
1.53 brouard 3192: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3193: fprintf(ficresprob,"# Age");
1.117 brouard 3194: pstamp(ficresprobcov);
1.53 brouard 3195: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3196: fprintf(ficresprobcov,"# Age");
1.117 brouard 3197: pstamp(ficresprobcor);
1.53 brouard 3198: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
1.117 brouard 3199: fprintf(ficresprobcor,"# Age");
1.53 brouard 3200:
3201:
3202: for(i=1; i<=nlstate;i++)
3203: for(j=1; j<=(nlstate+ndeath);j++){
3204: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3205: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3206: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3207: }
1.69 brouard 3208: /* fprintf(ficresprob,"\n");
1.53 brouard 3209: fprintf(ficresprobcov,"\n");
3210: fprintf(ficresprobcor,"\n");
1.69 brouard 3211: */
3212: xp=vector(1,npar);
1.53 brouard 3213: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3214: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3215: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3216: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3217: first=1;
1.88 brouard 3218: fprintf(ficgp,"\n# Routine varprob");
3219: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3220: fprintf(fichtm,"\n");
3221:
1.95 brouard 3222: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3223: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 3224: file %s<br>\n",optionfilehtmcov);
3225: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3226: and drawn. It helps understanding how is the covariance between two incidences.\
3227: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3228: 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. \
3229: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3230: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3231: standard deviations wide on each axis. <br>\
3232: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3233: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3234: 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 3235:
3236: cov[1]=1;
3237: tj=cptcoveff;
3238: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3239: j1=0;
3240: for(t=1; t<=tj;t++){
3241: for(i1=1; i1<=ncodemax[t];i1++){
3242: j1++;
3243: if (cptcovn>0) {
3244: fprintf(ficresprob, "\n#********** Variable ");
3245: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3246: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 3247: fprintf(ficresprobcov, "\n#********** Variable ");
3248: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3249: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 3250:
3251: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 3252: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3253: fprintf(ficgp, "**********\n#\n");
1.53 brouard 3254:
3255:
1.96 brouard 3256: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 3257: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 3258: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 3259:
3260: fprintf(ficresprobcor, "\n#********** Variable ");
3261: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3262: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 3263: }
3264:
3265: for (age=bage; age<=fage; age ++){
3266: cov[2]=age;
3267: for (k=1; k<=cptcovn;k++) {
3268: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3269: }
3270: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3271: for (k=1; k<=cptcovprod;k++)
3272: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3273:
3274: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3275: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3276: gp=vector(1,(nlstate)*(nlstate+ndeath));
3277: gm=vector(1,(nlstate)*(nlstate+ndeath));
3278:
3279: for(theta=1; theta <=npar; theta++){
3280: for(i=1; i<=npar; i++)
1.74 brouard 3281: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 3282:
3283: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3284:
3285: k=0;
3286: for(i=1; i<= (nlstate); i++){
3287: for(j=1; j<=(nlstate+ndeath);j++){
3288: k=k+1;
3289: gp[k]=pmmij[i][j];
3290: }
3291: }
3292:
3293: for(i=1; i<=npar; i++)
1.74 brouard 3294: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 3295:
3296: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3297: k=0;
3298: for(i=1; i<=(nlstate); i++){
3299: for(j=1; j<=(nlstate+ndeath);j++){
3300: k=k+1;
3301: gm[k]=pmmij[i][j];
3302: }
3303: }
3304:
3305: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 3306: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 3307: }
3308:
3309: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3310: for(theta=1; theta <=npar; theta++)
3311: trgradg[j][theta]=gradg[theta][j];
3312:
3313: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3314: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 3315: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3316: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3317: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3318: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3319:
1.53 brouard 3320: pmij(pmmij,cov,ncovmodel,x,nlstate);
3321:
3322: k=0;
3323: for(i=1; i<=(nlstate); i++){
3324: for(j=1; j<=(nlstate+ndeath);j++){
3325: k=k+1;
3326: mu[k][(int) age]=pmmij[i][j];
3327: }
3328: }
3329: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3330: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3331: varpij[i][j][(int)age] = doldm[i][j];
3332:
3333: /*printf("\n%d ",(int)age);
1.59 brouard 3334: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3335: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3336: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3337: }*/
1.53 brouard 3338:
3339: fprintf(ficresprob,"\n%d ",(int)age);
3340: fprintf(ficresprobcov,"\n%d ",(int)age);
3341: fprintf(ficresprobcor,"\n%d ",(int)age);
3342:
3343: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3344: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3345: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3346: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3347: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3348: }
3349: i=0;
3350: for (k=1; k<=(nlstate);k++){
3351: for (l=1; l<=(nlstate+ndeath);l++){
3352: i=i++;
3353: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3354: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3355: for (j=1; j<=i;j++){
3356: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3357: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3358: }
3359: }
3360: }/* end of loop for state */
3361: } /* end of loop for age */
3362:
3363: /* Confidence intervalle of pij */
3364: /*
1.59 brouard 3365: fprintf(ficgp,"\nset noparametric;unset label");
3366: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3367: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3368: 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);
3369: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3370: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3371: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3372: */
3373:
3374: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3375: first1=1;
3376: for (k2=1; k2<=(nlstate);k2++){
3377: for (l2=1; l2<=(nlstate+ndeath);l2++){
3378: if(l2==k2) continue;
3379: j=(k2-1)*(nlstate+ndeath)+l2;
3380: for (k1=1; k1<=(nlstate);k1++){
3381: for (l1=1; l1<=(nlstate+ndeath);l1++){
3382: if(l1==k1) continue;
3383: i=(k1-1)*(nlstate+ndeath)+l1;
3384: if(i<=j) continue;
3385: for (age=bage; age<=fage; age ++){
3386: if ((int)age %5==0){
3387: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3388: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3389: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3390: mu1=mu[i][(int) age]/stepm*YEARM ;
3391: mu2=mu[j][(int) age]/stepm*YEARM;
3392: c12=cv12/sqrt(v1*v2);
3393: /* Computing eigen value of matrix of covariance */
3394: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3395: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3396: /* Eigen vectors */
3397: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3398: /*v21=sqrt(1.-v11*v11); *//* error */
3399: v21=(lc1-v1)/cv12*v11;
3400: v12=-v21;
3401: v22=v11;
3402: tnalp=v21/v11;
3403: if(first1==1){
3404: first1=0;
3405: 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);
3406: }
3407: 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);
3408: /*printf(fignu*/
3409: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3410: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3411: if(first==1){
3412: first=0;
3413: fprintf(ficgp,"\nset parametric;unset label");
3414: 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);
3415: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3416: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3417: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3418: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3419: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3420: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3421: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3422: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3423: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3424: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3425: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3426: 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",\
3427: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3428: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3429: }else{
3430: first=0;
1.91 brouard 3431: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3432: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3433: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3434: 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",\
3435: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3436: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3437: }/* if first */
3438: } /* age mod 5 */
3439: } /* end loop age */
1.88 brouard 3440: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3441: first=1;
3442: } /*l12 */
3443: } /* k12 */
3444: } /*l1 */
3445: }/* k1 */
3446: } /* loop covariates */
3447: }
1.59 brouard 3448: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3449: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.113 brouard 3450: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3451: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
1.53 brouard 3452: free_vector(xp,1,npar);
3453: fclose(ficresprob);
3454: fclose(ficresprobcov);
3455: fclose(ficresprobcor);
1.91 brouard 3456: fflush(ficgp);
3457: fflush(fichtmcov);
1.53 brouard 3458: }
3459:
3460:
3461: /******************* Printing html file ***********/
3462: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3463: int lastpass, int stepm, int weightopt, char model[],\
3464: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3465: int popforecast, int estepm ,\
3466: double jprev1, double mprev1,double anprev1, \
3467: double jprev2, double mprev2,double anprev2){
3468: int jj1, k1, i1, cpt;
3469:
1.107 brouard 3470: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3471: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
1.106 brouard 3472: </ul>");
1.107 brouard 3473: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
1.96 brouard 3474: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3475: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3476: fprintf(fichtm,"\
3477: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3478: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3479: fprintf(fichtm,"\
1.117 brouard 3480: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.96 brouard 3481: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3482: fprintf(fichtm,"\
1.121 lievre 3483: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.96 brouard 3484: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3485: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.116 brouard 3486:
1.53 brouard 3487:
3488: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3489:
3490: m=cptcoveff;
3491: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3492:
3493: jj1=0;
3494: for(k1=1; k1<=m;k1++){
3495: for(i1=1; i1<=ncodemax[k1];i1++){
3496: jj1++;
3497: if (cptcovn > 0) {
3498: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3499: for (cpt=1; cpt<=cptcoveff;cpt++)
3500: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3501: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3502: }
3503: /* Pij */
1.117 brouard 3504: 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> \
3505: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3506: /* Quasi-incidences */
1.85 brouard 3507: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.117 brouard 3508: 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> \
3509: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3510: /* Period (stable) prevalence in each health state */
1.53 brouard 3511: for(cpt=1; cpt<nlstate;cpt++){
1.117 brouard 3512: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3513: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3514: }
3515: for(cpt=1; cpt<=nlstate;cpt++) {
1.117 brouard 3516: 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> \
3517: <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 3518: }
3519: } /* end i1 */
3520: }/* End k1 */
3521: fprintf(fichtm,"</ul>");
3522:
3523:
1.96 brouard 3524: fprintf(fichtm,"\
1.107 brouard 3525: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.96 brouard 3526: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3527:
3528: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3529: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3530: fprintf(fichtm,"\
3531: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3532: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3533:
3534: fprintf(fichtm,"\
3535: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3536: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3537: fprintf(fichtm,"\
1.117 brouard 3538: - 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): \
3539: <a href=\"%s\">%s</a> <br>\n</li>",
3540: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3541: fprintf(fichtm,"\
3542: - (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): \
3543: <a href=\"%s\">%s</a> <br>\n</li>",
3544: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3545: fprintf(fichtm,"\
3546: - 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 3547: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3548: fprintf(fichtm,"\
1.117 brouard 3549: - 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 3550: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3551: fprintf(fichtm,"\
1.117 brouard 3552: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.88 brouard 3553: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3554:
1.76 brouard 3555: /* if(popforecast==1) fprintf(fichtm,"\n */
3556: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3557: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3558: /* <br>",fileres,fileres,fileres,fileres); */
3559: /* else */
3560: /* 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 3561: fflush(fichtm);
3562: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3563:
3564: m=cptcoveff;
3565: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3566:
3567: jj1=0;
3568: for(k1=1; k1<=m;k1++){
3569: for(i1=1; i1<=ncodemax[k1];i1++){
3570: jj1++;
3571: if (cptcovn > 0) {
3572: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3573: for (cpt=1; cpt<=cptcoveff;cpt++)
3574: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3575: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3576: }
3577: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3578: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3579: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3580: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3581: }
1.96 brouard 3582: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3583: health expectancies in states (1) and (2): %s%d.png<br>\
3584: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3585: } /* end i1 */
3586: }/* End k1 */
3587: fprintf(fichtm,"</ul>");
1.87 brouard 3588: fflush(fichtm);
1.53 brouard 3589: }
3590:
3591: /******************* Gnuplot file **************/
1.89 brouard 3592: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3593:
1.88 brouard 3594: char dirfileres[132],optfileres[132];
1.53 brouard 3595: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3596: int ng;
1.88 brouard 3597: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3598: /* printf("Problem with file %s",optionfilegnuplot); */
3599: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3600: /* } */
1.53 brouard 3601:
1.54 brouard 3602: /*#ifdef windows */
1.89 brouard 3603: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3604: /*#endif */
1.88 brouard 3605: m=pow(2,cptcoveff);
3606:
3607: strcpy(dirfileres,optionfilefiname);
3608: strcpy(optfileres,"vpl");
1.53 brouard 3609: /* 1eme*/
3610: for (cpt=1; cpt<= nlstate ; cpt ++) {
3611: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3612: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3613: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3614: fprintf(ficgp,"set xlabel \"Age\" \n\
3615: set ylabel \"Probability\" \n\
3616: set ter png small\n\
3617: set size 0.65,0.65\n\
3618: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3619:
3620: for (i=1; i<= nlstate ; i ++) {
3621: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3622: else fprintf(ficgp," \%%*lf (\%%*lf)");
3623: }
1.117 brouard 3624: 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 3625: for (i=1; i<= nlstate ; i ++) {
3626: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3627: else fprintf(ficgp," \%%*lf (\%%*lf)");
3628: }
1.88 brouard 3629: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3630: for (i=1; i<= nlstate ; i ++) {
3631: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3632: else fprintf(ficgp," \%%*lf (\%%*lf)");
3633: }
1.88 brouard 3634: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3635: }
3636: }
3637: /*2 eme*/
3638:
3639: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3640: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3641: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3642:
3643: for (i=1; i<= nlstate+1 ; i ++) {
3644: k=2*i;
1.88 brouard 3645: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3646: for (j=1; j<= nlstate+1 ; j ++) {
3647: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3648: else fprintf(ficgp," \%%*lf (\%%*lf)");
3649: }
3650: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3651: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3652: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3653: for (j=1; j<= nlstate+1 ; j ++) {
3654: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3655: else fprintf(ficgp," \%%*lf (\%%*lf)");
3656: }
3657: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3658: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3659: for (j=1; j<= nlstate+1 ; j ++) {
3660: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3661: else fprintf(ficgp," \%%*lf (\%%*lf)");
3662: }
3663: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3664: else fprintf(ficgp,"\" t\"\" w l 0,");
3665: }
3666: }
3667:
3668: /*3eme*/
3669:
3670: for (k1=1; k1<= m ; k1 ++) {
3671: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.117 brouard 3672: /* k=2+nlstate*(2*cpt-2); */
3673: k=2+(nlstate+1)*(cpt-1);
1.88 brouard 3674: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3675: fprintf(ficgp,"set ter png small\n\
3676: set size 0.65,0.65\n\
3677: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3678: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3679: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3680: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3681: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3682: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3683: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3684:
3685: */
3686: for (i=1; i< nlstate ; i ++) {
1.117 brouard 3687: 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);
3688: /* 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 3689:
3690: }
1.117 brouard 3691: 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 3692: }
3693: }
3694:
1.76 brouard 3695: /* CV preval stable (period) */
1.53 brouard 3696: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3697: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3698: k=3;
1.88 brouard 3699: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3700: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3701: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3702: unset log y\n\
1.88 brouard 3703: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3704:
1.83 lievre 3705: for (i=1; i< nlstate ; i ++)
1.53 brouard 3706: fprintf(ficgp,"+$%d",k+i+1);
3707: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3708:
3709: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3710: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3711: for (i=1; i< nlstate ; i ++) {
3712: l=3+(nlstate+ndeath)*cpt;
3713: fprintf(ficgp,"+$%d",l+i+1);
3714: }
3715: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3716: }
3717: }
3718:
3719: /* proba elementaires */
3720: for(i=1,jk=1; i <=nlstate; i++){
3721: for(k=1; k <=(nlstate+ndeath); k++){
3722: if (k != i) {
3723: for(j=1; j <=ncovmodel; j++){
3724: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3725: jk++;
3726: fprintf(ficgp,"\n");
3727: }
3728: }
3729: }
3730: }
3731:
3732: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3733: for(jk=1; jk <=m; jk++) {
1.88 brouard 3734: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3735: if (ng==2)
3736: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3737: else
3738: fprintf(ficgp,"\nset title \"Probability\"\n");
3739: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3740: i=1;
3741: for(k2=1; k2<=nlstate; k2++) {
3742: k3=i;
3743: for(k=1; k<=(nlstate+ndeath); k++) {
3744: if (k != k2){
3745: if(ng==2)
3746: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3747: else
3748: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3749: ij=1;
3750: for(j=3; j <=ncovmodel; j++) {
3751: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3752: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3753: ij++;
3754: }
3755: else
3756: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3757: }
3758: fprintf(ficgp,")/(1");
3759:
3760: for(k1=1; k1 <=nlstate; k1++){
3761: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3762: ij=1;
3763: for(j=3; j <=ncovmodel; j++){
3764: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3765: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3766: ij++;
3767: }
3768: else
3769: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3770: }
3771: fprintf(ficgp,")");
3772: }
3773: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3774: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3775: i=i+ncovmodel;
3776: }
3777: } /* end k */
3778: } /* end k2 */
3779: } /* end jk */
3780: } /* end ng */
1.88 brouard 3781: fflush(ficgp);
1.53 brouard 3782: } /* end gnuplot */
3783:
3784:
3785: /*************** Moving average **************/
1.54 brouard 3786: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3787:
3788: int i, cpt, cptcod;
1.58 lievre 3789: int modcovmax =1;
1.54 brouard 3790: int mobilavrange, mob;
1.53 brouard 3791: double age;
1.58 lievre 3792:
3793: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3794: a covariate has 2 modalities */
3795: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3796:
1.54 brouard 3797: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3798: if(mobilav==1) mobilavrange=5; /* default */
3799: else mobilavrange=mobilav;
3800: for (age=bage; age<=fage; age++)
3801: for (i=1; i<=nlstate;i++)
1.58 lievre 3802: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3803: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3804: /* We keep the original values on the extreme ages bage, fage and for
3805: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3806: we use a 5 terms etc. until the borders are no more concerned.
3807: */
3808: for (mob=3;mob <=mobilavrange;mob=mob+2){
3809: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3810: for (i=1; i<=nlstate;i++){
1.58 lievre 3811: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3812: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3813: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3814: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3815: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3816: }
3817: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3818: }
1.53 brouard 3819: }
1.54 brouard 3820: }/* end age */
3821: }/* end mob */
3822: }else return -1;
3823: return 0;
3824: }/* End movingaverage */
1.53 brouard 3825:
3826:
3827: /************** Forecasting ******************/
1.70 brouard 3828: 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 3829: /* proj1, year, month, day of starting projection
3830: agemin, agemax range of age
3831: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3832: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3833: */
1.73 lievre 3834: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3835: int *popage;
1.70 brouard 3836: double agec; /* generic age */
3837: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3838: double *popeffectif,*popcount;
3839: double ***p3mat;
1.55 lievre 3840: double ***mobaverage;
1.53 brouard 3841: char fileresf[FILENAMELENGTH];
3842:
1.69 brouard 3843: agelim=AGESUP;
1.84 brouard 3844: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3845:
3846: strcpy(fileresf,"f");
3847: strcat(fileresf,fileres);
3848: if((ficresf=fopen(fileresf,"w"))==NULL) {
3849: printf("Problem with forecast resultfile: %s\n", fileresf);
3850: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3851: }
3852: printf("Computing forecasting: result on file '%s' \n", fileresf);
3853: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3854:
3855: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3856:
1.54 brouard 3857: if (mobilav!=0) {
1.53 brouard 3858: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3859: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3860: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3861: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3862: }
1.53 brouard 3863: }
3864:
3865: stepsize=(int) (stepm+YEARM-1)/YEARM;
3866: if (stepm<=12) stepsize=1;
1.74 brouard 3867: if(estepm < stepm){
3868: printf ("Problem %d lower than %d\n",estepm, stepm);
3869: }
3870: else hstepm=estepm;
3871:
1.53 brouard 3872: hstepm=hstepm/stepm;
1.69 brouard 3873: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3874: fractional in yp1 */
1.53 brouard 3875: anprojmean=yp;
3876: yp2=modf((yp1*12),&yp);
3877: mprojmean=yp;
3878: yp1=modf((yp2*30.5),&yp);
3879: jprojmean=yp;
3880: if(jprojmean==0) jprojmean=1;
3881: if(mprojmean==0) jprojmean=1;
1.73 lievre 3882:
3883: i1=cptcoveff;
3884: if (cptcovn < 1){i1=1;}
1.53 brouard 3885:
1.70 brouard 3886: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3887:
1.70 brouard 3888: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3889:
1.75 brouard 3890: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3891: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3892: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3893: k=k+1;
3894: fprintf(ficresf,"\n#******");
3895: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3896: 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 3897: }
3898: fprintf(ficresf,"******\n");
1.70 brouard 3899: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3900: for(j=1; j<=nlstate+ndeath;j++){
3901: for(i=1; i<=nlstate;i++)
3902: fprintf(ficresf," p%d%d",i,j);
3903: fprintf(ficresf," p.%d",j);
3904: }
1.74 brouard 3905: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3906: fprintf(ficresf,"\n");
1.70 brouard 3907: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3908:
1.71 brouard 3909: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3910: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3911: nhstepm = nhstepm/hstepm;
3912: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3913: oldm=oldms;savm=savms;
1.70 brouard 3914: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3915:
3916: for (h=0; h<=nhstepm; h++){
1.75 brouard 3917: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3918: fprintf(ficresf,"\n");
3919: for(j=1;j<=cptcoveff;j++)
3920: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3921: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3922: }
3923: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3924: ppij=0.;
1.71 brouard 3925: for(i=1; i<=nlstate;i++) {
1.53 brouard 3926: if (mobilav==1)
1.71 brouard 3927: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3928: else {
1.71 brouard 3929: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3930: }
1.75 brouard 3931: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3932: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3933: }
3934: } /* end i */
3935: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3936: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3937: }
1.75 brouard 3938: }/* end j */
3939: } /* end h */
1.53 brouard 3940: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3941: } /* end agec */
3942: } /* end yearp */
3943: } /* end cptcod */
3944: } /* end cptcov */
1.53 brouard 3945:
1.54 brouard 3946: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3947:
3948: fclose(ficresf);
3949: }
1.70 brouard 3950:
3951: /************** Forecasting *****not tested NB*************/
1.53 brouard 3952: 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){
3953:
3954: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3955: int *popage;
1.69 brouard 3956: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3957: double *popeffectif,*popcount;
3958: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3959: double ***mobaverage;
1.53 brouard 3960: char filerespop[FILENAMELENGTH];
3961:
3962: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3963: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3964: agelim=AGESUP;
1.69 brouard 3965: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3966:
1.84 brouard 3967: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3968:
3969:
3970: strcpy(filerespop,"pop");
3971: strcat(filerespop,fileres);
3972: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3973: printf("Problem with forecast resultfile: %s\n", filerespop);
3974: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3975: }
3976: printf("Computing forecasting: result on file '%s' \n", filerespop);
3977: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3978:
3979: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3980:
1.54 brouard 3981: if (mobilav!=0) {
1.53 brouard 3982: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3983: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3984: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3985: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3986: }
1.53 brouard 3987: }
3988:
3989: stepsize=(int) (stepm+YEARM-1)/YEARM;
3990: if (stepm<=12) stepsize=1;
3991:
3992: agelim=AGESUP;
3993:
3994: hstepm=1;
3995: hstepm=hstepm/stepm;
3996:
3997: if (popforecast==1) {
3998: if((ficpop=fopen(popfile,"r"))==NULL) {
3999: printf("Problem with population file : %s\n",popfile);exit(0);
4000: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4001: }
4002: popage=ivector(0,AGESUP);
4003: popeffectif=vector(0,AGESUP);
4004: popcount=vector(0,AGESUP);
4005:
4006: i=1;
4007: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4008:
4009: imx=i;
4010: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4011: }
4012:
1.69 brouard 4013: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 4014: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4015: k=k+1;
4016: fprintf(ficrespop,"\n#******");
4017: for(j=1;j<=cptcoveff;j++) {
4018: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4019: }
4020: fprintf(ficrespop,"******\n");
4021: fprintf(ficrespop,"# Age");
4022: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4023: if (popforecast==1) fprintf(ficrespop," [Population]");
4024:
4025: for (cpt=0; cpt<=0;cpt++) {
4026: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4027:
1.69 brouard 4028: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 4029: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4030: nhstepm = nhstepm/hstepm;
4031:
4032: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4033: oldm=oldms;savm=savms;
4034: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4035:
4036: for (h=0; h<=nhstepm; h++){
1.69 brouard 4037: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 4038: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4039: }
4040: for(j=1; j<=nlstate+ndeath;j++) {
4041: kk1=0.;kk2=0;
4042: for(i=1; i<=nlstate;i++) {
4043: if (mobilav==1)
4044: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4045: else {
4046: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4047: }
4048: }
1.69 brouard 4049: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 4050: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4051: /*fprintf(ficrespop," %.3f", kk1);
4052: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4053: }
4054: }
4055: for(i=1; i<=nlstate;i++){
4056: kk1=0.;
4057: for(j=1; j<=nlstate;j++){
4058: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4059: }
1.69 brouard 4060: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 4061: }
4062:
1.69 brouard 4063: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 4064: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4065: }
4066: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4067: }
4068: }
4069:
4070: /******/
4071:
4072: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4073: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 4074: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 4075: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4076: nhstepm = nhstepm/hstepm;
4077:
4078: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4079: oldm=oldms;savm=savms;
4080: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4081: for (h=0; h<=nhstepm; h++){
1.69 brouard 4082: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 4083: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4084: }
4085: for(j=1; j<=nlstate+ndeath;j++) {
4086: kk1=0.;kk2=0;
4087: for(i=1; i<=nlstate;i++) {
4088: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4089: }
1.69 brouard 4090: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 4091: }
4092: }
4093: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4094: }
4095: }
4096: }
4097: }
4098:
1.54 brouard 4099: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4100:
4101: if (popforecast==1) {
4102: free_ivector(popage,0,AGESUP);
4103: free_vector(popeffectif,0,AGESUP);
4104: free_vector(popcount,0,AGESUP);
4105: }
4106: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4107: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4108: fclose(ficrespop);
1.84 brouard 4109: } /* End of popforecast */
1.53 brouard 4110:
1.87 brouard 4111: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 4112: {
1.87 brouard 4113: if((fichier=fopen(optionfich,"a"))==NULL) {
4114: printf("Problem with file: %s\n", optionfich);
4115: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4116: return (0);
1.86 brouard 4117: }
1.87 brouard 4118: fflush(fichier);
4119: return (1);
1.86 brouard 4120: }
1.94 brouard 4121:
4122:
4123: /**************** function prwizard **********************/
1.88 brouard 4124: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4125: {
4126:
1.94 brouard 4127: /* Wizard to print covariance matrix template */
4128:
1.88 brouard 4129: char ca[32], cb[32], cc[32];
4130: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4131: int numlinepar;
4132:
4133: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4134: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4135: for(i=1; i <=nlstate; i++){
4136: jj=0;
4137: for(j=1; j <=nlstate+ndeath; j++){
4138: if(j==i) continue;
4139: jj++;
4140: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4141: printf("%1d%1d",i,j);
4142: fprintf(ficparo,"%1d%1d",i,j);
4143: for(k=1; k<=ncovmodel;k++){
4144: /* printf(" %lf",param[i][j][k]); */
4145: /* fprintf(ficparo," %lf",param[i][j][k]); */
4146: printf(" 0.");
4147: fprintf(ficparo," 0.");
4148: }
4149: printf("\n");
4150: fprintf(ficparo,"\n");
4151: }
4152: }
4153: printf("# Scales (for hessian or gradient estimation)\n");
4154: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4155: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4156: for(i=1; i <=nlstate; i++){
4157: jj=0;
4158: for(j=1; j <=nlstate+ndeath; j++){
4159: if(j==i) continue;
4160: jj++;
4161: fprintf(ficparo,"%1d%1d",i,j);
4162: printf("%1d%1d",i,j);
4163: fflush(stdout);
4164: for(k=1; k<=ncovmodel;k++){
4165: /* printf(" %le",delti3[i][j][k]); */
4166: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4167: printf(" 0.");
4168: fprintf(ficparo," 0.");
4169: }
4170: numlinepar++;
4171: printf("\n");
4172: fprintf(ficparo,"\n");
4173: }
4174: }
4175: printf("# Covariance matrix\n");
4176: /* # 121 Var(a12)\n\ */
4177: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4178: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4179: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4180: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4181: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4182: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4183: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4184: fflush(stdout);
4185: fprintf(ficparo,"# Covariance matrix\n");
4186: /* # 121 Var(a12)\n\ */
4187: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4188: /* # ...\n\ */
4189: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4190:
4191: for(itimes=1;itimes<=2;itimes++){
4192: jj=0;
4193: for(i=1; i <=nlstate; i++){
4194: for(j=1; j <=nlstate+ndeath; j++){
4195: if(j==i) continue;
4196: for(k=1; k<=ncovmodel;k++){
4197: jj++;
4198: ca[0]= k+'a'-1;ca[1]='\0';
4199: if(itimes==1){
4200: printf("#%1d%1d%d",i,j,k);
4201: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4202: }else{
4203: printf("%1d%1d%d",i,j,k);
4204: fprintf(ficparo,"%1d%1d%d",i,j,k);
4205: /* printf(" %.5le",matcov[i][j]); */
4206: }
4207: ll=0;
4208: for(li=1;li <=nlstate; li++){
4209: for(lj=1;lj <=nlstate+ndeath; lj++){
4210: if(lj==li) continue;
4211: for(lk=1;lk<=ncovmodel;lk++){
4212: ll++;
4213: if(ll<=jj){
4214: cb[0]= lk +'a'-1;cb[1]='\0';
4215: if(ll<jj){
4216: if(itimes==1){
4217: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4218: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4219: }else{
4220: printf(" 0.");
4221: fprintf(ficparo," 0.");
4222: }
4223: }else{
4224: if(itimes==1){
4225: printf(" Var(%s%1d%1d)",ca,i,j);
4226: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4227: }else{
4228: printf(" 0.");
4229: fprintf(ficparo," 0.");
4230: }
4231: }
4232: }
4233: } /* end lk */
4234: } /* end lj */
4235: } /* end li */
4236: printf("\n");
4237: fprintf(ficparo,"\n");
4238: numlinepar++;
4239: } /* end k*/
4240: } /*end j */
4241: } /* end i */
1.95 brouard 4242: } /* end itimes */
1.88 brouard 4243:
4244: } /* end of prwizard */
1.98 brouard 4245: /******************* Gompertz Likelihood ******************************/
4246: double gompertz(double x[])
4247: {
4248: double A,B,L=0.0,sump=0.,num=0.;
4249: int i,n=0; /* n is the size of the sample */
1.110 brouard 4250:
1.98 brouard 4251: for (i=0;i<=imx-1 ; i++) {
4252: sump=sump+weight[i];
1.103 lievre 4253: /* sump=sump+1;*/
1.98 brouard 4254: num=num+1;
4255: }
4256:
4257:
1.103 lievre 4258: /* for (i=0; i<=imx; i++)
1.98 brouard 4259: 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]);*/
4260:
1.103 lievre 4261: for (i=1;i<=imx ; i++)
1.98 brouard 4262: {
1.110 brouard 4263: if (cens[i] == 1 && wav[i]>1)
1.103 lievre 4264: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
1.98 brouard 4265:
1.110 brouard 4266: if (cens[i] == 0 && wav[i]>1)
1.103 lievre 4267: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4268: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
1.98 brouard 4269:
1.110 brouard 4270: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4271: if (wav[i] > 1 ) { /* ??? */
1.98 brouard 4272: L=L+A*weight[i];
4273: /* 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]);*/
4274: }
4275: }
4276:
4277: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4278:
4279: return -2*L*num/sump;
4280: }
4281:
4282: /******************* Printing html file ***********/
4283: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4284: int lastpass, int stepm, int weightopt, char model[],\
1.105 lievre 4285: int imx, double p[],double **matcov,double agemortsup){
4286: int i,k;
1.98 brouard 4287:
4288: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4289: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4290: for (i=1;i<=2;i++)
4291: 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]));
4292: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4293: fprintf(fichtm,"</ul>");
1.105 lievre 4294:
4295: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4296:
1.106 brouard 4297: 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 4298:
4299: for (k=agegomp;k<(agemortsup-2);k++)
4300: 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]);
4301:
4302:
1.98 brouard 4303: fflush(fichtm);
4304: }
4305:
4306: /******************* Gnuplot file **************/
4307: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4308:
4309: char dirfileres[132],optfileres[132];
4310: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4311: int ng;
4312:
4313:
4314: /*#ifdef windows */
4315: fprintf(ficgp,"cd \"%s\" \n",pathc);
4316: /*#endif */
4317:
4318:
4319: strcpy(dirfileres,optionfilefiname);
4320: strcpy(optfileres,"vpl");
4321: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4322: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4323: fprintf(ficgp, "set ter png small\n set log y\n");
4324: fprintf(ficgp, "set size 0.65,0.65\n");
4325: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4326:
4327: }
4328:
4329:
1.88 brouard 4330:
1.91 brouard 4331:
1.117 brouard 4332:
1.53 brouard 4333: /***********************************************/
4334: /**************** Main Program *****************/
4335: /***********************************************/
4336:
4337: int main(int argc, char *argv[])
4338: {
1.61 brouard 4339: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 4340: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.110 brouard 4341: int linei, month, year,iout;
1.95 brouard 4342: int jj, ll, li, lj, lk, imk;
1.85 brouard 4343: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 4344: int itimes;
1.98 brouard 4345: int NDIM=2;
1.95 brouard 4346:
4347: char ca[32], cb[32], cc[32];
1.111 brouard 4348: char dummy[]=" ";
1.87 brouard 4349: /* FILE *fichtm; *//* Html File */
4350: /* FILE *ficgp;*/ /*Gnuplot File */
1.107 brouard 4351: struct stat info;
1.53 brouard 4352: double agedeb, agefin,hf;
4353: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4354:
4355: double fret;
4356: double **xi,tmp,delta;
4357:
4358: double dum; /* Dummy variable */
4359: double ***p3mat;
4360: double ***mobaverage;
4361: int *indx;
4362: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 4363: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.99 brouard 4364: char pathr[MAXLINE], pathimach[MAXLINE];
1.114 brouard 4365: char **bp, *tok, *val; /* pathtot */
1.53 brouard 4366: int firstobs=1, lastobs=10;
4367: int sdeb, sfin; /* Status at beginning and end */
4368: int c, h , cpt,l;
4369: int ju,jl, mi;
4370: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 4371: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 4372: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 4373: int mobilav=0,popforecast=0;
4374: int hstepm, nhstepm;
1.105 lievre 4375: int agemortsup;
4376: float sumlpop=0.;
1.74 brouard 4377: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4378: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 4379:
4380: double bage, fage, age, agelim, agebase;
4381: double ftolpl=FTOL;
4382: double **prlim;
4383: double *severity;
4384: double ***param; /* Matrix of parameters */
4385: double *p;
4386: double **matcov; /* Matrix of covariance */
4387: double ***delti3; /* Scale */
4388: double *delti; /* Scale */
4389: double ***eij, ***vareij;
4390: double **varpl; /* Variances of prevalence limits by age */
4391: double *epj, vepp;
4392: double kk1, kk2;
1.74 brouard 4393: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 brouard 4394: double **ximort;
1.53 brouard 4395: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 brouard 4396: int *dcwave;
1.53 brouard 4397:
4398: char z[1]="c", occ;
1.86 brouard 4399:
1.53 brouard 4400: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.117 brouard 4401: char *strt, strtend[80];
1.85 brouard 4402: char *stratrunc;
4403: int lstra;
4404:
4405: long total_usecs;
1.53 brouard 4406:
1.95 brouard 4407: /* setlocale (LC_ALL, ""); */
4408: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4409: /* textdomain (PACKAGE); */
4410: /* setlocale (LC_CTYPE, ""); */
4411: /* setlocale (LC_MESSAGES, ""); */
4412:
1.85 brouard 4413: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4414: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4415: curr_time=start_time;
1.85 brouard 4416: tm = *localtime(&start_time.tv_sec);
4417: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4418: strcpy(strstart,asctime(&tm));
1.86 brouard 4419:
1.88 brouard 4420: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4421: /* tp.tv_sec = tp.tv_sec +86400; */
4422: /* tm = *localtime(&start_time.tv_sec); */
4423: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4424: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4425: /* tmg.tm_hour=tmg.tm_hour + 1; */
4426: /* tp.tv_sec = mktime(&tmg); */
4427: /* strt=asctime(&tmg); */
1.88 brouard 4428: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4429: /* (void) time (&time_value);
4430: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4431: * tm = *localtime(&time_value);
1.88 brouard 4432: * strstart=asctime(&tm);
4433: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4434: */
4435:
1.91 brouard 4436: nberr=0; /* Number of errors and warnings */
4437: nbwarn=0;
1.53 brouard 4438: getcwd(pathcd, size);
4439:
1.81 brouard 4440: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4441: if(argc <=1){
4442: printf("\nEnter the parameter file name: ");
1.114 brouard 4443: fgets(pathr,FILENAMELENGTH,stdin);
4444: i=strlen(pathr);
4445: if(pathr[i-1]=='\n')
4446: pathr[i-1]='\0';
4447: for (tok = pathr; tok != NULL; ){
4448: printf("Pathr |%s|\n",pathr);
4449: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4450: printf("val= |%s| pathr=%s\n",val,pathr);
4451: strcpy (pathtot, val);
1.119 brouard 4452: if(pathr[0] == '\0') break; /* Dirty */
1.114 brouard 4453: }
1.53 brouard 4454: }
4455: else{
4456: strcpy(pathtot,argv[1]);
4457: }
1.88 brouard 4458: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4459: /*cygwin_split_path(pathtot,path,optionfile);
4460: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4461: /* cutv(path,optionfile,pathtot,'\\');*/
4462:
1.107 brouard 4463: /* Split argv[0], imach program to get pathimach */
4464: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
1.99 brouard 4465: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4466: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.99 brouard 4467: /* strcpy(pathimach,argv[0]); */
1.107 brouard 4468: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
1.53 brouard 4469: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.107 brouard 4470: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.119 brouard 4471: chdir(path); /* Can be a relative path */
4472: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4473: printf("Current directory %s!\n",pathcd);
1.88 brouard 4474: strcpy(command,"mkdir ");
4475: strcat(command,optionfilefiname);
4476: if((outcmd=system(command)) != 0){
4477: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4478: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4479: /* fclose(ficlog); */
4480: /* exit(1); */
4481: }
4482: /* if((imk=mkdir(optionfilefiname))<0){ */
4483: /* perror("mkdir"); */
4484: /* } */
1.53 brouard 4485:
1.59 brouard 4486: /*-------- arguments in the command line --------*/
1.53 brouard 4487:
4488: /* Log file */
4489: strcat(filelog, optionfilefiname);
4490: strcat(filelog,".log"); /* */
4491: if((ficlog=fopen(filelog,"w"))==NULL) {
4492: printf("Problem with logfile %s\n",filelog);
4493: goto end;
4494: }
4495: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4496: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.99 brouard 4497: fprintf(ficlog,"\nEnter the parameter file name: \n");
4498: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
1.88 brouard 4499: path=%s \n\
4500: optionfile=%s\n\
4501: optionfilext=%s\n\
1.99 brouard 4502: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4503:
1.94 brouard 4504: printf("Local time (at start):%s",strstart);
4505: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4506: fflush(ficlog);
1.91 brouard 4507: /* (void) gettimeofday(&curr_time,&tzp); */
4508: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4509:
4510: /* */
4511: strcpy(fileres,"r");
4512: strcat(fileres, optionfilefiname);
4513: strcat(fileres,".txt"); /* Other files have txt extension */
4514:
4515: /*---------arguments file --------*/
4516:
4517: if((ficpar=fopen(optionfile,"r"))==NULL) {
4518: printf("Problem with optionfile %s\n",optionfile);
4519: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4520: fflush(ficlog);
1.53 brouard 4521: goto end;
4522: }
4523:
1.88 brouard 4524:
4525:
1.53 brouard 4526: strcpy(filereso,"o");
4527: strcat(filereso,fileres);
1.88 brouard 4528: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4529: printf("Problem with Output resultfile: %s\n", filereso);
4530: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4531: fflush(ficlog);
1.53 brouard 4532: goto end;
4533: }
4534:
4535: /* Reads comments: lines beginning with '#' */
1.85 brouard 4536: numlinepar=0;
1.53 brouard 4537: while((c=getc(ficpar))=='#' && c!= EOF){
4538: ungetc(c,ficpar);
4539: fgets(line, MAXLINE, ficpar);
1.85 brouard 4540: numlinepar++;
1.53 brouard 4541: puts(line);
4542: fputs(line,ficparo);
1.85 brouard 4543: fputs(line,ficlog);
1.53 brouard 4544: }
4545: ungetc(c,ficpar);
4546:
4547: 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 4548: numlinepar++;
1.53 brouard 4549: 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);
4550: 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 4551: 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);
4552: fflush(ficlog);
1.59 brouard 4553: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4554: ungetc(c,ficpar);
4555: fgets(line, MAXLINE, ficpar);
1.85 brouard 4556: numlinepar++;
1.53 brouard 4557: puts(line);
4558: fputs(line,ficparo);
1.85 brouard 4559: fputs(line,ficlog);
1.53 brouard 4560: }
4561: ungetc(c,ficpar);
1.85 brouard 4562:
1.53 brouard 4563:
4564: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4565: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4566: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4567:
1.58 lievre 4568: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4569: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 brouard 4570: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4571:
4572: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4573: delti=delti3[1][1];
4574: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4575: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4576: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4577: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4578: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 brouard 4579: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4580: fclose (ficparo);
4581: fclose (ficlog);
1.123 brouard 4582: goto end;
1.88 brouard 4583: exit(0);
4584: }
1.98 brouard 4585: else if(mle==-3) {
4586: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4587: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4588: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4589: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4590: matcov=matrix(1,npar,1,npar);
1.53 brouard 4591: }
1.98 brouard 4592: else{
4593: /* Read guess parameters */
4594: /* Reads comments: lines beginning with '#' */
4595: while((c=getc(ficpar))=='#' && c!= EOF){
4596: ungetc(c,ficpar);
4597: fgets(line, MAXLINE, ficpar);
1.85 brouard 4598: numlinepar++;
1.98 brouard 4599: puts(line);
4600: fputs(line,ficparo);
4601: fputs(line,ficlog);
1.53 brouard 4602: }
1.98 brouard 4603: ungetc(c,ficpar);
4604:
4605: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4606: for(i=1; i <=nlstate; i++){
4607: j=0;
4608: for(jj=1; jj <=nlstate+ndeath; jj++){
4609: if(jj==i) continue;
4610: j++;
4611: fscanf(ficpar,"%1d%1d",&i1,&j1);
4612: if ((i1 != i) && (j1 != j)){
1.123 brouard 4613: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4614: It might be a problem of design; if ncovcol and the model are correct\n \
4615: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.98 brouard 4616: exit(1);
4617: }
4618: fprintf(ficparo,"%1d%1d",i1,j1);
4619: if(mle==1)
4620: printf("%1d%1d",i,j);
4621: fprintf(ficlog,"%1d%1d",i,j);
4622: for(k=1; k<=ncovmodel;k++){
4623: fscanf(ficpar," %lf",¶m[i][j][k]);
4624: if(mle==1){
4625: printf(" %lf",param[i][j][k]);
4626: fprintf(ficlog," %lf",param[i][j][k]);
4627: }
4628: else
4629: fprintf(ficlog," %lf",param[i][j][k]);
4630: fprintf(ficparo," %lf",param[i][j][k]);
4631: }
4632: fscanf(ficpar,"\n");
4633: numlinepar++;
4634: if(mle==1)
4635: printf("\n");
4636: fprintf(ficlog,"\n");
4637: fprintf(ficparo,"\n");
4638: }
4639: }
4640: fflush(ficlog);
1.85 brouard 4641:
1.98 brouard 4642: p=param[1][1];
4643:
4644: /* Reads comments: lines beginning with '#' */
4645: while((c=getc(ficpar))=='#' && c!= EOF){
4646: ungetc(c,ficpar);
4647: fgets(line, MAXLINE, ficpar);
4648: numlinepar++;
4649: puts(line);
4650: fputs(line,ficparo);
4651: fputs(line,ficlog);
4652: }
1.53 brouard 4653: ungetc(c,ficpar);
4654:
1.98 brouard 4655: for(i=1; i <=nlstate; i++){
4656: for(j=1; j <=nlstate+ndeath-1; j++){
4657: fscanf(ficpar,"%1d%1d",&i1,&j1);
4658: if ((i1-i)*(j1-j)!=0){
4659: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4660: exit(1);
4661: }
4662: printf("%1d%1d",i,j);
4663: fprintf(ficparo,"%1d%1d",i1,j1);
4664: fprintf(ficlog,"%1d%1d",i1,j1);
4665: for(k=1; k<=ncovmodel;k++){
4666: fscanf(ficpar,"%le",&delti3[i][j][k]);
4667: printf(" %le",delti3[i][j][k]);
4668: fprintf(ficparo," %le",delti3[i][j][k]);
4669: fprintf(ficlog," %le",delti3[i][j][k]);
4670: }
4671: fscanf(ficpar,"\n");
4672: numlinepar++;
4673: printf("\n");
4674: fprintf(ficparo,"\n");
4675: fprintf(ficlog,"\n");
1.85 brouard 4676: }
1.53 brouard 4677: }
1.98 brouard 4678: fflush(ficlog);
1.85 brouard 4679:
1.98 brouard 4680: delti=delti3[1][1];
1.74 brouard 4681:
4682:
1.98 brouard 4683: /* 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 4684:
1.98 brouard 4685: /* Reads comments: lines beginning with '#' */
4686: while((c=getc(ficpar))=='#' && c!= EOF){
4687: ungetc(c,ficpar);
4688: fgets(line, MAXLINE, ficpar);
4689: numlinepar++;
4690: puts(line);
4691: fputs(line,ficparo);
4692: fputs(line,ficlog);
4693: }
1.53 brouard 4694: ungetc(c,ficpar);
4695:
1.98 brouard 4696: matcov=matrix(1,npar,1,npar);
4697: for(i=1; i <=npar; i++){
4698: fscanf(ficpar,"%s",&str);
4699: if(mle==1)
4700: printf("%s",str);
4701: fprintf(ficlog,"%s",str);
4702: fprintf(ficparo,"%s",str);
4703: for(j=1; j <=i; j++){
4704: fscanf(ficpar," %le",&matcov[i][j]);
4705: if(mle==1){
4706: printf(" %.5le",matcov[i][j]);
4707: }
4708: fprintf(ficlog," %.5le",matcov[i][j]);
4709: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4710: }
1.98 brouard 4711: fscanf(ficpar,"\n");
4712: numlinepar++;
4713: if(mle==1)
4714: printf("\n");
4715: fprintf(ficlog,"\n");
4716: fprintf(ficparo,"\n");
1.53 brouard 4717: }
1.98 brouard 4718: for(i=1; i <=npar; i++)
4719: for(j=i+1;j<=npar;j++)
4720: matcov[i][j]=matcov[j][i];
4721:
1.53 brouard 4722: if(mle==1)
4723: printf("\n");
4724: fprintf(ficlog,"\n");
1.98 brouard 4725:
4726: fflush(ficlog);
4727:
4728: /*-------- Rewriting parameter file ----------*/
4729: strcpy(rfileres,"r"); /* "Rparameterfile */
4730: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4731: strcat(rfileres,"."); /* */
4732: strcat(rfileres,optionfilext); /* Other files have txt extension */
4733: if((ficres =fopen(rfileres,"w"))==NULL) {
4734: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4735: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4736: }
4737: fprintf(ficres,"#%s\n",version);
4738: } /* End of mle != -3 */
1.53 brouard 4739:
1.59 brouard 4740: /*-------- data file ----------*/
4741: if((fic=fopen(datafile,"r"))==NULL) {
1.118 brouard 4742: printf("Problem while opening datafile: %s\n", datafile);goto end;
4743: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
1.59 brouard 4744: }
4745:
4746: n= lastobs;
4747: severity = vector(1,maxwav);
4748: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4749: num=lvector(1,n);
1.59 brouard 4750: moisnais=vector(1,n);
4751: annais=vector(1,n);
4752: moisdc=vector(1,n);
4753: andc=vector(1,n);
4754: agedc=vector(1,n);
4755: cod=ivector(1,n);
4756: weight=vector(1,n);
4757: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4758: mint=matrix(1,maxwav,1,n);
4759: anint=matrix(1,maxwav,1,n);
4760: s=imatrix(1,maxwav+1,1,n);
4761: tab=ivector(1,NCOVMAX);
4762: ncodemax=ivector(1,8);
4763:
4764: i=1;
1.109 brouard 4765: linei=0;
1.111 brouard 4766: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
1.109 brouard 4767: linei=linei+1;
4768: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
1.111 brouard 4769: if(line[j] == '\t')
4770: line[j] = ' ';
4771: }
4772: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4773: ;
4774: };
4775: line[j+1]=0; /* Trims blanks at end of line */
4776: if(line[0]=='#'){
4777: fprintf(ficlog,"Comment line\n%s\n",line);
4778: printf("Comment line\n%s\n",line);
4779: continue;
4780: }
1.109 brouard 4781:
1.111 brouard 4782: for (j=maxwav;j>=1;j--){
1.110 brouard 4783: cutv(stra, strb,line,' ');
1.111 brouard 4784: errno=0;
4785: lval=strtol(strb,&endptr,10);
4786: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4787: if( strb[0]=='\0' || (*endptr != '\0')){
4788: 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 4789: exit(1);
4790: }
1.111 brouard 4791: s[j][i]=lval;
4792:
1.109 brouard 4793: strcpy(line,stra);
1.111 brouard 4794: cutv(stra, strb,line,' ');
1.110 brouard 4795: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
1.109 brouard 4796: }
1.111 brouard 4797: else if(iout=sscanf(strb,"%s.") != 0){
1.110 brouard 4798: month=99;
4799: year=9999;
4800: }else{
1.111 brouard 4801: 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 4802: exit(1);
4803: }
1.111 brouard 4804: anint[j][i]= (double) year;
4805: mint[j][i]= (double)month;
1.109 brouard 4806: strcpy(line,stra);
1.111 brouard 4807: } /* ENd Waves */
4808:
4809: cutv(stra, strb,line,' ');
4810: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4811: }
4812: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4813: month=99;
4814: year=9999;
4815: }else{
4816: 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);
4817: exit(1);
4818: }
4819: andc[i]=(double) year;
4820: moisdc[i]=(double) month;
4821: strcpy(line,stra);
4822:
4823: cutv(stra, strb,line,' ');
4824: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4825: }
4826: else if(iout=sscanf(strb,"%s.") != 0){
4827: month=99;
4828: year=9999;
4829: }else{
4830: 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);
4831: exit(1);
4832: }
4833: annais[i]=(double)(year);
4834: moisnais[i]=(double)(month);
4835: strcpy(line,stra);
4836:
4837: cutv(stra, strb,line,' ');
4838: errno=0;
1.122 brouard 4839: dval=strtod(strb,&endptr);
1.111 brouard 4840: if( strb[0]=='\0' || (*endptr != '\0')){
1.122 brouard 4841: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.111 brouard 4842: exit(1);
4843: }
1.122 brouard 4844: weight[i]=dval;
1.111 brouard 4845: strcpy(line,stra);
4846:
4847: for (j=ncovcol;j>=1;j--){
1.109 brouard 4848: cutv(stra, strb,line,' ');
4849: errno=0;
4850: lval=strtol(strb,&endptr,10);
4851: if( strb[0]=='\0' || (*endptr != '\0')){
1.111 brouard 4852: 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);
4853: exit(1);
4854: }
4855: if(lval <-1 || lval >1){
1.122 brouard 4856: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4857: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4858: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4859: For example, for multinomial values like 1, 2 and 3,\n \
4860: build V1=0 V2=0 for the reference value (1),\n \
4861: V1=1 V2=0 for (2) \n \
4862: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4863: output of IMaCh is often meaningless.\n \
4864: Exiting.\n",lval,linei, i,line,j);
1.109 brouard 4865: exit(1);
4866: }
1.111 brouard 4867: covar[j][i]=(double)(lval);
1.109 brouard 4868: strcpy(line,stra);
1.111 brouard 4869: }
4870: lstra=strlen(stra);
4871:
4872: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4873: stratrunc = &(stra[lstra-9]);
4874: num[i]=atol(stratrunc);
4875: }
4876: else
4877: num[i]=atol(stra);
4878: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4879: 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;}*/
4880:
4881: i=i+1;
1.109 brouard 4882: } /* End loop reading data */
1.113 brouard 4883: fclose(fic);
1.59 brouard 4884: /* printf("ii=%d", ij);
4885: scanf("%d",i);*/
1.53 brouard 4886: imx=i-1; /* Number of individuals */
4887:
4888: /* for (i=1; i<=imx; i++){
4889: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4890: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4891: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4892: }*/
4893: /* for (i=1; i<=imx; i++){
4894: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4895: 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 4896:
1.106 brouard 4897: /* for (i=1; i<=imx; i++) */
1.53 brouard 4898:
1.71 brouard 4899: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4900: else weight[i]=1;*/
4901:
1.106 brouard 4902: /* Calculation of the number of parameters from char model */
1.53 brouard 4903: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4904: Tprod=ivector(1,15);
4905: Tvaraff=ivector(1,15);
4906: Tvard=imatrix(1,15,1,2);
4907: Tage=ivector(1,15);
4908:
1.58 lievre 4909: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4910: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4911: j=nbocc(model,'+'); /* j=Number of '+' */
4912: j1=nbocc(model,'*'); /* j1=Number of '*' */
4913: cptcovn=j+1;
4914: cptcovprod=j1; /*Number of products */
1.53 brouard 4915:
4916: strcpy(modelsav,model);
4917: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4918: printf("Error. Non available option model=%s ",model);
4919: fprintf(ficlog,"Error. Non available option model=%s ",model);
4920: goto end;
4921: }
4922:
1.59 brouard 4923: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4924:
1.53 brouard 4925: for(i=(j+1); i>=1;i--){
4926: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4927: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4928: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4929: /*scanf("%d",i);*/
4930: if (strchr(strb,'*')) { /* Model includes a product */
4931: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4932: if (strcmp(strc,"age")==0) { /* Vn*age */
4933: cptcovprod--;
4934: cutv(strb,stre,strd,'V');
4935: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4936: cptcovage++;
4937: Tage[cptcovage]=i;
4938: /*printf("stre=%s ", stre);*/
4939: }
4940: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4941: cptcovprod--;
4942: cutv(strb,stre,strc,'V');
4943: Tvar[i]=atoi(stre);
4944: cptcovage++;
4945: Tage[cptcovage]=i;
4946: }
4947: else { /* Age is not in the model */
4948: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4949: Tvar[i]=ncovcol+k1;
4950: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4951: Tprod[k1]=i;
4952: Tvard[k1][1]=atoi(strc); /* m*/
4953: Tvard[k1][2]=atoi(stre); /* n */
4954: Tvar[cptcovn+k2]=Tvard[k1][1];
4955: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4956: for (k=1; k<=lastobs;k++)
4957: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4958: k1++;
4959: k2=k2+2;
4960: }
4961: }
4962: else { /* no more sum */
4963: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4964: /* scanf("%d",i);*/
4965: cutv(strd,strc,strb,'V');
4966: Tvar[i]=atoi(strc);
4967: }
4968: strcpy(modelsav,stra);
4969: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4970: scanf("%d",i);*/
4971: } /* end of loop + */
4972: } /* end model */
4973:
1.58 lievre 4974: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4975: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4976:
1.53 brouard 4977: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4978: printf("cptcovprod=%d ", cptcovprod);
4979: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4980:
1.113 brouard 4981: scanf("%d ",i);*/
1.53 brouard 4982:
4983: /* if(mle==1){*/
1.59 brouard 4984: if (weightopt != 1) { /* Maximisation without weights*/
4985: for(i=1;i<=n;i++) weight[i]=1.0;
4986: }
1.53 brouard 4987: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4988: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4989:
1.59 brouard 4990: for (i=1; i<=imx; i++) {
4991: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4992: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4993: anint[m][i]=9999;
4994: s[m][i]=-1;
4995: }
1.76 brouard 4996: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4997: nberr++;
1.85 brouard 4998: 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);
4999: 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 5000: s[m][i]=-1;
5001: }
5002: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 5003: nberr++;
1.85 brouard 5004: 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]);
5005: 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 5006: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 5007: }
1.53 brouard 5008: }
1.59 brouard 5009: }
1.53 brouard 5010:
1.59 brouard 5011: for (i=1; i<=imx; i++) {
5012: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 5013: for(m=firstpass; (m<= lastpass); m++){
1.105 lievre 5014: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
1.59 brouard 5015: if (s[m][i] >= nlstate+1) {
5016: if(agedc[i]>0)
1.76 brouard 5017: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 5018: agev[m][i]=agedc[i];
1.59 brouard 5019: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5020: else {
1.76 brouard 5021: if ((int)andc[i]!=9999){
1.91 brouard 5022: nbwarn++;
1.85 brouard 5023: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5024: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 5025: agev[m][i]=-1;
1.53 brouard 5026: }
5027: }
1.70 brouard 5028: }
1.69 brouard 5029: else if(s[m][i] !=9){ /* Standard case, age in fractional
1.108 lievre 5030: years but with the precision of a month */
1.59 brouard 5031: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 5032: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 5033: agev[m][i]=1;
5034: else if(agev[m][i] <agemin){
5035: agemin=agev[m][i];
5036: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 5037: }
1.59 brouard 5038: else if(agev[m][i] >agemax){
5039: agemax=agev[m][i];
5040: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 5041: }
1.59 brouard 5042: /*agev[m][i]=anint[m][i]-annais[i];*/
5043: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 5044: }
1.59 brouard 5045: else { /* =9 */
1.53 brouard 5046: agev[m][i]=1;
1.59 brouard 5047: s[m][i]=-1;
5048: }
1.53 brouard 5049: }
1.59 brouard 5050: else /*= 0 Unknown */
5051: agev[m][i]=1;
5052: }
1.53 brouard 5053:
1.59 brouard 5054: }
5055: for (i=1; i<=imx; i++) {
1.71 brouard 5056: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 5057: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 5058: nberr++;
1.59 brouard 5059: 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);
5060: 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);
5061: goto end;
1.53 brouard 5062: }
5063: }
1.59 brouard 5064: }
1.53 brouard 5065:
1.71 brouard 5066: /*for (i=1; i<=imx; i++){
5067: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 5068: 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 5069: }
5070:
5071: }*/
5072:
1.97 lievre 5073:
1.59 brouard 5074: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5075: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5076:
1.98 brouard 5077: agegomp=(int)agemin;
1.59 brouard 5078: free_vector(severity,1,maxwav);
5079: free_imatrix(outcome,1,maxwav+1,1,n);
5080: free_vector(moisnais,1,n);
5081: free_vector(annais,1,n);
5082: /* free_matrix(mint,1,maxwav,1,n);
5083: free_matrix(anint,1,maxwav,1,n);*/
5084: free_vector(moisdc,1,n);
5085: free_vector(andc,1,n);
1.53 brouard 5086:
5087:
1.59 brouard 5088: wav=ivector(1,imx);
5089: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5090: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5091: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 5092:
1.59 brouard 5093: /* Concatenates waves */
5094: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 5095:
1.59 brouard 5096: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 5097:
1.59 brouard 5098: Tcode=ivector(1,100);
5099: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5100: ncodemax[1]=1;
5101: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 5102:
1.59 brouard 5103: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5104: the estimations*/
5105: h=0;
5106: m=pow(2,cptcoveff);
1.53 brouard 5107:
1.59 brouard 5108: for(k=1;k<=cptcoveff; k++){
5109: for(i=1; i <=(m/pow(2,k));i++){
5110: for(j=1; j <= ncodemax[k]; j++){
5111: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5112: h++;
5113: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5114: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5115: }
5116: }
5117: }
5118: }
5119: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5120: codtab[1][2]=1;codtab[2][2]=2; */
5121: /* for(i=1; i <=m ;i++){
5122: for(k=1; k <=cptcovn; k++){
5123: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5124: }
5125: printf("\n");
1.53 brouard 5126: }
1.59 brouard 5127: scanf("%d",i);*/
1.53 brouard 5128:
1.86 brouard 5129: /*------------ gnuplot -------------*/
5130: strcpy(optionfilegnuplot,optionfilefiname);
1.98 brouard 5131: if(mle==-3)
5132: strcat(optionfilegnuplot,"-mort");
1.86 brouard 5133: strcat(optionfilegnuplot,".gp");
1.98 brouard 5134:
1.86 brouard 5135: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5136: printf("Problem with file %s",optionfilegnuplot);
5137: }
5138: else{
5139: fprintf(ficgp,"\n# %s\n", version);
5140: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5141: fprintf(ficgp,"set missing 'NaNq'\n");
5142: }
1.88 brouard 5143: /* fclose(ficgp);*/
1.86 brouard 5144: /*--------- index.htm --------*/
5145:
1.91 brouard 5146: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 brouard 5147: if(mle==-3)
5148: strcat(optionfilehtm,"-mort");
1.86 brouard 5149: strcat(optionfilehtm,".htm");
5150: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5151: printf("Problem with %s \n",optionfilehtm), exit(0);
5152: }
5153:
1.91 brouard 5154: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5155: strcat(optionfilehtmcov,"-cov.htm");
5156: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5157: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5158: }
5159: else{
1.123 brouard 5160: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.91 brouard 5161: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5162: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
1.123 brouard 5163: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
1.91 brouard 5164: }
5165:
1.123 brouard 5166: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.86 brouard 5167: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5168: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5169: \n\
5170: <hr size=\"2\" color=\"#EC5E5E\">\
5171: <ul><li><h4>Parameter files</h4>\n\
1.117 brouard 5172: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
1.86 brouard 5173: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5174: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 5175: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 5176: - Date and time at start: %s</ul>\n",\
1.123 brouard 5177: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
1.117 brouard 5178: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
1.91 brouard 5179: fileres,fileres,\
1.88 brouard 5180: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 5181: fflush(fichtm);
1.86 brouard 5182:
1.88 brouard 5183: strcpy(pathr,path);
5184: strcat(pathr,optionfilefiname);
5185: chdir(optionfilefiname); /* Move to directory named optionfile */
5186:
1.59 brouard 5187: /* Calculates basic frequencies. Computes observed prevalence at single age
5188: and prints on file fileres'p'. */
1.105 lievre 5189: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
1.53 brouard 5190:
1.88 brouard 5191: fprintf(fichtm,"\n");
5192: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 5193: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5194: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 5195: imx,agemin,agemax,jmin,jmax,jmean);
5196: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 5197: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5198: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5199: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5200: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 5201:
5202:
1.59 brouard 5203: /* For Powell, parameters are in a vector p[] starting at p[1]
5204: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5205: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 5206:
1.86 brouard 5207: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.110 brouard 5208:
1.98 brouard 5209: if (mle==-3){
5210: ximort=matrix(1,NDIM,1,NDIM);
5211: cens=ivector(1,n);
5212: ageexmed=vector(1,n);
5213: agecens=vector(1,n);
5214: dcwave=ivector(1,n);
5215:
5216: for (i=1; i<=imx; i++){
5217: dcwave[i]=-1;
1.110 brouard 5218: for (m=firstpass; m<=lastpass; m++)
5219: if (s[m][i]>nlstate) {
5220: dcwave[i]=m;
1.98 brouard 5221: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5222: break;
5223: }
5224: }
5225:
5226: for (i=1; i<=imx; i++) {
5227: if (wav[i]>0){
5228: ageexmed[i]=agev[mw[1][i]][i];
1.110 brouard 5229: j=wav[i];
5230: agecens[i]=1.;
5231:
5232: if (ageexmed[i]> 1 && wav[i] > 0){
5233: agecens[i]=agev[mw[j][i]][i];
5234: cens[i]= 1;
5235: }else if (ageexmed[i]< 1)
5236: cens[i]= -1;
5237: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5238: cens[i]=0 ;
1.98 brouard 5239: }
5240: else cens[i]=-1;
5241: }
5242:
5243: for (i=1;i<=NDIM;i++) {
5244: for (j=1;j<=NDIM;j++)
5245: ximort[i][j]=(i == j ? 1.0 : 0.0);
5246: }
1.110 brouard 5247:
1.111 brouard 5248: p[1]=0.0268; p[NDIM]=0.083;
1.98 brouard 5249: /*printf("%lf %lf", p[1], p[2]);*/
5250:
5251:
1.110 brouard 5252: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5253: strcpy(filerespow,"pow-mort");
5254: strcat(filerespow,fileres);
5255: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5256: printf("Problem with resultfile: %s\n", filerespow);
5257: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5258: }
5259: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5260: /* for (i=1;i<=nlstate;i++)
5261: for(j=1;j<=nlstate+ndeath;j++)
5262: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5263: */
5264: fprintf(ficrespow,"\n");
5265:
1.98 brouard 5266: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5267: fclose(ficrespow);
1.53 brouard 5268:
1.110 brouard 5269: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
1.53 brouard 5270:
1.98 brouard 5271: for(i=1; i <=NDIM; i++)
5272: for(j=i+1;j<=NDIM;j++)
5273: matcov[i][j]=matcov[j][i];
5274:
5275: printf("\nCovariance matrix\n ");
5276: for(i=1; i <=NDIM; i++) {
5277: for(j=1;j<=NDIM;j++){
5278: printf("%f ",matcov[i][j]);
1.95 brouard 5279: }
1.98 brouard 5280: printf("\n ");
5281: }
5282:
5283: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5284: for (i=1;i<=NDIM;i++)
5285: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.105 lievre 5286:
1.110 brouard 5287: lsurv=vector(1,AGESUP);
1.105 lievre 5288: lpop=vector(1,AGESUP);
5289: tpop=vector(1,AGESUP);
5290: lsurv[agegomp]=100000;
1.110 brouard 5291:
5292: for (k=agegomp;k<=AGESUP;k++) {
1.105 lievre 5293: agemortsup=k;
5294: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5295: }
1.110 brouard 5296:
5297: for (k=agegomp;k<agemortsup;k++)
1.105 lievre 5298: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
1.110 brouard 5299:
1.105 lievre 5300: for (k=agegomp;k<agemortsup;k++){
5301: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5302: sumlpop=sumlpop+lpop[k];
5303: }
1.110 brouard 5304:
5305: tpop[agegomp]=sumlpop;
1.105 lievre 5306: for (k=agegomp;k<(agemortsup-3);k++){
5307: /* tpop[k+1]=2;*/
5308: tpop[k+1]=tpop[k]-lpop[k];
1.110 brouard 5309: }
5310:
5311:
5312: printf("\nAge lx qx dx Lx Tx e(x)\n");
1.105 lievre 5313: for (k=agegomp;k<(agemortsup-2);k++)
5314: 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 5315:
5316:
1.119 brouard 5317: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.98 brouard 5318: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5319:
5320: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5321: stepm, weightopt,\
1.105 lievre 5322: model,imx,p,matcov,agemortsup);
1.110 brouard 5323:
1.105 lievre 5324: free_vector(lsurv,1,AGESUP);
5325: free_vector(lpop,1,AGESUP);
5326: free_vector(tpop,1,AGESUP);
1.98 brouard 5327: } /* Endof if mle==-3 */
1.110 brouard 5328:
1.98 brouard 5329: else{ /* For mle >=1 */
5330:
5331: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5332: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5333: for (k=1; k<=npar;k++)
5334: printf(" %d %8.5f",k,p[k]);
5335: printf("\n");
5336: globpr=1; /* to print the contributions */
5337: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5338: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5339: for (k=1; k<=npar;k++)
5340: printf(" %d %8.5f",k,p[k]);
5341: printf("\n");
5342: if(mle>=1){ /* Could be 1 or 2 */
5343: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 5344: }
1.98 brouard 5345:
5346: /*--------- results files --------------*/
5347: 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);
5348:
5349:
5350: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5351: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5352: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5353: for(i=1,jk=1; i <=nlstate; i++){
5354: for(k=1; k <=(nlstate+ndeath); k++){
5355: if (k != i) {
5356: printf("%d%d ",i,k);
5357: fprintf(ficlog,"%d%d ",i,k);
5358: fprintf(ficres,"%1d%1d ",i,k);
5359: for(j=1; j <=ncovmodel; j++){
1.124 ! lievre 5360: printf("%lf ",p[jk]);
! 5361: fprintf(ficlog,"%lf ",p[jk]);
! 5362: fprintf(ficres,"%lf ",p[jk]);
1.98 brouard 5363: jk++;
5364: }
5365: printf("\n");
5366: fprintf(ficlog,"\n");
5367: fprintf(ficres,"\n");
1.59 brouard 5368: }
5369: }
5370: }
1.98 brouard 5371: if(mle!=0){
5372: /* Computing hessian and covariance matrix */
5373: ftolhess=ftol; /* Usually correct */
5374: hesscov(matcov, p, npar, delti, ftolhess, func);
5375: }
5376: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5377: printf("# Scales (for hessian or gradient estimation)\n");
5378: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5379: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 5380: for(j=1; j <=nlstate+ndeath; j++){
1.98 brouard 5381: if (j!=i) {
5382: fprintf(ficres,"%1d%1d",i,j);
5383: printf("%1d%1d",i,j);
5384: fprintf(ficlog,"%1d%1d",i,j);
5385: for(k=1; k<=ncovmodel;k++){
5386: printf(" %.5e",delti[jk]);
5387: fprintf(ficlog," %.5e",delti[jk]);
5388: fprintf(ficres," %.5e",delti[jk]);
5389: jk++;
1.95 brouard 5390: }
1.98 brouard 5391: printf("\n");
5392: fprintf(ficlog,"\n");
5393: fprintf(ficres,"\n");
5394: }
5395: }
5396: }
5397:
5398: 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");
5399: if(mle>=1)
5400: 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");
5401: 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");
5402: /* # 121 Var(a12)\n\ */
5403: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5404: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5405: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5406: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5407: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5408: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5409: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5410:
5411:
5412: /* Just to have a covariance matrix which will be more understandable
5413: even is we still don't want to manage dictionary of variables
5414: */
5415: for(itimes=1;itimes<=2;itimes++){
5416: jj=0;
5417: for(i=1; i <=nlstate; i++){
5418: for(j=1; j <=nlstate+ndeath; j++){
5419: if(j==i) continue;
5420: for(k=1; k<=ncovmodel;k++){
5421: jj++;
5422: ca[0]= k+'a'-1;ca[1]='\0';
5423: if(itimes==1){
5424: if(mle>=1)
5425: printf("#%1d%1d%d",i,j,k);
5426: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5427: fprintf(ficres,"#%1d%1d%d",i,j,k);
5428: }else{
5429: if(mle>=1)
5430: printf("%1d%1d%d",i,j,k);
5431: fprintf(ficlog,"%1d%1d%d",i,j,k);
5432: fprintf(ficres,"%1d%1d%d",i,j,k);
5433: }
5434: ll=0;
5435: for(li=1;li <=nlstate; li++){
5436: for(lj=1;lj <=nlstate+ndeath; lj++){
5437: if(lj==li) continue;
5438: for(lk=1;lk<=ncovmodel;lk++){
5439: ll++;
5440: if(ll<=jj){
5441: cb[0]= lk +'a'-1;cb[1]='\0';
5442: if(ll<jj){
5443: if(itimes==1){
5444: if(mle>=1)
5445: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5446: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5447: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5448: }else{
5449: if(mle>=1)
5450: printf(" %.5e",matcov[jj][ll]);
5451: fprintf(ficlog," %.5e",matcov[jj][ll]);
5452: fprintf(ficres," %.5e",matcov[jj][ll]);
5453: }
1.95 brouard 5454: }else{
1.98 brouard 5455: if(itimes==1){
5456: if(mle>=1)
5457: printf(" Var(%s%1d%1d)",ca,i,j);
5458: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5459: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5460: }else{
5461: if(mle>=1)
5462: printf(" %.5e",matcov[jj][ll]);
5463: fprintf(ficlog," %.5e",matcov[jj][ll]);
5464: fprintf(ficres," %.5e",matcov[jj][ll]);
5465: }
1.95 brouard 5466: }
5467: }
1.98 brouard 5468: } /* end lk */
5469: } /* end lj */
5470: } /* end li */
5471: if(mle>=1)
5472: printf("\n");
5473: fprintf(ficlog,"\n");
5474: fprintf(ficres,"\n");
5475: numlinepar++;
5476: } /* end k*/
5477: } /*end j */
5478: } /* end i */
5479: } /* end itimes */
5480:
5481: fflush(ficlog);
5482: fflush(ficres);
5483:
5484: while((c=getc(ficpar))=='#' && c!= EOF){
5485: ungetc(c,ficpar);
5486: fgets(line, MAXLINE, ficpar);
5487: puts(line);
5488: fputs(line,ficparo);
5489: }
1.59 brouard 5490: ungetc(c,ficpar);
1.98 brouard 5491:
5492: estepm=0;
5493: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5494: if (estepm==0 || estepm < stepm) estepm=stepm;
5495: if (fage <= 2) {
5496: bage = ageminpar;
5497: fage = agemaxpar;
5498: }
5499:
5500: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5501: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5502: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5503:
5504: while((c=getc(ficpar))=='#' && c!= EOF){
5505: ungetc(c,ficpar);
5506: fgets(line, MAXLINE, ficpar);
5507: puts(line);
5508: fputs(line,ficparo);
5509: }
1.59 brouard 5510: ungetc(c,ficpar);
1.98 brouard 5511:
5512: 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);
5513: 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);
5514: 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);
5515: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5516: 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);
5517:
5518: while((c=getc(ficpar))=='#' && c!= EOF){
5519: ungetc(c,ficpar);
5520: fgets(line, MAXLINE, ficpar);
5521: puts(line);
5522: fputs(line,ficparo);
5523: }
1.59 brouard 5524: ungetc(c,ficpar);
1.98 brouard 5525:
5526:
5527: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5528: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5529:
5530: fscanf(ficpar,"pop_based=%d\n",&popbased);
5531: fprintf(ficparo,"pop_based=%d\n",popbased);
5532: fprintf(ficres,"pop_based=%d\n",popbased);
5533:
5534: while((c=getc(ficpar))=='#' && c!= EOF){
5535: ungetc(c,ficpar);
5536: fgets(line, MAXLINE, ficpar);
5537: puts(line);
5538: fputs(line,ficparo);
5539: }
1.53 brouard 5540: ungetc(c,ficpar);
1.98 brouard 5541:
5542: 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);
5543: 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);
5544: 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);
5545: 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);
5546: 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);
5547: /* day and month of proj2 are not used but only year anproj2.*/
5548:
5549:
5550:
5551: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5552: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5553:
1.119 brouard 5554: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.98 brouard 5555: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5556:
5557: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5558: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5559: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5560:
5561: /*------------ free_vector -------------*/
5562: /* chdir(path); */
1.53 brouard 5563:
1.98 brouard 5564: free_ivector(wav,1,imx);
5565: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5566: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5567: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5568: free_lvector(num,1,n);
5569: free_vector(agedc,1,n);
5570: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5571: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5572: fclose(ficparo);
5573: fclose(ficres);
5574:
5575:
1.117 brouard 5576: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.98 brouard 5577:
5578: strcpy(filerespl,"pl");
5579: strcat(filerespl,fileres);
5580: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.117 brouard 5581: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5582: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
1.98 brouard 5583: }
1.117 brouard 5584: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5585: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5586: pstamp(ficrespl);
5587: fprintf(ficrespl,"# Period (stable) prevalence \n");
1.98 brouard 5588: fprintf(ficrespl,"#Age ");
5589: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5590: fprintf(ficrespl,"\n");
5591:
5592: prlim=matrix(1,nlstate,1,nlstate);
5593:
5594: agebase=ageminpar;
5595: agelim=agemaxpar;
5596: ftolpl=1.e-10;
5597: i1=cptcoveff;
5598: if (cptcovn < 1){i1=1;}
5599:
5600: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5601: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5602: k=k+1;
5603: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5604: fprintf(ficrespl,"\n#******");
5605: printf("\n#******");
5606: fprintf(ficlog,"\n#******");
5607: for(j=1;j<=cptcoveff;j++) {
5608: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5609: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5610: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5611: }
5612: fprintf(ficrespl,"******\n");
5613: printf("******\n");
5614: fprintf(ficlog,"******\n");
1.53 brouard 5615:
1.98 brouard 5616: for (age=agebase; age<=agelim; age++){
5617: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5618: fprintf(ficrespl,"%.0f ",age );
5619: for(j=1;j<=cptcoveff;j++)
5620: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5621: for(i=1; i<=nlstate;i++)
5622: fprintf(ficrespl," %.5f", prlim[i][i]);
5623: fprintf(ficrespl,"\n");
5624: }
1.53 brouard 5625: }
5626: }
1.98 brouard 5627: fclose(ficrespl);
1.53 brouard 5628:
1.98 brouard 5629: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5630:
1.98 brouard 5631: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5632: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5633: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5634: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5635: }
5636: printf("Computing pij: result on file '%s' \n", filerespij);
5637: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5638:
1.98 brouard 5639: stepsize=(int) (stepm+YEARM-1)/YEARM;
5640: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5641:
1.98 brouard 5642: agelim=AGESUP;
5643: hstepm=stepsize*YEARM; /* Every year of age */
5644: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5645:
1.98 brouard 5646: /* hstepm=1; aff par mois*/
1.117 brouard 5647: pstamp(ficrespij);
1.98 brouard 5648: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5649: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5650: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5651: k=k+1;
5652: fprintf(ficrespij,"\n#****** ");
5653: for(j=1;j<=cptcoveff;j++)
5654: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5655: fprintf(ficrespij,"******\n");
1.53 brouard 5656:
1.98 brouard 5657: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5658: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5659: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5660:
1.98 brouard 5661: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5662:
1.98 brouard 5663: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5664: oldm=oldms;savm=savms;
5665: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5666: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5667: for(i=1; i<=nlstate;i++)
5668: for(j=1; j<=nlstate+ndeath;j++)
1.98 brouard 5669: fprintf(ficrespij," %1d-%1d",i,j);
5670: fprintf(ficrespij,"\n");
5671: for (h=0; h<=nhstepm; h++){
5672: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5673: for(i=1; i<=nlstate;i++)
5674: for(j=1; j<=nlstate+ndeath;j++)
5675: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5676: fprintf(ficrespij,"\n");
5677: }
5678: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5679: fprintf(ficrespij,"\n");
5680: }
1.59 brouard 5681: }
1.53 brouard 5682: }
5683:
1.105 lievre 5684: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.53 brouard 5685:
1.98 brouard 5686: fclose(ficrespij);
1.53 brouard 5687:
1.98 brouard 5688: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5689: for(i=1;i<=AGESUP;i++)
5690: for(j=1;j<=NCOVMAX;j++)
5691: for(k=1;k<=NCOVMAX;k++)
5692: probs[i][j][k]=0.;
5693:
5694: /*---------- Forecasting ------------------*/
5695: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5696: if(prevfcast==1){
5697: /* if(stepm ==1){*/
1.70 brouard 5698: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5699: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 brouard 5700: /* } */
5701: /* else{ */
5702: /* erreur=108; */
5703: /* 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); */
5704: /* 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); */
5705: /* } */
5706: }
1.53 brouard 5707:
5708:
1.98 brouard 5709: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5710:
1.98 brouard 5711: strcpy(filerest,"t");
5712: strcat(filerest,fileres);
5713: if((ficrest=fopen(filerest,"w"))==NULL) {
5714: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5715: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5716: }
1.117 brouard 5717: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5718: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
1.53 brouard 5719:
5720:
1.98 brouard 5721: strcpy(filerese,"e");
5722: strcat(filerese,fileres);
5723: if((ficreseij=fopen(filerese,"w"))==NULL) {
5724: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5725: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5726: }
5727: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5728: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5729:
1.117 brouard 5730: strcpy(fileresstde,"stde");
5731: strcat(fileresstde,fileres);
5732: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5733: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5734: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5735: }
5736: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5737: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5738:
5739: strcpy(filerescve,"cve");
5740: strcat(filerescve,fileres);
5741: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5742: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5743: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5744: }
5745: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5746: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5747:
1.98 brouard 5748: strcpy(fileresv,"v");
5749: strcat(fileresv,fileres);
5750: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5751: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5752: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5753: }
5754: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5755: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5756:
1.98 brouard 5757: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5758: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5759: /* 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",\
5760: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5761: */
1.58 lievre 5762:
1.98 brouard 5763: if (mobilav!=0) {
5764: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5765: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5766: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5767: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5768: }
1.54 brouard 5769: }
1.53 brouard 5770:
1.98 brouard 5771: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5772: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5773: k=k+1;
5774: fprintf(ficrest,"\n#****** ");
5775: for(j=1;j<=cptcoveff;j++)
5776: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5777: fprintf(ficrest,"******\n");
5778:
5779: fprintf(ficreseij,"\n#****** ");
1.117 brouard 5780: fprintf(ficresstdeij,"\n#****** ");
5781: fprintf(ficrescveij,"\n#****** ");
5782: for(j=1;j<=cptcoveff;j++) {
1.98 brouard 5783: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.117 brouard 5784: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5785: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5786: }
1.98 brouard 5787: fprintf(ficreseij,"******\n");
1.117 brouard 5788: fprintf(ficresstdeij,"******\n");
5789: fprintf(ficrescveij,"******\n");
1.98 brouard 5790:
5791: fprintf(ficresvij,"\n#****** ");
5792: for(j=1;j<=cptcoveff;j++)
5793: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5794: fprintf(ficresvij,"******\n");
5795:
5796: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5797: oldm=oldms;savm=savms;
1.117 brouard 5798: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5799: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.53 brouard 5800:
1.98 brouard 5801: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5802: oldm=oldms;savm=savms;
1.105 lievre 5803: 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 5804: if(popbased==1){
1.105 lievre 5805: 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 5806: }
1.53 brouard 5807:
1.117 brouard 5808: pstamp(ficrest);
1.118 brouard 5809: 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 5810: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5811: fprintf(ficrest,"\n");
5812:
5813: epj=vector(1,nlstate+1);
5814: for(age=bage; age <=fage ;age++){
5815: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5816: if (popbased==1) {
5817: if(mobilav ==0){
5818: for(i=1; i<=nlstate;i++)
5819: prlim[i][i]=probs[(int)age][i][k];
5820: }else{ /* mobilav */
5821: for(i=1; i<=nlstate;i++)
5822: prlim[i][i]=mobaverage[(int)age][i][k];
5823: }
1.53 brouard 5824: }
5825:
1.98 brouard 5826: fprintf(ficrest," %4.0f",age);
5827: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5828: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5829: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5830: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5831: }
5832: epj[nlstate+1] +=epj[j];
1.53 brouard 5833: }
5834:
1.98 brouard 5835: for(i=1, vepp=0.;i <=nlstate;i++)
5836: for(j=1;j <=nlstate;j++)
5837: vepp += vareij[i][j][(int)age];
5838: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5839: for(j=1;j <=nlstate;j++){
5840: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5841: }
5842: fprintf(ficrest,"\n");
1.53 brouard 5843: }
1.98 brouard 5844: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5845: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5846: free_vector(epj,1,nlstate+1);
5847: }
5848: }
5849: free_vector(weight,1,n);
5850: free_imatrix(Tvard,1,15,1,2);
5851: free_imatrix(s,1,maxwav+1,1,n);
5852: free_matrix(anint,1,maxwav,1,n);
5853: free_matrix(mint,1,maxwav,1,n);
5854: free_ivector(cod,1,n);
5855: free_ivector(tab,1,NCOVMAX);
5856: fclose(ficreseij);
1.117 brouard 5857: fclose(ficresstdeij);
5858: fclose(ficrescveij);
1.98 brouard 5859: fclose(ficresvij);
5860: fclose(ficrest);
5861: fclose(ficpar);
5862:
1.117 brouard 5863: /*------- Variance of period (stable) prevalence------*/
1.98 brouard 5864:
5865: strcpy(fileresvpl,"vpl");
5866: strcat(fileresvpl,fileres);
5867: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.117 brouard 5868: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
1.98 brouard 5869: exit(0);
5870: }
1.117 brouard 5871: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
1.98 brouard 5872:
5873: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5874: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5875: k=k+1;
5876: fprintf(ficresvpl,"\n#****** ");
5877: for(j=1;j<=cptcoveff;j++)
5878: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5879: fprintf(ficresvpl,"******\n");
5880:
5881: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5882: oldm=oldms;savm=savms;
1.105 lievre 5883: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
1.98 brouard 5884: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5885: }
1.98 brouard 5886: }
1.53 brouard 5887:
1.98 brouard 5888: fclose(ficresvpl);
1.53 brouard 5889:
1.98 brouard 5890: /*---------- End : free ----------------*/
5891: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5892: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5893:
5894: } /* mle==-3 arrives here for freeing */
1.113 brouard 5895: free_matrix(prlim,1,nlstate,1,nlstate);
1.98 brouard 5896: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5897: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5898: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5899: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5900: free_matrix(covar,0,NCOVMAX,1,n);
5901: free_matrix(matcov,1,npar,1,npar);
5902: /*free_vector(delti,1,npar);*/
5903: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5904: free_matrix(agev,1,maxwav,1,imx);
5905: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5906:
5907: free_ivector(ncodemax,1,8);
5908: free_ivector(Tvar,1,15);
5909: free_ivector(Tprod,1,15);
5910: free_ivector(Tvaraff,1,15);
5911: free_ivector(Tage,1,15);
5912: free_ivector(Tcode,1,100);
1.74 brouard 5913:
1.113 brouard 5914: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5915: free_imatrix(codtab,1,100,1,10);
1.88 brouard 5916: fflush(fichtm);
5917: fflush(ficgp);
1.53 brouard 5918:
5919:
1.91 brouard 5920: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5921: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5922: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5923: }else{
1.91 brouard 5924: printf("End of Imach\n");
5925: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5926: }
5927: printf("See log file on %s\n",filelog);
5928: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5929: (void) gettimeofday(&end_time,&tzp);
5930: tm = *localtime(&end_time.tv_sec);
5931: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5932: strcpy(strtend,asctime(&tm));
1.105 lievre 5933: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
1.94 brouard 5934: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5935: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5936:
1.91 brouard 5937: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5938: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5939: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5940: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5941: /* if(fileappend(fichtm,optionfilehtm)){ */
1.123 brouard 5942: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
1.87 brouard 5943: fclose(fichtm);
1.123 brouard 5944: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
1.91 brouard 5945: fclose(fichtmcov);
1.88 brouard 5946: fclose(ficgp);
1.91 brouard 5947: fclose(ficlog);
1.53 brouard 5948: /*------ End -----------*/
5949:
1.119 brouard 5950:
5951: printf("Before Current directory %s!\n",pathcd);
5952: if(chdir(pathcd) != 0)
5953: printf("Can't move to directory %s!\n",path);
5954: if(getcwd(pathcd,MAXLINE) > 0)
5955: printf("Current directory %s!\n",pathcd);
1.107 brouard 5956: /*strcat(plotcmd,CHARSEPARATOR);*/
1.111 brouard 5957: sprintf(plotcmd,"gnuplot");
1.107 brouard 5958: #ifndef UNIX
1.112 brouard 5959: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
1.107 brouard 5960: #endif
1.111 brouard 5961: if(!stat(plotcmd,&info)){
1.107 brouard 5962: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
1.111 brouard 5963: if(!stat(getenv("GNUPLOTBIN"),&info)){
5964: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5965: }else
5966: strcpy(pplotcmd,plotcmd);
5967: #ifdef UNIX
5968: strcpy(plotcmd,GNUPLOTPROGRAM);
5969: if(!stat(plotcmd,&info)){
5970: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5971: }else
5972: strcpy(pplotcmd,plotcmd);
1.108 lievre 5973: #endif
1.111 brouard 5974: }else
5975: strcpy(pplotcmd,plotcmd);
5976:
5977: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5978: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
1.107 brouard 5979:
1.91 brouard 5980: if((outcmd=system(plotcmd)) != 0){
1.108 lievre 5981: printf("\n Problem with gnuplot\n");
1.91 brouard 5982: }
1.75 brouard 5983: printf(" Wait...");
1.53 brouard 5984: while (z[0] != 'q') {
5985: /* chdir(path); */
1.91 brouard 5986: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5987: scanf("%s",z);
1.91 brouard 5988: /* if (z[0] == 'c') system("./imach"); */
1.99 brouard 5989: if (z[0] == 'e') {
5990: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5991: system(optionfilehtm);
5992: }
1.53 brouard 5993: else if (z[0] == 'g') system(plotcmd);
5994: else if (z[0] == 'q') exit(0);
5995: }
1.91 brouard 5996: end:
5997: while (z[0] != 'q') {
5998: printf("\nType q for exiting: ");
5999: scanf("%s",z);
6000: }
1.53 brouard 6001: }
1.88 brouard 6002:
1.53 brouard 6003:
6004:
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