Annotation of imach/src/imach.c, revision 1.131
1.131 ! brouard 1: /* $Id: imach.c,v 1.130 2009/05/26 06:44:34 brouard Exp $
1.126 brouard 2: $State: Exp $
3: $Log: imach.c,v $
1.131 ! brouard 4: Revision 1.130 2009/05/26 06:44:34 brouard
! 5: (Module): Max Covariate is now set to 20 instead of 8. A
! 6: lot of cleaning with variables initialized to 0. Trying to make
! 7: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
! 8:
1.130 brouard 9: Revision 1.129 2007/08/31 13:49:27 lievre
10: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
11:
1.129 lievre 12: Revision 1.128 2006/06/30 13:02:05 brouard
13: (Module): Clarifications on computing e.j
14:
1.128 brouard 15: Revision 1.127 2006/04/28 18:11:50 brouard
16: (Module): Yes the sum of survivors was wrong since
17: imach-114 because nhstepm was no more computed in the age
18: loop. Now we define nhstepma in the age loop.
19: (Module): In order to speed up (in case of numerous covariates) we
20: compute health expectancies (without variances) in a first step
21: and then all the health expectancies with variances or standard
22: deviation (needs data from the Hessian matrices) which slows the
23: computation.
24: In the future we should be able to stop the program is only health
25: expectancies and graph are needed without standard deviations.
26:
1.127 brouard 27: Revision 1.126 2006/04/28 17:23:28 brouard
28: (Module): Yes the sum of survivors was wrong since
29: imach-114 because nhstepm was no more computed in the age
30: loop. Now we define nhstepma in the age loop.
31: Version 0.98h
32:
1.126 brouard 33: Revision 1.125 2006/04/04 15:20:31 lievre
34: Errors in calculation of health expectancies. Age was not initialized.
35: Forecasting file added.
36:
37: Revision 1.124 2006/03/22 17:13:53 lievre
38: Parameters are printed with %lf instead of %f (more numbers after the comma).
39: The log-likelihood is printed in the log file
40:
41: Revision 1.123 2006/03/20 10:52:43 brouard
42: * imach.c (Module): <title> changed, corresponds to .htm file
43: name. <head> headers where missing.
44:
45: * imach.c (Module): Weights can have a decimal point as for
46: English (a comma might work with a correct LC_NUMERIC environment,
47: otherwise the weight is truncated).
48: Modification of warning when the covariates values are not 0 or
49: 1.
50: Version 0.98g
51:
52: Revision 1.122 2006/03/20 09:45:41 brouard
53: (Module): Weights can have a decimal point as for
54: English (a comma might work with a correct LC_NUMERIC environment,
55: otherwise the weight is truncated).
56: Modification of warning when the covariates values are not 0 or
57: 1.
58: Version 0.98g
59:
60: Revision 1.121 2006/03/16 17:45:01 lievre
61: * imach.c (Module): Comments concerning covariates added
62:
63: * imach.c (Module): refinements in the computation of lli if
64: status=-2 in order to have more reliable computation if stepm is
65: not 1 month. Version 0.98f
66:
67: Revision 1.120 2006/03/16 15:10:38 lievre
68: (Module): refinements in the computation of lli if
69: status=-2 in order to have more reliable computation if stepm is
70: not 1 month. Version 0.98f
71:
72: Revision 1.119 2006/03/15 17:42:26 brouard
73: (Module): Bug if status = -2, the loglikelihood was
74: computed as likelihood omitting the logarithm. Version O.98e
75:
76: Revision 1.118 2006/03/14 18:20:07 brouard
77: (Module): varevsij Comments added explaining the second
78: table of variances if popbased=1 .
79: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
80: (Module): Function pstamp added
81: (Module): Version 0.98d
82:
83: Revision 1.117 2006/03/14 17:16:22 brouard
84: (Module): varevsij Comments added explaining the second
85: table of variances if popbased=1 .
86: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
87: (Module): Function pstamp added
88: (Module): Version 0.98d
89:
90: Revision 1.116 2006/03/06 10:29:27 brouard
91: (Module): Variance-covariance wrong links and
92: varian-covariance of ej. is needed (Saito).
93:
94: Revision 1.115 2006/02/27 12:17:45 brouard
95: (Module): One freematrix added in mlikeli! 0.98c
96:
97: Revision 1.114 2006/02/26 12:57:58 brouard
98: (Module): Some improvements in processing parameter
99: filename with strsep.
100:
101: Revision 1.113 2006/02/24 14:20:24 brouard
102: (Module): Memory leaks checks with valgrind and:
103: datafile was not closed, some imatrix were not freed and on matrix
104: allocation too.
105:
106: Revision 1.112 2006/01/30 09:55:26 brouard
107: (Module): Back to gnuplot.exe instead of wgnuplot.exe
108:
109: Revision 1.111 2006/01/25 20:38:18 brouard
110: (Module): Lots of cleaning and bugs added (Gompertz)
111: (Module): Comments can be added in data file. Missing date values
112: can be a simple dot '.'.
113:
114: Revision 1.110 2006/01/25 00:51:50 brouard
115: (Module): Lots of cleaning and bugs added (Gompertz)
116:
117: Revision 1.109 2006/01/24 19:37:15 brouard
118: (Module): Comments (lines starting with a #) are allowed in data.
119:
120: Revision 1.108 2006/01/19 18:05:42 lievre
121: Gnuplot problem appeared...
122: To be fixed
123:
124: Revision 1.107 2006/01/19 16:20:37 brouard
125: Test existence of gnuplot in imach path
126:
127: Revision 1.106 2006/01/19 13:24:36 brouard
128: Some cleaning and links added in html output
129:
130: Revision 1.105 2006/01/05 20:23:19 lievre
131: *** empty log message ***
132:
133: Revision 1.104 2005/09/30 16:11:43 lievre
134: (Module): sump fixed, loop imx fixed, and simplifications.
135: (Module): If the status is missing at the last wave but we know
136: that the person is alive, then we can code his/her status as -2
137: (instead of missing=-1 in earlier versions) and his/her
138: contributions to the likelihood is 1 - Prob of dying from last
139: health status (= 1-p13= p11+p12 in the easiest case of somebody in
140: the healthy state at last known wave). Version is 0.98
141:
142: Revision 1.103 2005/09/30 15:54:49 lievre
143: (Module): sump fixed, loop imx fixed, and simplifications.
144:
145: Revision 1.102 2004/09/15 17:31:30 brouard
146: Add the possibility to read data file including tab characters.
147:
148: Revision 1.101 2004/09/15 10:38:38 brouard
149: Fix on curr_time
150:
151: Revision 1.100 2004/07/12 18:29:06 brouard
152: Add version for Mac OS X. Just define UNIX in Makefile
153:
154: Revision 1.99 2004/06/05 08:57:40 brouard
155: *** empty log message ***
156:
157: Revision 1.98 2004/05/16 15:05:56 brouard
158: New version 0.97 . First attempt to estimate force of mortality
159: directly from the data i.e. without the need of knowing the health
160: state at each age, but using a Gompertz model: log u =a + b*age .
161: This is the basic analysis of mortality and should be done before any
162: other analysis, in order to test if the mortality estimated from the
163: cross-longitudinal survey is different from the mortality estimated
164: from other sources like vital statistic data.
165:
166: The same imach parameter file can be used but the option for mle should be -3.
167:
168: Agnès, who wrote this part of the code, tried to keep most of the
169: former routines in order to include the new code within the former code.
170:
171: The output is very simple: only an estimate of the intercept and of
172: the slope with 95% confident intervals.
173:
174: Current limitations:
175: A) Even if you enter covariates, i.e. with the
176: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
177: B) There is no computation of Life Expectancy nor Life Table.
178:
179: Revision 1.97 2004/02/20 13:25:42 lievre
180: Version 0.96d. Population forecasting command line is (temporarily)
181: suppressed.
182:
183: Revision 1.96 2003/07/15 15:38:55 brouard
184: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
185: rewritten within the same printf. Workaround: many printfs.
186:
187: Revision 1.95 2003/07/08 07:54:34 brouard
188: * imach.c (Repository):
189: (Repository): Using imachwizard code to output a more meaningful covariance
190: matrix (cov(a12,c31) instead of numbers.
191:
192: Revision 1.94 2003/06/27 13:00:02 brouard
193: Just cleaning
194:
195: Revision 1.93 2003/06/25 16:33:55 brouard
196: (Module): On windows (cygwin) function asctime_r doesn't
197: exist so I changed back to asctime which exists.
198: (Module): Version 0.96b
199:
200: Revision 1.92 2003/06/25 16:30:45 brouard
201: (Module): On windows (cygwin) function asctime_r doesn't
202: exist so I changed back to asctime which exists.
203:
204: Revision 1.91 2003/06/25 15:30:29 brouard
205: * imach.c (Repository): Duplicated warning errors corrected.
206: (Repository): Elapsed time after each iteration is now output. It
207: helps to forecast when convergence will be reached. Elapsed time
208: is stamped in powell. We created a new html file for the graphs
209: concerning matrix of covariance. It has extension -cov.htm.
210:
211: Revision 1.90 2003/06/24 12:34:15 brouard
212: (Module): Some bugs corrected for windows. Also, when
213: mle=-1 a template is output in file "or"mypar.txt with the design
214: of the covariance matrix to be input.
215:
216: Revision 1.89 2003/06/24 12:30:52 brouard
217: (Module): Some bugs corrected for windows. Also, when
218: mle=-1 a template is output in file "or"mypar.txt with the design
219: of the covariance matrix to be input.
220:
221: Revision 1.88 2003/06/23 17:54:56 brouard
222: * 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.
223:
224: Revision 1.87 2003/06/18 12:26:01 brouard
225: Version 0.96
226:
227: Revision 1.86 2003/06/17 20:04:08 brouard
228: (Module): Change position of html and gnuplot routines and added
229: routine fileappend.
230:
231: Revision 1.85 2003/06/17 13:12:43 brouard
232: * imach.c (Repository): Check when date of death was earlier that
233: current date of interview. It may happen when the death was just
234: prior to the death. In this case, dh was negative and likelihood
235: was wrong (infinity). We still send an "Error" but patch by
236: assuming that the date of death was just one stepm after the
237: interview.
238: (Repository): Because some people have very long ID (first column)
239: we changed int to long in num[] and we added a new lvector for
240: memory allocation. But we also truncated to 8 characters (left
241: truncation)
242: (Repository): No more line truncation errors.
243:
244: Revision 1.84 2003/06/13 21:44:43 brouard
245: * imach.c (Repository): Replace "freqsummary" at a correct
246: place. It differs from routine "prevalence" which may be called
247: many times. Probs is memory consuming and must be used with
248: parcimony.
249: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
250:
251: Revision 1.83 2003/06/10 13:39:11 lievre
252: *** empty log message ***
253:
254: Revision 1.82 2003/06/05 15:57:20 brouard
255: Add log in imach.c and fullversion number is now printed.
256:
257: */
258: /*
259: Interpolated Markov Chain
260:
261: Short summary of the programme:
262:
263: This program computes Healthy Life Expectancies from
264: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
265: first survey ("cross") where individuals from different ages are
266: interviewed on their health status or degree of disability (in the
267: case of a health survey which is our main interest) -2- at least a
268: second wave of interviews ("longitudinal") which measure each change
269: (if any) in individual health status. Health expectancies are
270: computed from the time spent in each health state according to a
271: model. More health states you consider, more time is necessary to reach the
272: Maximum Likelihood of the parameters involved in the model. The
273: simplest model is the multinomial logistic model where pij is the
274: probability to be observed in state j at the second wave
275: conditional to be observed in state i at the first wave. Therefore
276: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
277: 'age' is age and 'sex' is a covariate. If you want to have a more
278: complex model than "constant and age", you should modify the program
279: where the markup *Covariates have to be included here again* invites
280: you to do it. More covariates you add, slower the
281: convergence.
282:
283: The advantage of this computer programme, compared to a simple
284: multinomial logistic model, is clear when the delay between waves is not
285: identical for each individual. Also, if a individual missed an
286: intermediate interview, the information is lost, but taken into
287: account using an interpolation or extrapolation.
288:
289: hPijx is the probability to be observed in state i at age x+h
290: conditional to the observed state i at age x. The delay 'h' can be
291: split into an exact number (nh*stepm) of unobserved intermediate
292: states. This elementary transition (by month, quarter,
293: semester or year) is modelled as a multinomial logistic. The hPx
294: matrix is simply the matrix product of nh*stepm elementary matrices
295: and the contribution of each individual to the likelihood is simply
296: hPijx.
297:
298: Also this programme outputs the covariance matrix of the parameters but also
299: of the life expectancies. It also computes the period (stable) prevalence.
300:
301: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
302: Institut national d'études démographiques, Paris.
303: This software have been partly granted by Euro-REVES, a concerted action
304: from the European Union.
305: It is copyrighted identically to a GNU software product, ie programme and
306: software can be distributed freely for non commercial use. Latest version
307: can be accessed at http://euroreves.ined.fr/imach .
308:
309: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
310: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
311:
312: **********************************************************************/
313: /*
314: main
315: read parameterfile
316: read datafile
317: concatwav
318: freqsummary
319: if (mle >= 1)
320: mlikeli
321: print results files
322: if mle==1
323: computes hessian
324: read end of parameter file: agemin, agemax, bage, fage, estepm
325: begin-prev-date,...
326: open gnuplot file
327: open html file
328: period (stable) prevalence
329: for age prevalim()
330: h Pij x
331: variance of p varprob
332: forecasting if prevfcast==1 prevforecast call prevalence()
333: health expectancies
334: Variance-covariance of DFLE
335: prevalence()
336: movingaverage()
337: varevsij()
338: if popbased==1 varevsij(,popbased)
339: total life expectancies
340: Variance of period (stable) prevalence
341: end
342: */
343:
344:
345:
346:
347: #include <math.h>
348: #include <stdio.h>
349: #include <stdlib.h>
350: #include <string.h>
351: #include <unistd.h>
352:
353: #include <limits.h>
354: #include <sys/types.h>
355: #include <sys/stat.h>
356: #include <errno.h>
357: extern int errno;
358:
359: /* #include <sys/time.h> */
360: #include <time.h>
361: #include "timeval.h"
362:
363: /* #include <libintl.h> */
364: /* #define _(String) gettext (String) */
365:
366: #define MAXLINE 256
367:
368: #define GNUPLOTPROGRAM "gnuplot"
369: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
370: #define FILENAMELENGTH 132
371:
372: #define GLOCK_ERROR_NOPATH -1 /* empty path */
373: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
374:
1.131 ! brouard 375: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
1.126 brouard 376: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
377:
378: #define NINTERVMAX 8
379: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
380: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
1.130 brouard 381: #define NCOVMAX 20 /* Maximum number of covariates */
1.126 brouard 382: #define MAXN 20000
383: #define YEARM 12. /* Number of months per year */
384: #define AGESUP 130
385: #define AGEBASE 40
386: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
387: #ifdef UNIX
388: #define DIRSEPARATOR '/'
389: #define CHARSEPARATOR "/"
390: #define ODIRSEPARATOR '\\'
391: #else
392: #define DIRSEPARATOR '\\'
393: #define CHARSEPARATOR "\\"
394: #define ODIRSEPARATOR '/'
395: #endif
396:
1.131 ! brouard 397: /* $Id: imach.c,v 1.130 2009/05/26 06:44:34 brouard Exp $ */
1.126 brouard 398: /* $State: Exp $ */
399:
1.131 ! brouard 400: char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";
! 401: char fullversion[]="$Revision: 1.130 $ $Date: 2009/05/26 06:44:34 $";
1.126 brouard 402: char strstart[80];
403: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 404: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
405: int nvar=0;
406: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
1.126 brouard 407: int npar=NPARMAX;
408: int nlstate=2; /* Number of live states */
409: int ndeath=1; /* Number of dead states */
1.130 brouard 410: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 411: int popbased=0;
412:
413: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 414: int maxwav=0; /* Maxim number of waves */
415: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
416: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
417: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 418: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 419: int mle=1, weightopt=0;
1.126 brouard 420: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
421: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
422: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
423: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130 brouard 424: double jmean=1; /* Mean space between 2 waves */
1.126 brouard 425: double **oldm, **newm, **savm; /* Working pointers to matrices */
426: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
427: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
428: FILE *ficlog, *ficrespow;
1.130 brouard 429: int globpr=0; /* Global variable for printing or not */
1.126 brouard 430: double fretone; /* Only one call to likelihood */
1.130 brouard 431: long ipmx=0; /* Number of contributions */
1.126 brouard 432: double sw; /* Sum of weights */
433: char filerespow[FILENAMELENGTH];
434: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
435: FILE *ficresilk;
436: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
437: FILE *ficresprobmorprev;
438: FILE *fichtm, *fichtmcov; /* Html File */
439: FILE *ficreseij;
440: char filerese[FILENAMELENGTH];
441: FILE *ficresstdeij;
442: char fileresstde[FILENAMELENGTH];
443: FILE *ficrescveij;
444: char filerescve[FILENAMELENGTH];
445: FILE *ficresvij;
446: char fileresv[FILENAMELENGTH];
447: FILE *ficresvpl;
448: char fileresvpl[FILENAMELENGTH];
449: char title[MAXLINE];
450: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
451: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
452: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
453: char command[FILENAMELENGTH];
454: int outcmd=0;
455:
456: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
457:
458: char filelog[FILENAMELENGTH]; /* Log file */
459: char filerest[FILENAMELENGTH];
460: char fileregp[FILENAMELENGTH];
461: char popfile[FILENAMELENGTH];
462:
463: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
464:
465: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
466: struct timezone tzp;
467: extern int gettimeofday();
468: struct tm tmg, tm, tmf, *gmtime(), *localtime();
469: long time_value;
470: extern long time();
471: char strcurr[80], strfor[80];
472:
473: char *endptr;
474: long lval;
475: double dval;
476:
477: #define NR_END 1
478: #define FREE_ARG char*
479: #define FTOL 1.0e-10
480:
481: #define NRANSI
482: #define ITMAX 200
483:
484: #define TOL 2.0e-4
485:
486: #define CGOLD 0.3819660
487: #define ZEPS 1.0e-10
488: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
489:
490: #define GOLD 1.618034
491: #define GLIMIT 100.0
492: #define TINY 1.0e-20
493:
494: static double maxarg1,maxarg2;
495: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
496: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
497:
498: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
499: #define rint(a) floor(a+0.5)
500:
501: static double sqrarg;
502: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
503: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
504: int agegomp= AGEGOMP;
505:
506: int imx;
507: int stepm=1;
508: /* Stepm, step in month: minimum step interpolation*/
509:
510: int estepm;
511: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
512:
513: int m,nb;
514: long *num;
515: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
516: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
517: double **pmmij, ***probs;
518: double *ageexmed,*agecens;
519: double dateintmean=0;
520:
521: double *weight;
522: int **s; /* Status */
523: double *agedc, **covar, idx;
1.131 ! brouard 524: int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 525: double *lsurv, *lpop, *tpop;
526:
527: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
528: double ftolhess; /* Tolerance for computing hessian */
529:
530: /**************** split *************************/
531: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
532: {
533: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
534: the name of the file (name), its extension only (ext) and its first part of the name (finame)
535: */
536: char *ss; /* pointer */
537: int l1, l2; /* length counters */
538:
539: l1 = strlen(path ); /* length of path */
540: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
541: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
542: if ( ss == NULL ) { /* no directory, so determine current directory */
543: strcpy( name, path ); /* we got the fullname name because no directory */
544: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
545: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
546: /* get current working directory */
547: /* extern char* getcwd ( char *buf , int len);*/
548: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
549: return( GLOCK_ERROR_GETCWD );
550: }
551: /* got dirc from getcwd*/
552: printf(" DIRC = %s \n",dirc);
553: } else { /* strip direcotry from path */
554: ss++; /* after this, the filename */
555: l2 = strlen( ss ); /* length of filename */
556: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
557: strcpy( name, ss ); /* save file name */
558: strncpy( dirc, path, l1 - l2 ); /* now the directory */
559: dirc[l1-l2] = 0; /* add zero */
560: printf(" DIRC2 = %s \n",dirc);
561: }
562: /* We add a separator at the end of dirc if not exists */
563: l1 = strlen( dirc ); /* length of directory */
564: if( dirc[l1-1] != DIRSEPARATOR ){
565: dirc[l1] = DIRSEPARATOR;
566: dirc[l1+1] = 0;
567: printf(" DIRC3 = %s \n",dirc);
568: }
569: ss = strrchr( name, '.' ); /* find last / */
570: if (ss >0){
571: ss++;
572: strcpy(ext,ss); /* save extension */
573: l1= strlen( name);
574: l2= strlen(ss)+1;
575: strncpy( finame, name, l1-l2);
576: finame[l1-l2]= 0;
577: }
578:
579: return( 0 ); /* we're done */
580: }
581:
582:
583: /******************************************/
584:
585: void replace_back_to_slash(char *s, char*t)
586: {
587: int i;
588: int lg=0;
589: i=0;
590: lg=strlen(t);
591: for(i=0; i<= lg; i++) {
592: (s[i] = t[i]);
593: if (t[i]== '\\') s[i]='/';
594: }
595: }
596:
597: int nbocc(char *s, char occ)
598: {
599: int i,j=0;
600: int lg=20;
601: i=0;
602: lg=strlen(s);
603: for(i=0; i<= lg; i++) {
604: if (s[i] == occ ) j++;
605: }
606: return j;
607: }
608:
609: void cutv(char *u,char *v, char*t, char occ)
610: {
611: /* cuts string t into u and v where u ends before first occurence of char 'occ'
612: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
613: gives u="abcedf" and v="ghi2j" */
614: int i,lg,j,p=0;
615: i=0;
616: for(j=0; j<=strlen(t)-1; j++) {
617: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
618: }
619:
620: lg=strlen(t);
621: for(j=0; j<p; j++) {
622: (u[j] = t[j]);
623: }
624: u[p]='\0';
625:
626: for(j=0; j<= lg; j++) {
627: if (j>=(p+1))(v[j-p-1] = t[j]);
628: }
629: }
630:
631: /********************** nrerror ********************/
632:
633: void nrerror(char error_text[])
634: {
635: fprintf(stderr,"ERREUR ...\n");
636: fprintf(stderr,"%s\n",error_text);
637: exit(EXIT_FAILURE);
638: }
639: /*********************** vector *******************/
640: double *vector(int nl, int nh)
641: {
642: double *v;
643: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
644: if (!v) nrerror("allocation failure in vector");
645: return v-nl+NR_END;
646: }
647:
648: /************************ free vector ******************/
649: void free_vector(double*v, int nl, int nh)
650: {
651: free((FREE_ARG)(v+nl-NR_END));
652: }
653:
654: /************************ivector *******************************/
655: int *ivector(long nl,long nh)
656: {
657: int *v;
658: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
659: if (!v) nrerror("allocation failure in ivector");
660: return v-nl+NR_END;
661: }
662:
663: /******************free ivector **************************/
664: void free_ivector(int *v, long nl, long nh)
665: {
666: free((FREE_ARG)(v+nl-NR_END));
667: }
668:
669: /************************lvector *******************************/
670: long *lvector(long nl,long nh)
671: {
672: long *v;
673: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
674: if (!v) nrerror("allocation failure in ivector");
675: return v-nl+NR_END;
676: }
677:
678: /******************free lvector **************************/
679: void free_lvector(long *v, long nl, long nh)
680: {
681: free((FREE_ARG)(v+nl-NR_END));
682: }
683:
684: /******************* imatrix *******************************/
685: int **imatrix(long nrl, long nrh, long ncl, long nch)
686: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
687: {
688: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
689: int **m;
690:
691: /* allocate pointers to rows */
692: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
693: if (!m) nrerror("allocation failure 1 in matrix()");
694: m += NR_END;
695: m -= nrl;
696:
697:
698: /* allocate rows and set pointers to them */
699: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
700: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
701: m[nrl] += NR_END;
702: m[nrl] -= ncl;
703:
704: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
705:
706: /* return pointer to array of pointers to rows */
707: return m;
708: }
709:
710: /****************** free_imatrix *************************/
711: void free_imatrix(m,nrl,nrh,ncl,nch)
712: int **m;
713: long nch,ncl,nrh,nrl;
714: /* free an int matrix allocated by imatrix() */
715: {
716: free((FREE_ARG) (m[nrl]+ncl-NR_END));
717: free((FREE_ARG) (m+nrl-NR_END));
718: }
719:
720: /******************* matrix *******************************/
721: double **matrix(long nrl, long nrh, long ncl, long nch)
722: {
723: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
724: double **m;
725:
726: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
727: if (!m) nrerror("allocation failure 1 in matrix()");
728: m += NR_END;
729: m -= nrl;
730:
731: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
732: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
733: m[nrl] += NR_END;
734: m[nrl] -= ncl;
735:
736: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
737: return m;
738: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
739: */
740: }
741:
742: /*************************free matrix ************************/
743: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
744: {
745: free((FREE_ARG)(m[nrl]+ncl-NR_END));
746: free((FREE_ARG)(m+nrl-NR_END));
747: }
748:
749: /******************* ma3x *******************************/
750: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
751: {
752: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
753: double ***m;
754:
755: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
756: if (!m) nrerror("allocation failure 1 in matrix()");
757: m += NR_END;
758: m -= nrl;
759:
760: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
761: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
762: m[nrl] += NR_END;
763: m[nrl] -= ncl;
764:
765: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
766:
767: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
768: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
769: m[nrl][ncl] += NR_END;
770: m[nrl][ncl] -= nll;
771: for (j=ncl+1; j<=nch; j++)
772: m[nrl][j]=m[nrl][j-1]+nlay;
773:
774: for (i=nrl+1; i<=nrh; i++) {
775: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
776: for (j=ncl+1; j<=nch; j++)
777: m[i][j]=m[i][j-1]+nlay;
778: }
779: return m;
780: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
781: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
782: */
783: }
784:
785: /*************************free ma3x ************************/
786: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
787: {
788: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
789: free((FREE_ARG)(m[nrl]+ncl-NR_END));
790: free((FREE_ARG)(m+nrl-NR_END));
791: }
792:
793: /*************** function subdirf ***********/
794: char *subdirf(char fileres[])
795: {
796: /* Caution optionfilefiname is hidden */
797: strcpy(tmpout,optionfilefiname);
798: strcat(tmpout,"/"); /* Add to the right */
799: strcat(tmpout,fileres);
800: return tmpout;
801: }
802:
803: /*************** function subdirf2 ***********/
804: char *subdirf2(char fileres[], char *preop)
805: {
806:
807: /* Caution optionfilefiname is hidden */
808: strcpy(tmpout,optionfilefiname);
809: strcat(tmpout,"/");
810: strcat(tmpout,preop);
811: strcat(tmpout,fileres);
812: return tmpout;
813: }
814:
815: /*************** function subdirf3 ***********/
816: char *subdirf3(char fileres[], char *preop, char *preop2)
817: {
818:
819: /* Caution optionfilefiname is hidden */
820: strcpy(tmpout,optionfilefiname);
821: strcat(tmpout,"/");
822: strcat(tmpout,preop);
823: strcat(tmpout,preop2);
824: strcat(tmpout,fileres);
825: return tmpout;
826: }
827:
828: /***************** f1dim *************************/
829: extern int ncom;
830: extern double *pcom,*xicom;
831: extern double (*nrfunc)(double []);
832:
833: double f1dim(double x)
834: {
835: int j;
836: double f;
837: double *xt;
838:
839: xt=vector(1,ncom);
840: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
841: f=(*nrfunc)(xt);
842: free_vector(xt,1,ncom);
843: return f;
844: }
845:
846: /*****************brent *************************/
847: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
848: {
849: int iter;
850: double a,b,d,etemp;
851: double fu,fv,fw,fx;
852: double ftemp;
853: double p,q,r,tol1,tol2,u,v,w,x,xm;
854: double e=0.0;
855:
856: a=(ax < cx ? ax : cx);
857: b=(ax > cx ? ax : cx);
858: x=w=v=bx;
859: fw=fv=fx=(*f)(x);
860: for (iter=1;iter<=ITMAX;iter++) {
861: xm=0.5*(a+b);
862: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
863: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
864: printf(".");fflush(stdout);
865: fprintf(ficlog,".");fflush(ficlog);
866: #ifdef DEBUG
867: 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);
868: 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);
869: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
870: #endif
871: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
872: *xmin=x;
873: return fx;
874: }
875: ftemp=fu;
876: if (fabs(e) > tol1) {
877: r=(x-w)*(fx-fv);
878: q=(x-v)*(fx-fw);
879: p=(x-v)*q-(x-w)*r;
880: q=2.0*(q-r);
881: if (q > 0.0) p = -p;
882: q=fabs(q);
883: etemp=e;
884: e=d;
885: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
886: d=CGOLD*(e=(x >= xm ? a-x : b-x));
887: else {
888: d=p/q;
889: u=x+d;
890: if (u-a < tol2 || b-u < tol2)
891: d=SIGN(tol1,xm-x);
892: }
893: } else {
894: d=CGOLD*(e=(x >= xm ? a-x : b-x));
895: }
896: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
897: fu=(*f)(u);
898: if (fu <= fx) {
899: if (u >= x) a=x; else b=x;
900: SHFT(v,w,x,u)
901: SHFT(fv,fw,fx,fu)
902: } else {
903: if (u < x) a=u; else b=u;
904: if (fu <= fw || w == x) {
905: v=w;
906: w=u;
907: fv=fw;
908: fw=fu;
909: } else if (fu <= fv || v == x || v == w) {
910: v=u;
911: fv=fu;
912: }
913: }
914: }
915: nrerror("Too many iterations in brent");
916: *xmin=x;
917: return fx;
918: }
919:
920: /****************** mnbrak ***********************/
921:
922: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
923: double (*func)(double))
924: {
925: double ulim,u,r,q, dum;
926: double fu;
927:
928: *fa=(*func)(*ax);
929: *fb=(*func)(*bx);
930: if (*fb > *fa) {
931: SHFT(dum,*ax,*bx,dum)
932: SHFT(dum,*fb,*fa,dum)
933: }
934: *cx=(*bx)+GOLD*(*bx-*ax);
935: *fc=(*func)(*cx);
936: while (*fb > *fc) {
937: r=(*bx-*ax)*(*fb-*fc);
938: q=(*bx-*cx)*(*fb-*fa);
939: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
940: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
941: ulim=(*bx)+GLIMIT*(*cx-*bx);
942: if ((*bx-u)*(u-*cx) > 0.0) {
943: fu=(*func)(u);
944: } else if ((*cx-u)*(u-ulim) > 0.0) {
945: fu=(*func)(u);
946: if (fu < *fc) {
947: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
948: SHFT(*fb,*fc,fu,(*func)(u))
949: }
950: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
951: u=ulim;
952: fu=(*func)(u);
953: } else {
954: u=(*cx)+GOLD*(*cx-*bx);
955: fu=(*func)(u);
956: }
957: SHFT(*ax,*bx,*cx,u)
958: SHFT(*fa,*fb,*fc,fu)
959: }
960: }
961:
962: /*************** linmin ************************/
963:
964: int ncom;
965: double *pcom,*xicom;
966: double (*nrfunc)(double []);
967:
968: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
969: {
970: double brent(double ax, double bx, double cx,
971: double (*f)(double), double tol, double *xmin);
972: double f1dim(double x);
973: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
974: double *fc, double (*func)(double));
975: int j;
976: double xx,xmin,bx,ax;
977: double fx,fb,fa;
978:
979: ncom=n;
980: pcom=vector(1,n);
981: xicom=vector(1,n);
982: nrfunc=func;
983: for (j=1;j<=n;j++) {
984: pcom[j]=p[j];
985: xicom[j]=xi[j];
986: }
987: ax=0.0;
988: xx=1.0;
989: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
990: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
991: #ifdef DEBUG
992: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
993: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
994: #endif
995: for (j=1;j<=n;j++) {
996: xi[j] *= xmin;
997: p[j] += xi[j];
998: }
999: free_vector(xicom,1,n);
1000: free_vector(pcom,1,n);
1001: }
1002:
1003: char *asc_diff_time(long time_sec, char ascdiff[])
1004: {
1005: long sec_left, days, hours, minutes;
1006: days = (time_sec) / (60*60*24);
1007: sec_left = (time_sec) % (60*60*24);
1008: hours = (sec_left) / (60*60) ;
1009: sec_left = (sec_left) %(60*60);
1010: minutes = (sec_left) /60;
1011: sec_left = (sec_left) % (60);
1012: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1013: return ascdiff;
1014: }
1015:
1016: /*************** powell ************************/
1017: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1018: double (*func)(double []))
1019: {
1020: void linmin(double p[], double xi[], int n, double *fret,
1021: double (*func)(double []));
1022: int i,ibig,j;
1023: double del,t,*pt,*ptt,*xit;
1024: double fp,fptt;
1025: double *xits;
1026: int niterf, itmp;
1027:
1028: pt=vector(1,n);
1029: ptt=vector(1,n);
1030: xit=vector(1,n);
1031: xits=vector(1,n);
1032: *fret=(*func)(p);
1033: for (j=1;j<=n;j++) pt[j]=p[j];
1034: for (*iter=1;;++(*iter)) {
1035: fp=(*fret);
1036: ibig=0;
1037: del=0.0;
1038: last_time=curr_time;
1039: (void) gettimeofday(&curr_time,&tzp);
1040: 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);
1041: 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);
1042: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1043: for (i=1;i<=n;i++) {
1044: printf(" %d %.12f",i, p[i]);
1045: fprintf(ficlog," %d %.12lf",i, p[i]);
1046: fprintf(ficrespow," %.12lf", p[i]);
1047: }
1048: printf("\n");
1049: fprintf(ficlog,"\n");
1050: fprintf(ficrespow,"\n");fflush(ficrespow);
1051: if(*iter <=3){
1052: tm = *localtime(&curr_time.tv_sec);
1053: strcpy(strcurr,asctime(&tm));
1054: /* asctime_r(&tm,strcurr); */
1055: forecast_time=curr_time;
1056: itmp = strlen(strcurr);
1057: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1058: strcurr[itmp-1]='\0';
1059: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1060: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1061: for(niterf=10;niterf<=30;niterf+=10){
1062: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1063: tmf = *localtime(&forecast_time.tv_sec);
1064: /* asctime_r(&tmf,strfor); */
1065: strcpy(strfor,asctime(&tmf));
1066: itmp = strlen(strfor);
1067: if(strfor[itmp-1]=='\n')
1068: strfor[itmp-1]='\0';
1069: 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);
1070: 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);
1071: }
1072: }
1073: for (i=1;i<=n;i++) {
1074: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1075: fptt=(*fret);
1076: #ifdef DEBUG
1077: printf("fret=%lf \n",*fret);
1078: fprintf(ficlog,"fret=%lf \n",*fret);
1079: #endif
1080: printf("%d",i);fflush(stdout);
1081: fprintf(ficlog,"%d",i);fflush(ficlog);
1082: linmin(p,xit,n,fret,func);
1083: if (fabs(fptt-(*fret)) > del) {
1084: del=fabs(fptt-(*fret));
1085: ibig=i;
1086: }
1087: #ifdef DEBUG
1088: printf("%d %.12e",i,(*fret));
1089: fprintf(ficlog,"%d %.12e",i,(*fret));
1090: for (j=1;j<=n;j++) {
1091: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1092: printf(" x(%d)=%.12e",j,xit[j]);
1093: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1094: }
1095: for(j=1;j<=n;j++) {
1096: printf(" p=%.12e",p[j]);
1097: fprintf(ficlog," p=%.12e",p[j]);
1098: }
1099: printf("\n");
1100: fprintf(ficlog,"\n");
1101: #endif
1102: }
1103: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1104: #ifdef DEBUG
1105: int k[2],l;
1106: k[0]=1;
1107: k[1]=-1;
1108: printf("Max: %.12e",(*func)(p));
1109: fprintf(ficlog,"Max: %.12e",(*func)(p));
1110: for (j=1;j<=n;j++) {
1111: printf(" %.12e",p[j]);
1112: fprintf(ficlog," %.12e",p[j]);
1113: }
1114: printf("\n");
1115: fprintf(ficlog,"\n");
1116: for(l=0;l<=1;l++) {
1117: for (j=1;j<=n;j++) {
1118: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1119: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1120: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1121: }
1122: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1123: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1124: }
1125: #endif
1126:
1127:
1128: free_vector(xit,1,n);
1129: free_vector(xits,1,n);
1130: free_vector(ptt,1,n);
1131: free_vector(pt,1,n);
1132: return;
1133: }
1134: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1135: for (j=1;j<=n;j++) {
1136: ptt[j]=2.0*p[j]-pt[j];
1137: xit[j]=p[j]-pt[j];
1138: pt[j]=p[j];
1139: }
1140: fptt=(*func)(ptt);
1141: if (fptt < fp) {
1142: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1143: if (t < 0.0) {
1144: linmin(p,xit,n,fret,func);
1145: for (j=1;j<=n;j++) {
1146: xi[j][ibig]=xi[j][n];
1147: xi[j][n]=xit[j];
1148: }
1149: #ifdef DEBUG
1150: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1151: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1152: for(j=1;j<=n;j++){
1153: printf(" %.12e",xit[j]);
1154: fprintf(ficlog," %.12e",xit[j]);
1155: }
1156: printf("\n");
1157: fprintf(ficlog,"\n");
1158: #endif
1159: }
1160: }
1161: }
1162: }
1163:
1164: /**** Prevalence limit (stable or period prevalence) ****************/
1165:
1166: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1167: {
1168: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1169: matrix by transitions matrix until convergence is reached */
1170:
1171: int i, ii,j,k;
1172: double min, max, maxmin, maxmax,sumnew=0.;
1173: double **matprod2();
1.131 ! brouard 1174: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1175: double **newm;
1176: double agefin, delaymax=50 ; /* Max number of years to converge */
1177:
1178: for (ii=1;ii<=nlstate+ndeath;ii++)
1179: for (j=1;j<=nlstate+ndeath;j++){
1180: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1181: }
1182:
1183: cov[1]=1.;
1184:
1185: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1186: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1187: newm=savm;
1188: /* Covariates have to be included here again */
1189: cov[2]=agefin;
1190:
1191: for (k=1; k<=cptcovn;k++) {
1192: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1193: /* 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]]);*/
1194: }
1195: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1196: for (k=1; k<=cptcovprod;k++)
1197: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1198:
1199: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1200: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1201: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1202: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1203:
1204: savm=oldm;
1205: oldm=newm;
1206: maxmax=0.;
1207: for(j=1;j<=nlstate;j++){
1208: min=1.;
1209: max=0.;
1210: for(i=1; i<=nlstate; i++) {
1211: sumnew=0;
1212: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1213: prlim[i][j]= newm[i][j]/(1-sumnew);
1214: max=FMAX(max,prlim[i][j]);
1215: min=FMIN(min,prlim[i][j]);
1216: }
1217: maxmin=max-min;
1218: maxmax=FMAX(maxmax,maxmin);
1219: }
1220: if(maxmax < ftolpl){
1221: return prlim;
1222: }
1223: }
1224: }
1225:
1226: /*************** transition probabilities ***************/
1227:
1228: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1229: {
1230: double s1, s2;
1231: /*double t34;*/
1232: int i,j,j1, nc, ii, jj;
1233:
1234: for(i=1; i<= nlstate; i++){
1235: for(j=1; j<i;j++){
1236: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1237: /*s2 += param[i][j][nc]*cov[nc];*/
1238: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1239: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1240: }
1241: ps[i][j]=s2;
1242: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1243: }
1244: for(j=i+1; j<=nlstate+ndeath;j++){
1245: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1246: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1247: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1248: }
1249: ps[i][j]=s2;
1250: }
1251: }
1252: /*ps[3][2]=1;*/
1253:
1254: for(i=1; i<= nlstate; i++){
1255: s1=0;
1.131 ! brouard 1256: for(j=1; j<i; j++){
1.126 brouard 1257: s1+=exp(ps[i][j]);
1.131 ! brouard 1258: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 1259: }
! 1260: for(j=i+1; j<=nlstate+ndeath; j++){
1.126 brouard 1261: s1+=exp(ps[i][j]);
1.131 ! brouard 1262: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
! 1263: }
1.126 brouard 1264: ps[i][i]=1./(s1+1.);
1265: for(j=1; j<i; j++)
1266: ps[i][j]= exp(ps[i][j])*ps[i][i];
1267: for(j=i+1; j<=nlstate+ndeath; j++)
1268: ps[i][j]= exp(ps[i][j])*ps[i][i];
1269: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1270: } /* end i */
1271:
1272: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1273: for(jj=1; jj<= nlstate+ndeath; jj++){
1274: ps[ii][jj]=0;
1275: ps[ii][ii]=1;
1276: }
1277: }
1278:
1279:
1280: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1281: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1282: /* printf("ddd %lf ",ps[ii][jj]); */
1283: /* } */
1284: /* printf("\n "); */
1285: /* } */
1286: /* printf("\n ");printf("%lf ",cov[2]); */
1287: /*
1288: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1289: goto end;*/
1290: return ps;
1291: }
1292:
1293: /**************** Product of 2 matrices ******************/
1294:
1295: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1296: {
1297: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1298: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1299: /* in, b, out are matrice of pointers which should have been initialized
1300: before: only the contents of out is modified. The function returns
1301: a pointer to pointers identical to out */
1302: long i, j, k;
1303: for(i=nrl; i<= nrh; i++)
1304: for(k=ncolol; k<=ncoloh; k++)
1305: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1306: out[i][k] +=in[i][j]*b[j][k];
1307:
1308: return out;
1309: }
1310:
1311:
1312: /************* Higher Matrix Product ***************/
1313:
1314: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1315: {
1316: /* Computes the transition matrix starting at age 'age' over
1317: 'nhstepm*hstepm*stepm' months (i.e. until
1318: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1319: nhstepm*hstepm matrices.
1320: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1321: (typically every 2 years instead of every month which is too big
1322: for the memory).
1323: Model is determined by parameters x and covariates have to be
1324: included manually here.
1325:
1326: */
1327:
1328: int i, j, d, h, k;
1.131 ! brouard 1329: double **out, cov[NCOVMAX+1];
1.126 brouard 1330: double **newm;
1331:
1332: /* Hstepm could be zero and should return the unit matrix */
1333: for (i=1;i<=nlstate+ndeath;i++)
1334: for (j=1;j<=nlstate+ndeath;j++){
1335: oldm[i][j]=(i==j ? 1.0 : 0.0);
1336: po[i][j][0]=(i==j ? 1.0 : 0.0);
1337: }
1338: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1339: for(h=1; h <=nhstepm; h++){
1340: for(d=1; d <=hstepm; d++){
1341: newm=savm;
1342: /* Covariates have to be included here again */
1343: cov[1]=1.;
1344: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 ! brouard 1345: for (k=1; k<=cptcovn;k++)
! 1346: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1347: for (k=1; k<=cptcovage;k++)
1348: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1349: for (k=1; k<=cptcovprod;k++)
1350: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1351:
1352:
1353: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1354: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1355: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1356: pmij(pmmij,cov,ncovmodel,x,nlstate));
1357: savm=oldm;
1358: oldm=newm;
1359: }
1360: for(i=1; i<=nlstate+ndeath; i++)
1361: for(j=1;j<=nlstate+ndeath;j++) {
1362: po[i][j][h]=newm[i][j];
1.128 brouard 1363: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1364: }
1.128 brouard 1365: /*printf("h=%d ",h);*/
1.126 brouard 1366: } /* end h */
1.128 brouard 1367: /* printf("\n H=%d \n",h); */
1.126 brouard 1368: return po;
1369: }
1370:
1371:
1372: /*************** log-likelihood *************/
1373: double func( double *x)
1374: {
1375: int i, ii, j, k, mi, d, kk;
1.131 ! brouard 1376: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1377: double **out;
1378: double sw; /* Sum of weights */
1379: double lli; /* Individual log likelihood */
1380: int s1, s2;
1381: double bbh, survp;
1382: long ipmx;
1383: /*extern weight */
1384: /* We are differentiating ll according to initial status */
1385: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1386: /*for(i=1;i<imx;i++)
1387: printf(" %d\n",s[4][i]);
1388: */
1389: cov[1]=1.;
1390:
1391: for(k=1; k<=nlstate; k++) ll[k]=0.;
1392:
1393: if(mle==1){
1394: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1395: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1396: for(mi=1; mi<= wav[i]-1; mi++){
1397: for (ii=1;ii<=nlstate+ndeath;ii++)
1398: for (j=1;j<=nlstate+ndeath;j++){
1399: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1400: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1401: }
1402: for(d=0; d<dh[mi][i]; d++){
1403: newm=savm;
1404: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1405: for (kk=1; kk<=cptcovage;kk++) {
1406: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1407: }
1408: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1409: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1410: savm=oldm;
1411: oldm=newm;
1412: } /* end mult */
1413:
1414: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1415: /* But now since version 0.9 we anticipate for bias at large stepm.
1416: * If stepm is larger than one month (smallest stepm) and if the exact delay
1417: * (in months) between two waves is not a multiple of stepm, we rounded to
1418: * the nearest (and in case of equal distance, to the lowest) interval but now
1419: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1420: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1421: * probability in order to take into account the bias as a fraction of the way
1422: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1423: * -stepm/2 to stepm/2 .
1424: * For stepm=1 the results are the same as for previous versions of Imach.
1425: * For stepm > 1 the results are less biased than in previous versions.
1426: */
1427: s1=s[mw[mi][i]][i];
1428: s2=s[mw[mi+1][i]][i];
1429: bbh=(double)bh[mi][i]/(double)stepm;
1430: /* bias bh is positive if real duration
1431: * is higher than the multiple of stepm and negative otherwise.
1432: */
1433: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1434: if( s2 > nlstate){
1435: /* i.e. if s2 is a death state and if the date of death is known
1436: then the contribution to the likelihood is the probability to
1437: die between last step unit time and current step unit time,
1438: which is also equal to probability to die before dh
1439: minus probability to die before dh-stepm .
1440: In version up to 0.92 likelihood was computed
1441: as if date of death was unknown. Death was treated as any other
1442: health state: the date of the interview describes the actual state
1443: and not the date of a change in health state. The former idea was
1444: to consider that at each interview the state was recorded
1445: (healthy, disable or death) and IMaCh was corrected; but when we
1446: introduced the exact date of death then we should have modified
1447: the contribution of an exact death to the likelihood. This new
1448: contribution is smaller and very dependent of the step unit
1449: stepm. It is no more the probability to die between last interview
1450: and month of death but the probability to survive from last
1451: interview up to one month before death multiplied by the
1452: probability to die within a month. Thanks to Chris
1453: Jackson for correcting this bug. Former versions increased
1454: mortality artificially. The bad side is that we add another loop
1455: which slows down the processing. The difference can be up to 10%
1456: lower mortality.
1457: */
1458: lli=log(out[s1][s2] - savm[s1][s2]);
1459:
1460:
1461: } else if (s2==-2) {
1462: for (j=1,survp=0. ; j<=nlstate; j++)
1463: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1464: /*survp += out[s1][j]; */
1465: lli= log(survp);
1466: }
1467:
1468: else if (s2==-4) {
1469: for (j=3,survp=0. ; j<=nlstate; j++)
1470: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1471: lli= log(survp);
1472: }
1473:
1474: else if (s2==-5) {
1475: for (j=1,survp=0. ; j<=2; j++)
1476: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1477: lli= log(survp);
1478: }
1479:
1480: else{
1481: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1482: /* 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 */
1483: }
1484: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1485: /*if(lli ==000.0)*/
1486: /*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); */
1487: ipmx +=1;
1488: sw += weight[i];
1489: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1490: } /* end of wave */
1491: } /* end of individual */
1492: } else if(mle==2){
1493: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1494: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1495: for(mi=1; mi<= wav[i]-1; mi++){
1496: for (ii=1;ii<=nlstate+ndeath;ii++)
1497: for (j=1;j<=nlstate+ndeath;j++){
1498: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1499: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1500: }
1501: for(d=0; d<=dh[mi][i]; d++){
1502: newm=savm;
1503: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1504: for (kk=1; kk<=cptcovage;kk++) {
1505: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1506: }
1507: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1508: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1509: savm=oldm;
1510: oldm=newm;
1511: } /* end mult */
1512:
1513: s1=s[mw[mi][i]][i];
1514: s2=s[mw[mi+1][i]][i];
1515: bbh=(double)bh[mi][i]/(double)stepm;
1516: 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 */
1517: ipmx +=1;
1518: sw += weight[i];
1519: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1520: } /* end of wave */
1521: } /* end of individual */
1522: } else if(mle==3){ /* exponential inter-extrapolation */
1523: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1524: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1525: for(mi=1; mi<= wav[i]-1; mi++){
1526: for (ii=1;ii<=nlstate+ndeath;ii++)
1527: for (j=1;j<=nlstate+ndeath;j++){
1528: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1529: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1530: }
1531: for(d=0; d<dh[mi][i]; d++){
1532: newm=savm;
1533: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1534: for (kk=1; kk<=cptcovage;kk++) {
1535: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1536: }
1537: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1538: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1539: savm=oldm;
1540: oldm=newm;
1541: } /* end mult */
1542:
1543: s1=s[mw[mi][i]][i];
1544: s2=s[mw[mi+1][i]][i];
1545: bbh=(double)bh[mi][i]/(double)stepm;
1546: 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 */
1547: ipmx +=1;
1548: sw += weight[i];
1549: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1550: } /* end of wave */
1551: } /* end of individual */
1552: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1553: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1554: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1555: for(mi=1; mi<= wav[i]-1; mi++){
1556: for (ii=1;ii<=nlstate+ndeath;ii++)
1557: for (j=1;j<=nlstate+ndeath;j++){
1558: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1559: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1560: }
1561: for(d=0; d<dh[mi][i]; d++){
1562: newm=savm;
1563: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1564: for (kk=1; kk<=cptcovage;kk++) {
1565: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1566: }
1567:
1568: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1569: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1570: savm=oldm;
1571: oldm=newm;
1572: } /* end mult */
1573:
1574: s1=s[mw[mi][i]][i];
1575: s2=s[mw[mi+1][i]][i];
1576: if( s2 > nlstate){
1577: lli=log(out[s1][s2] - savm[s1][s2]);
1578: }else{
1579: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1580: }
1581: ipmx +=1;
1582: sw += weight[i];
1583: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1584: /* 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]); */
1585: } /* end of wave */
1586: } /* end of individual */
1587: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1588: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1589: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1590: for(mi=1; mi<= wav[i]-1; mi++){
1591: for (ii=1;ii<=nlstate+ndeath;ii++)
1592: for (j=1;j<=nlstate+ndeath;j++){
1593: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1594: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1595: }
1596: for(d=0; d<dh[mi][i]; d++){
1597: newm=savm;
1598: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1599: for (kk=1; kk<=cptcovage;kk++) {
1600: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1601: }
1602:
1603: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1604: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1605: savm=oldm;
1606: oldm=newm;
1607: } /* end mult */
1608:
1609: s1=s[mw[mi][i]][i];
1610: s2=s[mw[mi+1][i]][i];
1611: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1612: ipmx +=1;
1613: sw += weight[i];
1614: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1615: /*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]);*/
1616: } /* end of wave */
1617: } /* end of individual */
1618: } /* End of if */
1619: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1620: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1621: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1622: return -l;
1623: }
1624:
1625: /*************** log-likelihood *************/
1626: double funcone( double *x)
1627: {
1628: /* Same as likeli but slower because of a lot of printf and if */
1629: int i, ii, j, k, mi, d, kk;
1.131 ! brouard 1630: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1631: double **out;
1632: double lli; /* Individual log likelihood */
1633: double llt;
1634: int s1, s2;
1635: double bbh, survp;
1636: /*extern weight */
1637: /* We are differentiating ll according to initial status */
1638: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1639: /*for(i=1;i<imx;i++)
1640: printf(" %d\n",s[4][i]);
1641: */
1642: cov[1]=1.;
1643:
1644: for(k=1; k<=nlstate; k++) ll[k]=0.;
1645:
1646: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1647: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1648: for(mi=1; mi<= wav[i]-1; mi++){
1649: for (ii=1;ii<=nlstate+ndeath;ii++)
1650: for (j=1;j<=nlstate+ndeath;j++){
1651: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1652: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1653: }
1654: for(d=0; d<dh[mi][i]; d++){
1655: newm=savm;
1656: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1657: for (kk=1; kk<=cptcovage;kk++) {
1658: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1659: }
1660: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1661: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1662: savm=oldm;
1663: oldm=newm;
1664: } /* end mult */
1665:
1666: s1=s[mw[mi][i]][i];
1667: s2=s[mw[mi+1][i]][i];
1668: bbh=(double)bh[mi][i]/(double)stepm;
1669: /* bias is positive if real duration
1670: * is higher than the multiple of stepm and negative otherwise.
1671: */
1672: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1673: lli=log(out[s1][s2] - savm[s1][s2]);
1674: } else if (s2==-2) {
1675: for (j=1,survp=0. ; j<=nlstate; j++)
1676: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1677: lli= log(survp);
1678: }else if (mle==1){
1679: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1680: } else if(mle==2){
1681: 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 */
1682: } else if(mle==3){ /* exponential inter-extrapolation */
1683: 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 */
1684: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1685: lli=log(out[s1][s2]); /* Original formula */
1686: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1687: lli=log(out[s1][s2]); /* Original formula */
1688: } /* End of if */
1689: ipmx +=1;
1690: sw += weight[i];
1691: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.131 ! brouard 1692: 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]);
1.126 brouard 1693: if(globpr){
1694: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1695: %11.6f %11.6f %11.6f ", \
1696: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1697: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1698: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1699: llt +=ll[k]*gipmx/gsw;
1700: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1701: }
1702: fprintf(ficresilk," %10.6f\n", -llt);
1703: }
1704: } /* end of wave */
1705: } /* end of individual */
1706: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1707: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1708: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1709: if(globpr==0){ /* First time we count the contributions and weights */
1710: gipmx=ipmx;
1711: gsw=sw;
1712: }
1713: return -l;
1714: }
1715:
1716:
1717: /*************** function likelione ***********/
1718: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1719: {
1720: /* This routine should help understanding what is done with
1721: the selection of individuals/waves and
1722: to check the exact contribution to the likelihood.
1723: Plotting could be done.
1724: */
1725: int k;
1726:
1727: if(*globpri !=0){ /* Just counts and sums, no printings */
1728: strcpy(fileresilk,"ilk");
1729: strcat(fileresilk,fileres);
1730: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1731: printf("Problem with resultfile: %s\n", fileresilk);
1732: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1733: }
1734: 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");
1735: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1736: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1737: for(k=1; k<=nlstate; k++)
1738: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1739: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1740: }
1741:
1742: *fretone=(*funcone)(p);
1743: if(*globpri !=0){
1744: fclose(ficresilk);
1745: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1746: fflush(fichtm);
1747: }
1748: return;
1749: }
1750:
1751:
1752: /*********** Maximum Likelihood Estimation ***************/
1753:
1754: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1755: {
1756: int i,j, iter;
1757: double **xi;
1758: double fret;
1759: double fretone; /* Only one call to likelihood */
1760: /* char filerespow[FILENAMELENGTH];*/
1761: xi=matrix(1,npar,1,npar);
1762: for (i=1;i<=npar;i++)
1763: for (j=1;j<=npar;j++)
1764: xi[i][j]=(i==j ? 1.0 : 0.0);
1765: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1766: strcpy(filerespow,"pow");
1767: strcat(filerespow,fileres);
1768: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1769: printf("Problem with resultfile: %s\n", filerespow);
1770: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1771: }
1772: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1773: for (i=1;i<=nlstate;i++)
1774: for(j=1;j<=nlstate+ndeath;j++)
1775: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1776: fprintf(ficrespow,"\n");
1777:
1778: powell(p,xi,npar,ftol,&iter,&fret,func);
1779:
1780: free_matrix(xi,1,npar,1,npar);
1781: fclose(ficrespow);
1782: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1783: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1784: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1785:
1786: }
1787:
1788: /**** Computes Hessian and covariance matrix ***/
1789: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1790: {
1791: double **a,**y,*x,pd;
1792: double **hess;
1793: int i, j,jk;
1794: int *indx;
1795:
1796: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1797: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1798: void lubksb(double **a, int npar, int *indx, double b[]) ;
1799: void ludcmp(double **a, int npar, int *indx, double *d) ;
1800: double gompertz(double p[]);
1801: hess=matrix(1,npar,1,npar);
1802:
1803: printf("\nCalculation of the hessian matrix. Wait...\n");
1804: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1805: for (i=1;i<=npar;i++){
1806: printf("%d",i);fflush(stdout);
1807: fprintf(ficlog,"%d",i);fflush(ficlog);
1808:
1809: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1810:
1811: /* printf(" %f ",p[i]);
1812: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1813: }
1814:
1815: for (i=1;i<=npar;i++) {
1816: for (j=1;j<=npar;j++) {
1817: if (j>i) {
1818: printf(".%d%d",i,j);fflush(stdout);
1819: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1820: hess[i][j]=hessij(p,delti,i,j,func,npar);
1821:
1822: hess[j][i]=hess[i][j];
1823: /*printf(" %lf ",hess[i][j]);*/
1824: }
1825: }
1826: }
1827: printf("\n");
1828: fprintf(ficlog,"\n");
1829:
1830: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1831: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1832:
1833: a=matrix(1,npar,1,npar);
1834: y=matrix(1,npar,1,npar);
1835: x=vector(1,npar);
1836: indx=ivector(1,npar);
1837: for (i=1;i<=npar;i++)
1838: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1839: ludcmp(a,npar,indx,&pd);
1840:
1841: for (j=1;j<=npar;j++) {
1842: for (i=1;i<=npar;i++) x[i]=0;
1843: x[j]=1;
1844: lubksb(a,npar,indx,x);
1845: for (i=1;i<=npar;i++){
1846: matcov[i][j]=x[i];
1847: }
1848: }
1849:
1850: printf("\n#Hessian matrix#\n");
1851: fprintf(ficlog,"\n#Hessian matrix#\n");
1852: for (i=1;i<=npar;i++) {
1853: for (j=1;j<=npar;j++) {
1854: printf("%.3e ",hess[i][j]);
1855: fprintf(ficlog,"%.3e ",hess[i][j]);
1856: }
1857: printf("\n");
1858: fprintf(ficlog,"\n");
1859: }
1860:
1861: /* Recompute Inverse */
1862: for (i=1;i<=npar;i++)
1863: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1864: ludcmp(a,npar,indx,&pd);
1865:
1866: /* printf("\n#Hessian matrix recomputed#\n");
1867:
1868: for (j=1;j<=npar;j++) {
1869: for (i=1;i<=npar;i++) x[i]=0;
1870: x[j]=1;
1871: lubksb(a,npar,indx,x);
1872: for (i=1;i<=npar;i++){
1873: y[i][j]=x[i];
1874: printf("%.3e ",y[i][j]);
1875: fprintf(ficlog,"%.3e ",y[i][j]);
1876: }
1877: printf("\n");
1878: fprintf(ficlog,"\n");
1879: }
1880: */
1881:
1882: free_matrix(a,1,npar,1,npar);
1883: free_matrix(y,1,npar,1,npar);
1884: free_vector(x,1,npar);
1885: free_ivector(indx,1,npar);
1886: free_matrix(hess,1,npar,1,npar);
1887:
1888:
1889: }
1890:
1891: /*************** hessian matrix ****************/
1892: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1893: {
1894: int i;
1895: int l=1, lmax=20;
1896: double k1,k2;
1897: double p2[NPARMAX+1];
1898: double res;
1899: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1900: double fx;
1901: int k=0,kmax=10;
1902: double l1;
1903:
1904: fx=func(x);
1905: for (i=1;i<=npar;i++) p2[i]=x[i];
1906: for(l=0 ; l <=lmax; l++){
1907: l1=pow(10,l);
1908: delts=delt;
1909: for(k=1 ; k <kmax; k=k+1){
1910: delt = delta*(l1*k);
1911: p2[theta]=x[theta] +delt;
1912: k1=func(p2)-fx;
1913: p2[theta]=x[theta]-delt;
1914: k2=func(p2)-fx;
1915: /*res= (k1-2.0*fx+k2)/delt/delt; */
1916: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1917:
1918: #ifdef DEBUG
1919: 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);
1920: 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);
1921: #endif
1922: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1923: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1924: k=kmax;
1925: }
1926: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1927: k=kmax; l=lmax*10.;
1928: }
1929: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1930: delts=delt;
1931: }
1932: }
1933: }
1934: delti[theta]=delts;
1935: return res;
1936:
1937: }
1938:
1939: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1940: {
1941: int i;
1942: int l=1, l1, lmax=20;
1943: double k1,k2,k3,k4,res,fx;
1944: double p2[NPARMAX+1];
1945: int k;
1946:
1947: fx=func(x);
1948: for (k=1; k<=2; k++) {
1949: for (i=1;i<=npar;i++) p2[i]=x[i];
1950: p2[thetai]=x[thetai]+delti[thetai]/k;
1951: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1952: k1=func(p2)-fx;
1953:
1954: p2[thetai]=x[thetai]+delti[thetai]/k;
1955: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1956: k2=func(p2)-fx;
1957:
1958: p2[thetai]=x[thetai]-delti[thetai]/k;
1959: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1960: k3=func(p2)-fx;
1961:
1962: p2[thetai]=x[thetai]-delti[thetai]/k;
1963: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1964: k4=func(p2)-fx;
1965: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1966: #ifdef DEBUG
1967: 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);
1968: 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);
1969: #endif
1970: }
1971: return res;
1972: }
1973:
1974: /************** Inverse of matrix **************/
1975: void ludcmp(double **a, int n, int *indx, double *d)
1976: {
1977: int i,imax,j,k;
1978: double big,dum,sum,temp;
1979: double *vv;
1980:
1981: vv=vector(1,n);
1982: *d=1.0;
1983: for (i=1;i<=n;i++) {
1984: big=0.0;
1985: for (j=1;j<=n;j++)
1986: if ((temp=fabs(a[i][j])) > big) big=temp;
1987: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1988: vv[i]=1.0/big;
1989: }
1990: for (j=1;j<=n;j++) {
1991: for (i=1;i<j;i++) {
1992: sum=a[i][j];
1993: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1994: a[i][j]=sum;
1995: }
1996: big=0.0;
1997: for (i=j;i<=n;i++) {
1998: sum=a[i][j];
1999: for (k=1;k<j;k++)
2000: sum -= a[i][k]*a[k][j];
2001: a[i][j]=sum;
2002: if ( (dum=vv[i]*fabs(sum)) >= big) {
2003: big=dum;
2004: imax=i;
2005: }
2006: }
2007: if (j != imax) {
2008: for (k=1;k<=n;k++) {
2009: dum=a[imax][k];
2010: a[imax][k]=a[j][k];
2011: a[j][k]=dum;
2012: }
2013: *d = -(*d);
2014: vv[imax]=vv[j];
2015: }
2016: indx[j]=imax;
2017: if (a[j][j] == 0.0) a[j][j]=TINY;
2018: if (j != n) {
2019: dum=1.0/(a[j][j]);
2020: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2021: }
2022: }
2023: free_vector(vv,1,n); /* Doesn't work */
2024: ;
2025: }
2026:
2027: void lubksb(double **a, int n, int *indx, double b[])
2028: {
2029: int i,ii=0,ip,j;
2030: double sum;
2031:
2032: for (i=1;i<=n;i++) {
2033: ip=indx[i];
2034: sum=b[ip];
2035: b[ip]=b[i];
2036: if (ii)
2037: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2038: else if (sum) ii=i;
2039: b[i]=sum;
2040: }
2041: for (i=n;i>=1;i--) {
2042: sum=b[i];
2043: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2044: b[i]=sum/a[i][i];
2045: }
2046: }
2047:
2048: void pstamp(FILE *fichier)
2049: {
2050: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2051: }
2052:
2053: /************ Frequencies ********************/
2054: 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[])
2055: { /* Some frequencies */
2056:
1.130 brouard 2057: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2058: int first;
2059: double ***freq; /* Frequencies */
2060: double *pp, **prop;
2061: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2062: char fileresp[FILENAMELENGTH];
2063:
2064: pp=vector(1,nlstate);
2065: prop=matrix(1,nlstate,iagemin,iagemax+3);
2066: strcpy(fileresp,"p");
2067: strcat(fileresp,fileres);
2068: if((ficresp=fopen(fileresp,"w"))==NULL) {
2069: printf("Problem with prevalence resultfile: %s\n", fileresp);
2070: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2071: exit(0);
2072: }
2073: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2074: j1=0;
2075:
2076: j=cptcoveff;
2077: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2078:
2079: first=1;
2080:
2081: for(k1=1; k1<=j;k1++){
2082: for(i1=1; i1<=ncodemax[k1];i1++){
2083: j1++;
2084: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2085: scanf("%d", i);*/
2086: for (i=-5; i<=nlstate+ndeath; i++)
2087: for (jk=-5; jk<=nlstate+ndeath; jk++)
2088: for(m=iagemin; m <= iagemax+3; m++)
2089: freq[i][jk][m]=0;
2090:
2091: for (i=1; i<=nlstate; i++)
2092: for(m=iagemin; m <= iagemax+3; m++)
2093: prop[i][m]=0;
2094:
2095: dateintsum=0;
2096: k2cpt=0;
2097: for (i=1; i<=imx; i++) {
2098: bool=1;
2099: if (cptcovn>0) {
2100: for (z1=1; z1<=cptcoveff; z1++)
2101: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2102: bool=0;
2103: }
2104: if (bool==1){
2105: for(m=firstpass; m<=lastpass; m++){
2106: k2=anint[m][i]+(mint[m][i]/12.);
2107: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2108: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2109: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2110: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2111: if (m<lastpass) {
2112: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2113: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2114: }
2115:
2116: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2117: dateintsum=dateintsum+k2;
2118: k2cpt++;
2119: }
2120: /*}*/
2121: }
2122: }
2123: }
2124:
2125: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2126: pstamp(ficresp);
2127: if (cptcovn>0) {
2128: fprintf(ficresp, "\n#********** Variable ");
2129: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2130: fprintf(ficresp, "**********\n#");
2131: }
2132: for(i=1; i<=nlstate;i++)
2133: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2134: fprintf(ficresp, "\n");
2135:
2136: for(i=iagemin; i <= iagemax+3; i++){
2137: if(i==iagemax+3){
2138: fprintf(ficlog,"Total");
2139: }else{
2140: if(first==1){
2141: first=0;
2142: printf("See log file for details...\n");
2143: }
2144: fprintf(ficlog,"Age %d", i);
2145: }
2146: for(jk=1; jk <=nlstate ; jk++){
2147: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2148: pp[jk] += freq[jk][m][i];
2149: }
2150: for(jk=1; jk <=nlstate ; jk++){
2151: for(m=-1, pos=0; m <=0 ; m++)
2152: pos += freq[jk][m][i];
2153: if(pp[jk]>=1.e-10){
2154: if(first==1){
2155: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2156: }
2157: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2158: }else{
2159: if(first==1)
2160: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2161: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2162: }
2163: }
2164:
2165: for(jk=1; jk <=nlstate ; jk++){
2166: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2167: pp[jk] += freq[jk][m][i];
2168: }
2169: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2170: pos += pp[jk];
2171: posprop += prop[jk][i];
2172: }
2173: for(jk=1; jk <=nlstate ; jk++){
2174: if(pos>=1.e-5){
2175: if(first==1)
2176: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2177: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2178: }else{
2179: if(first==1)
2180: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2181: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2182: }
2183: if( i <= iagemax){
2184: if(pos>=1.e-5){
2185: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2186: /*probs[i][jk][j1]= pp[jk]/pos;*/
2187: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2188: }
2189: else
2190: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2191: }
2192: }
2193:
2194: for(jk=-1; jk <=nlstate+ndeath; jk++)
2195: for(m=-1; m <=nlstate+ndeath; m++)
2196: if(freq[jk][m][i] !=0 ) {
2197: if(first==1)
2198: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2199: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2200: }
2201: if(i <= iagemax)
2202: fprintf(ficresp,"\n");
2203: if(first==1)
2204: printf("Others in log...\n");
2205: fprintf(ficlog,"\n");
2206: }
2207: }
2208: }
2209: dateintmean=dateintsum/k2cpt;
2210:
2211: fclose(ficresp);
2212: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2213: free_vector(pp,1,nlstate);
2214: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2215: /* End of Freq */
2216: }
2217:
2218: /************ Prevalence ********************/
2219: 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)
2220: {
2221: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2222: in each health status at the date of interview (if between dateprev1 and dateprev2).
2223: We still use firstpass and lastpass as another selection.
2224: */
2225:
1.130 brouard 2226: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2227: double ***freq; /* Frequencies */
2228: double *pp, **prop;
2229: double pos,posprop;
2230: double y2; /* in fractional years */
2231: int iagemin, iagemax;
2232:
2233: iagemin= (int) agemin;
2234: iagemax= (int) agemax;
2235: /*pp=vector(1,nlstate);*/
2236: prop=matrix(1,nlstate,iagemin,iagemax+3);
2237: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2238: j1=0;
2239:
2240: j=cptcoveff;
2241: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2242:
2243: for(k1=1; k1<=j;k1++){
2244: for(i1=1; i1<=ncodemax[k1];i1++){
2245: j1++;
2246:
2247: for (i=1; i<=nlstate; i++)
2248: for(m=iagemin; m <= iagemax+3; m++)
2249: prop[i][m]=0.0;
2250:
2251: for (i=1; i<=imx; i++) { /* Each individual */
2252: bool=1;
2253: if (cptcovn>0) {
2254: for (z1=1; z1<=cptcoveff; z1++)
2255: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2256: bool=0;
2257: }
2258: if (bool==1) {
2259: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2260: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2261: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2262: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2263: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2264: 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);
2265: if (s[m][i]>0 && s[m][i]<=nlstate) {
2266: /*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]]);*/
2267: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2268: prop[s[m][i]][iagemax+3] += weight[i];
2269: }
2270: }
2271: } /* end selection of waves */
2272: }
2273: }
2274: for(i=iagemin; i <= iagemax+3; i++){
2275:
2276: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2277: posprop += prop[jk][i];
2278: }
2279:
2280: for(jk=1; jk <=nlstate ; jk++){
2281: if( i <= iagemax){
2282: if(posprop>=1.e-5){
2283: probs[i][jk][j1]= prop[jk][i]/posprop;
1.128 brouard 2284: } else
2285: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
1.126 brouard 2286: }
2287: }/* end jk */
2288: }/* end i */
2289: } /* end i1 */
2290: } /* end k1 */
2291:
2292: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2293: /*free_vector(pp,1,nlstate);*/
2294: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2295: } /* End of prevalence */
2296:
2297: /************* Waves Concatenation ***************/
2298:
2299: 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)
2300: {
2301: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2302: Death is a valid wave (if date is known).
2303: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2304: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2305: and mw[mi+1][i]. dh depends on stepm.
2306: */
2307:
2308: int i, mi, m;
2309: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2310: double sum=0., jmean=0.;*/
2311: int first;
2312: int j, k=0,jk, ju, jl;
2313: double sum=0.;
2314: first=0;
2315: jmin=1e+5;
2316: jmax=-1;
2317: jmean=0.;
2318: for(i=1; i<=imx; i++){
2319: mi=0;
2320: m=firstpass;
2321: while(s[m][i] <= nlstate){
2322: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2323: mw[++mi][i]=m;
2324: if(m >=lastpass)
2325: break;
2326: else
2327: m++;
2328: }/* end while */
2329: if (s[m][i] > nlstate){
2330: mi++; /* Death is another wave */
2331: /* if(mi==0) never been interviewed correctly before death */
2332: /* Only death is a correct wave */
2333: mw[mi][i]=m;
2334: }
2335:
2336: wav[i]=mi;
2337: if(mi==0){
2338: nbwarn++;
2339: if(first==0){
2340: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2341: first=1;
2342: }
2343: if(first==1){
2344: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2345: }
2346: } /* end mi==0 */
2347: } /* End individuals */
2348:
2349: for(i=1; i<=imx; i++){
2350: for(mi=1; mi<wav[i];mi++){
2351: if (stepm <=0)
2352: dh[mi][i]=1;
2353: else{
2354: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2355: if (agedc[i] < 2*AGESUP) {
2356: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2357: if(j==0) j=1; /* Survives at least one month after exam */
2358: else if(j<0){
2359: nberr++;
2360: 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]);
2361: j=1; /* Temporary Dangerous patch */
2362: 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);
2363: 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]);
2364: 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);
2365: }
2366: k=k+1;
2367: if (j >= jmax){
2368: jmax=j;
2369: ijmax=i;
2370: }
2371: if (j <= jmin){
2372: jmin=j;
2373: ijmin=i;
2374: }
2375: sum=sum+j;
2376: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2377: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2378: }
2379: }
2380: else{
2381: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2382: /* 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]); */
2383:
2384: k=k+1;
2385: if (j >= jmax) {
2386: jmax=j;
2387: ijmax=i;
2388: }
2389: else if (j <= jmin){
2390: jmin=j;
2391: ijmin=i;
2392: }
2393: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2394: /*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]);*/
2395: if(j<0){
2396: nberr++;
2397: 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]);
2398: 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]);
2399: }
2400: sum=sum+j;
2401: }
2402: jk= j/stepm;
2403: jl= j -jk*stepm;
2404: ju= j -(jk+1)*stepm;
2405: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2406: if(jl==0){
2407: dh[mi][i]=jk;
2408: bh[mi][i]=0;
2409: }else{ /* We want a negative bias in order to only have interpolation ie
2410: * at the price of an extra matrix product in likelihood */
2411: dh[mi][i]=jk+1;
2412: bh[mi][i]=ju;
2413: }
2414: }else{
2415: if(jl <= -ju){
2416: dh[mi][i]=jk;
2417: bh[mi][i]=jl; /* bias is positive if real duration
2418: * is higher than the multiple of stepm and negative otherwise.
2419: */
2420: }
2421: else{
2422: dh[mi][i]=jk+1;
2423: bh[mi][i]=ju;
2424: }
2425: if(dh[mi][i]==0){
2426: dh[mi][i]=1; /* At least one step */
2427: bh[mi][i]=ju; /* At least one step */
2428: /* 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);*/
2429: }
2430: } /* end if mle */
2431: }
2432: } /* end wave */
2433: }
2434: jmean=sum/k;
2435: 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);
2436: 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);
2437: }
2438:
2439: /*********** Tricode ****************************/
2440: void tricode(int *Tvar, int **nbcode, int imx)
2441: {
2442:
1.130 brouard 2443: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2444:
1.131 ! brouard 2445: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.126 brouard 2446: int cptcode=0;
2447: cptcoveff=0;
2448:
2449: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.131 ! brouard 2450: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
1.126 brouard 2451:
1.131 ! brouard 2452: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
1.126 brouard 2453: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2454: modality*/
1.131 ! brouard 2455: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
! 2456: Ndum[ij]++; /*counts the occurence of this modality */
1.126 brouard 2457: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.131 ! brouard 2458: if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now)
1.126 brouard 2459: Tvar[j]. If V=sex and male is 0 and
2460: female is 1, then cptcode=1.*/
2461: }
2462:
1.131 ! brouard 2463: for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
! 2464: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariate. In fact ncodemax[j]=2 (dichotom. variables only) but it can be more */
! 2465: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2466:
2467: ij=1;
1.131 ! brouard 2468: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
! 2469: for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
! 2470: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
! 2471: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
! 2472: k is a modality. If we have model=V1+V1*sex
! 2473: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2474: ij++;
2475: }
2476: if (ij > ncodemax[j]) break;
2477: }
2478: }
2479: }
2480:
2481: for (k=0; k< maxncov; k++) Ndum[k]=0;
2482:
1.131 ! brouard 2483: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
1.126 brouard 2484: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.131 ! brouard 2485: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.126 brouard 2486: Ndum[ij]++;
2487: }
2488:
2489: ij=1;
2490: for (i=1; i<= maxncov; i++) {
2491: if((Ndum[i]!=0) && (i<=ncovcol)){
2492: Tvaraff[ij]=i; /*For printing */
2493: ij++;
2494: }
2495: }
1.131 ! brouard 2496: ij--;
! 2497: cptcoveff=ij; /*Number of simple covariates*/
1.126 brouard 2498: }
2499:
2500: /*********** Health Expectancies ****************/
2501:
1.127 brouard 2502: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 2503:
2504: {
2505: /* Health expectancies, no variances */
2506: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2507: int nhstepma, nstepma; /* Decreasing with age */
2508: double age, agelim, hf;
2509: double ***p3mat;
2510: double eip;
2511:
2512: pstamp(ficreseij);
2513: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2514: fprintf(ficreseij,"# Age");
2515: for(i=1; i<=nlstate;i++){
2516: for(j=1; j<=nlstate;j++){
2517: fprintf(ficreseij," e%1d%1d ",i,j);
2518: }
2519: fprintf(ficreseij," e%1d. ",i);
2520: }
2521: fprintf(ficreseij,"\n");
2522:
2523:
2524: if(estepm < stepm){
2525: printf ("Problem %d lower than %d\n",estepm, stepm);
2526: }
2527: else hstepm=estepm;
2528: /* We compute the life expectancy from trapezoids spaced every estepm months
2529: * This is mainly to measure the difference between two models: for example
2530: * if stepm=24 months pijx are given only every 2 years and by summing them
2531: * we are calculating an estimate of the Life Expectancy assuming a linear
2532: * progression in between and thus overestimating or underestimating according
2533: * to the curvature of the survival function. If, for the same date, we
2534: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2535: * to compare the new estimate of Life expectancy with the same linear
2536: * hypothesis. A more precise result, taking into account a more precise
2537: * curvature will be obtained if estepm is as small as stepm. */
2538:
2539: /* For example we decided to compute the life expectancy with the smallest unit */
2540: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2541: nhstepm is the number of hstepm from age to agelim
2542: nstepm is the number of stepm from age to agelin.
2543: Look at hpijx to understand the reason of that which relies in memory size
2544: and note for a fixed period like estepm months */
2545: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2546: survival function given by stepm (the optimization length). Unfortunately it
2547: means that if the survival funtion is printed only each two years of age and if
2548: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2549: results. So we changed our mind and took the option of the best precision.
2550: */
2551: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2552:
2553: agelim=AGESUP;
2554: /* If stepm=6 months */
2555: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2556: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2557:
2558: /* nhstepm age range expressed in number of stepm */
2559: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2560: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2561: /* if (stepm >= YEARM) hstepm=1;*/
2562: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2563: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2564:
2565: for (age=bage; age<=fage; age ++){
2566: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2567: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2568: /* if (stepm >= YEARM) hstepm=1;*/
2569: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2570:
2571: /* If stepm=6 months */
2572: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2573: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2574:
2575: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2576:
2577: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2578:
2579: printf("%d|",(int)age);fflush(stdout);
2580: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2581:
2582: /* Computing expectancies */
2583: for(i=1; i<=nlstate;i++)
2584: for(j=1; j<=nlstate;j++)
2585: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2586: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2587:
2588: /* 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]);*/
2589:
2590: }
2591:
2592: fprintf(ficreseij,"%3.0f",age );
2593: for(i=1; i<=nlstate;i++){
2594: eip=0;
2595: for(j=1; j<=nlstate;j++){
2596: eip +=eij[i][j][(int)age];
2597: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2598: }
2599: fprintf(ficreseij,"%9.4f", eip );
2600: }
2601: fprintf(ficreseij,"\n");
2602:
2603: }
2604: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2605: printf("\n");
2606: fprintf(ficlog,"\n");
2607:
2608: }
2609:
1.127 brouard 2610: void cvevsij(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[] )
1.126 brouard 2611:
2612: {
2613: /* Covariances of health expectancies eij and of total life expectancies according
2614: to initial status i, ei. .
2615: */
2616: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2617: int nhstepma, nstepma; /* Decreasing with age */
2618: double age, agelim, hf;
2619: double ***p3matp, ***p3matm, ***varhe;
2620: double **dnewm,**doldm;
2621: double *xp, *xm;
2622: double **gp, **gm;
2623: double ***gradg, ***trgradg;
2624: int theta;
2625:
2626: double eip, vip;
2627:
2628: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2629: xp=vector(1,npar);
2630: xm=vector(1,npar);
2631: dnewm=matrix(1,nlstate*nlstate,1,npar);
2632: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2633:
2634: pstamp(ficresstdeij);
2635: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2636: fprintf(ficresstdeij,"# Age");
2637: for(i=1; i<=nlstate;i++){
2638: for(j=1; j<=nlstate;j++)
2639: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2640: fprintf(ficresstdeij," e%1d. ",i);
2641: }
2642: fprintf(ficresstdeij,"\n");
2643:
2644: pstamp(ficrescveij);
2645: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2646: fprintf(ficrescveij,"# Age");
2647: for(i=1; i<=nlstate;i++)
2648: for(j=1; j<=nlstate;j++){
2649: cptj= (j-1)*nlstate+i;
2650: for(i2=1; i2<=nlstate;i2++)
2651: for(j2=1; j2<=nlstate;j2++){
2652: cptj2= (j2-1)*nlstate+i2;
2653: if(cptj2 <= cptj)
2654: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2655: }
2656: }
2657: fprintf(ficrescveij,"\n");
2658:
2659: if(estepm < stepm){
2660: printf ("Problem %d lower than %d\n",estepm, stepm);
2661: }
2662: else hstepm=estepm;
2663: /* We compute the life expectancy from trapezoids spaced every estepm months
2664: * This is mainly to measure the difference between two models: for example
2665: * if stepm=24 months pijx are given only every 2 years and by summing them
2666: * we are calculating an estimate of the Life Expectancy assuming a linear
2667: * progression in between and thus overestimating or underestimating according
2668: * to the curvature of the survival function. If, for the same date, we
2669: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2670: * to compare the new estimate of Life expectancy with the same linear
2671: * hypothesis. A more precise result, taking into account a more precise
2672: * curvature will be obtained if estepm is as small as stepm. */
2673:
2674: /* For example we decided to compute the life expectancy with the smallest unit */
2675: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2676: nhstepm is the number of hstepm from age to agelim
2677: nstepm is the number of stepm from age to agelin.
2678: Look at hpijx to understand the reason of that which relies in memory size
2679: and note for a fixed period like estepm months */
2680: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2681: survival function given by stepm (the optimization length). Unfortunately it
2682: means that if the survival funtion is printed only each two years of age and if
2683: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2684: results. So we changed our mind and took the option of the best precision.
2685: */
2686: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2687:
2688: /* If stepm=6 months */
2689: /* nhstepm age range expressed in number of stepm */
2690: agelim=AGESUP;
2691: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2692: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2693: /* if (stepm >= YEARM) hstepm=1;*/
2694: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2695:
2696: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2697: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2698: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2699: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2700: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2701: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2702:
2703: for (age=bage; age<=fage; age ++){
2704: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2705: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2706: /* if (stepm >= YEARM) hstepm=1;*/
2707: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2708:
2709: /* If stepm=6 months */
2710: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2711: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2712:
2713: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2714:
2715: /* Computing Variances of health expectancies */
2716: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2717: decrease memory allocation */
2718: for(theta=1; theta <=npar; theta++){
2719: for(i=1; i<=npar; i++){
2720: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2721: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2722: }
2723: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2724: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2725:
2726: for(j=1; j<= nlstate; j++){
2727: for(i=1; i<=nlstate; i++){
2728: for(h=0; h<=nhstepm-1; h++){
2729: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2730: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2731: }
2732: }
2733: }
2734:
2735: for(ij=1; ij<= nlstate*nlstate; ij++)
2736: for(h=0; h<=nhstepm-1; h++){
2737: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2738: }
2739: }/* End theta */
2740:
2741:
2742: for(h=0; h<=nhstepm-1; h++)
2743: for(j=1; j<=nlstate*nlstate;j++)
2744: for(theta=1; theta <=npar; theta++)
2745: trgradg[h][j][theta]=gradg[h][theta][j];
2746:
2747:
2748: for(ij=1;ij<=nlstate*nlstate;ij++)
2749: for(ji=1;ji<=nlstate*nlstate;ji++)
2750: varhe[ij][ji][(int)age] =0.;
2751:
2752: printf("%d|",(int)age);fflush(stdout);
2753: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2754: for(h=0;h<=nhstepm-1;h++){
2755: for(k=0;k<=nhstepm-1;k++){
2756: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2757: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2758: for(ij=1;ij<=nlstate*nlstate;ij++)
2759: for(ji=1;ji<=nlstate*nlstate;ji++)
2760: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2761: }
2762: }
2763:
2764: /* Computing expectancies */
2765: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2766: for(i=1; i<=nlstate;i++)
2767: for(j=1; j<=nlstate;j++)
2768: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2769: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2770:
2771: /* 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]);*/
2772:
2773: }
2774:
2775: fprintf(ficresstdeij,"%3.0f",age );
2776: for(i=1; i<=nlstate;i++){
2777: eip=0.;
2778: vip=0.;
2779: for(j=1; j<=nlstate;j++){
2780: eip += eij[i][j][(int)age];
2781: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2782: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2783: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2784: }
2785: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2786: }
2787: fprintf(ficresstdeij,"\n");
2788:
2789: fprintf(ficrescveij,"%3.0f",age );
2790: for(i=1; i<=nlstate;i++)
2791: for(j=1; j<=nlstate;j++){
2792: cptj= (j-1)*nlstate+i;
2793: for(i2=1; i2<=nlstate;i2++)
2794: for(j2=1; j2<=nlstate;j2++){
2795: cptj2= (j2-1)*nlstate+i2;
2796: if(cptj2 <= cptj)
2797: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2798: }
2799: }
2800: fprintf(ficrescveij,"\n");
2801:
2802: }
2803: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2804: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2805: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2806: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2807: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2808: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2809: printf("\n");
2810: fprintf(ficlog,"\n");
2811:
2812: free_vector(xm,1,npar);
2813: free_vector(xp,1,npar);
2814: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2815: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2816: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2817: }
2818:
2819: /************ Variance ******************/
2820: 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[])
2821: {
2822: /* Variance of health expectancies */
2823: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2824: /* double **newm;*/
2825: double **dnewm,**doldm;
2826: double **dnewmp,**doldmp;
2827: int i, j, nhstepm, hstepm, h, nstepm ;
2828: int k, cptcode;
2829: double *xp;
2830: double **gp, **gm; /* for var eij */
2831: double ***gradg, ***trgradg; /*for var eij */
2832: double **gradgp, **trgradgp; /* for var p point j */
2833: double *gpp, *gmp; /* for var p point j */
2834: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2835: double ***p3mat;
2836: double age,agelim, hf;
2837: double ***mobaverage;
2838: int theta;
2839: char digit[4];
2840: char digitp[25];
2841:
2842: char fileresprobmorprev[FILENAMELENGTH];
2843:
2844: if(popbased==1){
2845: if(mobilav!=0)
2846: strcpy(digitp,"-populbased-mobilav-");
2847: else strcpy(digitp,"-populbased-nomobil-");
2848: }
2849: else
2850: strcpy(digitp,"-stablbased-");
2851:
2852: if (mobilav!=0) {
2853: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2854: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2855: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2856: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2857: }
2858: }
2859:
2860: strcpy(fileresprobmorprev,"prmorprev");
2861: sprintf(digit,"%-d",ij);
2862: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2863: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2864: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2865: strcat(fileresprobmorprev,fileres);
2866: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2867: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2868: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2869: }
2870: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2871:
2872: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2873: pstamp(ficresprobmorprev);
2874: 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);
2875: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2876: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2877: fprintf(ficresprobmorprev," p.%-d SE",j);
2878: for(i=1; i<=nlstate;i++)
2879: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2880: }
2881: fprintf(ficresprobmorprev,"\n");
2882: fprintf(ficgp,"\n# Routine varevsij");
2883: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2884: 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");
2885: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2886: /* } */
2887: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2888: pstamp(ficresvij);
2889: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2890: if(popbased==1)
1.128 brouard 2891: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 2892: else
2893: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2894: fprintf(ficresvij,"# Age");
2895: for(i=1; i<=nlstate;i++)
2896: for(j=1; j<=nlstate;j++)
2897: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2898: fprintf(ficresvij,"\n");
2899:
2900: xp=vector(1,npar);
2901: dnewm=matrix(1,nlstate,1,npar);
2902: doldm=matrix(1,nlstate,1,nlstate);
2903: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2904: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2905:
2906: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2907: gpp=vector(nlstate+1,nlstate+ndeath);
2908: gmp=vector(nlstate+1,nlstate+ndeath);
2909: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2910:
2911: if(estepm < stepm){
2912: printf ("Problem %d lower than %d\n",estepm, stepm);
2913: }
2914: else hstepm=estepm;
2915: /* For example we decided to compute the life expectancy with the smallest unit */
2916: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2917: nhstepm is the number of hstepm from age to agelim
2918: nstepm is the number of stepm from age to agelin.
1.128 brouard 2919: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 2920: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2921: survival function given by stepm (the optimization length). Unfortunately it
2922: means that if the survival funtion is printed every two years of age and if
2923: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2924: results. So we changed our mind and took the option of the best precision.
2925: */
2926: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2927: agelim = AGESUP;
2928: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2929: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2930: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2931: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2932: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2933: gp=matrix(0,nhstepm,1,nlstate);
2934: gm=matrix(0,nhstepm,1,nlstate);
2935:
2936:
2937: for(theta=1; theta <=npar; theta++){
2938: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2939: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2940: }
2941: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2942: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2943:
2944: if (popbased==1) {
2945: if(mobilav ==0){
2946: for(i=1; i<=nlstate;i++)
2947: prlim[i][i]=probs[(int)age][i][ij];
2948: }else{ /* mobilav */
2949: for(i=1; i<=nlstate;i++)
2950: prlim[i][i]=mobaverage[(int)age][i][ij];
2951: }
2952: }
2953:
2954: for(j=1; j<= nlstate; j++){
2955: for(h=0; h<=nhstepm; h++){
2956: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2957: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2958: }
2959: }
2960: /* This for computing probability of death (h=1 means
2961: computed over hstepm matrices product = hstepm*stepm months)
2962: as a weighted average of prlim.
2963: */
2964: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2965: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2966: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2967: }
2968: /* end probability of death */
2969:
2970: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2971: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2972: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2973: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2974:
2975: if (popbased==1) {
2976: if(mobilav ==0){
2977: for(i=1; i<=nlstate;i++)
2978: prlim[i][i]=probs[(int)age][i][ij];
2979: }else{ /* mobilav */
2980: for(i=1; i<=nlstate;i++)
2981: prlim[i][i]=mobaverage[(int)age][i][ij];
2982: }
2983: }
2984:
1.128 brouard 2985: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 2986: for(h=0; h<=nhstepm; h++){
2987: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2988: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2989: }
2990: }
2991: /* This for computing probability of death (h=1 means
2992: computed over hstepm matrices product = hstepm*stepm months)
2993: as a weighted average of prlim.
2994: */
2995: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2996: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2997: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2998: }
2999: /* end probability of death */
3000:
3001: for(j=1; j<= nlstate; j++) /* vareij */
3002: for(h=0; h<=nhstepm; h++){
3003: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3004: }
3005:
3006: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3007: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3008: }
3009:
3010: } /* End theta */
3011:
3012: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3013:
3014: for(h=0; h<=nhstepm; h++) /* veij */
3015: for(j=1; j<=nlstate;j++)
3016: for(theta=1; theta <=npar; theta++)
3017: trgradg[h][j][theta]=gradg[h][theta][j];
3018:
3019: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3020: for(theta=1; theta <=npar; theta++)
3021: trgradgp[j][theta]=gradgp[theta][j];
3022:
3023:
3024: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3025: for(i=1;i<=nlstate;i++)
3026: for(j=1;j<=nlstate;j++)
3027: vareij[i][j][(int)age] =0.;
3028:
3029: for(h=0;h<=nhstepm;h++){
3030: for(k=0;k<=nhstepm;k++){
3031: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3032: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3033: for(i=1;i<=nlstate;i++)
3034: for(j=1;j<=nlstate;j++)
3035: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3036: }
3037: }
3038:
3039: /* pptj */
3040: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3041: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3042: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3043: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3044: varppt[j][i]=doldmp[j][i];
3045: /* end ppptj */
3046: /* x centered again */
3047: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3048: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3049:
3050: if (popbased==1) {
3051: if(mobilav ==0){
3052: for(i=1; i<=nlstate;i++)
3053: prlim[i][i]=probs[(int)age][i][ij];
3054: }else{ /* mobilav */
3055: for(i=1; i<=nlstate;i++)
3056: prlim[i][i]=mobaverage[(int)age][i][ij];
3057: }
3058: }
3059:
3060: /* This for computing probability of death (h=1 means
3061: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3062: as a weighted average of prlim.
3063: */
3064: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3065: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3066: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3067: }
3068: /* end probability of death */
3069:
3070: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3071: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3072: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3073: for(i=1; i<=nlstate;i++){
3074: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3075: }
3076: }
3077: fprintf(ficresprobmorprev,"\n");
3078:
3079: fprintf(ficresvij,"%.0f ",age );
3080: for(i=1; i<=nlstate;i++)
3081: for(j=1; j<=nlstate;j++){
3082: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3083: }
3084: fprintf(ficresvij,"\n");
3085: free_matrix(gp,0,nhstepm,1,nlstate);
3086: free_matrix(gm,0,nhstepm,1,nlstate);
3087: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3088: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3089: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3090: } /* End age */
3091: free_vector(gpp,nlstate+1,nlstate+ndeath);
3092: free_vector(gmp,nlstate+1,nlstate+ndeath);
3093: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3094: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.131 ! brouard 3095: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
1.126 brouard 3096: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 ! brouard 3097: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3098: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3099: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3100: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3101: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3102: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3103: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3104: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3105: 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);
3106: /* 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);
3107: */
3108: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3109: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3110:
3111: free_vector(xp,1,npar);
3112: free_matrix(doldm,1,nlstate,1,nlstate);
3113: free_matrix(dnewm,1,nlstate,1,npar);
3114: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3115: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3116: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3117: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3118: fclose(ficresprobmorprev);
3119: fflush(ficgp);
3120: fflush(fichtm);
3121: } /* end varevsij */
3122:
3123: /************ Variance of prevlim ******************/
3124: 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[])
3125: {
3126: /* Variance of prevalence limit */
3127: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3128: double **newm;
3129: double **dnewm,**doldm;
3130: int i, j, nhstepm, hstepm;
3131: int k, cptcode;
3132: double *xp;
3133: double *gp, *gm;
3134: double **gradg, **trgradg;
3135: double age,agelim;
3136: int theta;
3137:
3138: pstamp(ficresvpl);
3139: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3140: fprintf(ficresvpl,"# Age");
3141: for(i=1; i<=nlstate;i++)
3142: fprintf(ficresvpl," %1d-%1d",i,i);
3143: fprintf(ficresvpl,"\n");
3144:
3145: xp=vector(1,npar);
3146: dnewm=matrix(1,nlstate,1,npar);
3147: doldm=matrix(1,nlstate,1,nlstate);
3148:
3149: hstepm=1*YEARM; /* Every year of age */
3150: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3151: agelim = AGESUP;
3152: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3153: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3154: if (stepm >= YEARM) hstepm=1;
3155: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3156: gradg=matrix(1,npar,1,nlstate);
3157: gp=vector(1,nlstate);
3158: gm=vector(1,nlstate);
3159:
3160: for(theta=1; theta <=npar; theta++){
3161: for(i=1; i<=npar; i++){ /* Computes gradient */
3162: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3163: }
3164: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3165: for(i=1;i<=nlstate;i++)
3166: gp[i] = prlim[i][i];
3167:
3168: for(i=1; i<=npar; i++) /* Computes gradient */
3169: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3170: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3171: for(i=1;i<=nlstate;i++)
3172: gm[i] = prlim[i][i];
3173:
3174: for(i=1;i<=nlstate;i++)
3175: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3176: } /* End theta */
3177:
3178: trgradg =matrix(1,nlstate,1,npar);
3179:
3180: for(j=1; j<=nlstate;j++)
3181: for(theta=1; theta <=npar; theta++)
3182: trgradg[j][theta]=gradg[theta][j];
3183:
3184: for(i=1;i<=nlstate;i++)
3185: varpl[i][(int)age] =0.;
3186: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3187: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3188: for(i=1;i<=nlstate;i++)
3189: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3190:
3191: fprintf(ficresvpl,"%.0f ",age );
3192: for(i=1; i<=nlstate;i++)
3193: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3194: fprintf(ficresvpl,"\n");
3195: free_vector(gp,1,nlstate);
3196: free_vector(gm,1,nlstate);
3197: free_matrix(gradg,1,npar,1,nlstate);
3198: free_matrix(trgradg,1,nlstate,1,npar);
3199: } /* End age */
3200:
3201: free_vector(xp,1,npar);
3202: free_matrix(doldm,1,nlstate,1,npar);
3203: free_matrix(dnewm,1,nlstate,1,nlstate);
3204:
3205: }
3206:
3207: /************ Variance of one-step probabilities ******************/
3208: 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[])
3209: {
3210: int i, j=0, i1, k1, l1, t, tj;
3211: int k2, l2, j1, z1;
3212: int k=0,l, cptcode;
3213: int first=1, first1;
3214: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3215: double **dnewm,**doldm;
3216: double *xp;
3217: double *gp, *gm;
3218: double **gradg, **trgradg;
3219: double **mu;
3220: double age,agelim, cov[NCOVMAX];
3221: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3222: int theta;
3223: char fileresprob[FILENAMELENGTH];
3224: char fileresprobcov[FILENAMELENGTH];
3225: char fileresprobcor[FILENAMELENGTH];
3226:
3227: double ***varpij;
3228:
3229: strcpy(fileresprob,"prob");
3230: strcat(fileresprob,fileres);
3231: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3232: printf("Problem with resultfile: %s\n", fileresprob);
3233: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3234: }
3235: strcpy(fileresprobcov,"probcov");
3236: strcat(fileresprobcov,fileres);
3237: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3238: printf("Problem with resultfile: %s\n", fileresprobcov);
3239: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3240: }
3241: strcpy(fileresprobcor,"probcor");
3242: strcat(fileresprobcor,fileres);
3243: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3244: printf("Problem with resultfile: %s\n", fileresprobcor);
3245: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3246: }
3247: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3248: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3249: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3250: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3251: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3252: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3253: pstamp(ficresprob);
3254: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3255: fprintf(ficresprob,"# Age");
3256: pstamp(ficresprobcov);
3257: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3258: fprintf(ficresprobcov,"# Age");
3259: pstamp(ficresprobcor);
3260: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3261: fprintf(ficresprobcor,"# Age");
3262:
3263:
3264: for(i=1; i<=nlstate;i++)
3265: for(j=1; j<=(nlstate+ndeath);j++){
3266: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3267: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3268: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3269: }
3270: /* fprintf(ficresprob,"\n");
3271: fprintf(ficresprobcov,"\n");
3272: fprintf(ficresprobcor,"\n");
3273: */
1.131 ! brouard 3274: xp=vector(1,npar);
1.126 brouard 3275: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3276: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3277: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3278: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3279: first=1;
3280: fprintf(ficgp,"\n# Routine varprob");
3281: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3282: fprintf(fichtm,"\n");
3283:
3284: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3285: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3286: file %s<br>\n",optionfilehtmcov);
3287: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3288: and drawn. It helps understanding how is the covariance between two incidences.\
3289: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3290: 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. \
3291: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3292: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3293: standard deviations wide on each axis. <br>\
3294: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3295: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3296: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3297:
3298: cov[1]=1;
3299: tj=cptcoveff;
3300: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3301: j1=0;
3302: for(t=1; t<=tj;t++){
3303: for(i1=1; i1<=ncodemax[t];i1++){
3304: j1++;
3305: if (cptcovn>0) {
3306: fprintf(ficresprob, "\n#********** Variable ");
3307: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3308: fprintf(ficresprob, "**********\n#\n");
3309: fprintf(ficresprobcov, "\n#********** Variable ");
3310: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3311: fprintf(ficresprobcov, "**********\n#\n");
3312:
3313: fprintf(ficgp, "\n#********** Variable ");
3314: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3315: fprintf(ficgp, "**********\n#\n");
3316:
3317:
3318: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3319: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3320: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3321:
3322: fprintf(ficresprobcor, "\n#********** Variable ");
3323: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3324: fprintf(ficresprobcor, "**********\n#");
3325: }
3326:
3327: for (age=bage; age<=fage; age ++){
3328: cov[2]=age;
3329: for (k=1; k<=cptcovn;k++) {
3330: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3331: }
3332: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3333: for (k=1; k<=cptcovprod;k++)
3334: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3335:
3336: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3337: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3338: gp=vector(1,(nlstate)*(nlstate+ndeath));
3339: gm=vector(1,(nlstate)*(nlstate+ndeath));
3340:
3341: for(theta=1; theta <=npar; theta++){
3342: for(i=1; i<=npar; i++)
3343: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3344:
3345: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3346:
3347: k=0;
3348: for(i=1; i<= (nlstate); i++){
3349: for(j=1; j<=(nlstate+ndeath);j++){
3350: k=k+1;
3351: gp[k]=pmmij[i][j];
3352: }
3353: }
3354:
3355: for(i=1; i<=npar; i++)
3356: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3357:
3358: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3359: k=0;
3360: for(i=1; i<=(nlstate); i++){
3361: for(j=1; j<=(nlstate+ndeath);j++){
3362: k=k+1;
3363: gm[k]=pmmij[i][j];
3364: }
3365: }
3366:
3367: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3368: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3369: }
3370:
3371: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3372: for(theta=1; theta <=npar; theta++)
3373: trgradg[j][theta]=gradg[theta][j];
3374:
3375: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3376: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3377: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3378: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3379: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3380: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3381:
3382: pmij(pmmij,cov,ncovmodel,x,nlstate);
3383:
3384: k=0;
3385: for(i=1; i<=(nlstate); i++){
3386: for(j=1; j<=(nlstate+ndeath);j++){
3387: k=k+1;
3388: mu[k][(int) age]=pmmij[i][j];
3389: }
3390: }
3391: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3392: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3393: varpij[i][j][(int)age] = doldm[i][j];
3394:
3395: /*printf("\n%d ",(int)age);
3396: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3397: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3398: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3399: }*/
3400:
3401: fprintf(ficresprob,"\n%d ",(int)age);
3402: fprintf(ficresprobcov,"\n%d ",(int)age);
3403: fprintf(ficresprobcor,"\n%d ",(int)age);
3404:
3405: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3406: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3407: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3408: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3409: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3410: }
3411: i=0;
3412: for (k=1; k<=(nlstate);k++){
3413: for (l=1; l<=(nlstate+ndeath);l++){
3414: i=i++;
3415: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3416: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3417: for (j=1; j<=i;j++){
3418: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3419: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3420: }
3421: }
3422: }/* end of loop for state */
3423: } /* end of loop for age */
3424:
3425: /* Confidence intervalle of pij */
3426: /*
1.131 ! brouard 3427: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3428: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3429: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3430: 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);
3431: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3432: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3433: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3434: */
3435:
3436: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3437: first1=1;
3438: for (k2=1; k2<=(nlstate);k2++){
3439: for (l2=1; l2<=(nlstate+ndeath);l2++){
3440: if(l2==k2) continue;
3441: j=(k2-1)*(nlstate+ndeath)+l2;
3442: for (k1=1; k1<=(nlstate);k1++){
3443: for (l1=1; l1<=(nlstate+ndeath);l1++){
3444: if(l1==k1) continue;
3445: i=(k1-1)*(nlstate+ndeath)+l1;
3446: if(i<=j) continue;
3447: for (age=bage; age<=fage; age ++){
3448: if ((int)age %5==0){
3449: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3450: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3451: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3452: mu1=mu[i][(int) age]/stepm*YEARM ;
3453: mu2=mu[j][(int) age]/stepm*YEARM;
3454: c12=cv12/sqrt(v1*v2);
3455: /* Computing eigen value of matrix of covariance */
3456: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3457: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3458: /* Eigen vectors */
3459: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3460: /*v21=sqrt(1.-v11*v11); *//* error */
3461: v21=(lc1-v1)/cv12*v11;
3462: v12=-v21;
3463: v22=v11;
3464: tnalp=v21/v11;
3465: if(first1==1){
3466: first1=0;
3467: 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);
3468: }
3469: 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);
3470: /*printf(fignu*/
3471: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3472: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3473: if(first==1){
3474: first=0;
3475: fprintf(ficgp,"\nset parametric;unset label");
3476: 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);
3477: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3478: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3479: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3480: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3481: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3482: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3483: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3484: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3485: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3486: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3487: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3488: 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",\
3489: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3490: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3491: }else{
3492: first=0;
3493: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3494: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3495: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3496: 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",\
3497: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3498: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3499: }/* if first */
3500: } /* age mod 5 */
3501: } /* end loop age */
3502: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3503: first=1;
3504: } /*l12 */
3505: } /* k12 */
3506: } /*l1 */
3507: }/* k1 */
3508: } /* loop covariates */
3509: }
3510: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3511: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3512: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3513: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3514: free_vector(xp,1,npar);
3515: fclose(ficresprob);
3516: fclose(ficresprobcov);
3517: fclose(ficresprobcor);
3518: fflush(ficgp);
3519: fflush(fichtmcov);
3520: }
3521:
3522:
3523: /******************* Printing html file ***********/
3524: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3525: int lastpass, int stepm, int weightopt, char model[],\
3526: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3527: int popforecast, int estepm ,\
3528: double jprev1, double mprev1,double anprev1, \
3529: double jprev2, double mprev2,double anprev2){
3530: int jj1, k1, i1, cpt;
3531:
3532: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3533: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3534: </ul>");
3535: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3536: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3537: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3538: fprintf(fichtm,"\
3539: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3540: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3541: fprintf(fichtm,"\
3542: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3543: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3544: fprintf(fichtm,"\
1.128 brouard 3545: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 3546: <a href=\"%s\">%s</a> <br>\n",
3547: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3548: fprintf(fichtm,"\
3549: - Population projections by age and states: \
3550: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3551:
3552: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3553:
3554: m=cptcoveff;
3555: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3556:
3557: jj1=0;
3558: for(k1=1; k1<=m;k1++){
3559: for(i1=1; i1<=ncodemax[k1];i1++){
3560: jj1++;
3561: if (cptcovn > 0) {
3562: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3563: for (cpt=1; cpt<=cptcoveff;cpt++)
3564: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3565: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3566: }
3567: /* Pij */
3568: 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> \
3569: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3570: /* Quasi-incidences */
3571: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3572: 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> \
3573: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3574: /* Period (stable) prevalence in each health state */
3575: for(cpt=1; cpt<nlstate;cpt++){
3576: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3577: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3578: }
3579: for(cpt=1; cpt<=nlstate;cpt++) {
3580: 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> \
3581: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3582: }
3583: } /* end i1 */
3584: }/* End k1 */
3585: fprintf(fichtm,"</ul>");
3586:
3587:
3588: fprintf(fichtm,"\
3589: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3590: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3591:
3592: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3593: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3594: fprintf(fichtm,"\
3595: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3596: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3597:
3598: fprintf(fichtm,"\
3599: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3600: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3601: fprintf(fichtm,"\
3602: - 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): \
3603: <a href=\"%s\">%s</a> <br>\n</li>",
3604: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3605: fprintf(fichtm,"\
3606: - (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): \
3607: <a href=\"%s\">%s</a> <br>\n</li>",
3608: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3609: fprintf(fichtm,"\
1.128 brouard 3610: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> 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",
1.126 brouard 3611: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3612: fprintf(fichtm,"\
1.128 brouard 3613: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (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",
3614: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3615: fprintf(fichtm,"\
3616: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3617: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3618:
3619: /* if(popforecast==1) fprintf(fichtm,"\n */
3620: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3621: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3622: /* <br>",fileres,fileres,fileres,fileres); */
3623: /* else */
3624: /* 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); */
3625: fflush(fichtm);
3626: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3627:
3628: m=cptcoveff;
3629: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3630:
3631: jj1=0;
3632: for(k1=1; k1<=m;k1++){
3633: for(i1=1; i1<=ncodemax[k1];i1++){
3634: jj1++;
3635: if (cptcovn > 0) {
3636: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3637: for (cpt=1; cpt<=cptcoveff;cpt++)
3638: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3639: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3640: }
3641: for(cpt=1; cpt<=nlstate;cpt++) {
3642: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3643: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3644: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3645: }
3646: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3647: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3648: true period expectancies (those weighted with period prevalences are also\
3649: drawn in addition to the population based expectancies computed using\
3650: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3651: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3652: } /* end i1 */
3653: }/* End k1 */
3654: fprintf(fichtm,"</ul>");
3655: fflush(fichtm);
3656: }
3657:
3658: /******************* Gnuplot file **************/
3659: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3660:
3661: char dirfileres[132],optfileres[132];
1.130 brouard 3662: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3663: int ng=0;
1.126 brouard 3664: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3665: /* printf("Problem with file %s",optionfilegnuplot); */
3666: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3667: /* } */
3668:
3669: /*#ifdef windows */
3670: fprintf(ficgp,"cd \"%s\" \n",pathc);
3671: /*#endif */
3672: m=pow(2,cptcoveff);
3673:
3674: strcpy(dirfileres,optionfilefiname);
3675: strcpy(optfileres,"vpl");
3676: /* 1eme*/
3677: for (cpt=1; cpt<= nlstate ; cpt ++) {
3678: for (k1=1; k1<= m ; k1 ++) {
3679: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3680: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3681: fprintf(ficgp,"set xlabel \"Age\" \n\
3682: set ylabel \"Probability\" \n\
3683: set ter png small\n\
3684: set size 0.65,0.65\n\
3685: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3686:
3687: for (i=1; i<= nlstate ; i ++) {
3688: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 ! brouard 3689: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 3690: }
3691: 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);
3692: for (i=1; i<= nlstate ; i ++) {
3693: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3694: else fprintf(ficgp," \%%*lf (\%%*lf)");
3695: }
3696: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3697: for (i=1; i<= nlstate ; i ++) {
3698: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3699: else fprintf(ficgp," \%%*lf (\%%*lf)");
3700: }
3701: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3702: }
3703: }
3704: /*2 eme*/
3705:
3706: for (k1=1; k1<= m ; k1 ++) {
3707: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3708: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3709:
3710: for (i=1; i<= nlstate+1 ; i ++) {
3711: k=2*i;
3712: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3713: for (j=1; j<= nlstate+1 ; j ++) {
3714: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3715: else fprintf(ficgp," \%%*lf (\%%*lf)");
3716: }
3717: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3718: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3719: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3720: for (j=1; j<= nlstate+1 ; j ++) {
3721: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3722: else fprintf(ficgp," \%%*lf (\%%*lf)");
3723: }
3724: fprintf(ficgp,"\" t\"\" w l 0,");
3725: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3726: for (j=1; j<= nlstate+1 ; j ++) {
3727: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3728: else fprintf(ficgp," \%%*lf (\%%*lf)");
3729: }
3730: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3731: else fprintf(ficgp,"\" t\"\" w l 0,");
3732: }
3733: }
3734:
3735: /*3eme*/
3736:
3737: for (k1=1; k1<= m ; k1 ++) {
3738: for (cpt=1; cpt<= nlstate ; cpt ++) {
3739: /* k=2+nlstate*(2*cpt-2); */
3740: k=2+(nlstate+1)*(cpt-1);
3741: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3742: fprintf(ficgp,"set ter png small\n\
3743: set size 0.65,0.65\n\
3744: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3745: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3746: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3747: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3748: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3749: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3750: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3751:
3752: */
3753: for (i=1; i< nlstate ; i ++) {
3754: 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);
3755: /* 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);*/
3756:
3757: }
3758: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3759: }
3760: }
3761:
3762: /* CV preval stable (period) */
3763: for (k1=1; k1<= m ; k1 ++) {
3764: for (cpt=1; cpt<=nlstate ; cpt ++) {
3765: k=3;
3766: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3767: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3768: set ter png small\nset size 0.65,0.65\n\
3769: unset log y\n\
3770: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3771:
3772: for (i=1; i< nlstate ; i ++)
3773: fprintf(ficgp,"+$%d",k+i+1);
3774: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3775:
3776: l=3+(nlstate+ndeath)*cpt;
3777: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3778: for (i=1; i< nlstate ; i ++) {
3779: l=3+(nlstate+ndeath)*cpt;
3780: fprintf(ficgp,"+$%d",l+i+1);
3781: }
3782: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3783: }
3784: }
3785:
3786: /* proba elementaires */
3787: for(i=1,jk=1; i <=nlstate; i++){
3788: for(k=1; k <=(nlstate+ndeath); k++){
3789: if (k != i) {
3790: for(j=1; j <=ncovmodel; j++){
3791: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3792: jk++;
3793: fprintf(ficgp,"\n");
3794: }
3795: }
3796: }
3797: }
3798:
3799: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3800: for(jk=1; jk <=m; jk++) {
3801: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3802: if (ng==2)
3803: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3804: else
3805: fprintf(ficgp,"\nset title \"Probability\"\n");
3806: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3807: i=1;
3808: for(k2=1; k2<=nlstate; k2++) {
3809: k3=i;
3810: for(k=1; k<=(nlstate+ndeath); k++) {
3811: if (k != k2){
3812: if(ng==2)
3813: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3814: else
3815: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3816: ij=1;
3817: for(j=3; j <=ncovmodel; j++) {
3818: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3819: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3820: ij++;
3821: }
3822: else
3823: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3824: }
3825: fprintf(ficgp,")/(1");
3826:
3827: for(k1=1; k1 <=nlstate; k1++){
3828: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3829: ij=1;
3830: for(j=3; j <=ncovmodel; j++){
3831: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3832: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3833: ij++;
3834: }
3835: else
3836: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3837: }
3838: fprintf(ficgp,")");
3839: }
3840: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3841: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3842: i=i+ncovmodel;
3843: }
3844: } /* end k */
3845: } /* end k2 */
3846: } /* end jk */
3847: } /* end ng */
3848: fflush(ficgp);
3849: } /* end gnuplot */
3850:
3851:
3852: /*************** Moving average **************/
3853: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3854:
3855: int i, cpt, cptcod;
3856: int modcovmax =1;
3857: int mobilavrange, mob;
3858: double age;
3859:
3860: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3861: a covariate has 2 modalities */
3862: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3863:
3864: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3865: if(mobilav==1) mobilavrange=5; /* default */
3866: else mobilavrange=mobilav;
3867: for (age=bage; age<=fage; age++)
3868: for (i=1; i<=nlstate;i++)
3869: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3870: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3871: /* We keep the original values on the extreme ages bage, fage and for
3872: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3873: we use a 5 terms etc. until the borders are no more concerned.
3874: */
3875: for (mob=3;mob <=mobilavrange;mob=mob+2){
3876: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3877: for (i=1; i<=nlstate;i++){
3878: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3879: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3880: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3881: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3882: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3883: }
3884: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3885: }
3886: }
3887: }/* end age */
3888: }/* end mob */
3889: }else return -1;
3890: return 0;
3891: }/* End movingaverage */
3892:
3893:
3894: /************** Forecasting ******************/
3895: 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){
3896: /* proj1, year, month, day of starting projection
3897: agemin, agemax range of age
3898: dateprev1 dateprev2 range of dates during which prevalence is computed
3899: anproj2 year of en of projection (same day and month as proj1).
3900: */
3901: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3902: int *popage;
3903: double agec; /* generic age */
3904: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3905: double *popeffectif,*popcount;
3906: double ***p3mat;
3907: double ***mobaverage;
3908: char fileresf[FILENAMELENGTH];
3909:
3910: agelim=AGESUP;
3911: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3912:
3913: strcpy(fileresf,"f");
3914: strcat(fileresf,fileres);
3915: if((ficresf=fopen(fileresf,"w"))==NULL) {
3916: printf("Problem with forecast resultfile: %s\n", fileresf);
3917: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3918: }
3919: printf("Computing forecasting: result on file '%s' \n", fileresf);
3920: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3921:
3922: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3923:
3924: if (mobilav!=0) {
3925: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3926: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3927: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3928: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3929: }
3930: }
3931:
3932: stepsize=(int) (stepm+YEARM-1)/YEARM;
3933: if (stepm<=12) stepsize=1;
3934: if(estepm < stepm){
3935: printf ("Problem %d lower than %d\n",estepm, stepm);
3936: }
3937: else hstepm=estepm;
3938:
3939: hstepm=hstepm/stepm;
3940: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3941: fractional in yp1 */
3942: anprojmean=yp;
3943: yp2=modf((yp1*12),&yp);
3944: mprojmean=yp;
3945: yp1=modf((yp2*30.5),&yp);
3946: jprojmean=yp;
3947: if(jprojmean==0) jprojmean=1;
3948: if(mprojmean==0) jprojmean=1;
3949:
3950: i1=cptcoveff;
3951: if (cptcovn < 1){i1=1;}
3952:
3953: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3954:
3955: fprintf(ficresf,"#****** Routine prevforecast **\n");
3956:
3957: /* if (h==(int)(YEARM*yearp)){ */
3958: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3959: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3960: k=k+1;
3961: fprintf(ficresf,"\n#******");
3962: for(j=1;j<=cptcoveff;j++) {
3963: 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]]);
3964: }
3965: fprintf(ficresf,"******\n");
3966: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3967: for(j=1; j<=nlstate+ndeath;j++){
3968: for(i=1; i<=nlstate;i++)
3969: fprintf(ficresf," p%d%d",i,j);
3970: fprintf(ficresf," p.%d",j);
3971: }
3972: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3973: fprintf(ficresf,"\n");
3974: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3975:
3976: for (agec=fage; agec>=(ageminpar-1); agec--){
3977: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3978: nhstepm = nhstepm/hstepm;
3979: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3980: oldm=oldms;savm=savms;
3981: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3982:
3983: for (h=0; h<=nhstepm; h++){
3984: if (h*hstepm/YEARM*stepm ==yearp) {
3985: fprintf(ficresf,"\n");
3986: for(j=1;j<=cptcoveff;j++)
3987: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3988: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3989: }
3990: for(j=1; j<=nlstate+ndeath;j++) {
3991: ppij=0.;
3992: for(i=1; i<=nlstate;i++) {
3993: if (mobilav==1)
3994: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3995: else {
3996: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3997: }
3998: if (h*hstepm/YEARM*stepm== yearp) {
3999: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4000: }
4001: } /* end i */
4002: if (h*hstepm/YEARM*stepm==yearp) {
4003: fprintf(ficresf," %.3f", ppij);
4004: }
4005: }/* end j */
4006: } /* end h */
4007: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4008: } /* end agec */
4009: } /* end yearp */
4010: } /* end cptcod */
4011: } /* end cptcov */
4012:
4013: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4014:
4015: fclose(ficresf);
4016: }
4017:
4018: /************** Forecasting *****not tested NB*************/
4019: 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){
4020:
4021: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4022: int *popage;
4023: double calagedatem, agelim, kk1, kk2;
4024: double *popeffectif,*popcount;
4025: double ***p3mat,***tabpop,***tabpopprev;
4026: double ***mobaverage;
4027: char filerespop[FILENAMELENGTH];
4028:
4029: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4030: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4031: agelim=AGESUP;
4032: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4033:
4034: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4035:
4036:
4037: strcpy(filerespop,"pop");
4038: strcat(filerespop,fileres);
4039: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4040: printf("Problem with forecast resultfile: %s\n", filerespop);
4041: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4042: }
4043: printf("Computing forecasting: result on file '%s' \n", filerespop);
4044: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4045:
4046: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4047:
4048: if (mobilav!=0) {
4049: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4050: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4051: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4052: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4053: }
4054: }
4055:
4056: stepsize=(int) (stepm+YEARM-1)/YEARM;
4057: if (stepm<=12) stepsize=1;
4058:
4059: agelim=AGESUP;
4060:
4061: hstepm=1;
4062: hstepm=hstepm/stepm;
4063:
4064: if (popforecast==1) {
4065: if((ficpop=fopen(popfile,"r"))==NULL) {
4066: printf("Problem with population file : %s\n",popfile);exit(0);
4067: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4068: }
4069: popage=ivector(0,AGESUP);
4070: popeffectif=vector(0,AGESUP);
4071: popcount=vector(0,AGESUP);
4072:
4073: i=1;
4074: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4075:
4076: imx=i;
4077: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4078: }
4079:
4080: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4081: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4082: k=k+1;
4083: fprintf(ficrespop,"\n#******");
4084: for(j=1;j<=cptcoveff;j++) {
4085: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4086: }
4087: fprintf(ficrespop,"******\n");
4088: fprintf(ficrespop,"# Age");
4089: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4090: if (popforecast==1) fprintf(ficrespop," [Population]");
4091:
4092: for (cpt=0; cpt<=0;cpt++) {
4093: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4094:
4095: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4096: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4097: nhstepm = nhstepm/hstepm;
4098:
4099: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4100: oldm=oldms;savm=savms;
4101: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4102:
4103: for (h=0; h<=nhstepm; h++){
4104: if (h==(int) (calagedatem+YEARM*cpt)) {
4105: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4106: }
4107: for(j=1; j<=nlstate+ndeath;j++) {
4108: kk1=0.;kk2=0;
4109: for(i=1; i<=nlstate;i++) {
4110: if (mobilav==1)
4111: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4112: else {
4113: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4114: }
4115: }
4116: if (h==(int)(calagedatem+12*cpt)){
4117: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4118: /*fprintf(ficrespop," %.3f", kk1);
4119: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4120: }
4121: }
4122: for(i=1; i<=nlstate;i++){
4123: kk1=0.;
4124: for(j=1; j<=nlstate;j++){
4125: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4126: }
4127: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4128: }
4129:
4130: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4131: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4132: }
4133: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4134: }
4135: }
4136:
4137: /******/
4138:
4139: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4140: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4141: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4142: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4143: nhstepm = nhstepm/hstepm;
4144:
4145: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4146: oldm=oldms;savm=savms;
4147: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4148: for (h=0; h<=nhstepm; h++){
4149: if (h==(int) (calagedatem+YEARM*cpt)) {
4150: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4151: }
4152: for(j=1; j<=nlstate+ndeath;j++) {
4153: kk1=0.;kk2=0;
4154: for(i=1; i<=nlstate;i++) {
4155: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4156: }
4157: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4158: }
4159: }
4160: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4161: }
4162: }
4163: }
4164: }
4165:
4166: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4167:
4168: if (popforecast==1) {
4169: free_ivector(popage,0,AGESUP);
4170: free_vector(popeffectif,0,AGESUP);
4171: free_vector(popcount,0,AGESUP);
4172: }
4173: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4174: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4175: fclose(ficrespop);
4176: } /* End of popforecast */
4177:
4178: int fileappend(FILE *fichier, char *optionfich)
4179: {
4180: if((fichier=fopen(optionfich,"a"))==NULL) {
4181: printf("Problem with file: %s\n", optionfich);
4182: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4183: return (0);
4184: }
4185: fflush(fichier);
4186: return (1);
4187: }
4188:
4189:
4190: /**************** function prwizard **********************/
4191: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4192: {
4193:
4194: /* Wizard to print covariance matrix template */
4195:
4196: char ca[32], cb[32], cc[32];
4197: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4198: int numlinepar;
4199:
4200: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4201: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4202: for(i=1; i <=nlstate; i++){
4203: jj=0;
4204: for(j=1; j <=nlstate+ndeath; j++){
4205: if(j==i) continue;
4206: jj++;
4207: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4208: printf("%1d%1d",i,j);
4209: fprintf(ficparo,"%1d%1d",i,j);
4210: for(k=1; k<=ncovmodel;k++){
4211: /* printf(" %lf",param[i][j][k]); */
4212: /* fprintf(ficparo," %lf",param[i][j][k]); */
4213: printf(" 0.");
4214: fprintf(ficparo," 0.");
4215: }
4216: printf("\n");
4217: fprintf(ficparo,"\n");
4218: }
4219: }
4220: printf("# Scales (for hessian or gradient estimation)\n");
4221: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4222: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4223: for(i=1; i <=nlstate; i++){
4224: jj=0;
4225: for(j=1; j <=nlstate+ndeath; j++){
4226: if(j==i) continue;
4227: jj++;
4228: fprintf(ficparo,"%1d%1d",i,j);
4229: printf("%1d%1d",i,j);
4230: fflush(stdout);
4231: for(k=1; k<=ncovmodel;k++){
4232: /* printf(" %le",delti3[i][j][k]); */
4233: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4234: printf(" 0.");
4235: fprintf(ficparo," 0.");
4236: }
4237: numlinepar++;
4238: printf("\n");
4239: fprintf(ficparo,"\n");
4240: }
4241: }
4242: printf("# Covariance matrix\n");
4243: /* # 121 Var(a12)\n\ */
4244: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4245: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4246: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4247: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4248: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4249: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4250: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4251: fflush(stdout);
4252: fprintf(ficparo,"# Covariance matrix\n");
4253: /* # 121 Var(a12)\n\ */
4254: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4255: /* # ...\n\ */
4256: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4257:
4258: for(itimes=1;itimes<=2;itimes++){
4259: jj=0;
4260: for(i=1; i <=nlstate; i++){
4261: for(j=1; j <=nlstate+ndeath; j++){
4262: if(j==i) continue;
4263: for(k=1; k<=ncovmodel;k++){
4264: jj++;
4265: ca[0]= k+'a'-1;ca[1]='\0';
4266: if(itimes==1){
4267: printf("#%1d%1d%d",i,j,k);
4268: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4269: }else{
4270: printf("%1d%1d%d",i,j,k);
4271: fprintf(ficparo,"%1d%1d%d",i,j,k);
4272: /* printf(" %.5le",matcov[i][j]); */
4273: }
4274: ll=0;
4275: for(li=1;li <=nlstate; li++){
4276: for(lj=1;lj <=nlstate+ndeath; lj++){
4277: if(lj==li) continue;
4278: for(lk=1;lk<=ncovmodel;lk++){
4279: ll++;
4280: if(ll<=jj){
4281: cb[0]= lk +'a'-1;cb[1]='\0';
4282: if(ll<jj){
4283: if(itimes==1){
4284: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4285: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4286: }else{
4287: printf(" 0.");
4288: fprintf(ficparo," 0.");
4289: }
4290: }else{
4291: if(itimes==1){
4292: printf(" Var(%s%1d%1d)",ca,i,j);
4293: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4294: }else{
4295: printf(" 0.");
4296: fprintf(ficparo," 0.");
4297: }
4298: }
4299: }
4300: } /* end lk */
4301: } /* end lj */
4302: } /* end li */
4303: printf("\n");
4304: fprintf(ficparo,"\n");
4305: numlinepar++;
4306: } /* end k*/
4307: } /*end j */
4308: } /* end i */
4309: } /* end itimes */
4310:
4311: } /* end of prwizard */
4312: /******************* Gompertz Likelihood ******************************/
4313: double gompertz(double x[])
4314: {
4315: double A,B,L=0.0,sump=0.,num=0.;
4316: int i,n=0; /* n is the size of the sample */
4317:
4318: for (i=0;i<=imx-1 ; i++) {
4319: sump=sump+weight[i];
4320: /* sump=sump+1;*/
4321: num=num+1;
4322: }
4323:
4324:
4325: /* for (i=0; i<=imx; i++)
4326: 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]);*/
4327:
4328: for (i=1;i<=imx ; i++)
4329: {
4330: if (cens[i] == 1 && wav[i]>1)
4331: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4332:
4333: if (cens[i] == 0 && wav[i]>1)
4334: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4335: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4336:
4337: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4338: if (wav[i] > 1 ) { /* ??? */
4339: L=L+A*weight[i];
4340: /* 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]);*/
4341: }
4342: }
4343:
4344: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4345:
4346: return -2*L*num/sump;
4347: }
4348:
4349: /******************* Printing html file ***********/
4350: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4351: int lastpass, int stepm, int weightopt, char model[],\
4352: int imx, double p[],double **matcov,double agemortsup){
4353: int i,k;
4354:
4355: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4356: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4357: for (i=1;i<=2;i++)
4358: 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]));
4359: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4360: fprintf(fichtm,"</ul>");
4361:
4362: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4363:
4364: 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>");
4365:
4366: for (k=agegomp;k<(agemortsup-2);k++)
4367: 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]);
4368:
4369:
4370: fflush(fichtm);
4371: }
4372:
4373: /******************* Gnuplot file **************/
4374: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4375:
4376: char dirfileres[132],optfileres[132];
4377: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4378: int ng;
4379:
4380:
4381: /*#ifdef windows */
4382: fprintf(ficgp,"cd \"%s\" \n",pathc);
4383: /*#endif */
4384:
4385:
4386: strcpy(dirfileres,optionfilefiname);
4387: strcpy(optfileres,"vpl");
4388: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4389: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4390: fprintf(ficgp, "set ter png small\n set log y\n");
4391: fprintf(ficgp, "set size 0.65,0.65\n");
4392: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4393:
4394: }
4395:
4396:
4397:
4398:
4399:
4400: /***********************************************/
4401: /**************** Main Program *****************/
4402: /***********************************************/
4403:
4404: int main(int argc, char *argv[])
4405: {
4406: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4407: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4408: int linei, month, year,iout;
4409: int jj, ll, li, lj, lk, imk;
4410: int numlinepar=0; /* Current linenumber of parameter file */
4411: int itimes;
4412: int NDIM=2;
1.128 brouard 4413: int vpopbased=0;
1.126 brouard 4414:
4415: char ca[32], cb[32], cc[32];
4416: char dummy[]=" ";
4417: /* FILE *fichtm; *//* Html File */
4418: /* FILE *ficgp;*/ /*Gnuplot File */
4419: struct stat info;
4420: double agedeb, agefin,hf;
4421: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4422:
4423: double fret;
4424: double **xi,tmp,delta;
4425:
4426: double dum; /* Dummy variable */
4427: double ***p3mat;
4428: double ***mobaverage;
4429: int *indx;
4430: char line[MAXLINE], linepar[MAXLINE];
4431: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4432: char pathr[MAXLINE], pathimach[MAXLINE];
4433: char **bp, *tok, *val; /* pathtot */
4434: int firstobs=1, lastobs=10;
4435: int sdeb, sfin; /* Status at beginning and end */
4436: int c, h , cpt,l;
4437: int ju,jl, mi;
4438: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4439: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4440: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4441: int mobilav=0,popforecast=0;
4442: int hstepm, nhstepm;
4443: int agemortsup;
4444: float sumlpop=0.;
4445: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4446: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4447:
4448: double bage, fage, age, agelim, agebase;
4449: double ftolpl=FTOL;
4450: double **prlim;
4451: double *severity;
4452: double ***param; /* Matrix of parameters */
4453: double *p;
4454: double **matcov; /* Matrix of covariance */
4455: double ***delti3; /* Scale */
4456: double *delti; /* Scale */
4457: double ***eij, ***vareij;
4458: double **varpl; /* Variances of prevalence limits by age */
4459: double *epj, vepp;
4460: double kk1, kk2;
4461: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4462: double **ximort;
4463: char *alph[]={"a","a","b","c","d","e"}, str[4];
4464: int *dcwave;
4465:
4466: char z[1]="c", occ;
4467:
4468: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4469: char *strt, strtend[80];
4470: char *stratrunc;
4471: int lstra;
4472:
4473: long total_usecs;
4474:
4475: /* setlocale (LC_ALL, ""); */
4476: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4477: /* textdomain (PACKAGE); */
4478: /* setlocale (LC_CTYPE, ""); */
4479: /* setlocale (LC_MESSAGES, ""); */
4480:
4481: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4482: (void) gettimeofday(&start_time,&tzp);
4483: curr_time=start_time;
4484: tm = *localtime(&start_time.tv_sec);
4485: tmg = *gmtime(&start_time.tv_sec);
4486: strcpy(strstart,asctime(&tm));
4487:
4488: /* printf("Localtime (at start)=%s",strstart); */
4489: /* tp.tv_sec = tp.tv_sec +86400; */
4490: /* tm = *localtime(&start_time.tv_sec); */
4491: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4492: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4493: /* tmg.tm_hour=tmg.tm_hour + 1; */
4494: /* tp.tv_sec = mktime(&tmg); */
4495: /* strt=asctime(&tmg); */
4496: /* printf("Time(after) =%s",strstart); */
4497: /* (void) time (&time_value);
4498: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4499: * tm = *localtime(&time_value);
4500: * strstart=asctime(&tm);
4501: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4502: */
4503:
4504: nberr=0; /* Number of errors and warnings */
4505: nbwarn=0;
4506: getcwd(pathcd, size);
4507:
4508: printf("\n%s\n%s",version,fullversion);
4509: if(argc <=1){
4510: printf("\nEnter the parameter file name: ");
4511: fgets(pathr,FILENAMELENGTH,stdin);
4512: i=strlen(pathr);
4513: if(pathr[i-1]=='\n')
4514: pathr[i-1]='\0';
4515: for (tok = pathr; tok != NULL; ){
4516: printf("Pathr |%s|\n",pathr);
4517: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4518: printf("val= |%s| pathr=%s\n",val,pathr);
4519: strcpy (pathtot, val);
4520: if(pathr[0] == '\0') break; /* Dirty */
4521: }
4522: }
4523: else{
4524: strcpy(pathtot,argv[1]);
4525: }
4526: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4527: /*cygwin_split_path(pathtot,path,optionfile);
4528: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4529: /* cutv(path,optionfile,pathtot,'\\');*/
4530:
4531: /* Split argv[0], imach program to get pathimach */
4532: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4533: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4534: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4535: /* strcpy(pathimach,argv[0]); */
4536: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4537: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4538: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4539: chdir(path); /* Can be a relative path */
4540: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4541: printf("Current directory %s!\n",pathcd);
4542: strcpy(command,"mkdir ");
4543: strcat(command,optionfilefiname);
4544: if((outcmd=system(command)) != 0){
4545: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4546: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4547: /* fclose(ficlog); */
4548: /* exit(1); */
4549: }
4550: /* if((imk=mkdir(optionfilefiname))<0){ */
4551: /* perror("mkdir"); */
4552: /* } */
4553:
4554: /*-------- arguments in the command line --------*/
4555:
4556: /* Log file */
4557: strcat(filelog, optionfilefiname);
4558: strcat(filelog,".log"); /* */
4559: if((ficlog=fopen(filelog,"w"))==NULL) {
4560: printf("Problem with logfile %s\n",filelog);
4561: goto end;
4562: }
4563: fprintf(ficlog,"Log filename:%s\n",filelog);
4564: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4565: fprintf(ficlog,"\nEnter the parameter file name: \n");
4566: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4567: path=%s \n\
4568: optionfile=%s\n\
4569: optionfilext=%s\n\
4570: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4571:
4572: printf("Local time (at start):%s",strstart);
4573: fprintf(ficlog,"Local time (at start): %s",strstart);
4574: fflush(ficlog);
4575: /* (void) gettimeofday(&curr_time,&tzp); */
4576: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4577:
4578: /* */
4579: strcpy(fileres,"r");
4580: strcat(fileres, optionfilefiname);
4581: strcat(fileres,".txt"); /* Other files have txt extension */
4582:
4583: /*---------arguments file --------*/
4584:
4585: if((ficpar=fopen(optionfile,"r"))==NULL) {
4586: printf("Problem with optionfile %s\n",optionfile);
4587: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4588: fflush(ficlog);
4589: goto end;
4590: }
4591:
4592:
4593:
4594: strcpy(filereso,"o");
4595: strcat(filereso,fileres);
4596: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4597: printf("Problem with Output resultfile: %s\n", filereso);
4598: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4599: fflush(ficlog);
4600: goto end;
4601: }
4602:
4603: /* Reads comments: lines beginning with '#' */
4604: numlinepar=0;
4605: while((c=getc(ficpar))=='#' && c!= EOF){
4606: ungetc(c,ficpar);
4607: fgets(line, MAXLINE, ficpar);
4608: numlinepar++;
4609: puts(line);
4610: fputs(line,ficparo);
4611: fputs(line,ficlog);
4612: }
4613: ungetc(c,ficpar);
4614:
4615: 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);
4616: numlinepar++;
4617: 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);
4618: 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);
4619: 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);
4620: fflush(ficlog);
4621: while((c=getc(ficpar))=='#' && c!= EOF){
4622: ungetc(c,ficpar);
4623: fgets(line, MAXLINE, ficpar);
4624: numlinepar++;
4625: puts(line);
4626: fputs(line,ficparo);
4627: fputs(line,ficlog);
4628: }
4629: ungetc(c,ficpar);
4630:
4631:
4632: covar=matrix(0,NCOVMAX,1,n);
4633: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4634: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4635:
4636: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4637: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4638: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.131 ! brouard 4639: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
! 4640: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
! 4641: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
! 4642: fflush(stdout);
! 4643: fclose (ficlog);
! 4644: goto end;
! 4645: }
1.126 brouard 4646: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4647: delti=delti3[1][1];
4648: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4649: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4650: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4651: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4652: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4653: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4654: fclose (ficparo);
4655: fclose (ficlog);
4656: goto end;
4657: exit(0);
4658: }
4659: else if(mle==-3) {
4660: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4661: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4662: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4663: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4664: matcov=matrix(1,npar,1,npar);
4665: }
4666: else{
4667: /* Read guess parameters */
4668: /* Reads comments: lines beginning with '#' */
4669: while((c=getc(ficpar))=='#' && c!= EOF){
4670: ungetc(c,ficpar);
4671: fgets(line, MAXLINE, ficpar);
4672: numlinepar++;
4673: puts(line);
4674: fputs(line,ficparo);
4675: fputs(line,ficlog);
4676: }
4677: ungetc(c,ficpar);
4678:
4679: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4680: for(i=1; i <=nlstate; i++){
4681: j=0;
4682: for(jj=1; jj <=nlstate+ndeath; jj++){
4683: if(jj==i) continue;
4684: j++;
4685: fscanf(ficpar,"%1d%1d",&i1,&j1);
4686: if ((i1 != i) && (j1 != j)){
4687: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4688: It might be a problem of design; if ncovcol and the model are correct\n \
4689: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
4690: exit(1);
4691: }
4692: fprintf(ficparo,"%1d%1d",i1,j1);
4693: if(mle==1)
4694: printf("%1d%1d",i,j);
4695: fprintf(ficlog,"%1d%1d",i,j);
4696: for(k=1; k<=ncovmodel;k++){
4697: fscanf(ficpar," %lf",¶m[i][j][k]);
4698: if(mle==1){
4699: printf(" %lf",param[i][j][k]);
4700: fprintf(ficlog," %lf",param[i][j][k]);
4701: }
4702: else
4703: fprintf(ficlog," %lf",param[i][j][k]);
4704: fprintf(ficparo," %lf",param[i][j][k]);
4705: }
4706: fscanf(ficpar,"\n");
4707: numlinepar++;
4708: if(mle==1)
4709: printf("\n");
4710: fprintf(ficlog,"\n");
4711: fprintf(ficparo,"\n");
4712: }
4713: }
4714: fflush(ficlog);
4715:
4716: p=param[1][1];
4717:
4718: /* Reads comments: lines beginning with '#' */
4719: while((c=getc(ficpar))=='#' && c!= EOF){
4720: ungetc(c,ficpar);
4721: fgets(line, MAXLINE, ficpar);
4722: numlinepar++;
4723: puts(line);
4724: fputs(line,ficparo);
4725: fputs(line,ficlog);
4726: }
4727: ungetc(c,ficpar);
4728:
4729: for(i=1; i <=nlstate; i++){
4730: for(j=1; j <=nlstate+ndeath-1; j++){
4731: fscanf(ficpar,"%1d%1d",&i1,&j1);
4732: if ((i1-i)*(j1-j)!=0){
4733: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4734: exit(1);
4735: }
4736: printf("%1d%1d",i,j);
4737: fprintf(ficparo,"%1d%1d",i1,j1);
4738: fprintf(ficlog,"%1d%1d",i1,j1);
4739: for(k=1; k<=ncovmodel;k++){
4740: fscanf(ficpar,"%le",&delti3[i][j][k]);
4741: printf(" %le",delti3[i][j][k]);
4742: fprintf(ficparo," %le",delti3[i][j][k]);
4743: fprintf(ficlog," %le",delti3[i][j][k]);
4744: }
4745: fscanf(ficpar,"\n");
4746: numlinepar++;
4747: printf("\n");
4748: fprintf(ficparo,"\n");
4749: fprintf(ficlog,"\n");
4750: }
4751: }
4752: fflush(ficlog);
4753:
4754: delti=delti3[1][1];
4755:
4756:
4757: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4758:
4759: /* Reads comments: lines beginning with '#' */
4760: while((c=getc(ficpar))=='#' && c!= EOF){
4761: ungetc(c,ficpar);
4762: fgets(line, MAXLINE, ficpar);
4763: numlinepar++;
4764: puts(line);
4765: fputs(line,ficparo);
4766: fputs(line,ficlog);
4767: }
4768: ungetc(c,ficpar);
4769:
4770: matcov=matrix(1,npar,1,npar);
1.131 ! brouard 4771: for(i=1; i <=npar; i++)
! 4772: for(j=1; j <=npar; j++) matcov[i][j]=0.;
! 4773:
1.126 brouard 4774: for(i=1; i <=npar; i++){
4775: fscanf(ficpar,"%s",&str);
4776: if(mle==1)
4777: printf("%s",str);
4778: fprintf(ficlog,"%s",str);
4779: fprintf(ficparo,"%s",str);
4780: for(j=1; j <=i; j++){
4781: fscanf(ficpar," %le",&matcov[i][j]);
4782: if(mle==1){
4783: printf(" %.5le",matcov[i][j]);
4784: }
4785: fprintf(ficlog," %.5le",matcov[i][j]);
4786: fprintf(ficparo," %.5le",matcov[i][j]);
4787: }
4788: fscanf(ficpar,"\n");
4789: numlinepar++;
4790: if(mle==1)
4791: printf("\n");
4792: fprintf(ficlog,"\n");
4793: fprintf(ficparo,"\n");
4794: }
4795: for(i=1; i <=npar; i++)
4796: for(j=i+1;j<=npar;j++)
4797: matcov[i][j]=matcov[j][i];
4798:
4799: if(mle==1)
4800: printf("\n");
4801: fprintf(ficlog,"\n");
4802:
4803: fflush(ficlog);
4804:
4805: /*-------- Rewriting parameter file ----------*/
4806: strcpy(rfileres,"r"); /* "Rparameterfile */
4807: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4808: strcat(rfileres,"."); /* */
4809: strcat(rfileres,optionfilext); /* Other files have txt extension */
4810: if((ficres =fopen(rfileres,"w"))==NULL) {
4811: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4812: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4813: }
4814: fprintf(ficres,"#%s\n",version);
4815: } /* End of mle != -3 */
4816:
4817: /*-------- data file ----------*/
4818: if((fic=fopen(datafile,"r"))==NULL) {
4819: printf("Problem while opening datafile: %s\n", datafile);goto end;
4820: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4821: }
4822:
4823: n= lastobs;
4824: severity = vector(1,maxwav);
4825: outcome=imatrix(1,maxwav+1,1,n);
4826: num=lvector(1,n);
4827: moisnais=vector(1,n);
4828: annais=vector(1,n);
4829: moisdc=vector(1,n);
4830: andc=vector(1,n);
4831: agedc=vector(1,n);
4832: cod=ivector(1,n);
4833: weight=vector(1,n);
4834: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4835: mint=matrix(1,maxwav,1,n);
4836: anint=matrix(1,maxwav,1,n);
1.131 ! brouard 4837: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 4838: tab=ivector(1,NCOVMAX);
4839: ncodemax=ivector(1,8);
4840:
4841: i=1;
4842: linei=0;
4843: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4844: linei=linei+1;
4845: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4846: if(line[j] == '\t')
4847: line[j] = ' ';
4848: }
4849: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4850: ;
4851: };
4852: line[j+1]=0; /* Trims blanks at end of line */
4853: if(line[0]=='#'){
4854: fprintf(ficlog,"Comment line\n%s\n",line);
4855: printf("Comment line\n%s\n",line);
4856: continue;
4857: }
4858:
4859: for (j=maxwav;j>=1;j--){
4860: cutv(stra, strb,line,' ');
1.131 ! brouard 4861: if(strb[0]=='.') { /* Missing status */
! 4862: lval=-1;
! 4863: }else{
! 4864: errno=0;
! 4865: lval=strtol(strb,&endptr,10);
1.126 brouard 4866: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
1.131 ! brouard 4867: if( strb[0]=='\0' || (*endptr != '\0')){
! 4868: printf("Error reading data around '%s' at line number %ld 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);
! 4869: fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);fflush(ficlog);
! 4870: goto end;
! 4871: }
1.126 brouard 4872: }
4873: s[j][i]=lval;
4874:
4875: strcpy(line,stra);
4876: cutv(stra, strb,line,' ');
4877: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4878: }
4879: else if(iout=sscanf(strb,"%s.") != 0){
4880: month=99;
4881: year=9999;
4882: }else{
1.131 ! brouard 4883: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
! 4884: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
! 4885: goto end;
1.126 brouard 4886: }
4887: anint[j][i]= (double) year;
4888: mint[j][i]= (double)month;
4889: strcpy(line,stra);
4890: } /* ENd Waves */
4891:
4892: cutv(stra, strb,line,' ');
4893: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4894: }
4895: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4896: month=99;
4897: year=9999;
4898: }else{
1.131 ! brouard 4899: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
! 4900: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
! 4901: goto end;
1.126 brouard 4902: }
4903: andc[i]=(double) year;
4904: moisdc[i]=(double) month;
4905: strcpy(line,stra);
4906:
4907: cutv(stra, strb,line,' ');
4908: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4909: }
4910: else if(iout=sscanf(strb,"%s.") != 0){
4911: month=99;
4912: year=9999;
4913: }else{
4914: 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);
1.131 ! brouard 4915: fprintf(ficlog,"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);fflush(ficlog);
! 4916: goto end;
1.126 brouard 4917: }
4918: annais[i]=(double)(year);
4919: moisnais[i]=(double)(month);
4920: strcpy(line,stra);
4921:
4922: cutv(stra, strb,line,' ');
4923: errno=0;
4924: dval=strtod(strb,&endptr);
4925: if( strb[0]=='\0' || (*endptr != '\0')){
4926: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.131 ! brouard 4927: fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
! 4928: fflush(ficlog);
! 4929: goto end;
1.126 brouard 4930: }
4931: weight[i]=dval;
4932: strcpy(line,stra);
4933:
4934: for (j=ncovcol;j>=1;j--){
4935: cutv(stra, strb,line,' ');
1.131 ! brouard 4936: if(strb[0]=='.') { /* Missing status */
! 4937: lval=-1;
! 4938: }else{
! 4939: errno=0;
! 4940: lval=strtol(strb,&endptr,10);
! 4941: if( strb[0]=='\0' || (*endptr != '\0')){
! 4942: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
! 4943: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
! 4944: goto end;
! 4945: }
1.126 brouard 4946: }
4947: if(lval <-1 || lval >1){
4948: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4949: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4950: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4951: For example, for multinomial values like 1, 2 and 3,\n \
4952: build V1=0 V2=0 for the reference value (1),\n \
4953: V1=1 V2=0 for (2) \n \
4954: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4955: output of IMaCh is often meaningless.\n \
4956: Exiting.\n",lval,linei, i,line,j);
1.131 ! brouard 4957: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
! 4958: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 4959: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 4960: For example, for multinomial values like 1, 2 and 3,\n \
! 4961: build V1=0 V2=0 for the reference value (1),\n \
! 4962: V1=1 V2=0 for (2) \n \
! 4963: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 4964: output of IMaCh is often meaningless.\n \
! 4965: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.129 lievre 4966: goto end;
1.126 brouard 4967: }
4968: covar[j][i]=(double)(lval);
4969: strcpy(line,stra);
1.129 lievre 4970: }
1.126 brouard 4971: lstra=strlen(stra);
1.129 lievre 4972:
1.126 brouard 4973: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4974: stratrunc = &(stra[lstra-9]);
4975: num[i]=atol(stratrunc);
4976: }
4977: else
4978: num[i]=atol(stra);
4979: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4980: 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;}*/
4981:
4982: i=i+1;
4983: } /* End loop reading data */
4984: fclose(fic);
4985: /* printf("ii=%d", ij);
4986: scanf("%d",i);*/
4987: imx=i-1; /* Number of individuals */
4988:
4989: /* for (i=1; i<=imx; i++){
4990: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4991: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4992: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4993: }*/
4994: /* for (i=1; i<=imx; i++){
4995: if (s[4][i]==9) s[4][i]=-1;
4996: 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]));}*/
4997:
4998: /* for (i=1; i<=imx; i++) */
4999:
5000: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
5001: else weight[i]=1;*/
5002:
5003: /* Calculation of the number of parameters from char model */
1.131 ! brouard 5004: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
1.126 brouard 5005: Tprod=ivector(1,15);
5006: Tvaraff=ivector(1,15);
5007: Tvard=imatrix(1,15,1,2);
5008: Tage=ivector(1,15);
5009:
5010: if (strlen(model) >1){ /* If there is at least 1 covariate */
5011: j=0, j1=0, k1=1, k2=1;
5012: j=nbocc(model,'+'); /* j=Number of '+' */
5013: j1=nbocc(model,'*'); /* j1=Number of '*' */
1.130 brouard 5014: cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
5015: cptcovprod=j1; /*Number of products V1*V2 =1 */
1.126 brouard 5016:
5017: strcpy(modelsav,model);
5018: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
5019: printf("Error. Non available option model=%s ",model);
1.131 ! brouard 5020: fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
1.126 brouard 5021: goto end;
5022: }
5023:
5024: /* This loop fills the array Tvar from the string 'model'.*/
1.130 brouard 5025: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.126 brouard 5026: for(i=(j+1); i>=1;i--){
1.130 brouard 5027: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5028: modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4
5029: stra=V2
5030: */
1.126 brouard 5031: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5032: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5033: /*scanf("%d",i);*/
1.130 brouard 5034: if (strchr(strb,'*')) { /* Model includes a product V1+V3*age+V2 strb=V3*age*/
5035: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
1.126 brouard 5036: if (strcmp(strc,"age")==0) { /* Vn*age */
5037: cptcovprod--;
5038: cutv(strb,stre,strd,'V');
1.130 brouard 5039: Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */
5040: cptcovage++; /* Sum the number of covariates including ages as a product */
5041: Tage[cptcovage]=i; /* Tage[1] =2 */
5042: /*printf("stre=%s ", stre);*/
1.126 brouard 5043: }
5044: else if (strcmp(strd,"age")==0) { /* or age*Vn */
5045: cptcovprod--;
5046: cutv(strb,stre,strc,'V');
5047: Tvar[i]=atoi(stre);
5048: cptcovage++;
5049: Tage[cptcovage]=i;
5050: }
1.130 brouard 5051: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
5052: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5053: Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
5054: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
1.126 brouard 5055: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
1.130 brouard 5056: Tprod[k1]=i; /* Tprod[1] */
1.126 brouard 5057: Tvard[k1][1]=atoi(strc); /* m*/
5058: Tvard[k1][2]=atoi(stre); /* n */
5059: Tvar[cptcovn+k2]=Tvard[k1][1];
5060: Tvar[cptcovn+k2+1]=Tvard[k1][2];
5061: for (k=1; k<=lastobs;k++)
5062: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
5063: k1++;
5064: k2=k2+2;
5065: }
5066: }
5067: else { /* no more sum */
5068: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5069: /* scanf("%d",i);*/
5070: cutv(strd,strc,strb,'V');
5071: Tvar[i]=atoi(strc);
5072: }
1.130 brouard 5073: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
1.126 brouard 5074: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5075: scanf("%d",i);*/
5076: } /* end of loop + */
5077: } /* end model */
5078:
5079: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5080: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5081:
5082: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5083: printf("cptcovprod=%d ", cptcovprod);
5084: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5085:
5086: scanf("%d ",i);*/
5087:
5088: /* if(mle==1){*/
5089: if (weightopt != 1) { /* Maximisation without weights*/
5090: for(i=1;i<=n;i++) weight[i]=1.0;
5091: }
5092: /*-calculation of age at interview from date of interview and age at death -*/
5093: agev=matrix(1,maxwav,1,imx);
5094:
5095: for (i=1; i<=imx; i++) {
5096: for(m=2; (m<= maxwav); m++) {
5097: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5098: anint[m][i]=9999;
5099: s[m][i]=-1;
5100: }
5101: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5102: nberr++;
5103: 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);
5104: 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);
5105: s[m][i]=-1;
5106: }
5107: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5108: nberr++;
5109: 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]);
5110: 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]);
5111: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5112: }
5113: }
5114: }
5115:
5116: for (i=1; i<=imx; i++) {
5117: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5118: for(m=firstpass; (m<= lastpass); m++){
5119: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5120: if (s[m][i] >= nlstate+1) {
5121: if(agedc[i]>0)
5122: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5123: agev[m][i]=agedc[i];
5124: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5125: else {
5126: if ((int)andc[i]!=9999){
5127: nbwarn++;
5128: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5129: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5130: agev[m][i]=-1;
5131: }
5132: }
5133: }
5134: else if(s[m][i] !=9){ /* Standard case, age in fractional
5135: years but with the precision of a month */
5136: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5137: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5138: agev[m][i]=1;
5139: else if(agev[m][i] <agemin){
5140: agemin=agev[m][i];
5141: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5142: }
5143: else if(agev[m][i] >agemax){
5144: agemax=agev[m][i];
5145: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5146: }
5147: /*agev[m][i]=anint[m][i]-annais[i];*/
5148: /* agev[m][i] = age[i]+2*m;*/
5149: }
5150: else { /* =9 */
5151: agev[m][i]=1;
5152: s[m][i]=-1;
5153: }
5154: }
5155: else /*= 0 Unknown */
5156: agev[m][i]=1;
5157: }
5158:
5159: }
5160: for (i=1; i<=imx; i++) {
5161: for(m=firstpass; (m<=lastpass); m++){
5162: if (s[m][i] > (nlstate+ndeath)) {
5163: nberr++;
5164: 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);
5165: 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);
5166: goto end;
5167: }
5168: }
5169: }
5170:
5171: /*for (i=1; i<=imx; i++){
5172: for (m=firstpass; (m<lastpass); m++){
5173: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5174: }
5175:
5176: }*/
5177:
5178:
5179: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5180: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5181:
5182: agegomp=(int)agemin;
5183: free_vector(severity,1,maxwav);
5184: free_imatrix(outcome,1,maxwav+1,1,n);
5185: free_vector(moisnais,1,n);
5186: free_vector(annais,1,n);
5187: /* free_matrix(mint,1,maxwav,1,n);
5188: free_matrix(anint,1,maxwav,1,n);*/
5189: free_vector(moisdc,1,n);
5190: free_vector(andc,1,n);
5191:
5192:
5193: wav=ivector(1,imx);
5194: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5195: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5196: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5197:
5198: /* Concatenates waves */
5199: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5200:
5201: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5202:
5203: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5204: ncodemax[1]=1;
5205: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5206:
5207: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5208: the estimations*/
5209: h=0;
5210: m=pow(2,cptcoveff);
5211:
1.131 ! brouard 5212: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
! 5213: for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
! 5214: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
! 5215: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 5216: h++;
1.131 ! brouard 5217: if (h>m)
! 5218: h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
1.130 brouard 5219: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
1.126 brouard 5220: }
5221: }
5222: }
5223: }
5224: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5225: codtab[1][2]=1;codtab[2][2]=2; */
5226: /* for(i=1; i <=m ;i++){
5227: for(k=1; k <=cptcovn; k++){
1.131 ! brouard 5228: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5229: }
5230: printf("\n");
5231: }
5232: scanf("%d",i);*/
5233:
5234: /*------------ gnuplot -------------*/
5235: strcpy(optionfilegnuplot,optionfilefiname);
5236: if(mle==-3)
5237: strcat(optionfilegnuplot,"-mort");
5238: strcat(optionfilegnuplot,".gp");
5239:
5240: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5241: printf("Problem with file %s",optionfilegnuplot);
5242: }
5243: else{
5244: fprintf(ficgp,"\n# %s\n", version);
5245: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5246: fprintf(ficgp,"set missing 'NaNq'\n");
5247: }
5248: /* fclose(ficgp);*/
5249: /*--------- index.htm --------*/
5250:
5251: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5252: if(mle==-3)
5253: strcat(optionfilehtm,"-mort");
5254: strcat(optionfilehtm,".htm");
5255: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 ! brouard 5256: printf("Problem with %s \n",optionfilehtm);
! 5257: exit(0);
1.126 brouard 5258: }
5259:
5260: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5261: strcat(optionfilehtmcov,"-cov.htm");
5262: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5263: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5264: }
5265: else{
5266: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5267: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5268: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5269: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5270: }
5271:
5272: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5273: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5274: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5275: \n\
5276: <hr size=\"2\" color=\"#EC5E5E\">\
5277: <ul><li><h4>Parameter files</h4>\n\
5278: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5279: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5280: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5281: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5282: - Date and time at start: %s</ul>\n",\
5283: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5284: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5285: fileres,fileres,\
5286: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5287: fflush(fichtm);
5288:
5289: strcpy(pathr,path);
5290: strcat(pathr,optionfilefiname);
5291: chdir(optionfilefiname); /* Move to directory named optionfile */
5292:
5293: /* Calculates basic frequencies. Computes observed prevalence at single age
5294: and prints on file fileres'p'. */
5295: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5296:
5297: fprintf(fichtm,"\n");
5298: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5299: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5300: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5301: imx,agemin,agemax,jmin,jmax,jmean);
5302: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5303: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5304: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5305: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5306: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5307:
5308:
5309: /* For Powell, parameters are in a vector p[] starting at p[1]
5310: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5311: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5312:
5313: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5314:
5315: if (mle==-3){
5316: ximort=matrix(1,NDIM,1,NDIM);
5317: cens=ivector(1,n);
5318: ageexmed=vector(1,n);
5319: agecens=vector(1,n);
5320: dcwave=ivector(1,n);
5321:
5322: for (i=1; i<=imx; i++){
5323: dcwave[i]=-1;
5324: for (m=firstpass; m<=lastpass; m++)
5325: if (s[m][i]>nlstate) {
5326: dcwave[i]=m;
5327: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5328: break;
5329: }
5330: }
5331:
5332: for (i=1; i<=imx; i++) {
5333: if (wav[i]>0){
5334: ageexmed[i]=agev[mw[1][i]][i];
5335: j=wav[i];
5336: agecens[i]=1.;
5337:
5338: if (ageexmed[i]> 1 && wav[i] > 0){
5339: agecens[i]=agev[mw[j][i]][i];
5340: cens[i]= 1;
5341: }else if (ageexmed[i]< 1)
5342: cens[i]= -1;
5343: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5344: cens[i]=0 ;
5345: }
5346: else cens[i]=-1;
5347: }
5348:
5349: for (i=1;i<=NDIM;i++) {
5350: for (j=1;j<=NDIM;j++)
5351: ximort[i][j]=(i == j ? 1.0 : 0.0);
5352: }
5353:
5354: p[1]=0.0268; p[NDIM]=0.083;
5355: /*printf("%lf %lf", p[1], p[2]);*/
5356:
5357:
5358: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5359: strcpy(filerespow,"pow-mort");
5360: strcat(filerespow,fileres);
5361: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5362: printf("Problem with resultfile: %s\n", filerespow);
5363: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5364: }
5365: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5366: /* for (i=1;i<=nlstate;i++)
5367: for(j=1;j<=nlstate+ndeath;j++)
5368: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5369: */
5370: fprintf(ficrespow,"\n");
5371:
5372: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5373: fclose(ficrespow);
5374:
5375: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5376:
5377: for(i=1; i <=NDIM; i++)
5378: for(j=i+1;j<=NDIM;j++)
5379: matcov[i][j]=matcov[j][i];
5380:
5381: printf("\nCovariance matrix\n ");
5382: for(i=1; i <=NDIM; i++) {
5383: for(j=1;j<=NDIM;j++){
5384: printf("%f ",matcov[i][j]);
5385: }
5386: printf("\n ");
5387: }
5388:
5389: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5390: for (i=1;i<=NDIM;i++)
5391: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5392:
5393: lsurv=vector(1,AGESUP);
5394: lpop=vector(1,AGESUP);
5395: tpop=vector(1,AGESUP);
5396: lsurv[agegomp]=100000;
5397:
5398: for (k=agegomp;k<=AGESUP;k++) {
5399: agemortsup=k;
5400: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5401: }
5402:
5403: for (k=agegomp;k<agemortsup;k++)
5404: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5405:
5406: for (k=agegomp;k<agemortsup;k++){
5407: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5408: sumlpop=sumlpop+lpop[k];
5409: }
5410:
5411: tpop[agegomp]=sumlpop;
5412: for (k=agegomp;k<(agemortsup-3);k++){
5413: /* tpop[k+1]=2;*/
5414: tpop[k+1]=tpop[k]-lpop[k];
5415: }
5416:
5417:
5418: printf("\nAge lx qx dx Lx Tx e(x)\n");
5419: for (k=agegomp;k<(agemortsup-2);k++)
5420: 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]);
5421:
5422:
5423: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5424: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5425:
5426: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5427: stepm, weightopt,\
5428: model,imx,p,matcov,agemortsup);
5429:
5430: free_vector(lsurv,1,AGESUP);
5431: free_vector(lpop,1,AGESUP);
5432: free_vector(tpop,1,AGESUP);
5433: } /* Endof if mle==-3 */
5434:
5435: else{ /* For mle >=1 */
1.131 ! brouard 5436: globpr=1;/* debug */
! 5437: /* likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone);*/ /* Prints the contributions to the likelihood */
1.126 brouard 5438: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5439: for (k=1; k<=npar;k++)
5440: printf(" %d %8.5f",k,p[k]);
5441: printf("\n");
5442: globpr=1; /* to print the contributions */
5443: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5444: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5445: for (k=1; k<=npar;k++)
5446: printf(" %d %8.5f",k,p[k]);
5447: printf("\n");
5448: if(mle>=1){ /* Could be 1 or 2 */
5449: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5450: }
5451:
5452: /*--------- results files --------------*/
5453: 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);
5454:
5455:
5456: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5457: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5458: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5459: for(i=1,jk=1; i <=nlstate; i++){
5460: for(k=1; k <=(nlstate+ndeath); k++){
5461: if (k != i) {
5462: printf("%d%d ",i,k);
5463: fprintf(ficlog,"%d%d ",i,k);
5464: fprintf(ficres,"%1d%1d ",i,k);
5465: for(j=1; j <=ncovmodel; j++){
5466: printf("%lf ",p[jk]);
5467: fprintf(ficlog,"%lf ",p[jk]);
5468: fprintf(ficres,"%lf ",p[jk]);
5469: jk++;
5470: }
5471: printf("\n");
5472: fprintf(ficlog,"\n");
5473: fprintf(ficres,"\n");
5474: }
5475: }
5476: }
5477: if(mle!=0){
5478: /* Computing hessian and covariance matrix */
5479: ftolhess=ftol; /* Usually correct */
5480: hesscov(matcov, p, npar, delti, ftolhess, func);
5481: }
5482: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5483: printf("# Scales (for hessian or gradient estimation)\n");
5484: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5485: for(i=1,jk=1; i <=nlstate; i++){
5486: for(j=1; j <=nlstate+ndeath; j++){
5487: if (j!=i) {
5488: fprintf(ficres,"%1d%1d",i,j);
5489: printf("%1d%1d",i,j);
5490: fprintf(ficlog,"%1d%1d",i,j);
5491: for(k=1; k<=ncovmodel;k++){
5492: printf(" %.5e",delti[jk]);
5493: fprintf(ficlog," %.5e",delti[jk]);
5494: fprintf(ficres," %.5e",delti[jk]);
5495: jk++;
5496: }
5497: printf("\n");
5498: fprintf(ficlog,"\n");
5499: fprintf(ficres,"\n");
5500: }
5501: }
5502: }
5503:
5504: 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");
5505: if(mle>=1)
5506: 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");
5507: 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");
5508: /* # 121 Var(a12)\n\ */
5509: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5510: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5511: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5512: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5513: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5514: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5515: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5516:
5517:
5518: /* Just to have a covariance matrix which will be more understandable
5519: even is we still don't want to manage dictionary of variables
5520: */
5521: for(itimes=1;itimes<=2;itimes++){
5522: jj=0;
5523: for(i=1; i <=nlstate; i++){
5524: for(j=1; j <=nlstate+ndeath; j++){
5525: if(j==i) continue;
5526: for(k=1; k<=ncovmodel;k++){
5527: jj++;
5528: ca[0]= k+'a'-1;ca[1]='\0';
5529: if(itimes==1){
5530: if(mle>=1)
5531: printf("#%1d%1d%d",i,j,k);
5532: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5533: fprintf(ficres,"#%1d%1d%d",i,j,k);
5534: }else{
5535: if(mle>=1)
5536: printf("%1d%1d%d",i,j,k);
5537: fprintf(ficlog,"%1d%1d%d",i,j,k);
5538: fprintf(ficres,"%1d%1d%d",i,j,k);
5539: }
5540: ll=0;
5541: for(li=1;li <=nlstate; li++){
5542: for(lj=1;lj <=nlstate+ndeath; lj++){
5543: if(lj==li) continue;
5544: for(lk=1;lk<=ncovmodel;lk++){
5545: ll++;
5546: if(ll<=jj){
5547: cb[0]= lk +'a'-1;cb[1]='\0';
5548: if(ll<jj){
5549: if(itimes==1){
5550: if(mle>=1)
5551: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5552: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5553: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5554: }else{
5555: if(mle>=1)
5556: printf(" %.5e",matcov[jj][ll]);
5557: fprintf(ficlog," %.5e",matcov[jj][ll]);
5558: fprintf(ficres," %.5e",matcov[jj][ll]);
5559: }
5560: }else{
5561: if(itimes==1){
5562: if(mle>=1)
5563: printf(" Var(%s%1d%1d)",ca,i,j);
5564: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5565: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5566: }else{
5567: if(mle>=1)
5568: printf(" %.5e",matcov[jj][ll]);
5569: fprintf(ficlog," %.5e",matcov[jj][ll]);
5570: fprintf(ficres," %.5e",matcov[jj][ll]);
5571: }
5572: }
5573: }
5574: } /* end lk */
5575: } /* end lj */
5576: } /* end li */
5577: if(mle>=1)
5578: printf("\n");
5579: fprintf(ficlog,"\n");
5580: fprintf(ficres,"\n");
5581: numlinepar++;
5582: } /* end k*/
5583: } /*end j */
5584: } /* end i */
5585: } /* end itimes */
5586:
5587: fflush(ficlog);
5588: fflush(ficres);
5589:
5590: while((c=getc(ficpar))=='#' && c!= EOF){
5591: ungetc(c,ficpar);
5592: fgets(line, MAXLINE, ficpar);
5593: puts(line);
5594: fputs(line,ficparo);
5595: }
5596: ungetc(c,ficpar);
5597:
5598: estepm=0;
5599: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5600: if (estepm==0 || estepm < stepm) estepm=stepm;
5601: if (fage <= 2) {
5602: bage = ageminpar;
5603: fage = agemaxpar;
5604: }
5605:
5606: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5607: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5608: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5609:
5610: while((c=getc(ficpar))=='#' && c!= EOF){
5611: ungetc(c,ficpar);
5612: fgets(line, MAXLINE, ficpar);
5613: puts(line);
5614: fputs(line,ficparo);
5615: }
5616: ungetc(c,ficpar);
5617:
5618: 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);
5619: 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);
5620: 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);
5621: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5622: 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);
5623:
5624: while((c=getc(ficpar))=='#' && c!= EOF){
5625: ungetc(c,ficpar);
5626: fgets(line, MAXLINE, ficpar);
5627: puts(line);
5628: fputs(line,ficparo);
5629: }
5630: ungetc(c,ficpar);
5631:
5632:
5633: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5634: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5635:
5636: fscanf(ficpar,"pop_based=%d\n",&popbased);
5637: fprintf(ficparo,"pop_based=%d\n",popbased);
5638: fprintf(ficres,"pop_based=%d\n",popbased);
5639:
5640: while((c=getc(ficpar))=='#' && c!= EOF){
5641: ungetc(c,ficpar);
5642: fgets(line, MAXLINE, ficpar);
5643: puts(line);
5644: fputs(line,ficparo);
5645: }
5646: ungetc(c,ficpar);
5647:
5648: 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);
5649: 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);
5650: 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);
5651: 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);
5652: 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);
5653: /* day and month of proj2 are not used but only year anproj2.*/
5654:
5655:
5656:
5657: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5658: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5659:
5660: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5661: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5662:
5663: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5664: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5665: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5666:
5667: /*------------ free_vector -------------*/
5668: /* chdir(path); */
5669:
5670: free_ivector(wav,1,imx);
5671: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5672: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5673: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5674: free_lvector(num,1,n);
5675: free_vector(agedc,1,n);
5676: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5677: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5678: fclose(ficparo);
5679: fclose(ficres);
5680:
5681:
5682: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5683:
5684: strcpy(filerespl,"pl");
5685: strcat(filerespl,fileres);
5686: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5687: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5688: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5689: }
5690: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5691: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5692: pstamp(ficrespl);
5693: fprintf(ficrespl,"# Period (stable) prevalence \n");
5694: fprintf(ficrespl,"#Age ");
5695: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5696: fprintf(ficrespl,"\n");
5697:
5698: prlim=matrix(1,nlstate,1,nlstate);
5699:
5700: agebase=ageminpar;
5701: agelim=agemaxpar;
5702: ftolpl=1.e-10;
5703: i1=cptcoveff;
5704: if (cptcovn < 1){i1=1;}
5705:
5706: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5707: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5708: k=k+1;
1.131 ! brouard 5709: /* to clean */
! 5710: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
1.126 brouard 5711: fprintf(ficrespl,"\n#******");
5712: printf("\n#******");
5713: fprintf(ficlog,"\n#******");
5714: for(j=1;j<=cptcoveff;j++) {
5715: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5716: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5717: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5718: }
5719: fprintf(ficrespl,"******\n");
5720: printf("******\n");
5721: fprintf(ficlog,"******\n");
5722:
5723: for (age=agebase; age<=agelim; age++){
5724: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5725: fprintf(ficrespl,"%.0f ",age );
5726: for(j=1;j<=cptcoveff;j++)
5727: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5728: for(i=1; i<=nlstate;i++)
5729: fprintf(ficrespl," %.5f", prlim[i][i]);
5730: fprintf(ficrespl,"\n");
5731: }
5732: }
5733: }
5734: fclose(ficrespl);
5735:
5736: /*------------- h Pij x at various ages ------------*/
5737:
5738: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5739: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5740: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5741: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5742: }
5743: printf("Computing pij: result on file '%s' \n", filerespij);
5744: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5745:
5746: stepsize=(int) (stepm+YEARM-1)/YEARM;
5747: /*if (stepm<=24) stepsize=2;*/
5748:
5749: agelim=AGESUP;
5750: hstepm=stepsize*YEARM; /* Every year of age */
5751: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5752:
5753: /* hstepm=1; aff par mois*/
5754: pstamp(ficrespij);
5755: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5756: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5757: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5758: k=k+1;
5759: fprintf(ficrespij,"\n#****** ");
5760: for(j=1;j<=cptcoveff;j++)
5761: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5762: fprintf(ficrespij,"******\n");
5763:
5764: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5765: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5766: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5767:
5768: /* nhstepm=nhstepm*YEARM; aff par mois*/
5769:
5770: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5771: oldm=oldms;savm=savms;
5772: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5773: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5774: for(i=1; i<=nlstate;i++)
5775: for(j=1; j<=nlstate+ndeath;j++)
5776: fprintf(ficrespij," %1d-%1d",i,j);
5777: fprintf(ficrespij,"\n");
5778: for (h=0; h<=nhstepm; h++){
5779: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5780: for(i=1; i<=nlstate;i++)
5781: for(j=1; j<=nlstate+ndeath;j++)
5782: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5783: fprintf(ficrespij,"\n");
5784: }
5785: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5786: fprintf(ficrespij,"\n");
5787: }
5788: }
5789: }
5790:
5791: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5792:
5793: fclose(ficrespij);
5794:
5795: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5796: for(i=1;i<=AGESUP;i++)
5797: for(j=1;j<=NCOVMAX;j++)
5798: for(k=1;k<=NCOVMAX;k++)
5799: probs[i][j][k]=0.;
5800:
5801: /*---------- Forecasting ------------------*/
5802: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5803: if(prevfcast==1){
5804: /* if(stepm ==1){*/
5805: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5806: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5807: /* } */
5808: /* else{ */
5809: /* erreur=108; */
5810: /* 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); */
5811: /* 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); */
5812: /* } */
5813: }
5814:
5815:
1.127 brouard 5816: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5817:
5818: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5819: /* 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",\
5820: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5821: */
1.126 brouard 5822:
1.127 brouard 5823: if (mobilav!=0) {
5824: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5825: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5826: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5827: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5828: }
1.126 brouard 5829: }
5830:
5831:
1.127 brouard 5832: /*---------- Health expectancies, no variances ------------*/
5833:
1.126 brouard 5834: strcpy(filerese,"e");
5835: strcat(filerese,fileres);
5836: if((ficreseij=fopen(filerese,"w"))==NULL) {
5837: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5838: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5839: }
5840: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5841: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.127 brouard 5842: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5843: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5844: k=k+1;
5845: fprintf(ficreseij,"\n#****** ");
5846: for(j=1;j<=cptcoveff;j++) {
5847: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5848: }
5849: fprintf(ficreseij,"******\n");
5850:
5851: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5852: oldm=oldms;savm=savms;
5853: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5854:
5855: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5856: }
5857: }
5858: fclose(ficreseij);
5859:
5860:
5861: /*---------- Health expectancies and variances ------------*/
5862:
5863:
5864: strcpy(filerest,"t");
5865: strcat(filerest,fileres);
5866: if((ficrest=fopen(filerest,"w"))==NULL) {
5867: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5868: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5869: }
5870: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5871: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5872:
1.126 brouard 5873:
5874: strcpy(fileresstde,"stde");
5875: strcat(fileresstde,fileres);
5876: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5877: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5878: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5879: }
5880: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5881: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5882:
5883: strcpy(filerescve,"cve");
5884: strcat(filerescve,fileres);
5885: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5886: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5887: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5888: }
5889: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5890: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5891:
5892: strcpy(fileresv,"v");
5893: strcat(fileresv,fileres);
5894: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5895: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5896: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5897: }
5898: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5899: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5900:
5901: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5902: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5903: k=k+1;
5904: fprintf(ficrest,"\n#****** ");
5905: for(j=1;j<=cptcoveff;j++)
5906: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5907: fprintf(ficrest,"******\n");
5908:
5909: fprintf(ficresstdeij,"\n#****** ");
5910: fprintf(ficrescveij,"\n#****** ");
5911: for(j=1;j<=cptcoveff;j++) {
5912: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5913: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5914: }
5915: fprintf(ficresstdeij,"******\n");
5916: fprintf(ficrescveij,"******\n");
5917:
5918: fprintf(ficresvij,"\n#****** ");
5919: for(j=1;j<=cptcoveff;j++)
5920: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5921: fprintf(ficresvij,"******\n");
5922:
5923: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5924: oldm=oldms;savm=savms;
1.127 brouard 5925: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.126 brouard 5926:
5927: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5928: pstamp(ficrest);
1.128 brouard 5929: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5930: oldm=oldms;savm=savms;
5931: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
5932: if(vpopbased==1)
5933: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
5934: else
5935: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
5936: fprintf(ficrest,"# Age e.. (std) ");
5937: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5938: fprintf(ficrest,"\n");
1.126 brouard 5939:
1.128 brouard 5940: epj=vector(1,nlstate+1);
5941: for(age=bage; age <=fage ;age++){
5942: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5943: if (vpopbased==1) {
5944: if(mobilav ==0){
5945: for(i=1; i<=nlstate;i++)
5946: prlim[i][i]=probs[(int)age][i][k];
5947: }else{ /* mobilav */
5948: for(i=1; i<=nlstate;i++)
5949: prlim[i][i]=mobaverage[(int)age][i][k];
5950: }
1.126 brouard 5951: }
5952:
1.128 brouard 5953: fprintf(ficrest," %4.0f",age);
5954: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5955: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5956: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5957: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5958: }
5959: epj[nlstate+1] +=epj[j];
1.126 brouard 5960: }
5961:
1.128 brouard 5962: for(i=1, vepp=0.;i <=nlstate;i++)
5963: for(j=1;j <=nlstate;j++)
5964: vepp += vareij[i][j][(int)age];
5965: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5966: for(j=1;j <=nlstate;j++){
5967: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5968: }
5969: fprintf(ficrest,"\n");
1.126 brouard 5970: }
5971: }
5972: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5973: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5974: free_vector(epj,1,nlstate+1);
5975: }
5976: }
5977: free_vector(weight,1,n);
5978: free_imatrix(Tvard,1,15,1,2);
5979: free_imatrix(s,1,maxwav+1,1,n);
5980: free_matrix(anint,1,maxwav,1,n);
5981: free_matrix(mint,1,maxwav,1,n);
5982: free_ivector(cod,1,n);
5983: free_ivector(tab,1,NCOVMAX);
5984: fclose(ficresstdeij);
5985: fclose(ficrescveij);
5986: fclose(ficresvij);
5987: fclose(ficrest);
5988: fclose(ficpar);
5989:
5990: /*------- Variance of period (stable) prevalence------*/
5991:
5992: strcpy(fileresvpl,"vpl");
5993: strcat(fileresvpl,fileres);
5994: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5995: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5996: exit(0);
5997: }
5998: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5999:
6000: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6001: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6002: k=k+1;
6003: fprintf(ficresvpl,"\n#****** ");
6004: for(j=1;j<=cptcoveff;j++)
6005: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6006: fprintf(ficresvpl,"******\n");
6007:
6008: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6009: oldm=oldms;savm=savms;
6010: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6011: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6012: }
6013: }
6014:
6015: fclose(ficresvpl);
6016:
6017: /*---------- End : free ----------------*/
6018: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6019: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6020:
6021: } /* mle==-3 arrives here for freeing */
1.131 ! brouard 6022: endfree:
1.126 brouard 6023: free_matrix(prlim,1,nlstate,1,nlstate);
6024: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6025: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6026: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6027: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6028: free_matrix(covar,0,NCOVMAX,1,n);
6029: free_matrix(matcov,1,npar,1,npar);
6030: /*free_vector(delti,1,npar);*/
6031: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6032: free_matrix(agev,1,maxwav,1,imx);
6033: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6034:
6035: free_ivector(ncodemax,1,8);
6036: free_ivector(Tvar,1,15);
6037: free_ivector(Tprod,1,15);
6038: free_ivector(Tvaraff,1,15);
6039: free_ivector(Tage,1,15);
6040:
6041: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6042: free_imatrix(codtab,1,100,1,10);
6043: fflush(fichtm);
6044: fflush(ficgp);
6045:
6046:
6047: if((nberr >0) || (nbwarn>0)){
6048: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6049: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6050: }else{
6051: printf("End of Imach\n");
6052: fprintf(ficlog,"End of Imach\n");
6053: }
6054: printf("See log file on %s\n",filelog);
6055: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6056: (void) gettimeofday(&end_time,&tzp);
6057: tm = *localtime(&end_time.tv_sec);
6058: tmg = *gmtime(&end_time.tv_sec);
6059: strcpy(strtend,asctime(&tm));
6060: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6061: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6062: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6063:
6064: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6065: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6066: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6067: /* printf("Total time was %d uSec.\n", total_usecs);*/
6068: /* if(fileappend(fichtm,optionfilehtm)){ */
6069: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6070: fclose(fichtm);
6071: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6072: fclose(fichtmcov);
6073: fclose(ficgp);
6074: fclose(ficlog);
6075: /*------ End -----------*/
6076:
6077:
6078: printf("Before Current directory %s!\n",pathcd);
6079: if(chdir(pathcd) != 0)
6080: printf("Can't move to directory %s!\n",path);
6081: if(getcwd(pathcd,MAXLINE) > 0)
6082: printf("Current directory %s!\n",pathcd);
6083: /*strcat(plotcmd,CHARSEPARATOR);*/
6084: sprintf(plotcmd,"gnuplot");
6085: #ifndef UNIX
6086: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6087: #endif
6088: if(!stat(plotcmd,&info)){
6089: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6090: if(!stat(getenv("GNUPLOTBIN"),&info)){
6091: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6092: }else
6093: strcpy(pplotcmd,plotcmd);
6094: #ifdef UNIX
6095: strcpy(plotcmd,GNUPLOTPROGRAM);
6096: if(!stat(plotcmd,&info)){
6097: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6098: }else
6099: strcpy(pplotcmd,plotcmd);
6100: #endif
6101: }else
6102: strcpy(pplotcmd,plotcmd);
6103:
6104: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6105: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6106:
6107: if((outcmd=system(plotcmd)) != 0){
6108: printf("\n Problem with gnuplot\n");
6109: }
6110: printf(" Wait...");
6111: while (z[0] != 'q') {
6112: /* chdir(path); */
6113: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6114: scanf("%s",z);
6115: /* if (z[0] == 'c') system("./imach"); */
6116: if (z[0] == 'e') {
6117: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6118: system(optionfilehtm);
6119: }
6120: else if (z[0] == 'g') system(plotcmd);
6121: else if (z[0] == 'q') exit(0);
6122: }
6123: end:
6124: while (z[0] != 'q') {
6125: printf("\nType q for exiting: ");
6126: scanf("%s",z);
6127: }
6128: }
6129:
6130:
6131:
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