Annotation of imach/src/imach.c, revision 1.133
1.133 ! brouard 1: /* $Id: imach.c,v 1.132 2009/07/06 08:22:05 brouard Exp $
1.126 brouard 2: $State: Exp $
3: $Log: imach.c,v $
1.133 ! brouard 4: Revision 1.132 2009/07/06 08:22:05 brouard
! 5: Many tings
! 6:
1.132 brouard 7: Revision 1.131 2009/06/20 16:22:47 brouard
8: Some dimensions resccaled
9:
1.131 brouard 10: Revision 1.130 2009/05/26 06:44:34 brouard
11: (Module): Max Covariate is now set to 20 instead of 8. A
12: lot of cleaning with variables initialized to 0. Trying to make
13: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
14:
1.130 brouard 15: Revision 1.129 2007/08/31 13:49:27 lievre
16: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
17:
1.129 lievre 18: Revision 1.128 2006/06/30 13:02:05 brouard
19: (Module): Clarifications on computing e.j
20:
1.128 brouard 21: Revision 1.127 2006/04/28 18:11:50 brouard
22: (Module): Yes the sum of survivors was wrong since
23: imach-114 because nhstepm was no more computed in the age
24: loop. Now we define nhstepma in the age loop.
25: (Module): In order to speed up (in case of numerous covariates) we
26: compute health expectancies (without variances) in a first step
27: and then all the health expectancies with variances or standard
28: deviation (needs data from the Hessian matrices) which slows the
29: computation.
30: In the future we should be able to stop the program is only health
31: expectancies and graph are needed without standard deviations.
32:
1.127 brouard 33: Revision 1.126 2006/04/28 17:23:28 brouard
34: (Module): Yes the sum of survivors was wrong since
35: imach-114 because nhstepm was no more computed in the age
36: loop. Now we define nhstepma in the age loop.
37: Version 0.98h
38:
1.126 brouard 39: Revision 1.125 2006/04/04 15:20:31 lievre
40: Errors in calculation of health expectancies. Age was not initialized.
41: Forecasting file added.
42:
43: Revision 1.124 2006/03/22 17:13:53 lievre
44: Parameters are printed with %lf instead of %f (more numbers after the comma).
45: The log-likelihood is printed in the log file
46:
47: Revision 1.123 2006/03/20 10:52:43 brouard
48: * imach.c (Module): <title> changed, corresponds to .htm file
49: name. <head> headers where missing.
50:
51: * imach.c (Module): Weights can have a decimal point as for
52: English (a comma might work with a correct LC_NUMERIC environment,
53: otherwise the weight is truncated).
54: Modification of warning when the covariates values are not 0 or
55: 1.
56: Version 0.98g
57:
58: Revision 1.122 2006/03/20 09:45:41 brouard
59: (Module): Weights can have a decimal point as for
60: English (a comma might work with a correct LC_NUMERIC environment,
61: otherwise the weight is truncated).
62: Modification of warning when the covariates values are not 0 or
63: 1.
64: Version 0.98g
65:
66: Revision 1.121 2006/03/16 17:45:01 lievre
67: * imach.c (Module): Comments concerning covariates added
68:
69: * imach.c (Module): refinements in the computation of lli if
70: status=-2 in order to have more reliable computation if stepm is
71: not 1 month. Version 0.98f
72:
73: Revision 1.120 2006/03/16 15:10:38 lievre
74: (Module): refinements in the computation of lli if
75: status=-2 in order to have more reliable computation if stepm is
76: not 1 month. Version 0.98f
77:
78: Revision 1.119 2006/03/15 17:42:26 brouard
79: (Module): Bug if status = -2, the loglikelihood was
80: computed as likelihood omitting the logarithm. Version O.98e
81:
82: Revision 1.118 2006/03/14 18:20:07 brouard
83: (Module): varevsij Comments added explaining the second
84: table of variances if popbased=1 .
85: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
86: (Module): Function pstamp added
87: (Module): Version 0.98d
88:
89: Revision 1.117 2006/03/14 17:16:22 brouard
90: (Module): varevsij Comments added explaining the second
91: table of variances if popbased=1 .
92: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
93: (Module): Function pstamp added
94: (Module): Version 0.98d
95:
96: Revision 1.116 2006/03/06 10:29:27 brouard
97: (Module): Variance-covariance wrong links and
98: varian-covariance of ej. is needed (Saito).
99:
100: Revision 1.115 2006/02/27 12:17:45 brouard
101: (Module): One freematrix added in mlikeli! 0.98c
102:
103: Revision 1.114 2006/02/26 12:57:58 brouard
104: (Module): Some improvements in processing parameter
105: filename with strsep.
106:
107: Revision 1.113 2006/02/24 14:20:24 brouard
108: (Module): Memory leaks checks with valgrind and:
109: datafile was not closed, some imatrix were not freed and on matrix
110: allocation too.
111:
112: Revision 1.112 2006/01/30 09:55:26 brouard
113: (Module): Back to gnuplot.exe instead of wgnuplot.exe
114:
115: Revision 1.111 2006/01/25 20:38:18 brouard
116: (Module): Lots of cleaning and bugs added (Gompertz)
117: (Module): Comments can be added in data file. Missing date values
118: can be a simple dot '.'.
119:
120: Revision 1.110 2006/01/25 00:51:50 brouard
121: (Module): Lots of cleaning and bugs added (Gompertz)
122:
123: Revision 1.109 2006/01/24 19:37:15 brouard
124: (Module): Comments (lines starting with a #) are allowed in data.
125:
126: Revision 1.108 2006/01/19 18:05:42 lievre
127: Gnuplot problem appeared...
128: To be fixed
129:
130: Revision 1.107 2006/01/19 16:20:37 brouard
131: Test existence of gnuplot in imach path
132:
133: Revision 1.106 2006/01/19 13:24:36 brouard
134: Some cleaning and links added in html output
135:
136: Revision 1.105 2006/01/05 20:23:19 lievre
137: *** empty log message ***
138:
139: Revision 1.104 2005/09/30 16:11:43 lievre
140: (Module): sump fixed, loop imx fixed, and simplifications.
141: (Module): If the status is missing at the last wave but we know
142: that the person is alive, then we can code his/her status as -2
143: (instead of missing=-1 in earlier versions) and his/her
144: contributions to the likelihood is 1 - Prob of dying from last
145: health status (= 1-p13= p11+p12 in the easiest case of somebody in
146: the healthy state at last known wave). Version is 0.98
147:
148: Revision 1.103 2005/09/30 15:54:49 lievre
149: (Module): sump fixed, loop imx fixed, and simplifications.
150:
151: Revision 1.102 2004/09/15 17:31:30 brouard
152: Add the possibility to read data file including tab characters.
153:
154: Revision 1.101 2004/09/15 10:38:38 brouard
155: Fix on curr_time
156:
157: Revision 1.100 2004/07/12 18:29:06 brouard
158: Add version for Mac OS X. Just define UNIX in Makefile
159:
160: Revision 1.99 2004/06/05 08:57:40 brouard
161: *** empty log message ***
162:
163: Revision 1.98 2004/05/16 15:05:56 brouard
164: New version 0.97 . First attempt to estimate force of mortality
165: directly from the data i.e. without the need of knowing the health
166: state at each age, but using a Gompertz model: log u =a + b*age .
167: This is the basic analysis of mortality and should be done before any
168: other analysis, in order to test if the mortality estimated from the
169: cross-longitudinal survey is different from the mortality estimated
170: from other sources like vital statistic data.
171:
172: The same imach parameter file can be used but the option for mle should be -3.
173:
1.133 ! brouard 174: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 175: former routines in order to include the new code within the former code.
176:
177: The output is very simple: only an estimate of the intercept and of
178: the slope with 95% confident intervals.
179:
180: Current limitations:
181: A) Even if you enter covariates, i.e. with the
182: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
183: B) There is no computation of Life Expectancy nor Life Table.
184:
185: Revision 1.97 2004/02/20 13:25:42 lievre
186: Version 0.96d. Population forecasting command line is (temporarily)
187: suppressed.
188:
189: Revision 1.96 2003/07/15 15:38:55 brouard
190: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
191: rewritten within the same printf. Workaround: many printfs.
192:
193: Revision 1.95 2003/07/08 07:54:34 brouard
194: * imach.c (Repository):
195: (Repository): Using imachwizard code to output a more meaningful covariance
196: matrix (cov(a12,c31) instead of numbers.
197:
198: Revision 1.94 2003/06/27 13:00:02 brouard
199: Just cleaning
200:
201: Revision 1.93 2003/06/25 16:33:55 brouard
202: (Module): On windows (cygwin) function asctime_r doesn't
203: exist so I changed back to asctime which exists.
204: (Module): Version 0.96b
205:
206: Revision 1.92 2003/06/25 16:30:45 brouard
207: (Module): On windows (cygwin) function asctime_r doesn't
208: exist so I changed back to asctime which exists.
209:
210: Revision 1.91 2003/06/25 15:30:29 brouard
211: * imach.c (Repository): Duplicated warning errors corrected.
212: (Repository): Elapsed time after each iteration is now output. It
213: helps to forecast when convergence will be reached. Elapsed time
214: is stamped in powell. We created a new html file for the graphs
215: concerning matrix of covariance. It has extension -cov.htm.
216:
217: Revision 1.90 2003/06/24 12:34:15 brouard
218: (Module): Some bugs corrected for windows. Also, when
219: mle=-1 a template is output in file "or"mypar.txt with the design
220: of the covariance matrix to be input.
221:
222: Revision 1.89 2003/06/24 12:30:52 brouard
223: (Module): Some bugs corrected for windows. Also, when
224: mle=-1 a template is output in file "or"mypar.txt with the design
225: of the covariance matrix to be input.
226:
227: Revision 1.88 2003/06/23 17:54:56 brouard
228: * 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.
229:
230: Revision 1.87 2003/06/18 12:26:01 brouard
231: Version 0.96
232:
233: Revision 1.86 2003/06/17 20:04:08 brouard
234: (Module): Change position of html and gnuplot routines and added
235: routine fileappend.
236:
237: Revision 1.85 2003/06/17 13:12:43 brouard
238: * imach.c (Repository): Check when date of death was earlier that
239: current date of interview. It may happen when the death was just
240: prior to the death. In this case, dh was negative and likelihood
241: was wrong (infinity). We still send an "Error" but patch by
242: assuming that the date of death was just one stepm after the
243: interview.
244: (Repository): Because some people have very long ID (first column)
245: we changed int to long in num[] and we added a new lvector for
246: memory allocation. But we also truncated to 8 characters (left
247: truncation)
248: (Repository): No more line truncation errors.
249:
250: Revision 1.84 2003/06/13 21:44:43 brouard
251: * imach.c (Repository): Replace "freqsummary" at a correct
252: place. It differs from routine "prevalence" which may be called
253: many times. Probs is memory consuming and must be used with
254: parcimony.
255: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
256:
257: Revision 1.83 2003/06/10 13:39:11 lievre
258: *** empty log message ***
259:
260: Revision 1.82 2003/06/05 15:57:20 brouard
261: Add log in imach.c and fullversion number is now printed.
262:
263: */
264: /*
265: Interpolated Markov Chain
266:
267: Short summary of the programme:
268:
269: This program computes Healthy Life Expectancies from
270: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
271: first survey ("cross") where individuals from different ages are
272: interviewed on their health status or degree of disability (in the
273: case of a health survey which is our main interest) -2- at least a
274: second wave of interviews ("longitudinal") which measure each change
275: (if any) in individual health status. Health expectancies are
276: computed from the time spent in each health state according to a
277: model. More health states you consider, more time is necessary to reach the
278: Maximum Likelihood of the parameters involved in the model. The
279: simplest model is the multinomial logistic model where pij is the
280: probability to be observed in state j at the second wave
281: conditional to be observed in state i at the first wave. Therefore
282: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
283: 'age' is age and 'sex' is a covariate. If you want to have a more
284: complex model than "constant and age", you should modify the program
285: where the markup *Covariates have to be included here again* invites
286: you to do it. More covariates you add, slower the
287: convergence.
288:
289: The advantage of this computer programme, compared to a simple
290: multinomial logistic model, is clear when the delay between waves is not
291: identical for each individual. Also, if a individual missed an
292: intermediate interview, the information is lost, but taken into
293: account using an interpolation or extrapolation.
294:
295: hPijx is the probability to be observed in state i at age x+h
296: conditional to the observed state i at age x. The delay 'h' can be
297: split into an exact number (nh*stepm) of unobserved intermediate
298: states. This elementary transition (by month, quarter,
299: semester or year) is modelled as a multinomial logistic. The hPx
300: matrix is simply the matrix product of nh*stepm elementary matrices
301: and the contribution of each individual to the likelihood is simply
302: hPijx.
303:
304: Also this programme outputs the covariance matrix of the parameters but also
305: of the life expectancies. It also computes the period (stable) prevalence.
306:
1.133 ! brouard 307: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
! 308: Institut national d'études démographiques, Paris.
1.126 brouard 309: This software have been partly granted by Euro-REVES, a concerted action
310: from the European Union.
311: It is copyrighted identically to a GNU software product, ie programme and
312: software can be distributed freely for non commercial use. Latest version
313: can be accessed at http://euroreves.ined.fr/imach .
314:
315: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
316: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
317:
318: **********************************************************************/
319: /*
320: main
321: read parameterfile
322: read datafile
323: concatwav
324: freqsummary
325: if (mle >= 1)
326: mlikeli
327: print results files
328: if mle==1
329: computes hessian
330: read end of parameter file: agemin, agemax, bage, fage, estepm
331: begin-prev-date,...
332: open gnuplot file
333: open html file
334: period (stable) prevalence
335: for age prevalim()
336: h Pij x
337: variance of p varprob
338: forecasting if prevfcast==1 prevforecast call prevalence()
339: health expectancies
340: Variance-covariance of DFLE
341: prevalence()
342: movingaverage()
343: varevsij()
344: if popbased==1 varevsij(,popbased)
345: total life expectancies
346: Variance of period (stable) prevalence
347: end
348: */
349:
350:
351:
352:
353: #include <math.h>
354: #include <stdio.h>
355: #include <stdlib.h>
356: #include <string.h>
357: #include <unistd.h>
358:
359: #include <limits.h>
360: #include <sys/types.h>
361: #include <sys/stat.h>
362: #include <errno.h>
363: extern int errno;
364:
365: /* #include <sys/time.h> */
366: #include <time.h>
367: #include "timeval.h"
368:
369: /* #include <libintl.h> */
370: /* #define _(String) gettext (String) */
371:
372: #define MAXLINE 256
373:
374: #define GNUPLOTPROGRAM "gnuplot"
375: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
376: #define FILENAMELENGTH 132
377:
378: #define GLOCK_ERROR_NOPATH -1 /* empty path */
379: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
380:
1.131 brouard 381: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
1.126 brouard 382: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
383:
384: #define NINTERVMAX 8
385: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
386: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
1.130 brouard 387: #define NCOVMAX 20 /* Maximum number of covariates */
1.126 brouard 388: #define MAXN 20000
389: #define YEARM 12. /* Number of months per year */
390: #define AGESUP 130
391: #define AGEBASE 40
392: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
393: #ifdef UNIX
394: #define DIRSEPARATOR '/'
395: #define CHARSEPARATOR "/"
396: #define ODIRSEPARATOR '\\'
397: #else
398: #define DIRSEPARATOR '\\'
399: #define CHARSEPARATOR "\\"
400: #define ODIRSEPARATOR '/'
401: #endif
402:
1.133 ! brouard 403: /* $Id: imach.c,v 1.132 2009/07/06 08:22:05 brouard Exp $ */
1.126 brouard 404: /* $State: Exp $ */
405:
1.133 ! brouard 406: char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
! 407: char fullversion[]="$Revision: 1.132 $ $Date: 2009/07/06 08:22:05 $";
1.126 brouard 408: char strstart[80];
409: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 410: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 ! brouard 411: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.130 brouard 412: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
1.126 brouard 413: int npar=NPARMAX;
414: int nlstate=2; /* Number of live states */
415: int ndeath=1; /* Number of dead states */
1.130 brouard 416: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 417: int popbased=0;
418:
419: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 420: int maxwav=0; /* Maxim number of waves */
421: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
422: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
423: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 424: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 425: int mle=1, weightopt=0;
1.126 brouard 426: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
427: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
428: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
429: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130 brouard 430: double jmean=1; /* Mean space between 2 waves */
1.126 brouard 431: double **oldm, **newm, **savm; /* Working pointers to matrices */
432: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
433: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
434: FILE *ficlog, *ficrespow;
1.130 brouard 435: int globpr=0; /* Global variable for printing or not */
1.126 brouard 436: double fretone; /* Only one call to likelihood */
1.130 brouard 437: long ipmx=0; /* Number of contributions */
1.126 brouard 438: double sw; /* Sum of weights */
439: char filerespow[FILENAMELENGTH];
440: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
441: FILE *ficresilk;
442: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
443: FILE *ficresprobmorprev;
444: FILE *fichtm, *fichtmcov; /* Html File */
445: FILE *ficreseij;
446: char filerese[FILENAMELENGTH];
447: FILE *ficresstdeij;
448: char fileresstde[FILENAMELENGTH];
449: FILE *ficrescveij;
450: char filerescve[FILENAMELENGTH];
451: FILE *ficresvij;
452: char fileresv[FILENAMELENGTH];
453: FILE *ficresvpl;
454: char fileresvpl[FILENAMELENGTH];
455: char title[MAXLINE];
456: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
457: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
458: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
459: char command[FILENAMELENGTH];
460: int outcmd=0;
461:
462: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
463:
464: char filelog[FILENAMELENGTH]; /* Log file */
465: char filerest[FILENAMELENGTH];
466: char fileregp[FILENAMELENGTH];
467: char popfile[FILENAMELENGTH];
468:
469: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
470:
471: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
472: struct timezone tzp;
473: extern int gettimeofday();
474: struct tm tmg, tm, tmf, *gmtime(), *localtime();
475: long time_value;
476: extern long time();
477: char strcurr[80], strfor[80];
478:
479: char *endptr;
480: long lval;
481: double dval;
482:
483: #define NR_END 1
484: #define FREE_ARG char*
485: #define FTOL 1.0e-10
486:
487: #define NRANSI
488: #define ITMAX 200
489:
490: #define TOL 2.0e-4
491:
492: #define CGOLD 0.3819660
493: #define ZEPS 1.0e-10
494: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
495:
496: #define GOLD 1.618034
497: #define GLIMIT 100.0
498: #define TINY 1.0e-20
499:
500: static double maxarg1,maxarg2;
501: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
502: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
503:
504: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
505: #define rint(a) floor(a+0.5)
506:
507: static double sqrarg;
508: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
509: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
510: int agegomp= AGEGOMP;
511:
512: int imx;
513: int stepm=1;
514: /* Stepm, step in month: minimum step interpolation*/
515:
516: int estepm;
517: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
518:
519: int m,nb;
520: long *num;
521: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
522: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
523: double **pmmij, ***probs;
524: double *ageexmed,*agecens;
525: double dateintmean=0;
526:
527: double *weight;
528: int **s; /* Status */
529: double *agedc, **covar, idx;
1.131 brouard 530: int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 531: double *lsurv, *lpop, *tpop;
532:
533: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
534: double ftolhess; /* Tolerance for computing hessian */
535:
536: /**************** split *************************/
537: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
538: {
539: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
540: the name of the file (name), its extension only (ext) and its first part of the name (finame)
541: */
542: char *ss; /* pointer */
543: int l1, l2; /* length counters */
544:
545: l1 = strlen(path ); /* length of path */
546: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
547: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
548: if ( ss == NULL ) { /* no directory, so determine current directory */
549: strcpy( name, path ); /* we got the fullname name because no directory */
550: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
551: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
552: /* get current working directory */
553: /* extern char* getcwd ( char *buf , int len);*/
554: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
555: return( GLOCK_ERROR_GETCWD );
556: }
557: /* got dirc from getcwd*/
558: printf(" DIRC = %s \n",dirc);
559: } else { /* strip direcotry from path */
560: ss++; /* after this, the filename */
561: l2 = strlen( ss ); /* length of filename */
562: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
563: strcpy( name, ss ); /* save file name */
564: strncpy( dirc, path, l1 - l2 ); /* now the directory */
565: dirc[l1-l2] = 0; /* add zero */
566: printf(" DIRC2 = %s \n",dirc);
567: }
568: /* We add a separator at the end of dirc if not exists */
569: l1 = strlen( dirc ); /* length of directory */
570: if( dirc[l1-1] != DIRSEPARATOR ){
571: dirc[l1] = DIRSEPARATOR;
572: dirc[l1+1] = 0;
573: printf(" DIRC3 = %s \n",dirc);
574: }
575: ss = strrchr( name, '.' ); /* find last / */
576: if (ss >0){
577: ss++;
578: strcpy(ext,ss); /* save extension */
579: l1= strlen( name);
580: l2= strlen(ss)+1;
581: strncpy( finame, name, l1-l2);
582: finame[l1-l2]= 0;
583: }
584:
585: return( 0 ); /* we're done */
586: }
587:
588:
589: /******************************************/
590:
591: void replace_back_to_slash(char *s, char*t)
592: {
593: int i;
594: int lg=0;
595: i=0;
596: lg=strlen(t);
597: for(i=0; i<= lg; i++) {
598: (s[i] = t[i]);
599: if (t[i]== '\\') s[i]='/';
600: }
601: }
602:
1.132 brouard 603: char *trimbb(char *out, char *in)
604: { /* Trim multiple blanks in line */
605: char *s;
606: s=out;
607: while (*in != '\0'){
608: while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
609: in++;
610: }
611: *out++ = *in++;
612: }
613: *out='\0';
614: return s;
615: }
616:
1.126 brouard 617: int nbocc(char *s, char occ)
618: {
619: int i,j=0;
620: int lg=20;
621: i=0;
622: lg=strlen(s);
623: for(i=0; i<= lg; i++) {
624: if (s[i] == occ ) j++;
625: }
626: return j;
627: }
628:
629: void cutv(char *u,char *v, char*t, char occ)
630: {
631: /* cuts string t into u and v where u ends before first occurence of char 'occ'
632: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
633: gives u="abcedf" and v="ghi2j" */
634: int i,lg,j,p=0;
635: i=0;
636: for(j=0; j<=strlen(t)-1; j++) {
637: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
638: }
639:
640: lg=strlen(t);
641: for(j=0; j<p; j++) {
642: (u[j] = t[j]);
643: }
644: u[p]='\0';
645:
646: for(j=0; j<= lg; j++) {
647: if (j>=(p+1))(v[j-p-1] = t[j]);
648: }
649: }
650:
651: /********************** nrerror ********************/
652:
653: void nrerror(char error_text[])
654: {
655: fprintf(stderr,"ERREUR ...\n");
656: fprintf(stderr,"%s\n",error_text);
657: exit(EXIT_FAILURE);
658: }
659: /*********************** vector *******************/
660: double *vector(int nl, int nh)
661: {
662: double *v;
663: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
664: if (!v) nrerror("allocation failure in vector");
665: return v-nl+NR_END;
666: }
667:
668: /************************ free vector ******************/
669: void free_vector(double*v, int nl, int nh)
670: {
671: free((FREE_ARG)(v+nl-NR_END));
672: }
673:
674: /************************ivector *******************************/
675: int *ivector(long nl,long nh)
676: {
677: int *v;
678: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
679: if (!v) nrerror("allocation failure in ivector");
680: return v-nl+NR_END;
681: }
682:
683: /******************free ivector **************************/
684: void free_ivector(int *v, long nl, long nh)
685: {
686: free((FREE_ARG)(v+nl-NR_END));
687: }
688:
689: /************************lvector *******************************/
690: long *lvector(long nl,long nh)
691: {
692: long *v;
693: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
694: if (!v) nrerror("allocation failure in ivector");
695: return v-nl+NR_END;
696: }
697:
698: /******************free lvector **************************/
699: void free_lvector(long *v, long nl, long nh)
700: {
701: free((FREE_ARG)(v+nl-NR_END));
702: }
703:
704: /******************* imatrix *******************************/
705: int **imatrix(long nrl, long nrh, long ncl, long nch)
706: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
707: {
708: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
709: int **m;
710:
711: /* allocate pointers to rows */
712: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
713: if (!m) nrerror("allocation failure 1 in matrix()");
714: m += NR_END;
715: m -= nrl;
716:
717:
718: /* allocate rows and set pointers to them */
719: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
720: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
721: m[nrl] += NR_END;
722: m[nrl] -= ncl;
723:
724: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
725:
726: /* return pointer to array of pointers to rows */
727: return m;
728: }
729:
730: /****************** free_imatrix *************************/
731: void free_imatrix(m,nrl,nrh,ncl,nch)
732: int **m;
733: long nch,ncl,nrh,nrl;
734: /* free an int matrix allocated by imatrix() */
735: {
736: free((FREE_ARG) (m[nrl]+ncl-NR_END));
737: free((FREE_ARG) (m+nrl-NR_END));
738: }
739:
740: /******************* matrix *******************************/
741: double **matrix(long nrl, long nrh, long ncl, long nch)
742: {
743: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
744: double **m;
745:
746: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
747: if (!m) nrerror("allocation failure 1 in matrix()");
748: m += NR_END;
749: m -= nrl;
750:
751: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
752: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
753: m[nrl] += NR_END;
754: m[nrl] -= ncl;
755:
756: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
757: return m;
758: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
759: */
760: }
761:
762: /*************************free matrix ************************/
763: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
764: {
765: free((FREE_ARG)(m[nrl]+ncl-NR_END));
766: free((FREE_ARG)(m+nrl-NR_END));
767: }
768:
769: /******************* ma3x *******************************/
770: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
771: {
772: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
773: double ***m;
774:
775: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
776: if (!m) nrerror("allocation failure 1 in matrix()");
777: m += NR_END;
778: m -= nrl;
779:
780: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
781: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
782: m[nrl] += NR_END;
783: m[nrl] -= ncl;
784:
785: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
786:
787: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
788: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
789: m[nrl][ncl] += NR_END;
790: m[nrl][ncl] -= nll;
791: for (j=ncl+1; j<=nch; j++)
792: m[nrl][j]=m[nrl][j-1]+nlay;
793:
794: for (i=nrl+1; i<=nrh; i++) {
795: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
796: for (j=ncl+1; j<=nch; j++)
797: m[i][j]=m[i][j-1]+nlay;
798: }
799: return m;
800: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
801: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
802: */
803: }
804:
805: /*************************free ma3x ************************/
806: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
807: {
808: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
809: free((FREE_ARG)(m[nrl]+ncl-NR_END));
810: free((FREE_ARG)(m+nrl-NR_END));
811: }
812:
813: /*************** function subdirf ***********/
814: char *subdirf(char fileres[])
815: {
816: /* Caution optionfilefiname is hidden */
817: strcpy(tmpout,optionfilefiname);
818: strcat(tmpout,"/"); /* Add to the right */
819: strcat(tmpout,fileres);
820: return tmpout;
821: }
822:
823: /*************** function subdirf2 ***********/
824: char *subdirf2(char fileres[], char *preop)
825: {
826:
827: /* Caution optionfilefiname is hidden */
828: strcpy(tmpout,optionfilefiname);
829: strcat(tmpout,"/");
830: strcat(tmpout,preop);
831: strcat(tmpout,fileres);
832: return tmpout;
833: }
834:
835: /*************** function subdirf3 ***********/
836: char *subdirf3(char fileres[], char *preop, char *preop2)
837: {
838:
839: /* Caution optionfilefiname is hidden */
840: strcpy(tmpout,optionfilefiname);
841: strcat(tmpout,"/");
842: strcat(tmpout,preop);
843: strcat(tmpout,preop2);
844: strcat(tmpout,fileres);
845: return tmpout;
846: }
847:
848: /***************** f1dim *************************/
849: extern int ncom;
850: extern double *pcom,*xicom;
851: extern double (*nrfunc)(double []);
852:
853: double f1dim(double x)
854: {
855: int j;
856: double f;
857: double *xt;
858:
859: xt=vector(1,ncom);
860: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
861: f=(*nrfunc)(xt);
862: free_vector(xt,1,ncom);
863: return f;
864: }
865:
866: /*****************brent *************************/
867: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
868: {
869: int iter;
870: double a,b,d,etemp;
871: double fu,fv,fw,fx;
872: double ftemp;
873: double p,q,r,tol1,tol2,u,v,w,x,xm;
874: double e=0.0;
875:
876: a=(ax < cx ? ax : cx);
877: b=(ax > cx ? ax : cx);
878: x=w=v=bx;
879: fw=fv=fx=(*f)(x);
880: for (iter=1;iter<=ITMAX;iter++) {
881: xm=0.5*(a+b);
882: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
883: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
884: printf(".");fflush(stdout);
885: fprintf(ficlog,".");fflush(ficlog);
886: #ifdef DEBUG
887: 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);
888: 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);
889: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
890: #endif
891: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
892: *xmin=x;
893: return fx;
894: }
895: ftemp=fu;
896: if (fabs(e) > tol1) {
897: r=(x-w)*(fx-fv);
898: q=(x-v)*(fx-fw);
899: p=(x-v)*q-(x-w)*r;
900: q=2.0*(q-r);
901: if (q > 0.0) p = -p;
902: q=fabs(q);
903: etemp=e;
904: e=d;
905: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
906: d=CGOLD*(e=(x >= xm ? a-x : b-x));
907: else {
908: d=p/q;
909: u=x+d;
910: if (u-a < tol2 || b-u < tol2)
911: d=SIGN(tol1,xm-x);
912: }
913: } else {
914: d=CGOLD*(e=(x >= xm ? a-x : b-x));
915: }
916: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
917: fu=(*f)(u);
918: if (fu <= fx) {
919: if (u >= x) a=x; else b=x;
920: SHFT(v,w,x,u)
921: SHFT(fv,fw,fx,fu)
922: } else {
923: if (u < x) a=u; else b=u;
924: if (fu <= fw || w == x) {
925: v=w;
926: w=u;
927: fv=fw;
928: fw=fu;
929: } else if (fu <= fv || v == x || v == w) {
930: v=u;
931: fv=fu;
932: }
933: }
934: }
935: nrerror("Too many iterations in brent");
936: *xmin=x;
937: return fx;
938: }
939:
940: /****************** mnbrak ***********************/
941:
942: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
943: double (*func)(double))
944: {
945: double ulim,u,r,q, dum;
946: double fu;
947:
948: *fa=(*func)(*ax);
949: *fb=(*func)(*bx);
950: if (*fb > *fa) {
951: SHFT(dum,*ax,*bx,dum)
952: SHFT(dum,*fb,*fa,dum)
953: }
954: *cx=(*bx)+GOLD*(*bx-*ax);
955: *fc=(*func)(*cx);
956: while (*fb > *fc) {
957: r=(*bx-*ax)*(*fb-*fc);
958: q=(*bx-*cx)*(*fb-*fa);
959: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
960: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
961: ulim=(*bx)+GLIMIT*(*cx-*bx);
962: if ((*bx-u)*(u-*cx) > 0.0) {
963: fu=(*func)(u);
964: } else if ((*cx-u)*(u-ulim) > 0.0) {
965: fu=(*func)(u);
966: if (fu < *fc) {
967: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
968: SHFT(*fb,*fc,fu,(*func)(u))
969: }
970: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
971: u=ulim;
972: fu=(*func)(u);
973: } else {
974: u=(*cx)+GOLD*(*cx-*bx);
975: fu=(*func)(u);
976: }
977: SHFT(*ax,*bx,*cx,u)
978: SHFT(*fa,*fb,*fc,fu)
979: }
980: }
981:
982: /*************** linmin ************************/
983:
984: int ncom;
985: double *pcom,*xicom;
986: double (*nrfunc)(double []);
987:
988: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
989: {
990: double brent(double ax, double bx, double cx,
991: double (*f)(double), double tol, double *xmin);
992: double f1dim(double x);
993: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
994: double *fc, double (*func)(double));
995: int j;
996: double xx,xmin,bx,ax;
997: double fx,fb,fa;
998:
999: ncom=n;
1000: pcom=vector(1,n);
1001: xicom=vector(1,n);
1002: nrfunc=func;
1003: for (j=1;j<=n;j++) {
1004: pcom[j]=p[j];
1005: xicom[j]=xi[j];
1006: }
1007: ax=0.0;
1008: xx=1.0;
1009: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1010: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1011: #ifdef DEBUG
1012: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1013: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1014: #endif
1015: for (j=1;j<=n;j++) {
1016: xi[j] *= xmin;
1017: p[j] += xi[j];
1018: }
1019: free_vector(xicom,1,n);
1020: free_vector(pcom,1,n);
1021: }
1022:
1023: char *asc_diff_time(long time_sec, char ascdiff[])
1024: {
1025: long sec_left, days, hours, minutes;
1026: days = (time_sec) / (60*60*24);
1027: sec_left = (time_sec) % (60*60*24);
1028: hours = (sec_left) / (60*60) ;
1029: sec_left = (sec_left) %(60*60);
1030: minutes = (sec_left) /60;
1031: sec_left = (sec_left) % (60);
1032: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1033: return ascdiff;
1034: }
1035:
1036: /*************** powell ************************/
1037: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1038: double (*func)(double []))
1039: {
1040: void linmin(double p[], double xi[], int n, double *fret,
1041: double (*func)(double []));
1042: int i,ibig,j;
1043: double del,t,*pt,*ptt,*xit;
1044: double fp,fptt;
1045: double *xits;
1046: int niterf, itmp;
1047:
1048: pt=vector(1,n);
1049: ptt=vector(1,n);
1050: xit=vector(1,n);
1051: xits=vector(1,n);
1052: *fret=(*func)(p);
1053: for (j=1;j<=n;j++) pt[j]=p[j];
1054: for (*iter=1;;++(*iter)) {
1055: fp=(*fret);
1056: ibig=0;
1057: del=0.0;
1058: last_time=curr_time;
1059: (void) gettimeofday(&curr_time,&tzp);
1060: 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);
1061: 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);
1062: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1063: for (i=1;i<=n;i++) {
1064: printf(" %d %.12f",i, p[i]);
1065: fprintf(ficlog," %d %.12lf",i, p[i]);
1066: fprintf(ficrespow," %.12lf", p[i]);
1067: }
1068: printf("\n");
1069: fprintf(ficlog,"\n");
1070: fprintf(ficrespow,"\n");fflush(ficrespow);
1071: if(*iter <=3){
1072: tm = *localtime(&curr_time.tv_sec);
1073: strcpy(strcurr,asctime(&tm));
1074: /* asctime_r(&tm,strcurr); */
1075: forecast_time=curr_time;
1076: itmp = strlen(strcurr);
1077: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1078: strcurr[itmp-1]='\0';
1079: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1080: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1081: for(niterf=10;niterf<=30;niterf+=10){
1082: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1083: tmf = *localtime(&forecast_time.tv_sec);
1084: /* asctime_r(&tmf,strfor); */
1085: strcpy(strfor,asctime(&tmf));
1086: itmp = strlen(strfor);
1087: if(strfor[itmp-1]=='\n')
1088: strfor[itmp-1]='\0';
1089: 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);
1090: 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);
1091: }
1092: }
1093: for (i=1;i<=n;i++) {
1094: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1095: fptt=(*fret);
1096: #ifdef DEBUG
1097: printf("fret=%lf \n",*fret);
1098: fprintf(ficlog,"fret=%lf \n",*fret);
1099: #endif
1100: printf("%d",i);fflush(stdout);
1101: fprintf(ficlog,"%d",i);fflush(ficlog);
1102: linmin(p,xit,n,fret,func);
1103: if (fabs(fptt-(*fret)) > del) {
1104: del=fabs(fptt-(*fret));
1105: ibig=i;
1106: }
1107: #ifdef DEBUG
1108: printf("%d %.12e",i,(*fret));
1109: fprintf(ficlog,"%d %.12e",i,(*fret));
1110: for (j=1;j<=n;j++) {
1111: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1112: printf(" x(%d)=%.12e",j,xit[j]);
1113: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1114: }
1115: for(j=1;j<=n;j++) {
1116: printf(" p=%.12e",p[j]);
1117: fprintf(ficlog," p=%.12e",p[j]);
1118: }
1119: printf("\n");
1120: fprintf(ficlog,"\n");
1121: #endif
1122: }
1123: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1124: #ifdef DEBUG
1125: int k[2],l;
1126: k[0]=1;
1127: k[1]=-1;
1128: printf("Max: %.12e",(*func)(p));
1129: fprintf(ficlog,"Max: %.12e",(*func)(p));
1130: for (j=1;j<=n;j++) {
1131: printf(" %.12e",p[j]);
1132: fprintf(ficlog," %.12e",p[j]);
1133: }
1134: printf("\n");
1135: fprintf(ficlog,"\n");
1136: for(l=0;l<=1;l++) {
1137: for (j=1;j<=n;j++) {
1138: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1139: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1140: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1141: }
1142: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1143: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1144: }
1145: #endif
1146:
1147:
1148: free_vector(xit,1,n);
1149: free_vector(xits,1,n);
1150: free_vector(ptt,1,n);
1151: free_vector(pt,1,n);
1152: return;
1153: }
1154: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1155: for (j=1;j<=n;j++) {
1156: ptt[j]=2.0*p[j]-pt[j];
1157: xit[j]=p[j]-pt[j];
1158: pt[j]=p[j];
1159: }
1160: fptt=(*func)(ptt);
1161: if (fptt < fp) {
1162: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1163: if (t < 0.0) {
1164: linmin(p,xit,n,fret,func);
1165: for (j=1;j<=n;j++) {
1166: xi[j][ibig]=xi[j][n];
1167: xi[j][n]=xit[j];
1168: }
1169: #ifdef DEBUG
1170: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1171: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1172: for(j=1;j<=n;j++){
1173: printf(" %.12e",xit[j]);
1174: fprintf(ficlog," %.12e",xit[j]);
1175: }
1176: printf("\n");
1177: fprintf(ficlog,"\n");
1178: #endif
1179: }
1180: }
1181: }
1182: }
1183:
1184: /**** Prevalence limit (stable or period prevalence) ****************/
1185:
1186: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1187: {
1188: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1189: matrix by transitions matrix until convergence is reached */
1190:
1191: int i, ii,j,k;
1192: double min, max, maxmin, maxmax,sumnew=0.;
1193: double **matprod2();
1.131 brouard 1194: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1195: double **newm;
1196: double agefin, delaymax=50 ; /* Max number of years to converge */
1197:
1198: for (ii=1;ii<=nlstate+ndeath;ii++)
1199: for (j=1;j<=nlstate+ndeath;j++){
1200: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1201: }
1202:
1203: cov[1]=1.;
1204:
1205: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1206: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1207: newm=savm;
1208: /* Covariates have to be included here again */
1209: cov[2]=agefin;
1210:
1211: for (k=1; k<=cptcovn;k++) {
1212: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1213: /* 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]]);*/
1214: }
1215: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1216: for (k=1; k<=cptcovprod;k++)
1217: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1218:
1219: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1220: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1221: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1222: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1223:
1224: savm=oldm;
1225: oldm=newm;
1226: maxmax=0.;
1227: for(j=1;j<=nlstate;j++){
1228: min=1.;
1229: max=0.;
1230: for(i=1; i<=nlstate; i++) {
1231: sumnew=0;
1232: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1233: prlim[i][j]= newm[i][j]/(1-sumnew);
1234: max=FMAX(max,prlim[i][j]);
1235: min=FMIN(min,prlim[i][j]);
1236: }
1237: maxmin=max-min;
1238: maxmax=FMAX(maxmax,maxmin);
1239: }
1240: if(maxmax < ftolpl){
1241: return prlim;
1242: }
1243: }
1244: }
1245:
1246: /*************** transition probabilities ***************/
1247:
1248: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1249: {
1250: double s1, s2;
1251: /*double t34;*/
1252: int i,j,j1, nc, ii, jj;
1253:
1254: for(i=1; i<= nlstate; i++){
1255: for(j=1; j<i;j++){
1256: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1257: /*s2 += param[i][j][nc]*cov[nc];*/
1258: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1259: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1260: }
1261: ps[i][j]=s2;
1262: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1263: }
1264: for(j=i+1; j<=nlstate+ndeath;j++){
1265: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1266: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1267: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1268: }
1269: ps[i][j]=s2;
1270: }
1271: }
1272: /*ps[3][2]=1;*/
1273:
1274: for(i=1; i<= nlstate; i++){
1275: s1=0;
1.131 brouard 1276: for(j=1; j<i; j++){
1.126 brouard 1277: s1+=exp(ps[i][j]);
1.131 brouard 1278: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1279: }
1280: for(j=i+1; j<=nlstate+ndeath; j++){
1.126 brouard 1281: s1+=exp(ps[i][j]);
1.131 brouard 1282: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1283: }
1.126 brouard 1284: ps[i][i]=1./(s1+1.);
1285: for(j=1; j<i; j++)
1286: ps[i][j]= exp(ps[i][j])*ps[i][i];
1287: for(j=i+1; j<=nlstate+ndeath; j++)
1288: ps[i][j]= exp(ps[i][j])*ps[i][i];
1289: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1290: } /* end i */
1291:
1292: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1293: for(jj=1; jj<= nlstate+ndeath; jj++){
1294: ps[ii][jj]=0;
1295: ps[ii][ii]=1;
1296: }
1297: }
1298:
1299:
1300: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1301: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1302: /* printf("ddd %lf ",ps[ii][jj]); */
1303: /* } */
1304: /* printf("\n "); */
1305: /* } */
1306: /* printf("\n ");printf("%lf ",cov[2]); */
1307: /*
1308: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1309: goto end;*/
1310: return ps;
1311: }
1312:
1313: /**************** Product of 2 matrices ******************/
1314:
1315: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1316: {
1317: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1318: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1319: /* in, b, out are matrice of pointers which should have been initialized
1320: before: only the contents of out is modified. The function returns
1321: a pointer to pointers identical to out */
1322: long i, j, k;
1323: for(i=nrl; i<= nrh; i++)
1324: for(k=ncolol; k<=ncoloh; k++)
1325: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1326: out[i][k] +=in[i][j]*b[j][k];
1327:
1328: return out;
1329: }
1330:
1331:
1332: /************* Higher Matrix Product ***************/
1333:
1334: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1335: {
1336: /* Computes the transition matrix starting at age 'age' over
1337: 'nhstepm*hstepm*stepm' months (i.e. until
1338: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1339: nhstepm*hstepm matrices.
1340: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1341: (typically every 2 years instead of every month which is too big
1342: for the memory).
1343: Model is determined by parameters x and covariates have to be
1344: included manually here.
1345:
1346: */
1347:
1348: int i, j, d, h, k;
1.131 brouard 1349: double **out, cov[NCOVMAX+1];
1.126 brouard 1350: double **newm;
1351:
1352: /* Hstepm could be zero and should return the unit matrix */
1353: for (i=1;i<=nlstate+ndeath;i++)
1354: for (j=1;j<=nlstate+ndeath;j++){
1355: oldm[i][j]=(i==j ? 1.0 : 0.0);
1356: po[i][j][0]=(i==j ? 1.0 : 0.0);
1357: }
1358: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1359: for(h=1; h <=nhstepm; h++){
1360: for(d=1; d <=hstepm; d++){
1361: newm=savm;
1362: /* Covariates have to be included here again */
1363: cov[1]=1.;
1364: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1365: for (k=1; k<=cptcovn;k++)
1366: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1367: for (k=1; k<=cptcovage;k++)
1368: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1369: for (k=1; k<=cptcovprod;k++)
1370: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1371:
1372:
1373: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1374: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1375: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1376: pmij(pmmij,cov,ncovmodel,x,nlstate));
1377: savm=oldm;
1378: oldm=newm;
1379: }
1380: for(i=1; i<=nlstate+ndeath; i++)
1381: for(j=1;j<=nlstate+ndeath;j++) {
1382: po[i][j][h]=newm[i][j];
1.128 brouard 1383: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1384: }
1.128 brouard 1385: /*printf("h=%d ",h);*/
1.126 brouard 1386: } /* end h */
1.128 brouard 1387: /* printf("\n H=%d \n",h); */
1.126 brouard 1388: return po;
1389: }
1390:
1391:
1392: /*************** log-likelihood *************/
1393: double func( double *x)
1394: {
1395: int i, ii, j, k, mi, d, kk;
1.131 brouard 1396: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1397: double **out;
1398: double sw; /* Sum of weights */
1399: double lli; /* Individual log likelihood */
1400: int s1, s2;
1401: double bbh, survp;
1402: long ipmx;
1403: /*extern weight */
1404: /* We are differentiating ll according to initial status */
1405: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1406: /*for(i=1;i<imx;i++)
1407: printf(" %d\n",s[4][i]);
1408: */
1409: cov[1]=1.;
1410:
1411: for(k=1; k<=nlstate; k++) ll[k]=0.;
1412:
1413: if(mle==1){
1414: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1415: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1416: for(mi=1; mi<= wav[i]-1; mi++){
1417: for (ii=1;ii<=nlstate+ndeath;ii++)
1418: for (j=1;j<=nlstate+ndeath;j++){
1419: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1420: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1421: }
1422: for(d=0; d<dh[mi][i]; d++){
1423: newm=savm;
1424: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1425: for (kk=1; kk<=cptcovage;kk++) {
1426: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1427: }
1428: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1429: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1430: savm=oldm;
1431: oldm=newm;
1432: } /* end mult */
1433:
1434: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1435: /* But now since version 0.9 we anticipate for bias at large stepm.
1436: * If stepm is larger than one month (smallest stepm) and if the exact delay
1437: * (in months) between two waves is not a multiple of stepm, we rounded to
1438: * the nearest (and in case of equal distance, to the lowest) interval but now
1439: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1440: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1441: * probability in order to take into account the bias as a fraction of the way
1442: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1443: * -stepm/2 to stepm/2 .
1444: * For stepm=1 the results are the same as for previous versions of Imach.
1445: * For stepm > 1 the results are less biased than in previous versions.
1446: */
1447: s1=s[mw[mi][i]][i];
1448: s2=s[mw[mi+1][i]][i];
1449: bbh=(double)bh[mi][i]/(double)stepm;
1450: /* bias bh is positive if real duration
1451: * is higher than the multiple of stepm and negative otherwise.
1452: */
1453: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1454: if( s2 > nlstate){
1455: /* i.e. if s2 is a death state and if the date of death is known
1456: then the contribution to the likelihood is the probability to
1457: die between last step unit time and current step unit time,
1458: which is also equal to probability to die before dh
1459: minus probability to die before dh-stepm .
1460: In version up to 0.92 likelihood was computed
1461: as if date of death was unknown. Death was treated as any other
1462: health state: the date of the interview describes the actual state
1463: and not the date of a change in health state. The former idea was
1464: to consider that at each interview the state was recorded
1465: (healthy, disable or death) and IMaCh was corrected; but when we
1466: introduced the exact date of death then we should have modified
1467: the contribution of an exact death to the likelihood. This new
1468: contribution is smaller and very dependent of the step unit
1469: stepm. It is no more the probability to die between last interview
1470: and month of death but the probability to survive from last
1471: interview up to one month before death multiplied by the
1472: probability to die within a month. Thanks to Chris
1473: Jackson for correcting this bug. Former versions increased
1474: mortality artificially. The bad side is that we add another loop
1475: which slows down the processing. The difference can be up to 10%
1476: lower mortality.
1477: */
1478: lli=log(out[s1][s2] - savm[s1][s2]);
1479:
1480:
1481: } else if (s2==-2) {
1482: for (j=1,survp=0. ; j<=nlstate; j++)
1483: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1484: /*survp += out[s1][j]; */
1485: lli= log(survp);
1486: }
1487:
1488: else if (s2==-4) {
1489: for (j=3,survp=0. ; j<=nlstate; j++)
1490: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1491: lli= log(survp);
1492: }
1493:
1494: else if (s2==-5) {
1495: for (j=1,survp=0. ; j<=2; j++)
1496: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1497: lli= log(survp);
1498: }
1499:
1500: else{
1501: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1502: /* 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 */
1503: }
1504: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1505: /*if(lli ==000.0)*/
1506: /*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); */
1507: ipmx +=1;
1508: sw += weight[i];
1509: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1510: } /* end of wave */
1511: } /* end of individual */
1512: } else if(mle==2){
1513: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1514: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1515: for(mi=1; mi<= wav[i]-1; mi++){
1516: for (ii=1;ii<=nlstate+ndeath;ii++)
1517: for (j=1;j<=nlstate+ndeath;j++){
1518: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1519: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1520: }
1521: for(d=0; d<=dh[mi][i]; d++){
1522: newm=savm;
1523: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1524: for (kk=1; kk<=cptcovage;kk++) {
1525: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1526: }
1527: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1528: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1529: savm=oldm;
1530: oldm=newm;
1531: } /* end mult */
1532:
1533: s1=s[mw[mi][i]][i];
1534: s2=s[mw[mi+1][i]][i];
1535: bbh=(double)bh[mi][i]/(double)stepm;
1536: 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 */
1537: ipmx +=1;
1538: sw += weight[i];
1539: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1540: } /* end of wave */
1541: } /* end of individual */
1542: } else if(mle==3){ /* exponential inter-extrapolation */
1543: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1544: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1545: for(mi=1; mi<= wav[i]-1; mi++){
1546: for (ii=1;ii<=nlstate+ndeath;ii++)
1547: for (j=1;j<=nlstate+ndeath;j++){
1548: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1549: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1550: }
1551: for(d=0; d<dh[mi][i]; d++){
1552: newm=savm;
1553: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1554: for (kk=1; kk<=cptcovage;kk++) {
1555: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1556: }
1557: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1558: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1559: savm=oldm;
1560: oldm=newm;
1561: } /* end mult */
1562:
1563: s1=s[mw[mi][i]][i];
1564: s2=s[mw[mi+1][i]][i];
1565: bbh=(double)bh[mi][i]/(double)stepm;
1566: 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 */
1567: ipmx +=1;
1568: sw += weight[i];
1569: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1570: } /* end of wave */
1571: } /* end of individual */
1572: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1573: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1574: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1575: for(mi=1; mi<= wav[i]-1; mi++){
1576: for (ii=1;ii<=nlstate+ndeath;ii++)
1577: for (j=1;j<=nlstate+ndeath;j++){
1578: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1579: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1580: }
1581: for(d=0; d<dh[mi][i]; d++){
1582: newm=savm;
1583: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1584: for (kk=1; kk<=cptcovage;kk++) {
1585: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1586: }
1587:
1588: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1589: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1590: savm=oldm;
1591: oldm=newm;
1592: } /* end mult */
1593:
1594: s1=s[mw[mi][i]][i];
1595: s2=s[mw[mi+1][i]][i];
1596: if( s2 > nlstate){
1597: lli=log(out[s1][s2] - savm[s1][s2]);
1598: }else{
1599: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1600: }
1601: ipmx +=1;
1602: sw += weight[i];
1603: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1604: /* 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]); */
1605: } /* end of wave */
1606: } /* end of individual */
1607: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1608: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1609: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1610: for(mi=1; mi<= wav[i]-1; mi++){
1611: for (ii=1;ii<=nlstate+ndeath;ii++)
1612: for (j=1;j<=nlstate+ndeath;j++){
1613: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1614: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1615: }
1616: for(d=0; d<dh[mi][i]; d++){
1617: newm=savm;
1618: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1619: for (kk=1; kk<=cptcovage;kk++) {
1620: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1621: }
1622:
1623: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1624: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1625: savm=oldm;
1626: oldm=newm;
1627: } /* end mult */
1628:
1629: s1=s[mw[mi][i]][i];
1630: s2=s[mw[mi+1][i]][i];
1631: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1632: ipmx +=1;
1633: sw += weight[i];
1634: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1635: /*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]);*/
1636: } /* end of wave */
1637: } /* end of individual */
1638: } /* End of if */
1639: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1640: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1641: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1642: return -l;
1643: }
1644:
1645: /*************** log-likelihood *************/
1646: double funcone( double *x)
1647: {
1648: /* Same as likeli but slower because of a lot of printf and if */
1649: int i, ii, j, k, mi, d, kk;
1.131 brouard 1650: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1651: double **out;
1652: double lli; /* Individual log likelihood */
1653: double llt;
1654: int s1, s2;
1655: double bbh, survp;
1656: /*extern weight */
1657: /* We are differentiating ll according to initial status */
1658: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1659: /*for(i=1;i<imx;i++)
1660: printf(" %d\n",s[4][i]);
1661: */
1662: cov[1]=1.;
1663:
1664: for(k=1; k<=nlstate; k++) ll[k]=0.;
1665:
1666: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1667: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1668: for(mi=1; mi<= wav[i]-1; mi++){
1669: for (ii=1;ii<=nlstate+ndeath;ii++)
1670: for (j=1;j<=nlstate+ndeath;j++){
1671: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1672: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1673: }
1674: for(d=0; d<dh[mi][i]; d++){
1675: newm=savm;
1676: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1677: for (kk=1; kk<=cptcovage;kk++) {
1678: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1679: }
1680: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1681: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1682: savm=oldm;
1683: oldm=newm;
1684: } /* end mult */
1685:
1686: s1=s[mw[mi][i]][i];
1687: s2=s[mw[mi+1][i]][i];
1688: bbh=(double)bh[mi][i]/(double)stepm;
1689: /* bias is positive if real duration
1690: * is higher than the multiple of stepm and negative otherwise.
1691: */
1692: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1693: lli=log(out[s1][s2] - savm[s1][s2]);
1694: } else if (s2==-2) {
1695: for (j=1,survp=0. ; j<=nlstate; j++)
1696: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1697: lli= log(survp);
1698: }else if (mle==1){
1699: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1700: } else if(mle==2){
1701: 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 */
1702: } else if(mle==3){ /* exponential inter-extrapolation */
1703: 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 */
1704: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1705: lli=log(out[s1][s2]); /* Original formula */
1706: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1707: lli=log(out[s1][s2]); /* Original formula */
1708: } /* End of if */
1709: ipmx +=1;
1710: sw += weight[i];
1711: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 1712: /*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 1713: if(globpr){
1714: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1715: %11.6f %11.6f %11.6f ", \
1716: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1717: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1718: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1719: llt +=ll[k]*gipmx/gsw;
1720: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1721: }
1722: fprintf(ficresilk," %10.6f\n", -llt);
1723: }
1724: } /* end of wave */
1725: } /* end of individual */
1726: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1727: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1728: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1729: if(globpr==0){ /* First time we count the contributions and weights */
1730: gipmx=ipmx;
1731: gsw=sw;
1732: }
1733: return -l;
1734: }
1735:
1736:
1737: /*************** function likelione ***********/
1738: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1739: {
1740: /* This routine should help understanding what is done with
1741: the selection of individuals/waves and
1742: to check the exact contribution to the likelihood.
1743: Plotting could be done.
1744: */
1745: int k;
1746:
1747: if(*globpri !=0){ /* Just counts and sums, no printings */
1748: strcpy(fileresilk,"ilk");
1749: strcat(fileresilk,fileres);
1750: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1751: printf("Problem with resultfile: %s\n", fileresilk);
1752: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1753: }
1754: 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");
1755: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1756: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1757: for(k=1; k<=nlstate; k++)
1758: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1759: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1760: }
1761:
1762: *fretone=(*funcone)(p);
1763: if(*globpri !=0){
1764: fclose(ficresilk);
1765: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1766: fflush(fichtm);
1767: }
1768: return;
1769: }
1770:
1771:
1772: /*********** Maximum Likelihood Estimation ***************/
1773:
1774: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1775: {
1776: int i,j, iter;
1777: double **xi;
1778: double fret;
1779: double fretone; /* Only one call to likelihood */
1780: /* char filerespow[FILENAMELENGTH];*/
1781: xi=matrix(1,npar,1,npar);
1782: for (i=1;i<=npar;i++)
1783: for (j=1;j<=npar;j++)
1784: xi[i][j]=(i==j ? 1.0 : 0.0);
1785: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1786: strcpy(filerespow,"pow");
1787: strcat(filerespow,fileres);
1788: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1789: printf("Problem with resultfile: %s\n", filerespow);
1790: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1791: }
1792: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1793: for (i=1;i<=nlstate;i++)
1794: for(j=1;j<=nlstate+ndeath;j++)
1795: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1796: fprintf(ficrespow,"\n");
1797:
1798: powell(p,xi,npar,ftol,&iter,&fret,func);
1799:
1800: free_matrix(xi,1,npar,1,npar);
1801: fclose(ficrespow);
1802: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1803: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1804: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1805:
1806: }
1807:
1808: /**** Computes Hessian and covariance matrix ***/
1809: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1810: {
1811: double **a,**y,*x,pd;
1812: double **hess;
1813: int i, j,jk;
1814: int *indx;
1815:
1816: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1817: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1818: void lubksb(double **a, int npar, int *indx, double b[]) ;
1819: void ludcmp(double **a, int npar, int *indx, double *d) ;
1820: double gompertz(double p[]);
1821: hess=matrix(1,npar,1,npar);
1822:
1823: printf("\nCalculation of the hessian matrix. Wait...\n");
1824: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1825: for (i=1;i<=npar;i++){
1826: printf("%d",i);fflush(stdout);
1827: fprintf(ficlog,"%d",i);fflush(ficlog);
1828:
1829: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1830:
1831: /* printf(" %f ",p[i]);
1832: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1833: }
1834:
1835: for (i=1;i<=npar;i++) {
1836: for (j=1;j<=npar;j++) {
1837: if (j>i) {
1838: printf(".%d%d",i,j);fflush(stdout);
1839: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1840: hess[i][j]=hessij(p,delti,i,j,func,npar);
1841:
1842: hess[j][i]=hess[i][j];
1843: /*printf(" %lf ",hess[i][j]);*/
1844: }
1845: }
1846: }
1847: printf("\n");
1848: fprintf(ficlog,"\n");
1849:
1850: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1851: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1852:
1853: a=matrix(1,npar,1,npar);
1854: y=matrix(1,npar,1,npar);
1855: x=vector(1,npar);
1856: indx=ivector(1,npar);
1857: for (i=1;i<=npar;i++)
1858: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1859: ludcmp(a,npar,indx,&pd);
1860:
1861: for (j=1;j<=npar;j++) {
1862: for (i=1;i<=npar;i++) x[i]=0;
1863: x[j]=1;
1864: lubksb(a,npar,indx,x);
1865: for (i=1;i<=npar;i++){
1866: matcov[i][j]=x[i];
1867: }
1868: }
1869:
1870: printf("\n#Hessian matrix#\n");
1871: fprintf(ficlog,"\n#Hessian matrix#\n");
1872: for (i=1;i<=npar;i++) {
1873: for (j=1;j<=npar;j++) {
1874: printf("%.3e ",hess[i][j]);
1875: fprintf(ficlog,"%.3e ",hess[i][j]);
1876: }
1877: printf("\n");
1878: fprintf(ficlog,"\n");
1879: }
1880:
1881: /* Recompute Inverse */
1882: for (i=1;i<=npar;i++)
1883: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1884: ludcmp(a,npar,indx,&pd);
1885:
1886: /* printf("\n#Hessian matrix recomputed#\n");
1887:
1888: for (j=1;j<=npar;j++) {
1889: for (i=1;i<=npar;i++) x[i]=0;
1890: x[j]=1;
1891: lubksb(a,npar,indx,x);
1892: for (i=1;i<=npar;i++){
1893: y[i][j]=x[i];
1894: printf("%.3e ",y[i][j]);
1895: fprintf(ficlog,"%.3e ",y[i][j]);
1896: }
1897: printf("\n");
1898: fprintf(ficlog,"\n");
1899: }
1900: */
1901:
1902: free_matrix(a,1,npar,1,npar);
1903: free_matrix(y,1,npar,1,npar);
1904: free_vector(x,1,npar);
1905: free_ivector(indx,1,npar);
1906: free_matrix(hess,1,npar,1,npar);
1907:
1908:
1909: }
1910:
1911: /*************** hessian matrix ****************/
1912: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1913: {
1914: int i;
1915: int l=1, lmax=20;
1916: double k1,k2;
1.132 brouard 1917: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 1918: double res;
1919: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1920: double fx;
1921: int k=0,kmax=10;
1922: double l1;
1923:
1924: fx=func(x);
1925: for (i=1;i<=npar;i++) p2[i]=x[i];
1926: for(l=0 ; l <=lmax; l++){
1927: l1=pow(10,l);
1928: delts=delt;
1929: for(k=1 ; k <kmax; k=k+1){
1930: delt = delta*(l1*k);
1931: p2[theta]=x[theta] +delt;
1932: k1=func(p2)-fx;
1933: p2[theta]=x[theta]-delt;
1934: k2=func(p2)-fx;
1935: /*res= (k1-2.0*fx+k2)/delt/delt; */
1936: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1937:
1.132 brouard 1938: #ifdef DEBUGHESS
1.126 brouard 1939: 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);
1940: 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);
1941: #endif
1942: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1943: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1944: k=kmax;
1945: }
1946: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1947: k=kmax; l=lmax*10.;
1948: }
1949: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1950: delts=delt;
1951: }
1952: }
1953: }
1954: delti[theta]=delts;
1955: return res;
1956:
1957: }
1958:
1959: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1960: {
1961: int i;
1962: int l=1, l1, lmax=20;
1963: double k1,k2,k3,k4,res,fx;
1.132 brouard 1964: double p2[MAXPARM+1];
1.126 brouard 1965: int k;
1966:
1967: fx=func(x);
1968: for (k=1; k<=2; k++) {
1969: for (i=1;i<=npar;i++) p2[i]=x[i];
1970: p2[thetai]=x[thetai]+delti[thetai]/k;
1971: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1972: k1=func(p2)-fx;
1973:
1974: p2[thetai]=x[thetai]+delti[thetai]/k;
1975: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1976: k2=func(p2)-fx;
1977:
1978: p2[thetai]=x[thetai]-delti[thetai]/k;
1979: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1980: k3=func(p2)-fx;
1981:
1982: p2[thetai]=x[thetai]-delti[thetai]/k;
1983: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1984: k4=func(p2)-fx;
1985: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1986: #ifdef DEBUG
1987: 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);
1988: 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);
1989: #endif
1990: }
1991: return res;
1992: }
1993:
1994: /************** Inverse of matrix **************/
1995: void ludcmp(double **a, int n, int *indx, double *d)
1996: {
1997: int i,imax,j,k;
1998: double big,dum,sum,temp;
1999: double *vv;
2000:
2001: vv=vector(1,n);
2002: *d=1.0;
2003: for (i=1;i<=n;i++) {
2004: big=0.0;
2005: for (j=1;j<=n;j++)
2006: if ((temp=fabs(a[i][j])) > big) big=temp;
2007: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2008: vv[i]=1.0/big;
2009: }
2010: for (j=1;j<=n;j++) {
2011: for (i=1;i<j;i++) {
2012: sum=a[i][j];
2013: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2014: a[i][j]=sum;
2015: }
2016: big=0.0;
2017: for (i=j;i<=n;i++) {
2018: sum=a[i][j];
2019: for (k=1;k<j;k++)
2020: sum -= a[i][k]*a[k][j];
2021: a[i][j]=sum;
2022: if ( (dum=vv[i]*fabs(sum)) >= big) {
2023: big=dum;
2024: imax=i;
2025: }
2026: }
2027: if (j != imax) {
2028: for (k=1;k<=n;k++) {
2029: dum=a[imax][k];
2030: a[imax][k]=a[j][k];
2031: a[j][k]=dum;
2032: }
2033: *d = -(*d);
2034: vv[imax]=vv[j];
2035: }
2036: indx[j]=imax;
2037: if (a[j][j] == 0.0) a[j][j]=TINY;
2038: if (j != n) {
2039: dum=1.0/(a[j][j]);
2040: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2041: }
2042: }
2043: free_vector(vv,1,n); /* Doesn't work */
2044: ;
2045: }
2046:
2047: void lubksb(double **a, int n, int *indx, double b[])
2048: {
2049: int i,ii=0,ip,j;
2050: double sum;
2051:
2052: for (i=1;i<=n;i++) {
2053: ip=indx[i];
2054: sum=b[ip];
2055: b[ip]=b[i];
2056: if (ii)
2057: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2058: else if (sum) ii=i;
2059: b[i]=sum;
2060: }
2061: for (i=n;i>=1;i--) {
2062: sum=b[i];
2063: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2064: b[i]=sum/a[i][i];
2065: }
2066: }
2067:
2068: void pstamp(FILE *fichier)
2069: {
2070: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2071: }
2072:
2073: /************ Frequencies ********************/
2074: 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[])
2075: { /* Some frequencies */
2076:
1.130 brouard 2077: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2078: int first;
2079: double ***freq; /* Frequencies */
2080: double *pp, **prop;
2081: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2082: char fileresp[FILENAMELENGTH];
2083:
2084: pp=vector(1,nlstate);
2085: prop=matrix(1,nlstate,iagemin,iagemax+3);
2086: strcpy(fileresp,"p");
2087: strcat(fileresp,fileres);
2088: if((ficresp=fopen(fileresp,"w"))==NULL) {
2089: printf("Problem with prevalence resultfile: %s\n", fileresp);
2090: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2091: exit(0);
2092: }
2093: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2094: j1=0;
2095:
2096: j=cptcoveff;
2097: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2098:
2099: first=1;
2100:
2101: for(k1=1; k1<=j;k1++){
2102: for(i1=1; i1<=ncodemax[k1];i1++){
2103: j1++;
2104: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2105: scanf("%d", i);*/
2106: for (i=-5; i<=nlstate+ndeath; i++)
2107: for (jk=-5; jk<=nlstate+ndeath; jk++)
2108: for(m=iagemin; m <= iagemax+3; m++)
2109: freq[i][jk][m]=0;
2110:
2111: for (i=1; i<=nlstate; i++)
2112: for(m=iagemin; m <= iagemax+3; m++)
2113: prop[i][m]=0;
2114:
2115: dateintsum=0;
2116: k2cpt=0;
2117: for (i=1; i<=imx; i++) {
2118: bool=1;
2119: if (cptcovn>0) {
2120: for (z1=1; z1<=cptcoveff; z1++)
2121: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2122: bool=0;
2123: }
2124: if (bool==1){
2125: for(m=firstpass; m<=lastpass; m++){
2126: k2=anint[m][i]+(mint[m][i]/12.);
2127: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2128: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2129: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2130: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2131: if (m<lastpass) {
2132: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2133: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2134: }
2135:
2136: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2137: dateintsum=dateintsum+k2;
2138: k2cpt++;
2139: }
2140: /*}*/
2141: }
2142: }
2143: }
2144:
2145: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2146: pstamp(ficresp);
2147: if (cptcovn>0) {
2148: fprintf(ficresp, "\n#********** Variable ");
2149: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2150: fprintf(ficresp, "**********\n#");
2151: }
2152: for(i=1; i<=nlstate;i++)
2153: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2154: fprintf(ficresp, "\n");
2155:
2156: for(i=iagemin; i <= iagemax+3; i++){
2157: if(i==iagemax+3){
2158: fprintf(ficlog,"Total");
2159: }else{
2160: if(first==1){
2161: first=0;
2162: printf("See log file for details...\n");
2163: }
2164: fprintf(ficlog,"Age %d", i);
2165: }
2166: for(jk=1; jk <=nlstate ; jk++){
2167: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2168: pp[jk] += freq[jk][m][i];
2169: }
2170: for(jk=1; jk <=nlstate ; jk++){
2171: for(m=-1, pos=0; m <=0 ; m++)
2172: pos += freq[jk][m][i];
2173: if(pp[jk]>=1.e-10){
2174: if(first==1){
1.132 brouard 2175: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2176: }
2177: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2178: }else{
2179: if(first==1)
2180: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2181: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2182: }
2183: }
2184:
2185: for(jk=1; jk <=nlstate ; jk++){
2186: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2187: pp[jk] += freq[jk][m][i];
2188: }
2189: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2190: pos += pp[jk];
2191: posprop += prop[jk][i];
2192: }
2193: for(jk=1; jk <=nlstate ; jk++){
2194: if(pos>=1.e-5){
2195: if(first==1)
2196: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2197: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2198: }else{
2199: if(first==1)
2200: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2201: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2202: }
2203: if( i <= iagemax){
2204: if(pos>=1.e-5){
2205: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2206: /*probs[i][jk][j1]= pp[jk]/pos;*/
2207: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2208: }
2209: else
2210: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2211: }
2212: }
2213:
2214: for(jk=-1; jk <=nlstate+ndeath; jk++)
2215: for(m=-1; m <=nlstate+ndeath; m++)
2216: if(freq[jk][m][i] !=0 ) {
2217: if(first==1)
2218: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2219: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2220: }
2221: if(i <= iagemax)
2222: fprintf(ficresp,"\n");
2223: if(first==1)
2224: printf("Others in log...\n");
2225: fprintf(ficlog,"\n");
2226: }
2227: }
2228: }
2229: dateintmean=dateintsum/k2cpt;
2230:
2231: fclose(ficresp);
2232: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2233: free_vector(pp,1,nlstate);
2234: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2235: /* End of Freq */
2236: }
2237:
2238: /************ Prevalence ********************/
2239: 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)
2240: {
2241: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2242: in each health status at the date of interview (if between dateprev1 and dateprev2).
2243: We still use firstpass and lastpass as another selection.
2244: */
2245:
1.130 brouard 2246: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2247: double ***freq; /* Frequencies */
2248: double *pp, **prop;
2249: double pos,posprop;
2250: double y2; /* in fractional years */
2251: int iagemin, iagemax;
2252:
2253: iagemin= (int) agemin;
2254: iagemax= (int) agemax;
2255: /*pp=vector(1,nlstate);*/
2256: prop=matrix(1,nlstate,iagemin,iagemax+3);
2257: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2258: j1=0;
2259:
2260: j=cptcoveff;
2261: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2262:
2263: for(k1=1; k1<=j;k1++){
2264: for(i1=1; i1<=ncodemax[k1];i1++){
2265: j1++;
2266:
2267: for (i=1; i<=nlstate; i++)
2268: for(m=iagemin; m <= iagemax+3; m++)
2269: prop[i][m]=0.0;
2270:
2271: for (i=1; i<=imx; i++) { /* Each individual */
2272: bool=1;
2273: if (cptcovn>0) {
2274: for (z1=1; z1<=cptcoveff; z1++)
2275: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2276: bool=0;
2277: }
2278: if (bool==1) {
2279: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2280: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2281: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2282: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2283: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2284: 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);
2285: if (s[m][i]>0 && s[m][i]<=nlstate) {
2286: /*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]]);*/
2287: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2288: prop[s[m][i]][iagemax+3] += weight[i];
2289: }
2290: }
2291: } /* end selection of waves */
2292: }
2293: }
2294: for(i=iagemin; i <= iagemax+3; i++){
2295:
2296: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2297: posprop += prop[jk][i];
2298: }
2299:
2300: for(jk=1; jk <=nlstate ; jk++){
2301: if( i <= iagemax){
2302: if(posprop>=1.e-5){
2303: probs[i][jk][j1]= prop[jk][i]/posprop;
1.128 brouard 2304: } else
2305: 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 2306: }
2307: }/* end jk */
2308: }/* end i */
2309: } /* end i1 */
2310: } /* end k1 */
2311:
2312: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2313: /*free_vector(pp,1,nlstate);*/
2314: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2315: } /* End of prevalence */
2316:
2317: /************* Waves Concatenation ***************/
2318:
2319: 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)
2320: {
2321: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2322: Death is a valid wave (if date is known).
2323: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2324: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2325: and mw[mi+1][i]. dh depends on stepm.
2326: */
2327:
2328: int i, mi, m;
2329: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2330: double sum=0., jmean=0.;*/
2331: int first;
2332: int j, k=0,jk, ju, jl;
2333: double sum=0.;
2334: first=0;
2335: jmin=1e+5;
2336: jmax=-1;
2337: jmean=0.;
2338: for(i=1; i<=imx; i++){
2339: mi=0;
2340: m=firstpass;
2341: while(s[m][i] <= nlstate){
2342: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2343: mw[++mi][i]=m;
2344: if(m >=lastpass)
2345: break;
2346: else
2347: m++;
2348: }/* end while */
2349: if (s[m][i] > nlstate){
2350: mi++; /* Death is another wave */
2351: /* if(mi==0) never been interviewed correctly before death */
2352: /* Only death is a correct wave */
2353: mw[mi][i]=m;
2354: }
2355:
2356: wav[i]=mi;
2357: if(mi==0){
2358: nbwarn++;
2359: if(first==0){
2360: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2361: first=1;
2362: }
2363: if(first==1){
2364: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2365: }
2366: } /* end mi==0 */
2367: } /* End individuals */
2368:
2369: for(i=1; i<=imx; i++){
2370: for(mi=1; mi<wav[i];mi++){
2371: if (stepm <=0)
2372: dh[mi][i]=1;
2373: else{
2374: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2375: if (agedc[i] < 2*AGESUP) {
2376: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2377: if(j==0) j=1; /* Survives at least one month after exam */
2378: else if(j<0){
2379: nberr++;
2380: 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]);
2381: j=1; /* Temporary Dangerous patch */
2382: 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);
2383: 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]);
2384: 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);
2385: }
2386: k=k+1;
2387: if (j >= jmax){
2388: jmax=j;
2389: ijmax=i;
2390: }
2391: if (j <= jmin){
2392: jmin=j;
2393: ijmin=i;
2394: }
2395: sum=sum+j;
2396: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2397: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2398: }
2399: }
2400: else{
2401: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2402: /* 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]); */
2403:
2404: k=k+1;
2405: if (j >= jmax) {
2406: jmax=j;
2407: ijmax=i;
2408: }
2409: else if (j <= jmin){
2410: jmin=j;
2411: ijmin=i;
2412: }
2413: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2414: /*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]);*/
2415: if(j<0){
2416: nberr++;
2417: 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]);
2418: 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]);
2419: }
2420: sum=sum+j;
2421: }
2422: jk= j/stepm;
2423: jl= j -jk*stepm;
2424: ju= j -(jk+1)*stepm;
2425: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2426: if(jl==0){
2427: dh[mi][i]=jk;
2428: bh[mi][i]=0;
2429: }else{ /* We want a negative bias in order to only have interpolation ie
2430: * at the price of an extra matrix product in likelihood */
2431: dh[mi][i]=jk+1;
2432: bh[mi][i]=ju;
2433: }
2434: }else{
2435: if(jl <= -ju){
2436: dh[mi][i]=jk;
2437: bh[mi][i]=jl; /* bias is positive if real duration
2438: * is higher than the multiple of stepm and negative otherwise.
2439: */
2440: }
2441: else{
2442: dh[mi][i]=jk+1;
2443: bh[mi][i]=ju;
2444: }
2445: if(dh[mi][i]==0){
2446: dh[mi][i]=1; /* At least one step */
2447: bh[mi][i]=ju; /* At least one step */
2448: /* 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);*/
2449: }
2450: } /* end if mle */
2451: }
2452: } /* end wave */
2453: }
2454: jmean=sum/k;
2455: 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);
2456: 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);
2457: }
2458:
2459: /*********** Tricode ****************************/
2460: void tricode(int *Tvar, int **nbcode, int imx)
2461: {
2462:
1.130 brouard 2463: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2464:
1.131 brouard 2465: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.126 brouard 2466: int cptcode=0;
2467: cptcoveff=0;
2468:
2469: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.131 brouard 2470: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
1.126 brouard 2471:
1.131 brouard 2472: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
1.126 brouard 2473: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2474: modality*/
1.131 brouard 2475: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
2476: Ndum[ij]++; /*counts the occurence of this modality */
1.126 brouard 2477: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.131 brouard 2478: if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now)
1.126 brouard 2479: Tvar[j]. If V=sex and male is 0 and
2480: female is 1, then cptcode=1.*/
2481: }
2482:
1.131 brouard 2483: for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
1.132 brouard 2484: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
2485: th covariate. In fact
2486: ncodemax[j]=2
2487: (dichotom. variables only) but
2488: it can be more */
1.131 brouard 2489: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2490:
2491: ij=1;
1.131 brouard 2492: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
2493: for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
2494: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2495: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2496: k is a modality. If we have model=V1+V1*sex
2497: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2498: ij++;
2499: }
2500: if (ij > ncodemax[j]) break;
2501: }
2502: }
2503: }
2504:
2505: for (k=0; k< maxncov; k++) Ndum[k]=0;
2506:
1.131 brouard 2507: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
1.126 brouard 2508: /* 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 2509: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.126 brouard 2510: Ndum[ij]++;
2511: }
2512:
2513: ij=1;
2514: for (i=1; i<= maxncov; i++) {
2515: if((Ndum[i]!=0) && (i<=ncovcol)){
2516: Tvaraff[ij]=i; /*For printing */
2517: ij++;
2518: }
2519: }
1.131 brouard 2520: ij--;
2521: cptcoveff=ij; /*Number of simple covariates*/
1.126 brouard 2522: }
2523:
2524: /*********** Health Expectancies ****************/
2525:
1.127 brouard 2526: 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 2527:
2528: {
2529: /* Health expectancies, no variances */
2530: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2531: int nhstepma, nstepma; /* Decreasing with age */
2532: double age, agelim, hf;
2533: double ***p3mat;
2534: double eip;
2535:
2536: pstamp(ficreseij);
2537: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2538: fprintf(ficreseij,"# Age");
2539: for(i=1; i<=nlstate;i++){
2540: for(j=1; j<=nlstate;j++){
2541: fprintf(ficreseij," e%1d%1d ",i,j);
2542: }
2543: fprintf(ficreseij," e%1d. ",i);
2544: }
2545: fprintf(ficreseij,"\n");
2546:
2547:
2548: if(estepm < stepm){
2549: printf ("Problem %d lower than %d\n",estepm, stepm);
2550: }
2551: else hstepm=estepm;
2552: /* We compute the life expectancy from trapezoids spaced every estepm months
2553: * This is mainly to measure the difference between two models: for example
2554: * if stepm=24 months pijx are given only every 2 years and by summing them
2555: * we are calculating an estimate of the Life Expectancy assuming a linear
2556: * progression in between and thus overestimating or underestimating according
2557: * to the curvature of the survival function. If, for the same date, we
2558: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2559: * to compare the new estimate of Life expectancy with the same linear
2560: * hypothesis. A more precise result, taking into account a more precise
2561: * curvature will be obtained if estepm is as small as stepm. */
2562:
2563: /* For example we decided to compute the life expectancy with the smallest unit */
2564: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2565: nhstepm is the number of hstepm from age to agelim
2566: nstepm is the number of stepm from age to agelin.
2567: Look at hpijx to understand the reason of that which relies in memory size
2568: and note for a fixed period like estepm months */
2569: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2570: survival function given by stepm (the optimization length). Unfortunately it
2571: means that if the survival funtion is printed only each two years of age and if
2572: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2573: results. So we changed our mind and took the option of the best precision.
2574: */
2575: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2576:
2577: agelim=AGESUP;
2578: /* If stepm=6 months */
2579: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2580: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2581:
2582: /* nhstepm age range expressed in number of stepm */
2583: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2584: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2585: /* if (stepm >= YEARM) hstepm=1;*/
2586: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2587: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2588:
2589: for (age=bage; age<=fage; age ++){
2590: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2591: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2592: /* if (stepm >= YEARM) hstepm=1;*/
2593: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2594:
2595: /* If stepm=6 months */
2596: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2597: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2598:
2599: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2600:
2601: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2602:
2603: printf("%d|",(int)age);fflush(stdout);
2604: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2605:
2606: /* Computing expectancies */
2607: for(i=1; i<=nlstate;i++)
2608: for(j=1; j<=nlstate;j++)
2609: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2610: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2611:
2612: /* 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]);*/
2613:
2614: }
2615:
2616: fprintf(ficreseij,"%3.0f",age );
2617: for(i=1; i<=nlstate;i++){
2618: eip=0;
2619: for(j=1; j<=nlstate;j++){
2620: eip +=eij[i][j][(int)age];
2621: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2622: }
2623: fprintf(ficreseij,"%9.4f", eip );
2624: }
2625: fprintf(ficreseij,"\n");
2626:
2627: }
2628: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2629: printf("\n");
2630: fprintf(ficlog,"\n");
2631:
2632: }
2633:
1.127 brouard 2634: 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 2635:
2636: {
2637: /* Covariances of health expectancies eij and of total life expectancies according
2638: to initial status i, ei. .
2639: */
2640: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2641: int nhstepma, nstepma; /* Decreasing with age */
2642: double age, agelim, hf;
2643: double ***p3matp, ***p3matm, ***varhe;
2644: double **dnewm,**doldm;
2645: double *xp, *xm;
2646: double **gp, **gm;
2647: double ***gradg, ***trgradg;
2648: int theta;
2649:
2650: double eip, vip;
2651:
2652: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2653: xp=vector(1,npar);
2654: xm=vector(1,npar);
2655: dnewm=matrix(1,nlstate*nlstate,1,npar);
2656: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2657:
2658: pstamp(ficresstdeij);
2659: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2660: fprintf(ficresstdeij,"# Age");
2661: for(i=1; i<=nlstate;i++){
2662: for(j=1; j<=nlstate;j++)
2663: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2664: fprintf(ficresstdeij," e%1d. ",i);
2665: }
2666: fprintf(ficresstdeij,"\n");
2667:
2668: pstamp(ficrescveij);
2669: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2670: fprintf(ficrescveij,"# Age");
2671: for(i=1; i<=nlstate;i++)
2672: for(j=1; j<=nlstate;j++){
2673: cptj= (j-1)*nlstate+i;
2674: for(i2=1; i2<=nlstate;i2++)
2675: for(j2=1; j2<=nlstate;j2++){
2676: cptj2= (j2-1)*nlstate+i2;
2677: if(cptj2 <= cptj)
2678: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2679: }
2680: }
2681: fprintf(ficrescveij,"\n");
2682:
2683: if(estepm < stepm){
2684: printf ("Problem %d lower than %d\n",estepm, stepm);
2685: }
2686: else hstepm=estepm;
2687: /* We compute the life expectancy from trapezoids spaced every estepm months
2688: * This is mainly to measure the difference between two models: for example
2689: * if stepm=24 months pijx are given only every 2 years and by summing them
2690: * we are calculating an estimate of the Life Expectancy assuming a linear
2691: * progression in between and thus overestimating or underestimating according
2692: * to the curvature of the survival function. If, for the same date, we
2693: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2694: * to compare the new estimate of Life expectancy with the same linear
2695: * hypothesis. A more precise result, taking into account a more precise
2696: * curvature will be obtained if estepm is as small as stepm. */
2697:
2698: /* For example we decided to compute the life expectancy with the smallest unit */
2699: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2700: nhstepm is the number of hstepm from age to agelim
2701: nstepm is the number of stepm from age to agelin.
2702: Look at hpijx to understand the reason of that which relies in memory size
2703: and note for a fixed period like estepm months */
2704: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2705: survival function given by stepm (the optimization length). Unfortunately it
2706: means that if the survival funtion is printed only each two years of age and if
2707: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2708: results. So we changed our mind and took the option of the best precision.
2709: */
2710: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2711:
2712: /* If stepm=6 months */
2713: /* nhstepm age range expressed in number of stepm */
2714: agelim=AGESUP;
2715: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2716: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2717: /* if (stepm >= YEARM) hstepm=1;*/
2718: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2719:
2720: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2721: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2722: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2723: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2724: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2725: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2726:
2727: for (age=bage; age<=fage; age ++){
2728: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2729: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2730: /* if (stepm >= YEARM) hstepm=1;*/
2731: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2732:
2733: /* If stepm=6 months */
2734: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2735: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2736:
2737: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2738:
2739: /* Computing Variances of health expectancies */
2740: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2741: decrease memory allocation */
2742: for(theta=1; theta <=npar; theta++){
2743: for(i=1; i<=npar; i++){
2744: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2745: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2746: }
2747: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2748: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2749:
2750: for(j=1; j<= nlstate; j++){
2751: for(i=1; i<=nlstate; i++){
2752: for(h=0; h<=nhstepm-1; h++){
2753: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2754: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2755: }
2756: }
2757: }
2758:
2759: for(ij=1; ij<= nlstate*nlstate; ij++)
2760: for(h=0; h<=nhstepm-1; h++){
2761: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2762: }
2763: }/* End theta */
2764:
2765:
2766: for(h=0; h<=nhstepm-1; h++)
2767: for(j=1; j<=nlstate*nlstate;j++)
2768: for(theta=1; theta <=npar; theta++)
2769: trgradg[h][j][theta]=gradg[h][theta][j];
2770:
2771:
2772: for(ij=1;ij<=nlstate*nlstate;ij++)
2773: for(ji=1;ji<=nlstate*nlstate;ji++)
2774: varhe[ij][ji][(int)age] =0.;
2775:
2776: printf("%d|",(int)age);fflush(stdout);
2777: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2778: for(h=0;h<=nhstepm-1;h++){
2779: for(k=0;k<=nhstepm-1;k++){
2780: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2781: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2782: for(ij=1;ij<=nlstate*nlstate;ij++)
2783: for(ji=1;ji<=nlstate*nlstate;ji++)
2784: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2785: }
2786: }
2787:
2788: /* Computing expectancies */
2789: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2790: for(i=1; i<=nlstate;i++)
2791: for(j=1; j<=nlstate;j++)
2792: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2793: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2794:
2795: /* 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]);*/
2796:
2797: }
2798:
2799: fprintf(ficresstdeij,"%3.0f",age );
2800: for(i=1; i<=nlstate;i++){
2801: eip=0.;
2802: vip=0.;
2803: for(j=1; j<=nlstate;j++){
2804: eip += eij[i][j][(int)age];
2805: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2806: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2807: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2808: }
2809: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2810: }
2811: fprintf(ficresstdeij,"\n");
2812:
2813: fprintf(ficrescveij,"%3.0f",age );
2814: for(i=1; i<=nlstate;i++)
2815: for(j=1; j<=nlstate;j++){
2816: cptj= (j-1)*nlstate+i;
2817: for(i2=1; i2<=nlstate;i2++)
2818: for(j2=1; j2<=nlstate;j2++){
2819: cptj2= (j2-1)*nlstate+i2;
2820: if(cptj2 <= cptj)
2821: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2822: }
2823: }
2824: fprintf(ficrescveij,"\n");
2825:
2826: }
2827: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2828: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2829: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2830: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2831: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2832: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2833: printf("\n");
2834: fprintf(ficlog,"\n");
2835:
2836: free_vector(xm,1,npar);
2837: free_vector(xp,1,npar);
2838: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2839: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2840: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2841: }
2842:
2843: /************ Variance ******************/
2844: 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[])
2845: {
2846: /* Variance of health expectancies */
2847: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2848: /* double **newm;*/
2849: double **dnewm,**doldm;
2850: double **dnewmp,**doldmp;
2851: int i, j, nhstepm, hstepm, h, nstepm ;
2852: int k, cptcode;
2853: double *xp;
2854: double **gp, **gm; /* for var eij */
2855: double ***gradg, ***trgradg; /*for var eij */
2856: double **gradgp, **trgradgp; /* for var p point j */
2857: double *gpp, *gmp; /* for var p point j */
2858: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2859: double ***p3mat;
2860: double age,agelim, hf;
2861: double ***mobaverage;
2862: int theta;
2863: char digit[4];
2864: char digitp[25];
2865:
2866: char fileresprobmorprev[FILENAMELENGTH];
2867:
2868: if(popbased==1){
2869: if(mobilav!=0)
2870: strcpy(digitp,"-populbased-mobilav-");
2871: else strcpy(digitp,"-populbased-nomobil-");
2872: }
2873: else
2874: strcpy(digitp,"-stablbased-");
2875:
2876: if (mobilav!=0) {
2877: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2878: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2879: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2880: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2881: }
2882: }
2883:
2884: strcpy(fileresprobmorprev,"prmorprev");
2885: sprintf(digit,"%-d",ij);
2886: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2887: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2888: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2889: strcat(fileresprobmorprev,fileres);
2890: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2891: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2892: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2893: }
2894: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2895:
2896: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2897: pstamp(ficresprobmorprev);
2898: 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);
2899: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2900: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2901: fprintf(ficresprobmorprev," p.%-d SE",j);
2902: for(i=1; i<=nlstate;i++)
2903: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2904: }
2905: fprintf(ficresprobmorprev,"\n");
2906: fprintf(ficgp,"\n# Routine varevsij");
2907: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2908: 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");
2909: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2910: /* } */
2911: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2912: pstamp(ficresvij);
2913: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2914: if(popbased==1)
1.128 brouard 2915: 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 2916: else
2917: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2918: fprintf(ficresvij,"# Age");
2919: for(i=1; i<=nlstate;i++)
2920: for(j=1; j<=nlstate;j++)
2921: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2922: fprintf(ficresvij,"\n");
2923:
2924: xp=vector(1,npar);
2925: dnewm=matrix(1,nlstate,1,npar);
2926: doldm=matrix(1,nlstate,1,nlstate);
2927: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2928: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2929:
2930: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2931: gpp=vector(nlstate+1,nlstate+ndeath);
2932: gmp=vector(nlstate+1,nlstate+ndeath);
2933: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2934:
2935: if(estepm < stepm){
2936: printf ("Problem %d lower than %d\n",estepm, stepm);
2937: }
2938: else hstepm=estepm;
2939: /* For example we decided to compute the life expectancy with the smallest unit */
2940: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2941: nhstepm is the number of hstepm from age to agelim
2942: nstepm is the number of stepm from age to agelin.
1.128 brouard 2943: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 2944: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2945: survival function given by stepm (the optimization length). Unfortunately it
2946: means that if the survival funtion is printed every two years of age and if
2947: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2948: results. So we changed our mind and took the option of the best precision.
2949: */
2950: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2951: agelim = AGESUP;
2952: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2953: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2954: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2955: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2956: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2957: gp=matrix(0,nhstepm,1,nlstate);
2958: gm=matrix(0,nhstepm,1,nlstate);
2959:
2960:
2961: for(theta=1; theta <=npar; theta++){
2962: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2963: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2964: }
2965: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2966: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2967:
2968: if (popbased==1) {
2969: if(mobilav ==0){
2970: for(i=1; i<=nlstate;i++)
2971: prlim[i][i]=probs[(int)age][i][ij];
2972: }else{ /* mobilav */
2973: for(i=1; i<=nlstate;i++)
2974: prlim[i][i]=mobaverage[(int)age][i][ij];
2975: }
2976: }
2977:
2978: for(j=1; j<= nlstate; j++){
2979: for(h=0; h<=nhstepm; h++){
2980: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2981: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2982: }
2983: }
2984: /* This for computing probability of death (h=1 means
2985: computed over hstepm matrices product = hstepm*stepm months)
2986: as a weighted average of prlim.
2987: */
2988: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2989: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2990: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2991: }
2992: /* end probability of death */
2993:
2994: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2995: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2996: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2997: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2998:
2999: if (popbased==1) {
3000: if(mobilav ==0){
3001: for(i=1; i<=nlstate;i++)
3002: prlim[i][i]=probs[(int)age][i][ij];
3003: }else{ /* mobilav */
3004: for(i=1; i<=nlstate;i++)
3005: prlim[i][i]=mobaverage[(int)age][i][ij];
3006: }
3007: }
3008:
1.128 brouard 3009: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3010: for(h=0; h<=nhstepm; h++){
3011: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3012: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3013: }
3014: }
3015: /* This for computing probability of death (h=1 means
3016: computed over hstepm matrices product = hstepm*stepm months)
3017: as a weighted average of prlim.
3018: */
3019: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3020: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3021: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3022: }
3023: /* end probability of death */
3024:
3025: for(j=1; j<= nlstate; j++) /* vareij */
3026: for(h=0; h<=nhstepm; h++){
3027: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3028: }
3029:
3030: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3031: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3032: }
3033:
3034: } /* End theta */
3035:
3036: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3037:
3038: for(h=0; h<=nhstepm; h++) /* veij */
3039: for(j=1; j<=nlstate;j++)
3040: for(theta=1; theta <=npar; theta++)
3041: trgradg[h][j][theta]=gradg[h][theta][j];
3042:
3043: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3044: for(theta=1; theta <=npar; theta++)
3045: trgradgp[j][theta]=gradgp[theta][j];
3046:
3047:
3048: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3049: for(i=1;i<=nlstate;i++)
3050: for(j=1;j<=nlstate;j++)
3051: vareij[i][j][(int)age] =0.;
3052:
3053: for(h=0;h<=nhstepm;h++){
3054: for(k=0;k<=nhstepm;k++){
3055: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3056: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3057: for(i=1;i<=nlstate;i++)
3058: for(j=1;j<=nlstate;j++)
3059: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3060: }
3061: }
3062:
3063: /* pptj */
3064: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3065: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3066: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3067: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3068: varppt[j][i]=doldmp[j][i];
3069: /* end ppptj */
3070: /* x centered again */
3071: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3072: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3073:
3074: if (popbased==1) {
3075: if(mobilav ==0){
3076: for(i=1; i<=nlstate;i++)
3077: prlim[i][i]=probs[(int)age][i][ij];
3078: }else{ /* mobilav */
3079: for(i=1; i<=nlstate;i++)
3080: prlim[i][i]=mobaverage[(int)age][i][ij];
3081: }
3082: }
3083:
3084: /* This for computing probability of death (h=1 means
3085: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3086: as a weighted average of prlim.
3087: */
3088: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3089: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3090: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3091: }
3092: /* end probability of death */
3093:
3094: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3095: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3096: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3097: for(i=1; i<=nlstate;i++){
3098: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3099: }
3100: }
3101: fprintf(ficresprobmorprev,"\n");
3102:
3103: fprintf(ficresvij,"%.0f ",age );
3104: for(i=1; i<=nlstate;i++)
3105: for(j=1; j<=nlstate;j++){
3106: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3107: }
3108: fprintf(ficresvij,"\n");
3109: free_matrix(gp,0,nhstepm,1,nlstate);
3110: free_matrix(gm,0,nhstepm,1,nlstate);
3111: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3112: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3113: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3114: } /* End age */
3115: free_vector(gpp,nlstate+1,nlstate+ndeath);
3116: free_vector(gmp,nlstate+1,nlstate+ndeath);
3117: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3118: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.131 brouard 3119: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
1.126 brouard 3120: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3121: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3122: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3123: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3124: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3125: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3126: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3127: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3128: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3129: 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);
3130: /* 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);
3131: */
3132: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3133: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3134:
3135: free_vector(xp,1,npar);
3136: free_matrix(doldm,1,nlstate,1,nlstate);
3137: free_matrix(dnewm,1,nlstate,1,npar);
3138: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3139: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3140: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3141: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3142: fclose(ficresprobmorprev);
3143: fflush(ficgp);
3144: fflush(fichtm);
3145: } /* end varevsij */
3146:
3147: /************ Variance of prevlim ******************/
3148: 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[])
3149: {
3150: /* Variance of prevalence limit */
3151: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3152: double **newm;
3153: double **dnewm,**doldm;
3154: int i, j, nhstepm, hstepm;
3155: int k, cptcode;
3156: double *xp;
3157: double *gp, *gm;
3158: double **gradg, **trgradg;
3159: double age,agelim;
3160: int theta;
3161:
3162: pstamp(ficresvpl);
3163: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3164: fprintf(ficresvpl,"# Age");
3165: for(i=1; i<=nlstate;i++)
3166: fprintf(ficresvpl," %1d-%1d",i,i);
3167: fprintf(ficresvpl,"\n");
3168:
3169: xp=vector(1,npar);
3170: dnewm=matrix(1,nlstate,1,npar);
3171: doldm=matrix(1,nlstate,1,nlstate);
3172:
3173: hstepm=1*YEARM; /* Every year of age */
3174: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3175: agelim = AGESUP;
3176: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3177: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3178: if (stepm >= YEARM) hstepm=1;
3179: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3180: gradg=matrix(1,npar,1,nlstate);
3181: gp=vector(1,nlstate);
3182: gm=vector(1,nlstate);
3183:
3184: for(theta=1; theta <=npar; theta++){
3185: for(i=1; i<=npar; i++){ /* Computes gradient */
3186: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3187: }
3188: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3189: for(i=1;i<=nlstate;i++)
3190: gp[i] = prlim[i][i];
3191:
3192: for(i=1; i<=npar; i++) /* Computes gradient */
3193: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3194: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3195: for(i=1;i<=nlstate;i++)
3196: gm[i] = prlim[i][i];
3197:
3198: for(i=1;i<=nlstate;i++)
3199: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3200: } /* End theta */
3201:
3202: trgradg =matrix(1,nlstate,1,npar);
3203:
3204: for(j=1; j<=nlstate;j++)
3205: for(theta=1; theta <=npar; theta++)
3206: trgradg[j][theta]=gradg[theta][j];
3207:
3208: for(i=1;i<=nlstate;i++)
3209: varpl[i][(int)age] =0.;
3210: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3211: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3212: for(i=1;i<=nlstate;i++)
3213: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3214:
3215: fprintf(ficresvpl,"%.0f ",age );
3216: for(i=1; i<=nlstate;i++)
3217: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3218: fprintf(ficresvpl,"\n");
3219: free_vector(gp,1,nlstate);
3220: free_vector(gm,1,nlstate);
3221: free_matrix(gradg,1,npar,1,nlstate);
3222: free_matrix(trgradg,1,nlstate,1,npar);
3223: } /* End age */
3224:
3225: free_vector(xp,1,npar);
3226: free_matrix(doldm,1,nlstate,1,npar);
3227: free_matrix(dnewm,1,nlstate,1,nlstate);
3228:
3229: }
3230:
3231: /************ Variance of one-step probabilities ******************/
3232: 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[])
3233: {
3234: int i, j=0, i1, k1, l1, t, tj;
3235: int k2, l2, j1, z1;
3236: int k=0,l, cptcode;
3237: int first=1, first1;
3238: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3239: double **dnewm,**doldm;
3240: double *xp;
3241: double *gp, *gm;
3242: double **gradg, **trgradg;
3243: double **mu;
3244: double age,agelim, cov[NCOVMAX];
3245: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3246: int theta;
3247: char fileresprob[FILENAMELENGTH];
3248: char fileresprobcov[FILENAMELENGTH];
3249: char fileresprobcor[FILENAMELENGTH];
3250:
3251: double ***varpij;
3252:
3253: strcpy(fileresprob,"prob");
3254: strcat(fileresprob,fileres);
3255: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3256: printf("Problem with resultfile: %s\n", fileresprob);
3257: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3258: }
3259: strcpy(fileresprobcov,"probcov");
3260: strcat(fileresprobcov,fileres);
3261: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3262: printf("Problem with resultfile: %s\n", fileresprobcov);
3263: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3264: }
3265: strcpy(fileresprobcor,"probcor");
3266: strcat(fileresprobcor,fileres);
3267: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3268: printf("Problem with resultfile: %s\n", fileresprobcor);
3269: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3270: }
3271: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3272: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3273: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3274: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3275: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3276: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3277: pstamp(ficresprob);
3278: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3279: fprintf(ficresprob,"# Age");
3280: pstamp(ficresprobcov);
3281: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3282: fprintf(ficresprobcov,"# Age");
3283: pstamp(ficresprobcor);
3284: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3285: fprintf(ficresprobcor,"# Age");
3286:
3287:
3288: for(i=1; i<=nlstate;i++)
3289: for(j=1; j<=(nlstate+ndeath);j++){
3290: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3291: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3292: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3293: }
3294: /* fprintf(ficresprob,"\n");
3295: fprintf(ficresprobcov,"\n");
3296: fprintf(ficresprobcor,"\n");
3297: */
1.131 brouard 3298: xp=vector(1,npar);
1.126 brouard 3299: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3300: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3301: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3302: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3303: first=1;
3304: fprintf(ficgp,"\n# Routine varprob");
3305: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3306: fprintf(fichtm,"\n");
3307:
3308: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3309: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3310: file %s<br>\n",optionfilehtmcov);
3311: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3312: and drawn. It helps understanding how is the covariance between two incidences.\
3313: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3314: 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. \
3315: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3316: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3317: standard deviations wide on each axis. <br>\
3318: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3319: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3320: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3321:
3322: cov[1]=1;
3323: tj=cptcoveff;
3324: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3325: j1=0;
3326: for(t=1; t<=tj;t++){
3327: for(i1=1; i1<=ncodemax[t];i1++){
3328: j1++;
3329: if (cptcovn>0) {
3330: fprintf(ficresprob, "\n#********** Variable ");
3331: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3332: fprintf(ficresprob, "**********\n#\n");
3333: fprintf(ficresprobcov, "\n#********** Variable ");
3334: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3335: fprintf(ficresprobcov, "**********\n#\n");
3336:
3337: fprintf(ficgp, "\n#********** Variable ");
3338: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3339: fprintf(ficgp, "**********\n#\n");
3340:
3341:
3342: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3343: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3344: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3345:
3346: fprintf(ficresprobcor, "\n#********** Variable ");
3347: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3348: fprintf(ficresprobcor, "**********\n#");
3349: }
3350:
3351: for (age=bage; age<=fage; age ++){
3352: cov[2]=age;
3353: for (k=1; k<=cptcovn;k++) {
3354: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3355: }
3356: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3357: for (k=1; k<=cptcovprod;k++)
3358: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3359:
3360: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3361: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3362: gp=vector(1,(nlstate)*(nlstate+ndeath));
3363: gm=vector(1,(nlstate)*(nlstate+ndeath));
3364:
3365: for(theta=1; theta <=npar; theta++){
3366: for(i=1; i<=npar; i++)
3367: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3368:
3369: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3370:
3371: k=0;
3372: for(i=1; i<= (nlstate); i++){
3373: for(j=1; j<=(nlstate+ndeath);j++){
3374: k=k+1;
3375: gp[k]=pmmij[i][j];
3376: }
3377: }
3378:
3379: for(i=1; i<=npar; i++)
3380: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3381:
3382: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3383: k=0;
3384: for(i=1; i<=(nlstate); i++){
3385: for(j=1; j<=(nlstate+ndeath);j++){
3386: k=k+1;
3387: gm[k]=pmmij[i][j];
3388: }
3389: }
3390:
3391: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3392: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3393: }
3394:
3395: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3396: for(theta=1; theta <=npar; theta++)
3397: trgradg[j][theta]=gradg[theta][j];
3398:
3399: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3400: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3401: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3402: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3403: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3404: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3405:
3406: pmij(pmmij,cov,ncovmodel,x,nlstate);
3407:
3408: k=0;
3409: for(i=1; i<=(nlstate); i++){
3410: for(j=1; j<=(nlstate+ndeath);j++){
3411: k=k+1;
3412: mu[k][(int) age]=pmmij[i][j];
3413: }
3414: }
3415: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3416: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3417: varpij[i][j][(int)age] = doldm[i][j];
3418:
3419: /*printf("\n%d ",(int)age);
3420: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3421: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3422: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3423: }*/
3424:
3425: fprintf(ficresprob,"\n%d ",(int)age);
3426: fprintf(ficresprobcov,"\n%d ",(int)age);
3427: fprintf(ficresprobcor,"\n%d ",(int)age);
3428:
3429: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3430: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3431: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3432: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3433: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3434: }
3435: i=0;
3436: for (k=1; k<=(nlstate);k++){
3437: for (l=1; l<=(nlstate+ndeath);l++){
3438: i=i++;
3439: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3440: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3441: for (j=1; j<=i;j++){
3442: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3443: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3444: }
3445: }
3446: }/* end of loop for state */
3447: } /* end of loop for age */
3448:
3449: /* Confidence intervalle of pij */
3450: /*
1.131 brouard 3451: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3452: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3453: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3454: 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);
3455: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3456: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3457: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3458: */
3459:
3460: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3461: first1=1;
3462: for (k2=1; k2<=(nlstate);k2++){
3463: for (l2=1; l2<=(nlstate+ndeath);l2++){
3464: if(l2==k2) continue;
3465: j=(k2-1)*(nlstate+ndeath)+l2;
3466: for (k1=1; k1<=(nlstate);k1++){
3467: for (l1=1; l1<=(nlstate+ndeath);l1++){
3468: if(l1==k1) continue;
3469: i=(k1-1)*(nlstate+ndeath)+l1;
3470: if(i<=j) continue;
3471: for (age=bage; age<=fage; age ++){
3472: if ((int)age %5==0){
3473: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3474: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3475: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3476: mu1=mu[i][(int) age]/stepm*YEARM ;
3477: mu2=mu[j][(int) age]/stepm*YEARM;
3478: c12=cv12/sqrt(v1*v2);
3479: /* Computing eigen value of matrix of covariance */
3480: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3481: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3482: /* Eigen vectors */
3483: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3484: /*v21=sqrt(1.-v11*v11); *//* error */
3485: v21=(lc1-v1)/cv12*v11;
3486: v12=-v21;
3487: v22=v11;
3488: tnalp=v21/v11;
3489: if(first1==1){
3490: first1=0;
3491: 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);
3492: }
3493: 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);
3494: /*printf(fignu*/
3495: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3496: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3497: if(first==1){
3498: first=0;
3499: fprintf(ficgp,"\nset parametric;unset label");
3500: 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);
3501: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3502: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3503: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3504: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3505: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3506: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3507: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3508: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3509: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3510: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3511: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3512: 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",\
3513: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3514: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3515: }else{
3516: first=0;
3517: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3518: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3519: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3520: 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",\
3521: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3522: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3523: }/* if first */
3524: } /* age mod 5 */
3525: } /* end loop age */
3526: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3527: first=1;
3528: } /*l12 */
3529: } /* k12 */
3530: } /*l1 */
3531: }/* k1 */
3532: } /* loop covariates */
3533: }
3534: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3535: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3536: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3537: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3538: free_vector(xp,1,npar);
3539: fclose(ficresprob);
3540: fclose(ficresprobcov);
3541: fclose(ficresprobcor);
3542: fflush(ficgp);
3543: fflush(fichtmcov);
3544: }
3545:
3546:
3547: /******************* Printing html file ***********/
3548: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3549: int lastpass, int stepm, int weightopt, char model[],\
3550: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3551: int popforecast, int estepm ,\
3552: double jprev1, double mprev1,double anprev1, \
3553: double jprev2, double mprev2,double anprev2){
3554: int jj1, k1, i1, cpt;
3555:
3556: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3557: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3558: </ul>");
3559: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3560: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3561: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3562: fprintf(fichtm,"\
3563: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3564: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3565: fprintf(fichtm,"\
3566: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3567: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3568: fprintf(fichtm,"\
1.128 brouard 3569: - (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 3570: <a href=\"%s\">%s</a> <br>\n",
3571: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3572: fprintf(fichtm,"\
3573: - Population projections by age and states: \
3574: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3575:
3576: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3577:
3578: m=cptcoveff;
3579: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3580:
3581: jj1=0;
3582: for(k1=1; k1<=m;k1++){
3583: for(i1=1; i1<=ncodemax[k1];i1++){
3584: jj1++;
3585: if (cptcovn > 0) {
3586: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3587: for (cpt=1; cpt<=cptcoveff;cpt++)
3588: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3589: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3590: }
3591: /* Pij */
3592: 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> \
3593: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3594: /* Quasi-incidences */
3595: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3596: 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> \
3597: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3598: /* Period (stable) prevalence in each health state */
3599: for(cpt=1; cpt<nlstate;cpt++){
3600: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3601: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3602: }
3603: for(cpt=1; cpt<=nlstate;cpt++) {
3604: 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> \
3605: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3606: }
3607: } /* end i1 */
3608: }/* End k1 */
3609: fprintf(fichtm,"</ul>");
3610:
3611:
3612: fprintf(fichtm,"\
3613: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3614: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3615:
3616: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3617: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3618: fprintf(fichtm,"\
3619: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3620: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3621:
3622: fprintf(fichtm,"\
3623: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3624: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3625: fprintf(fichtm,"\
3626: - 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): \
3627: <a href=\"%s\">%s</a> <br>\n</li>",
3628: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3629: fprintf(fichtm,"\
3630: - (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): \
3631: <a href=\"%s\">%s</a> <br>\n</li>",
3632: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3633: fprintf(fichtm,"\
1.128 brouard 3634: - 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 3635: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3636: fprintf(fichtm,"\
1.128 brouard 3637: - 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",
3638: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3639: fprintf(fichtm,"\
3640: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3641: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3642:
3643: /* if(popforecast==1) fprintf(fichtm,"\n */
3644: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3645: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3646: /* <br>",fileres,fileres,fileres,fileres); */
3647: /* else */
3648: /* 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); */
3649: fflush(fichtm);
3650: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3651:
3652: m=cptcoveff;
3653: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3654:
3655: jj1=0;
3656: for(k1=1; k1<=m;k1++){
3657: for(i1=1; i1<=ncodemax[k1];i1++){
3658: jj1++;
3659: if (cptcovn > 0) {
3660: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3661: for (cpt=1; cpt<=cptcoveff;cpt++)
3662: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3663: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3664: }
3665: for(cpt=1; cpt<=nlstate;cpt++) {
3666: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3667: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3668: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3669: }
3670: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3671: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3672: true period expectancies (those weighted with period prevalences are also\
3673: drawn in addition to the population based expectancies computed using\
3674: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3675: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3676: } /* end i1 */
3677: }/* End k1 */
3678: fprintf(fichtm,"</ul>");
3679: fflush(fichtm);
3680: }
3681:
3682: /******************* Gnuplot file **************/
3683: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3684:
3685: char dirfileres[132],optfileres[132];
1.130 brouard 3686: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3687: int ng=0;
1.126 brouard 3688: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3689: /* printf("Problem with file %s",optionfilegnuplot); */
3690: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3691: /* } */
3692:
3693: /*#ifdef windows */
3694: fprintf(ficgp,"cd \"%s\" \n",pathc);
3695: /*#endif */
3696: m=pow(2,cptcoveff);
3697:
3698: strcpy(dirfileres,optionfilefiname);
3699: strcpy(optfileres,"vpl");
3700: /* 1eme*/
3701: for (cpt=1; cpt<= nlstate ; cpt ++) {
3702: for (k1=1; k1<= m ; k1 ++) {
3703: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3704: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3705: fprintf(ficgp,"set xlabel \"Age\" \n\
3706: set ylabel \"Probability\" \n\
3707: set ter png small\n\
3708: set size 0.65,0.65\n\
3709: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3710:
3711: for (i=1; i<= nlstate ; i ++) {
3712: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 3713: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 3714: }
3715: 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);
3716: for (i=1; i<= nlstate ; i ++) {
3717: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3718: else fprintf(ficgp," \%%*lf (\%%*lf)");
3719: }
3720: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3721: for (i=1; i<= nlstate ; i ++) {
3722: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3723: else fprintf(ficgp," \%%*lf (\%%*lf)");
3724: }
3725: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3726: }
3727: }
3728: /*2 eme*/
3729:
3730: for (k1=1; k1<= m ; k1 ++) {
3731: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3732: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3733:
3734: for (i=1; i<= nlstate+1 ; i ++) {
3735: k=2*i;
3736: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3737: for (j=1; j<= nlstate+1 ; j ++) {
3738: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3739: else fprintf(ficgp," \%%*lf (\%%*lf)");
3740: }
3741: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3742: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3743: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3744: for (j=1; j<= nlstate+1 ; j ++) {
3745: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3746: else fprintf(ficgp," \%%*lf (\%%*lf)");
3747: }
3748: fprintf(ficgp,"\" t\"\" w l 0,");
3749: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3750: for (j=1; j<= nlstate+1 ; j ++) {
3751: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3752: else fprintf(ficgp," \%%*lf (\%%*lf)");
3753: }
3754: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3755: else fprintf(ficgp,"\" t\"\" w l 0,");
3756: }
3757: }
3758:
3759: /*3eme*/
3760:
3761: for (k1=1; k1<= m ; k1 ++) {
3762: for (cpt=1; cpt<= nlstate ; cpt ++) {
3763: /* k=2+nlstate*(2*cpt-2); */
3764: k=2+(nlstate+1)*(cpt-1);
3765: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3766: fprintf(ficgp,"set ter png small\n\
3767: set size 0.65,0.65\n\
3768: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3769: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3770: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3771: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3772: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3773: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3774: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3775:
3776: */
3777: for (i=1; i< nlstate ; i ++) {
3778: 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);
3779: /* 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);*/
3780:
3781: }
3782: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3783: }
3784: }
3785:
3786: /* CV preval stable (period) */
3787: for (k1=1; k1<= m ; k1 ++) {
3788: for (cpt=1; cpt<=nlstate ; cpt ++) {
3789: k=3;
3790: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3791: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3792: set ter png small\nset size 0.65,0.65\n\
3793: unset log y\n\
3794: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3795:
3796: for (i=1; i< nlstate ; i ++)
3797: fprintf(ficgp,"+$%d",k+i+1);
3798: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3799:
3800: l=3+(nlstate+ndeath)*cpt;
3801: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3802: for (i=1; i< nlstate ; i ++) {
3803: l=3+(nlstate+ndeath)*cpt;
3804: fprintf(ficgp,"+$%d",l+i+1);
3805: }
3806: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3807: }
3808: }
3809:
3810: /* proba elementaires */
3811: for(i=1,jk=1; i <=nlstate; i++){
3812: for(k=1; k <=(nlstate+ndeath); k++){
3813: if (k != i) {
3814: for(j=1; j <=ncovmodel; j++){
3815: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3816: jk++;
3817: fprintf(ficgp,"\n");
3818: }
3819: }
3820: }
3821: }
3822:
3823: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3824: for(jk=1; jk <=m; jk++) {
3825: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3826: if (ng==2)
3827: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3828: else
3829: fprintf(ficgp,"\nset title \"Probability\"\n");
3830: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3831: i=1;
3832: for(k2=1; k2<=nlstate; k2++) {
3833: k3=i;
3834: for(k=1; k<=(nlstate+ndeath); k++) {
3835: if (k != k2){
3836: if(ng==2)
3837: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3838: else
3839: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3840: ij=1;
3841: for(j=3; j <=ncovmodel; j++) {
3842: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3843: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3844: ij++;
3845: }
3846: else
3847: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3848: }
3849: fprintf(ficgp,")/(1");
3850:
3851: for(k1=1; k1 <=nlstate; k1++){
3852: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3853: ij=1;
3854: for(j=3; j <=ncovmodel; j++){
3855: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3856: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3857: ij++;
3858: }
3859: else
3860: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3861: }
3862: fprintf(ficgp,")");
3863: }
3864: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3865: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3866: i=i+ncovmodel;
3867: }
3868: } /* end k */
3869: } /* end k2 */
3870: } /* end jk */
3871: } /* end ng */
3872: fflush(ficgp);
3873: } /* end gnuplot */
3874:
3875:
3876: /*************** Moving average **************/
3877: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3878:
3879: int i, cpt, cptcod;
3880: int modcovmax =1;
3881: int mobilavrange, mob;
3882: double age;
3883:
3884: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3885: a covariate has 2 modalities */
3886: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3887:
3888: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3889: if(mobilav==1) mobilavrange=5; /* default */
3890: else mobilavrange=mobilav;
3891: for (age=bage; age<=fage; age++)
3892: for (i=1; i<=nlstate;i++)
3893: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3894: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3895: /* We keep the original values on the extreme ages bage, fage and for
3896: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3897: we use a 5 terms etc. until the borders are no more concerned.
3898: */
3899: for (mob=3;mob <=mobilavrange;mob=mob+2){
3900: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3901: for (i=1; i<=nlstate;i++){
3902: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3903: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3904: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3905: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3906: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3907: }
3908: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3909: }
3910: }
3911: }/* end age */
3912: }/* end mob */
3913: }else return -1;
3914: return 0;
3915: }/* End movingaverage */
3916:
3917:
3918: /************** Forecasting ******************/
3919: 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){
3920: /* proj1, year, month, day of starting projection
3921: agemin, agemax range of age
3922: dateprev1 dateprev2 range of dates during which prevalence is computed
3923: anproj2 year of en of projection (same day and month as proj1).
3924: */
3925: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3926: int *popage;
3927: double agec; /* generic age */
3928: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3929: double *popeffectif,*popcount;
3930: double ***p3mat;
3931: double ***mobaverage;
3932: char fileresf[FILENAMELENGTH];
3933:
3934: agelim=AGESUP;
3935: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3936:
3937: strcpy(fileresf,"f");
3938: strcat(fileresf,fileres);
3939: if((ficresf=fopen(fileresf,"w"))==NULL) {
3940: printf("Problem with forecast resultfile: %s\n", fileresf);
3941: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3942: }
3943: printf("Computing forecasting: result on file '%s' \n", fileresf);
3944: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3945:
3946: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3947:
3948: if (mobilav!=0) {
3949: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3950: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3951: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3952: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3953: }
3954: }
3955:
3956: stepsize=(int) (stepm+YEARM-1)/YEARM;
3957: if (stepm<=12) stepsize=1;
3958: if(estepm < stepm){
3959: printf ("Problem %d lower than %d\n",estepm, stepm);
3960: }
3961: else hstepm=estepm;
3962:
3963: hstepm=hstepm/stepm;
3964: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3965: fractional in yp1 */
3966: anprojmean=yp;
3967: yp2=modf((yp1*12),&yp);
3968: mprojmean=yp;
3969: yp1=modf((yp2*30.5),&yp);
3970: jprojmean=yp;
3971: if(jprojmean==0) jprojmean=1;
3972: if(mprojmean==0) jprojmean=1;
3973:
3974: i1=cptcoveff;
3975: if (cptcovn < 1){i1=1;}
3976:
3977: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3978:
3979: fprintf(ficresf,"#****** Routine prevforecast **\n");
3980:
3981: /* if (h==(int)(YEARM*yearp)){ */
3982: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3983: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3984: k=k+1;
3985: fprintf(ficresf,"\n#******");
3986: for(j=1;j<=cptcoveff;j++) {
3987: 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]]);
3988: }
3989: fprintf(ficresf,"******\n");
3990: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3991: for(j=1; j<=nlstate+ndeath;j++){
3992: for(i=1; i<=nlstate;i++)
3993: fprintf(ficresf," p%d%d",i,j);
3994: fprintf(ficresf," p.%d",j);
3995: }
3996: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3997: fprintf(ficresf,"\n");
3998: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3999:
4000: for (agec=fage; agec>=(ageminpar-1); agec--){
4001: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4002: nhstepm = nhstepm/hstepm;
4003: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4004: oldm=oldms;savm=savms;
4005: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4006:
4007: for (h=0; h<=nhstepm; h++){
4008: if (h*hstepm/YEARM*stepm ==yearp) {
4009: fprintf(ficresf,"\n");
4010: for(j=1;j<=cptcoveff;j++)
4011: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4012: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4013: }
4014: for(j=1; j<=nlstate+ndeath;j++) {
4015: ppij=0.;
4016: for(i=1; i<=nlstate;i++) {
4017: if (mobilav==1)
4018: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4019: else {
4020: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4021: }
4022: if (h*hstepm/YEARM*stepm== yearp) {
4023: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4024: }
4025: } /* end i */
4026: if (h*hstepm/YEARM*stepm==yearp) {
4027: fprintf(ficresf," %.3f", ppij);
4028: }
4029: }/* end j */
4030: } /* end h */
4031: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4032: } /* end agec */
4033: } /* end yearp */
4034: } /* end cptcod */
4035: } /* end cptcov */
4036:
4037: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4038:
4039: fclose(ficresf);
4040: }
4041:
4042: /************** Forecasting *****not tested NB*************/
4043: 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){
4044:
4045: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4046: int *popage;
4047: double calagedatem, agelim, kk1, kk2;
4048: double *popeffectif,*popcount;
4049: double ***p3mat,***tabpop,***tabpopprev;
4050: double ***mobaverage;
4051: char filerespop[FILENAMELENGTH];
4052:
4053: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4054: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4055: agelim=AGESUP;
4056: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4057:
4058: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4059:
4060:
4061: strcpy(filerespop,"pop");
4062: strcat(filerespop,fileres);
4063: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4064: printf("Problem with forecast resultfile: %s\n", filerespop);
4065: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4066: }
4067: printf("Computing forecasting: result on file '%s' \n", filerespop);
4068: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4069:
4070: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4071:
4072: if (mobilav!=0) {
4073: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4074: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4075: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4076: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4077: }
4078: }
4079:
4080: stepsize=(int) (stepm+YEARM-1)/YEARM;
4081: if (stepm<=12) stepsize=1;
4082:
4083: agelim=AGESUP;
4084:
4085: hstepm=1;
4086: hstepm=hstepm/stepm;
4087:
4088: if (popforecast==1) {
4089: if((ficpop=fopen(popfile,"r"))==NULL) {
4090: printf("Problem with population file : %s\n",popfile);exit(0);
4091: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4092: }
4093: popage=ivector(0,AGESUP);
4094: popeffectif=vector(0,AGESUP);
4095: popcount=vector(0,AGESUP);
4096:
4097: i=1;
4098: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4099:
4100: imx=i;
4101: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4102: }
4103:
4104: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4105: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4106: k=k+1;
4107: fprintf(ficrespop,"\n#******");
4108: for(j=1;j<=cptcoveff;j++) {
4109: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4110: }
4111: fprintf(ficrespop,"******\n");
4112: fprintf(ficrespop,"# Age");
4113: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4114: if (popforecast==1) fprintf(ficrespop," [Population]");
4115:
4116: for (cpt=0; cpt<=0;cpt++) {
4117: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4118:
4119: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4120: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4121: nhstepm = nhstepm/hstepm;
4122:
4123: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4124: oldm=oldms;savm=savms;
4125: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4126:
4127: for (h=0; h<=nhstepm; h++){
4128: if (h==(int) (calagedatem+YEARM*cpt)) {
4129: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4130: }
4131: for(j=1; j<=nlstate+ndeath;j++) {
4132: kk1=0.;kk2=0;
4133: for(i=1; i<=nlstate;i++) {
4134: if (mobilav==1)
4135: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4136: else {
4137: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4138: }
4139: }
4140: if (h==(int)(calagedatem+12*cpt)){
4141: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4142: /*fprintf(ficrespop," %.3f", kk1);
4143: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4144: }
4145: }
4146: for(i=1; i<=nlstate;i++){
4147: kk1=0.;
4148: for(j=1; j<=nlstate;j++){
4149: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4150: }
4151: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4152: }
4153:
4154: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4155: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4156: }
4157: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4158: }
4159: }
4160:
4161: /******/
4162:
4163: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4164: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4165: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4166: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4167: nhstepm = nhstepm/hstepm;
4168:
4169: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4170: oldm=oldms;savm=savms;
4171: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4172: for (h=0; h<=nhstepm; h++){
4173: if (h==(int) (calagedatem+YEARM*cpt)) {
4174: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4175: }
4176: for(j=1; j<=nlstate+ndeath;j++) {
4177: kk1=0.;kk2=0;
4178: for(i=1; i<=nlstate;i++) {
4179: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4180: }
4181: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4182: }
4183: }
4184: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4185: }
4186: }
4187: }
4188: }
4189:
4190: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4191:
4192: if (popforecast==1) {
4193: free_ivector(popage,0,AGESUP);
4194: free_vector(popeffectif,0,AGESUP);
4195: free_vector(popcount,0,AGESUP);
4196: }
4197: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4198: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4199: fclose(ficrespop);
4200: } /* End of popforecast */
4201:
4202: int fileappend(FILE *fichier, char *optionfich)
4203: {
4204: if((fichier=fopen(optionfich,"a"))==NULL) {
4205: printf("Problem with file: %s\n", optionfich);
4206: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4207: return (0);
4208: }
4209: fflush(fichier);
4210: return (1);
4211: }
4212:
4213:
4214: /**************** function prwizard **********************/
4215: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4216: {
4217:
4218: /* Wizard to print covariance matrix template */
4219:
4220: char ca[32], cb[32], cc[32];
4221: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4222: int numlinepar;
4223:
4224: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4225: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4226: for(i=1; i <=nlstate; i++){
4227: jj=0;
4228: for(j=1; j <=nlstate+ndeath; j++){
4229: if(j==i) continue;
4230: jj++;
4231: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4232: printf("%1d%1d",i,j);
4233: fprintf(ficparo,"%1d%1d",i,j);
4234: for(k=1; k<=ncovmodel;k++){
4235: /* printf(" %lf",param[i][j][k]); */
4236: /* fprintf(ficparo," %lf",param[i][j][k]); */
4237: printf(" 0.");
4238: fprintf(ficparo," 0.");
4239: }
4240: printf("\n");
4241: fprintf(ficparo,"\n");
4242: }
4243: }
4244: printf("# Scales (for hessian or gradient estimation)\n");
4245: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4246: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4247: for(i=1; i <=nlstate; i++){
4248: jj=0;
4249: for(j=1; j <=nlstate+ndeath; j++){
4250: if(j==i) continue;
4251: jj++;
4252: fprintf(ficparo,"%1d%1d",i,j);
4253: printf("%1d%1d",i,j);
4254: fflush(stdout);
4255: for(k=1; k<=ncovmodel;k++){
4256: /* printf(" %le",delti3[i][j][k]); */
4257: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4258: printf(" 0.");
4259: fprintf(ficparo," 0.");
4260: }
4261: numlinepar++;
4262: printf("\n");
4263: fprintf(ficparo,"\n");
4264: }
4265: }
4266: printf("# Covariance matrix\n");
4267: /* # 121 Var(a12)\n\ */
4268: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4269: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4270: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4271: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4272: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4273: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4274: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4275: fflush(stdout);
4276: fprintf(ficparo,"# Covariance matrix\n");
4277: /* # 121 Var(a12)\n\ */
4278: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4279: /* # ...\n\ */
4280: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4281:
4282: for(itimes=1;itimes<=2;itimes++){
4283: jj=0;
4284: for(i=1; i <=nlstate; i++){
4285: for(j=1; j <=nlstate+ndeath; j++){
4286: if(j==i) continue;
4287: for(k=1; k<=ncovmodel;k++){
4288: jj++;
4289: ca[0]= k+'a'-1;ca[1]='\0';
4290: if(itimes==1){
4291: printf("#%1d%1d%d",i,j,k);
4292: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4293: }else{
4294: printf("%1d%1d%d",i,j,k);
4295: fprintf(ficparo,"%1d%1d%d",i,j,k);
4296: /* printf(" %.5le",matcov[i][j]); */
4297: }
4298: ll=0;
4299: for(li=1;li <=nlstate; li++){
4300: for(lj=1;lj <=nlstate+ndeath; lj++){
4301: if(lj==li) continue;
4302: for(lk=1;lk<=ncovmodel;lk++){
4303: ll++;
4304: if(ll<=jj){
4305: cb[0]= lk +'a'-1;cb[1]='\0';
4306: if(ll<jj){
4307: if(itimes==1){
4308: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4309: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4310: }else{
4311: printf(" 0.");
4312: fprintf(ficparo," 0.");
4313: }
4314: }else{
4315: if(itimes==1){
4316: printf(" Var(%s%1d%1d)",ca,i,j);
4317: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4318: }else{
4319: printf(" 0.");
4320: fprintf(ficparo," 0.");
4321: }
4322: }
4323: }
4324: } /* end lk */
4325: } /* end lj */
4326: } /* end li */
4327: printf("\n");
4328: fprintf(ficparo,"\n");
4329: numlinepar++;
4330: } /* end k*/
4331: } /*end j */
4332: } /* end i */
4333: } /* end itimes */
4334:
4335: } /* end of prwizard */
4336: /******************* Gompertz Likelihood ******************************/
4337: double gompertz(double x[])
4338: {
4339: double A,B,L=0.0,sump=0.,num=0.;
4340: int i,n=0; /* n is the size of the sample */
4341:
4342: for (i=0;i<=imx-1 ; i++) {
4343: sump=sump+weight[i];
4344: /* sump=sump+1;*/
4345: num=num+1;
4346: }
4347:
4348:
4349: /* for (i=0; i<=imx; i++)
4350: 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]);*/
4351:
4352: for (i=1;i<=imx ; i++)
4353: {
4354: if (cens[i] == 1 && wav[i]>1)
4355: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4356:
4357: if (cens[i] == 0 && wav[i]>1)
4358: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4359: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4360:
4361: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4362: if (wav[i] > 1 ) { /* ??? */
4363: L=L+A*weight[i];
4364: /* 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]);*/
4365: }
4366: }
4367:
4368: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4369:
4370: return -2*L*num/sump;
4371: }
4372:
4373: /******************* Printing html file ***********/
4374: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4375: int lastpass, int stepm, int weightopt, char model[],\
4376: int imx, double p[],double **matcov,double agemortsup){
4377: int i,k;
4378:
4379: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4380: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4381: for (i=1;i<=2;i++)
4382: 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]));
4383: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4384: fprintf(fichtm,"</ul>");
4385:
4386: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4387:
4388: 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>");
4389:
4390: for (k=agegomp;k<(agemortsup-2);k++)
4391: 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]);
4392:
4393:
4394: fflush(fichtm);
4395: }
4396:
4397: /******************* Gnuplot file **************/
4398: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4399:
4400: char dirfileres[132],optfileres[132];
4401: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4402: int ng;
4403:
4404:
4405: /*#ifdef windows */
4406: fprintf(ficgp,"cd \"%s\" \n",pathc);
4407: /*#endif */
4408:
4409:
4410: strcpy(dirfileres,optionfilefiname);
4411: strcpy(optfileres,"vpl");
4412: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4413: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4414: fprintf(ficgp, "set ter png small\n set log y\n");
4415: fprintf(ficgp, "set size 0.65,0.65\n");
4416: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4417:
4418: }
4419:
4420:
4421:
4422:
4423:
4424: /***********************************************/
4425: /**************** Main Program *****************/
4426: /***********************************************/
4427:
4428: int main(int argc, char *argv[])
4429: {
4430: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4431: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4432: int linei, month, year,iout;
4433: int jj, ll, li, lj, lk, imk;
4434: int numlinepar=0; /* Current linenumber of parameter file */
4435: int itimes;
4436: int NDIM=2;
1.128 brouard 4437: int vpopbased=0;
1.126 brouard 4438:
4439: char ca[32], cb[32], cc[32];
4440: char dummy[]=" ";
4441: /* FILE *fichtm; *//* Html File */
4442: /* FILE *ficgp;*/ /*Gnuplot File */
4443: struct stat info;
4444: double agedeb, agefin,hf;
4445: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4446:
4447: double fret;
4448: double **xi,tmp,delta;
4449:
4450: double dum; /* Dummy variable */
4451: double ***p3mat;
4452: double ***mobaverage;
4453: int *indx;
4454: char line[MAXLINE], linepar[MAXLINE];
1.132 brouard 4455: char linetmp[MAXLINE];
4456: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.126 brouard 4457: char pathr[MAXLINE], pathimach[MAXLINE];
4458: char **bp, *tok, *val; /* pathtot */
4459: int firstobs=1, lastobs=10;
4460: int sdeb, sfin; /* Status at beginning and end */
4461: int c, h , cpt,l;
4462: int ju,jl, mi;
4463: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4464: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4465: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4466: int mobilav=0,popforecast=0;
4467: int hstepm, nhstepm;
4468: int agemortsup;
4469: float sumlpop=0.;
4470: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4471: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4472:
4473: double bage, fage, age, agelim, agebase;
4474: double ftolpl=FTOL;
4475: double **prlim;
4476: double *severity;
4477: double ***param; /* Matrix of parameters */
4478: double *p;
4479: double **matcov; /* Matrix of covariance */
4480: double ***delti3; /* Scale */
4481: double *delti; /* Scale */
4482: double ***eij, ***vareij;
4483: double **varpl; /* Variances of prevalence limits by age */
4484: double *epj, vepp;
4485: double kk1, kk2;
4486: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4487: double **ximort;
4488: char *alph[]={"a","a","b","c","d","e"}, str[4];
4489: int *dcwave;
4490:
4491: char z[1]="c", occ;
4492:
4493: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4494: char *strt, strtend[80];
4495: char *stratrunc;
4496: int lstra;
4497:
4498: long total_usecs;
4499:
4500: /* setlocale (LC_ALL, ""); */
4501: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4502: /* textdomain (PACKAGE); */
4503: /* setlocale (LC_CTYPE, ""); */
4504: /* setlocale (LC_MESSAGES, ""); */
4505:
4506: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4507: (void) gettimeofday(&start_time,&tzp);
4508: curr_time=start_time;
4509: tm = *localtime(&start_time.tv_sec);
4510: tmg = *gmtime(&start_time.tv_sec);
4511: strcpy(strstart,asctime(&tm));
4512:
4513: /* printf("Localtime (at start)=%s",strstart); */
4514: /* tp.tv_sec = tp.tv_sec +86400; */
4515: /* tm = *localtime(&start_time.tv_sec); */
4516: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4517: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4518: /* tmg.tm_hour=tmg.tm_hour + 1; */
4519: /* tp.tv_sec = mktime(&tmg); */
4520: /* strt=asctime(&tmg); */
4521: /* printf("Time(after) =%s",strstart); */
4522: /* (void) time (&time_value);
4523: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4524: * tm = *localtime(&time_value);
4525: * strstart=asctime(&tm);
4526: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4527: */
4528:
4529: nberr=0; /* Number of errors and warnings */
4530: nbwarn=0;
4531: getcwd(pathcd, size);
4532:
4533: printf("\n%s\n%s",version,fullversion);
4534: if(argc <=1){
4535: printf("\nEnter the parameter file name: ");
4536: fgets(pathr,FILENAMELENGTH,stdin);
4537: i=strlen(pathr);
4538: if(pathr[i-1]=='\n')
4539: pathr[i-1]='\0';
4540: for (tok = pathr; tok != NULL; ){
4541: printf("Pathr |%s|\n",pathr);
4542: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4543: printf("val= |%s| pathr=%s\n",val,pathr);
4544: strcpy (pathtot, val);
4545: if(pathr[0] == '\0') break; /* Dirty */
4546: }
4547: }
4548: else{
4549: strcpy(pathtot,argv[1]);
4550: }
4551: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4552: /*cygwin_split_path(pathtot,path,optionfile);
4553: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4554: /* cutv(path,optionfile,pathtot,'\\');*/
4555:
4556: /* Split argv[0], imach program to get pathimach */
4557: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4558: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4559: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4560: /* strcpy(pathimach,argv[0]); */
4561: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4562: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4563: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4564: chdir(path); /* Can be a relative path */
4565: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4566: printf("Current directory %s!\n",pathcd);
4567: strcpy(command,"mkdir ");
4568: strcat(command,optionfilefiname);
4569: if((outcmd=system(command)) != 0){
4570: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4571: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4572: /* fclose(ficlog); */
4573: /* exit(1); */
4574: }
4575: /* if((imk=mkdir(optionfilefiname))<0){ */
4576: /* perror("mkdir"); */
4577: /* } */
4578:
4579: /*-------- arguments in the command line --------*/
4580:
4581: /* Log file */
4582: strcat(filelog, optionfilefiname);
4583: strcat(filelog,".log"); /* */
4584: if((ficlog=fopen(filelog,"w"))==NULL) {
4585: printf("Problem with logfile %s\n",filelog);
4586: goto end;
4587: }
4588: fprintf(ficlog,"Log filename:%s\n",filelog);
4589: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4590: fprintf(ficlog,"\nEnter the parameter file name: \n");
4591: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4592: path=%s \n\
4593: optionfile=%s\n\
4594: optionfilext=%s\n\
4595: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4596:
4597: printf("Local time (at start):%s",strstart);
4598: fprintf(ficlog,"Local time (at start): %s",strstart);
4599: fflush(ficlog);
4600: /* (void) gettimeofday(&curr_time,&tzp); */
4601: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4602:
4603: /* */
4604: strcpy(fileres,"r");
4605: strcat(fileres, optionfilefiname);
4606: strcat(fileres,".txt"); /* Other files have txt extension */
4607:
4608: /*---------arguments file --------*/
4609:
4610: if((ficpar=fopen(optionfile,"r"))==NULL) {
4611: printf("Problem with optionfile %s\n",optionfile);
4612: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4613: fflush(ficlog);
4614: goto end;
4615: }
4616:
4617:
4618:
4619: strcpy(filereso,"o");
4620: strcat(filereso,fileres);
4621: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4622: printf("Problem with Output resultfile: %s\n", filereso);
4623: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4624: fflush(ficlog);
4625: goto end;
4626: }
4627:
4628: /* Reads comments: lines beginning with '#' */
4629: numlinepar=0;
4630: while((c=getc(ficpar))=='#' && c!= EOF){
4631: ungetc(c,ficpar);
4632: fgets(line, MAXLINE, ficpar);
4633: numlinepar++;
4634: puts(line);
4635: fputs(line,ficparo);
4636: fputs(line,ficlog);
4637: }
4638: ungetc(c,ficpar);
4639:
4640: 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);
4641: numlinepar++;
4642: 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);
4643: 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);
4644: 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);
4645: fflush(ficlog);
4646: while((c=getc(ficpar))=='#' && c!= EOF){
4647: ungetc(c,ficpar);
4648: fgets(line, MAXLINE, ficpar);
4649: numlinepar++;
4650: puts(line);
4651: fputs(line,ficparo);
4652: fputs(line,ficlog);
4653: }
4654: ungetc(c,ficpar);
4655:
4656:
4657: covar=matrix(0,NCOVMAX,1,n);
4658: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4659: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
1.132 brouard 4660: /* where is ncovprod ?*/
4661: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
1.126 brouard 4662: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 ! brouard 4663: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
! 4664: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 4665: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
4666: 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);
4667: 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);
4668: fflush(stdout);
4669: fclose (ficlog);
4670: goto end;
4671: }
1.126 brouard 4672: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4673: delti=delti3[1][1];
4674: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4675: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4676: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4677: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4678: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4679: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4680: fclose (ficparo);
4681: fclose (ficlog);
4682: goto end;
4683: exit(0);
4684: }
4685: else if(mle==-3) {
4686: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4687: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4688: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4689: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4690: matcov=matrix(1,npar,1,npar);
4691: }
4692: else{
4693: /* Read guess parameters */
4694: /* Reads comments: lines beginning with '#' */
4695: while((c=getc(ficpar))=='#' && c!= EOF){
4696: ungetc(c,ficpar);
4697: fgets(line, MAXLINE, ficpar);
4698: numlinepar++;
4699: puts(line);
4700: fputs(line,ficparo);
4701: fputs(line,ficlog);
4702: }
4703: ungetc(c,ficpar);
4704:
4705: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4706: for(i=1; i <=nlstate; i++){
4707: j=0;
4708: for(jj=1; jj <=nlstate+ndeath; jj++){
4709: if(jj==i) continue;
4710: j++;
4711: fscanf(ficpar,"%1d%1d",&i1,&j1);
4712: if ((i1 != i) && (j1 != j)){
4713: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4714: It might be a problem of design; if ncovcol and the model are correct\n \
4715: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
4716: exit(1);
4717: }
4718: fprintf(ficparo,"%1d%1d",i1,j1);
4719: if(mle==1)
4720: printf("%1d%1d",i,j);
4721: fprintf(ficlog,"%1d%1d",i,j);
4722: for(k=1; k<=ncovmodel;k++){
4723: fscanf(ficpar," %lf",¶m[i][j][k]);
4724: if(mle==1){
4725: printf(" %lf",param[i][j][k]);
4726: fprintf(ficlog," %lf",param[i][j][k]);
4727: }
4728: else
4729: fprintf(ficlog," %lf",param[i][j][k]);
4730: fprintf(ficparo," %lf",param[i][j][k]);
4731: }
4732: fscanf(ficpar,"\n");
4733: numlinepar++;
4734: if(mle==1)
4735: printf("\n");
4736: fprintf(ficlog,"\n");
4737: fprintf(ficparo,"\n");
4738: }
4739: }
4740: fflush(ficlog);
4741:
4742: p=param[1][1];
4743:
4744: /* Reads comments: lines beginning with '#' */
4745: while((c=getc(ficpar))=='#' && c!= EOF){
4746: ungetc(c,ficpar);
4747: fgets(line, MAXLINE, ficpar);
4748: numlinepar++;
4749: puts(line);
4750: fputs(line,ficparo);
4751: fputs(line,ficlog);
4752: }
4753: ungetc(c,ficpar);
4754:
4755: for(i=1; i <=nlstate; i++){
4756: for(j=1; j <=nlstate+ndeath-1; j++){
4757: fscanf(ficpar,"%1d%1d",&i1,&j1);
4758: if ((i1-i)*(j1-j)!=0){
4759: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4760: exit(1);
4761: }
4762: printf("%1d%1d",i,j);
4763: fprintf(ficparo,"%1d%1d",i1,j1);
4764: fprintf(ficlog,"%1d%1d",i1,j1);
4765: for(k=1; k<=ncovmodel;k++){
4766: fscanf(ficpar,"%le",&delti3[i][j][k]);
4767: printf(" %le",delti3[i][j][k]);
4768: fprintf(ficparo," %le",delti3[i][j][k]);
4769: fprintf(ficlog," %le",delti3[i][j][k]);
4770: }
4771: fscanf(ficpar,"\n");
4772: numlinepar++;
4773: printf("\n");
4774: fprintf(ficparo,"\n");
4775: fprintf(ficlog,"\n");
4776: }
4777: }
4778: fflush(ficlog);
4779:
4780: delti=delti3[1][1];
4781:
4782:
4783: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4784:
4785: /* Reads comments: lines beginning with '#' */
4786: while((c=getc(ficpar))=='#' && c!= EOF){
4787: ungetc(c,ficpar);
4788: fgets(line, MAXLINE, ficpar);
4789: numlinepar++;
4790: puts(line);
4791: fputs(line,ficparo);
4792: fputs(line,ficlog);
4793: }
4794: ungetc(c,ficpar);
4795:
4796: matcov=matrix(1,npar,1,npar);
1.131 brouard 4797: for(i=1; i <=npar; i++)
4798: for(j=1; j <=npar; j++) matcov[i][j]=0.;
4799:
1.126 brouard 4800: for(i=1; i <=npar; i++){
4801: fscanf(ficpar,"%s",&str);
4802: if(mle==1)
4803: printf("%s",str);
4804: fprintf(ficlog,"%s",str);
4805: fprintf(ficparo,"%s",str);
4806: for(j=1; j <=i; j++){
4807: fscanf(ficpar," %le",&matcov[i][j]);
4808: if(mle==1){
4809: printf(" %.5le",matcov[i][j]);
4810: }
4811: fprintf(ficlog," %.5le",matcov[i][j]);
4812: fprintf(ficparo," %.5le",matcov[i][j]);
4813: }
4814: fscanf(ficpar,"\n");
4815: numlinepar++;
4816: if(mle==1)
4817: printf("\n");
4818: fprintf(ficlog,"\n");
4819: fprintf(ficparo,"\n");
4820: }
4821: for(i=1; i <=npar; i++)
4822: for(j=i+1;j<=npar;j++)
4823: matcov[i][j]=matcov[j][i];
4824:
4825: if(mle==1)
4826: printf("\n");
4827: fprintf(ficlog,"\n");
4828:
4829: fflush(ficlog);
4830:
4831: /*-------- Rewriting parameter file ----------*/
4832: strcpy(rfileres,"r"); /* "Rparameterfile */
4833: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4834: strcat(rfileres,"."); /* */
4835: strcat(rfileres,optionfilext); /* Other files have txt extension */
4836: if((ficres =fopen(rfileres,"w"))==NULL) {
4837: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4838: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4839: }
4840: fprintf(ficres,"#%s\n",version);
4841: } /* End of mle != -3 */
4842:
4843: /*-------- data file ----------*/
4844: if((fic=fopen(datafile,"r"))==NULL) {
4845: printf("Problem while opening datafile: %s\n", datafile);goto end;
4846: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4847: }
4848:
4849: n= lastobs;
4850: severity = vector(1,maxwav);
4851: outcome=imatrix(1,maxwav+1,1,n);
4852: num=lvector(1,n);
4853: moisnais=vector(1,n);
4854: annais=vector(1,n);
4855: moisdc=vector(1,n);
4856: andc=vector(1,n);
4857: agedc=vector(1,n);
4858: cod=ivector(1,n);
4859: weight=vector(1,n);
4860: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4861: mint=matrix(1,maxwav,1,n);
4862: anint=matrix(1,maxwav,1,n);
1.131 brouard 4863: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 4864: tab=ivector(1,NCOVMAX);
4865: ncodemax=ivector(1,8);
4866:
4867: i=1;
4868: linei=0;
4869: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4870: linei=linei+1;
4871: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4872: if(line[j] == '\t')
4873: line[j] = ' ';
4874: }
4875: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4876: ;
4877: };
4878: line[j+1]=0; /* Trims blanks at end of line */
4879: if(line[0]=='#'){
4880: fprintf(ficlog,"Comment line\n%s\n",line);
4881: printf("Comment line\n%s\n",line);
4882: continue;
4883: }
1.132 brouard 4884: trimbb(linetmp,line); /* Trims multiple blanks in line */
4885: for (j=0; line[j]!='\0';j++){
4886: line[j]=linetmp[j];
4887: }
4888:
1.126 brouard 4889:
4890: for (j=maxwav;j>=1;j--){
4891: cutv(stra, strb,line,' ');
1.131 brouard 4892: if(strb[0]=='.') { /* Missing status */
4893: lval=-1;
4894: }else{
4895: errno=0;
4896: lval=strtol(strb,&endptr,10);
1.126 brouard 4897: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
1.131 brouard 4898: if( strb[0]=='\0' || (*endptr != '\0')){
4899: 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);
4900: 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);
4901: goto end;
4902: }
1.126 brouard 4903: }
4904: s[j][i]=lval;
4905:
4906: strcpy(line,stra);
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{
1.131 brouard 4914: 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);
4915: 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);
4916: goto end;
1.126 brouard 4917: }
4918: anint[j][i]= (double) year;
4919: mint[j][i]= (double)month;
4920: strcpy(line,stra);
4921: } /* ENd Waves */
4922:
4923: cutv(stra, strb,line,' ');
4924: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4925: }
4926: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4927: month=99;
4928: year=9999;
4929: }else{
1.131 brouard 4930: 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);
4931: 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);
4932: goto end;
1.126 brouard 4933: }
4934: andc[i]=(double) year;
4935: moisdc[i]=(double) month;
4936: strcpy(line,stra);
4937:
4938: cutv(stra, strb,line,' ');
4939: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4940: }
4941: else if(iout=sscanf(strb,"%s.") != 0){
4942: month=99;
4943: year=9999;
4944: }else{
4945: 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 4946: 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);
4947: goto end;
1.126 brouard 4948: }
4949: annais[i]=(double)(year);
4950: moisnais[i]=(double)(month);
4951: strcpy(line,stra);
4952:
4953: cutv(stra, strb,line,' ');
4954: errno=0;
4955: dval=strtod(strb,&endptr);
4956: if( strb[0]=='\0' || (*endptr != '\0')){
4957: 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 4958: 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);
4959: fflush(ficlog);
4960: goto end;
1.126 brouard 4961: }
4962: weight[i]=dval;
4963: strcpy(line,stra);
4964:
4965: for (j=ncovcol;j>=1;j--){
4966: cutv(stra, strb,line,' ');
1.131 brouard 4967: if(strb[0]=='.') { /* Missing status */
4968: lval=-1;
4969: }else{
4970: errno=0;
4971: lval=strtol(strb,&endptr,10);
4972: if( strb[0]=='\0' || (*endptr != '\0')){
4973: 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);
4974: 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);
4975: goto end;
4976: }
1.126 brouard 4977: }
4978: if(lval <-1 || lval >1){
4979: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4980: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4981: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4982: For example, for multinomial values like 1, 2 and 3,\n \
4983: build V1=0 V2=0 for the reference value (1),\n \
4984: V1=1 V2=0 for (2) \n \
4985: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4986: output of IMaCh is often meaningless.\n \
4987: Exiting.\n",lval,linei, i,line,j);
1.131 brouard 4988: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4989: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4990: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4991: For example, for multinomial values like 1, 2 and 3,\n \
4992: build V1=0 V2=0 for the reference value (1),\n \
4993: V1=1 V2=0 for (2) \n \
4994: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4995: output of IMaCh is often meaningless.\n \
4996: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.129 lievre 4997: goto end;
1.126 brouard 4998: }
4999: covar[j][i]=(double)(lval);
5000: strcpy(line,stra);
1.129 lievre 5001: }
1.126 brouard 5002: lstra=strlen(stra);
1.129 lievre 5003:
1.126 brouard 5004: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5005: stratrunc = &(stra[lstra-9]);
5006: num[i]=atol(stratrunc);
5007: }
5008: else
5009: num[i]=atol(stra);
5010: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5011: 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;}*/
5012:
5013: i=i+1;
5014: } /* End loop reading data */
5015: fclose(fic);
5016: /* printf("ii=%d", ij);
5017: scanf("%d",i);*/
5018: imx=i-1; /* Number of individuals */
5019:
5020: /* for (i=1; i<=imx; i++){
5021: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
5022: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
5023: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
5024: }*/
5025: /* for (i=1; i<=imx; i++){
5026: if (s[4][i]==9) s[4][i]=-1;
5027: 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]));}*/
5028:
5029: /* for (i=1; i<=imx; i++) */
5030:
5031: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
5032: else weight[i]=1;*/
5033:
5034: /* Calculation of the number of parameters from char model */
1.131 brouard 5035: 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 5036: Tprod=ivector(1,15);
5037: Tvaraff=ivector(1,15);
5038: Tvard=imatrix(1,15,1,2);
5039: Tage=ivector(1,15);
5040:
5041: if (strlen(model) >1){ /* If there is at least 1 covariate */
5042: j=0, j1=0, k1=1, k2=1;
5043: j=nbocc(model,'+'); /* j=Number of '+' */
5044: j1=nbocc(model,'*'); /* j1=Number of '*' */
1.130 brouard 5045: cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
5046: cptcovprod=j1; /*Number of products V1*V2 =1 */
1.126 brouard 5047:
5048: strcpy(modelsav,model);
5049: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
5050: printf("Error. Non available option model=%s ",model);
1.131 brouard 5051: fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
1.126 brouard 5052: goto end;
5053: }
5054:
5055: /* This loop fills the array Tvar from the string 'model'.*/
1.130 brouard 5056: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.126 brouard 5057: for(i=(j+1); i>=1;i--){
1.130 brouard 5058: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5059: modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4
5060: stra=V2
5061: */
1.126 brouard 5062: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5063: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5064: /*scanf("%d",i);*/
1.130 brouard 5065: if (strchr(strb,'*')) { /* Model includes a product V1+V3*age+V2 strb=V3*age*/
5066: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
1.126 brouard 5067: if (strcmp(strc,"age")==0) { /* Vn*age */
5068: cptcovprod--;
5069: cutv(strb,stre,strd,'V');
1.130 brouard 5070: Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */
1.132 brouard 5071: cptcovage++; /* Sums the number of covariates including age as a product */
1.130 brouard 5072: Tage[cptcovage]=i; /* Tage[1] =2 */
5073: /*printf("stre=%s ", stre);*/
1.126 brouard 5074: }
5075: else if (strcmp(strd,"age")==0) { /* or age*Vn */
5076: cptcovprod--;
5077: cutv(strb,stre,strc,'V');
5078: Tvar[i]=atoi(stre);
5079: cptcovage++;
5080: Tage[cptcovage]=i;
5081: }
1.130 brouard 5082: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
5083: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5084: Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
5085: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
1.126 brouard 5086: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
1.130 brouard 5087: Tprod[k1]=i; /* Tprod[1] */
1.126 brouard 5088: Tvard[k1][1]=atoi(strc); /* m*/
5089: Tvard[k1][2]=atoi(stre); /* n */
5090: Tvar[cptcovn+k2]=Tvard[k1][1];
5091: Tvar[cptcovn+k2+1]=Tvard[k1][2];
5092: for (k=1; k<=lastobs;k++)
5093: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
5094: k1++;
5095: k2=k2+2;
5096: }
5097: }
5098: else { /* no more sum */
5099: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5100: /* scanf("%d",i);*/
5101: cutv(strd,strc,strb,'V');
5102: Tvar[i]=atoi(strc);
5103: }
1.130 brouard 5104: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
1.126 brouard 5105: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5106: scanf("%d",i);*/
5107: } /* end of loop + */
5108: } /* end model */
5109:
5110: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5111: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5112:
5113: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5114: printf("cptcovprod=%d ", cptcovprod);
5115: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5116:
5117: scanf("%d ",i);*/
5118:
5119: /* if(mle==1){*/
5120: if (weightopt != 1) { /* Maximisation without weights*/
5121: for(i=1;i<=n;i++) weight[i]=1.0;
5122: }
5123: /*-calculation of age at interview from date of interview and age at death -*/
5124: agev=matrix(1,maxwav,1,imx);
5125:
5126: for (i=1; i<=imx; i++) {
5127: for(m=2; (m<= maxwav); m++) {
5128: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5129: anint[m][i]=9999;
5130: s[m][i]=-1;
5131: }
5132: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5133: nberr++;
5134: 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);
5135: 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);
5136: s[m][i]=-1;
5137: }
5138: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5139: nberr++;
5140: 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]);
5141: 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]);
5142: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5143: }
5144: }
5145: }
5146:
5147: for (i=1; i<=imx; i++) {
5148: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5149: for(m=firstpass; (m<= lastpass); m++){
5150: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5151: if (s[m][i] >= nlstate+1) {
5152: if(agedc[i]>0)
5153: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5154: agev[m][i]=agedc[i];
5155: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5156: else {
5157: if ((int)andc[i]!=9999){
5158: nbwarn++;
5159: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5160: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5161: agev[m][i]=-1;
5162: }
5163: }
5164: }
5165: else if(s[m][i] !=9){ /* Standard case, age in fractional
5166: years but with the precision of a month */
5167: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5168: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5169: agev[m][i]=1;
5170: else if(agev[m][i] <agemin){
5171: agemin=agev[m][i];
5172: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5173: }
5174: else if(agev[m][i] >agemax){
5175: agemax=agev[m][i];
5176: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5177: }
5178: /*agev[m][i]=anint[m][i]-annais[i];*/
5179: /* agev[m][i] = age[i]+2*m;*/
5180: }
5181: else { /* =9 */
5182: agev[m][i]=1;
5183: s[m][i]=-1;
5184: }
5185: }
5186: else /*= 0 Unknown */
5187: agev[m][i]=1;
5188: }
5189:
5190: }
5191: for (i=1; i<=imx; i++) {
5192: for(m=firstpass; (m<=lastpass); m++){
5193: if (s[m][i] > (nlstate+ndeath)) {
5194: nberr++;
5195: 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);
5196: 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);
5197: goto end;
5198: }
5199: }
5200: }
5201:
5202: /*for (i=1; i<=imx; i++){
5203: for (m=firstpass; (m<lastpass); m++){
5204: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5205: }
5206:
5207: }*/
5208:
5209:
5210: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5211: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5212:
5213: agegomp=(int)agemin;
5214: free_vector(severity,1,maxwav);
5215: free_imatrix(outcome,1,maxwav+1,1,n);
5216: free_vector(moisnais,1,n);
5217: free_vector(annais,1,n);
5218: /* free_matrix(mint,1,maxwav,1,n);
5219: free_matrix(anint,1,maxwav,1,n);*/
5220: free_vector(moisdc,1,n);
5221: free_vector(andc,1,n);
5222:
5223:
5224: wav=ivector(1,imx);
5225: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5226: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5227: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5228:
5229: /* Concatenates waves */
5230: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5231:
5232: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5233:
5234: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5235: ncodemax[1]=1;
5236: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5237:
5238: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5239: the estimations*/
5240: h=0;
5241: m=pow(2,cptcoveff);
5242:
1.131 brouard 5243: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5244: 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 */
5245: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
5246: 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 5247: h++;
1.131 brouard 5248: if (h>m)
5249: h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
1.130 brouard 5250: 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 5251: }
5252: }
5253: }
5254: }
5255: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5256: codtab[1][2]=1;codtab[2][2]=2; */
5257: /* for(i=1; i <=m ;i++){
5258: for(k=1; k <=cptcovn; k++){
1.131 brouard 5259: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5260: }
5261: printf("\n");
5262: }
5263: scanf("%d",i);*/
5264:
5265: /*------------ gnuplot -------------*/
5266: strcpy(optionfilegnuplot,optionfilefiname);
5267: if(mle==-3)
5268: strcat(optionfilegnuplot,"-mort");
5269: strcat(optionfilegnuplot,".gp");
5270:
5271: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5272: printf("Problem with file %s",optionfilegnuplot);
5273: }
5274: else{
5275: fprintf(ficgp,"\n# %s\n", version);
5276: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5277: fprintf(ficgp,"set missing 'NaNq'\n");
5278: }
5279: /* fclose(ficgp);*/
5280: /*--------- index.htm --------*/
5281:
5282: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5283: if(mle==-3)
5284: strcat(optionfilehtm,"-mort");
5285: strcat(optionfilehtm,".htm");
5286: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 5287: printf("Problem with %s \n",optionfilehtm);
5288: exit(0);
1.126 brouard 5289: }
5290:
5291: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5292: strcat(optionfilehtmcov,"-cov.htm");
5293: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5294: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5295: }
5296: else{
5297: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5298: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5299: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5300: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5301: }
5302:
5303: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5304: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5305: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5306: \n\
5307: <hr size=\"2\" color=\"#EC5E5E\">\
5308: <ul><li><h4>Parameter files</h4>\n\
5309: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5310: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5311: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5312: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5313: - Date and time at start: %s</ul>\n",\
5314: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5315: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5316: fileres,fileres,\
5317: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5318: fflush(fichtm);
5319:
5320: strcpy(pathr,path);
5321: strcat(pathr,optionfilefiname);
5322: chdir(optionfilefiname); /* Move to directory named optionfile */
5323:
5324: /* Calculates basic frequencies. Computes observed prevalence at single age
5325: and prints on file fileres'p'. */
5326: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5327:
5328: fprintf(fichtm,"\n");
5329: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5330: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5331: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5332: imx,agemin,agemax,jmin,jmax,jmean);
5333: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5334: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5335: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5336: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5337: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5338:
5339:
5340: /* For Powell, parameters are in a vector p[] starting at p[1]
5341: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5342: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5343:
5344: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5345:
5346: if (mle==-3){
5347: ximort=matrix(1,NDIM,1,NDIM);
5348: cens=ivector(1,n);
5349: ageexmed=vector(1,n);
5350: agecens=vector(1,n);
5351: dcwave=ivector(1,n);
5352:
5353: for (i=1; i<=imx; i++){
5354: dcwave[i]=-1;
5355: for (m=firstpass; m<=lastpass; m++)
5356: if (s[m][i]>nlstate) {
5357: dcwave[i]=m;
5358: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5359: break;
5360: }
5361: }
5362:
5363: for (i=1; i<=imx; i++) {
5364: if (wav[i]>0){
5365: ageexmed[i]=agev[mw[1][i]][i];
5366: j=wav[i];
5367: agecens[i]=1.;
5368:
5369: if (ageexmed[i]> 1 && wav[i] > 0){
5370: agecens[i]=agev[mw[j][i]][i];
5371: cens[i]= 1;
5372: }else if (ageexmed[i]< 1)
5373: cens[i]= -1;
5374: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5375: cens[i]=0 ;
5376: }
5377: else cens[i]=-1;
5378: }
5379:
5380: for (i=1;i<=NDIM;i++) {
5381: for (j=1;j<=NDIM;j++)
5382: ximort[i][j]=(i == j ? 1.0 : 0.0);
5383: }
5384:
5385: p[1]=0.0268; p[NDIM]=0.083;
5386: /*printf("%lf %lf", p[1], p[2]);*/
5387:
5388:
5389: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5390: strcpy(filerespow,"pow-mort");
5391: strcat(filerespow,fileres);
5392: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5393: printf("Problem with resultfile: %s\n", filerespow);
5394: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5395: }
5396: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5397: /* for (i=1;i<=nlstate;i++)
5398: for(j=1;j<=nlstate+ndeath;j++)
5399: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5400: */
5401: fprintf(ficrespow,"\n");
5402:
5403: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5404: fclose(ficrespow);
5405:
5406: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5407:
5408: for(i=1; i <=NDIM; i++)
5409: for(j=i+1;j<=NDIM;j++)
5410: matcov[i][j]=matcov[j][i];
5411:
5412: printf("\nCovariance matrix\n ");
5413: for(i=1; i <=NDIM; i++) {
5414: for(j=1;j<=NDIM;j++){
5415: printf("%f ",matcov[i][j]);
5416: }
5417: printf("\n ");
5418: }
5419:
5420: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5421: for (i=1;i<=NDIM;i++)
5422: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5423:
5424: lsurv=vector(1,AGESUP);
5425: lpop=vector(1,AGESUP);
5426: tpop=vector(1,AGESUP);
5427: lsurv[agegomp]=100000;
5428:
5429: for (k=agegomp;k<=AGESUP;k++) {
5430: agemortsup=k;
5431: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5432: }
5433:
5434: for (k=agegomp;k<agemortsup;k++)
5435: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5436:
5437: for (k=agegomp;k<agemortsup;k++){
5438: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5439: sumlpop=sumlpop+lpop[k];
5440: }
5441:
5442: tpop[agegomp]=sumlpop;
5443: for (k=agegomp;k<(agemortsup-3);k++){
5444: /* tpop[k+1]=2;*/
5445: tpop[k+1]=tpop[k]-lpop[k];
5446: }
5447:
5448:
5449: printf("\nAge lx qx dx Lx Tx e(x)\n");
5450: for (k=agegomp;k<(agemortsup-2);k++)
5451: 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]);
5452:
5453:
5454: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5455: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5456:
5457: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5458: stepm, weightopt,\
5459: model,imx,p,matcov,agemortsup);
5460:
5461: free_vector(lsurv,1,AGESUP);
5462: free_vector(lpop,1,AGESUP);
5463: free_vector(tpop,1,AGESUP);
5464: } /* Endof if mle==-3 */
5465:
5466: else{ /* For mle >=1 */
1.132 brouard 5467: globpr=0;/* debug */
5468: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 5469: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5470: for (k=1; k<=npar;k++)
5471: printf(" %d %8.5f",k,p[k]);
5472: printf("\n");
5473: globpr=1; /* to print the contributions */
5474: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5475: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5476: for (k=1; k<=npar;k++)
5477: printf(" %d %8.5f",k,p[k]);
5478: printf("\n");
5479: if(mle>=1){ /* Could be 1 or 2 */
5480: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5481: }
5482:
5483: /*--------- results files --------------*/
5484: 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);
5485:
5486:
5487: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5488: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5489: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5490: for(i=1,jk=1; i <=nlstate; i++){
5491: for(k=1; k <=(nlstate+ndeath); k++){
5492: if (k != i) {
5493: printf("%d%d ",i,k);
5494: fprintf(ficlog,"%d%d ",i,k);
5495: fprintf(ficres,"%1d%1d ",i,k);
5496: for(j=1; j <=ncovmodel; j++){
5497: printf("%lf ",p[jk]);
5498: fprintf(ficlog,"%lf ",p[jk]);
5499: fprintf(ficres,"%lf ",p[jk]);
5500: jk++;
5501: }
5502: printf("\n");
5503: fprintf(ficlog,"\n");
5504: fprintf(ficres,"\n");
5505: }
5506: }
5507: }
5508: if(mle!=0){
5509: /* Computing hessian and covariance matrix */
5510: ftolhess=ftol; /* Usually correct */
5511: hesscov(matcov, p, npar, delti, ftolhess, func);
5512: }
5513: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5514: printf("# Scales (for hessian or gradient estimation)\n");
5515: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5516: for(i=1,jk=1; i <=nlstate; i++){
5517: for(j=1; j <=nlstate+ndeath; j++){
5518: if (j!=i) {
5519: fprintf(ficres,"%1d%1d",i,j);
5520: printf("%1d%1d",i,j);
5521: fprintf(ficlog,"%1d%1d",i,j);
5522: for(k=1; k<=ncovmodel;k++){
5523: printf(" %.5e",delti[jk]);
5524: fprintf(ficlog," %.5e",delti[jk]);
5525: fprintf(ficres," %.5e",delti[jk]);
5526: jk++;
5527: }
5528: printf("\n");
5529: fprintf(ficlog,"\n");
5530: fprintf(ficres,"\n");
5531: }
5532: }
5533: }
5534:
5535: 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");
5536: if(mle>=1)
5537: 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");
5538: 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");
5539: /* # 121 Var(a12)\n\ */
5540: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5541: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5542: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5543: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5544: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5545: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5546: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5547:
5548:
5549: /* Just to have a covariance matrix which will be more understandable
5550: even is we still don't want to manage dictionary of variables
5551: */
5552: for(itimes=1;itimes<=2;itimes++){
5553: jj=0;
5554: for(i=1; i <=nlstate; i++){
5555: for(j=1; j <=nlstate+ndeath; j++){
5556: if(j==i) continue;
5557: for(k=1; k<=ncovmodel;k++){
5558: jj++;
5559: ca[0]= k+'a'-1;ca[1]='\0';
5560: if(itimes==1){
5561: if(mle>=1)
5562: printf("#%1d%1d%d",i,j,k);
5563: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5564: fprintf(ficres,"#%1d%1d%d",i,j,k);
5565: }else{
5566: if(mle>=1)
5567: printf("%1d%1d%d",i,j,k);
5568: fprintf(ficlog,"%1d%1d%d",i,j,k);
5569: fprintf(ficres,"%1d%1d%d",i,j,k);
5570: }
5571: ll=0;
5572: for(li=1;li <=nlstate; li++){
5573: for(lj=1;lj <=nlstate+ndeath; lj++){
5574: if(lj==li) continue;
5575: for(lk=1;lk<=ncovmodel;lk++){
5576: ll++;
5577: if(ll<=jj){
5578: cb[0]= lk +'a'-1;cb[1]='\0';
5579: if(ll<jj){
5580: if(itimes==1){
5581: if(mle>=1)
5582: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5583: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5584: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5585: }else{
5586: if(mle>=1)
5587: printf(" %.5e",matcov[jj][ll]);
5588: fprintf(ficlog," %.5e",matcov[jj][ll]);
5589: fprintf(ficres," %.5e",matcov[jj][ll]);
5590: }
5591: }else{
5592: if(itimes==1){
5593: if(mle>=1)
5594: printf(" Var(%s%1d%1d)",ca,i,j);
5595: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5596: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5597: }else{
5598: if(mle>=1)
5599: printf(" %.5e",matcov[jj][ll]);
5600: fprintf(ficlog," %.5e",matcov[jj][ll]);
5601: fprintf(ficres," %.5e",matcov[jj][ll]);
5602: }
5603: }
5604: }
5605: } /* end lk */
5606: } /* end lj */
5607: } /* end li */
5608: if(mle>=1)
5609: printf("\n");
5610: fprintf(ficlog,"\n");
5611: fprintf(ficres,"\n");
5612: numlinepar++;
5613: } /* end k*/
5614: } /*end j */
5615: } /* end i */
5616: } /* end itimes */
5617:
5618: fflush(ficlog);
5619: fflush(ficres);
5620:
5621: while((c=getc(ficpar))=='#' && c!= EOF){
5622: ungetc(c,ficpar);
5623: fgets(line, MAXLINE, ficpar);
5624: puts(line);
5625: fputs(line,ficparo);
5626: }
5627: ungetc(c,ficpar);
5628:
5629: estepm=0;
5630: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5631: if (estepm==0 || estepm < stepm) estepm=stepm;
5632: if (fage <= 2) {
5633: bage = ageminpar;
5634: fage = agemaxpar;
5635: }
5636:
5637: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5638: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5639: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5640:
5641: while((c=getc(ficpar))=='#' && c!= EOF){
5642: ungetc(c,ficpar);
5643: fgets(line, MAXLINE, ficpar);
5644: puts(line);
5645: fputs(line,ficparo);
5646: }
5647: ungetc(c,ficpar);
5648:
5649: 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);
5650: 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);
5651: 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);
5652: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5653: 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);
5654:
5655: while((c=getc(ficpar))=='#' && c!= EOF){
5656: ungetc(c,ficpar);
5657: fgets(line, MAXLINE, ficpar);
5658: puts(line);
5659: fputs(line,ficparo);
5660: }
5661: ungetc(c,ficpar);
5662:
5663:
5664: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5665: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5666:
5667: fscanf(ficpar,"pop_based=%d\n",&popbased);
5668: fprintf(ficparo,"pop_based=%d\n",popbased);
5669: fprintf(ficres,"pop_based=%d\n",popbased);
5670:
5671: while((c=getc(ficpar))=='#' && c!= EOF){
5672: ungetc(c,ficpar);
5673: fgets(line, MAXLINE, ficpar);
5674: puts(line);
5675: fputs(line,ficparo);
5676: }
5677: ungetc(c,ficpar);
5678:
5679: 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);
5680: 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);
5681: 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);
5682: 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);
5683: 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);
5684: /* day and month of proj2 are not used but only year anproj2.*/
5685:
5686:
5687:
5688: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5689: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5690:
5691: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5692: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5693:
5694: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5695: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5696: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5697:
5698: /*------------ free_vector -------------*/
5699: /* chdir(path); */
5700:
5701: free_ivector(wav,1,imx);
5702: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5703: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5704: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5705: free_lvector(num,1,n);
5706: free_vector(agedc,1,n);
5707: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5708: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5709: fclose(ficparo);
5710: fclose(ficres);
5711:
5712:
5713: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5714:
5715: strcpy(filerespl,"pl");
5716: strcat(filerespl,fileres);
5717: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5718: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5719: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5720: }
5721: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5722: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5723: pstamp(ficrespl);
5724: fprintf(ficrespl,"# Period (stable) prevalence \n");
5725: fprintf(ficrespl,"#Age ");
5726: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5727: fprintf(ficrespl,"\n");
5728:
5729: prlim=matrix(1,nlstate,1,nlstate);
5730:
5731: agebase=ageminpar;
5732: agelim=agemaxpar;
5733: ftolpl=1.e-10;
5734: i1=cptcoveff;
5735: if (cptcovn < 1){i1=1;}
5736:
5737: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5738: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5739: k=k+1;
1.131 brouard 5740: /* to clean */
5741: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
1.126 brouard 5742: fprintf(ficrespl,"\n#******");
5743: printf("\n#******");
5744: fprintf(ficlog,"\n#******");
5745: for(j=1;j<=cptcoveff;j++) {
5746: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5747: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5748: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5749: }
5750: fprintf(ficrespl,"******\n");
5751: printf("******\n");
5752: fprintf(ficlog,"******\n");
5753:
5754: for (age=agebase; age<=agelim; age++){
5755: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5756: fprintf(ficrespl,"%.0f ",age );
5757: for(j=1;j<=cptcoveff;j++)
5758: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5759: for(i=1; i<=nlstate;i++)
5760: fprintf(ficrespl," %.5f", prlim[i][i]);
5761: fprintf(ficrespl,"\n");
5762: }
5763: }
5764: }
5765: fclose(ficrespl);
5766:
5767: /*------------- h Pij x at various ages ------------*/
5768:
5769: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5770: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5771: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5772: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5773: }
5774: printf("Computing pij: result on file '%s' \n", filerespij);
5775: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5776:
5777: stepsize=(int) (stepm+YEARM-1)/YEARM;
5778: /*if (stepm<=24) stepsize=2;*/
5779:
5780: agelim=AGESUP;
5781: hstepm=stepsize*YEARM; /* Every year of age */
5782: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5783:
5784: /* hstepm=1; aff par mois*/
5785: pstamp(ficrespij);
5786: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5787: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5788: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5789: k=k+1;
5790: fprintf(ficrespij,"\n#****** ");
5791: for(j=1;j<=cptcoveff;j++)
5792: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5793: fprintf(ficrespij,"******\n");
5794:
5795: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5796: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5797: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5798:
5799: /* nhstepm=nhstepm*YEARM; aff par mois*/
5800:
5801: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5802: oldm=oldms;savm=savms;
5803: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5804: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5805: for(i=1; i<=nlstate;i++)
5806: for(j=1; j<=nlstate+ndeath;j++)
5807: fprintf(ficrespij," %1d-%1d",i,j);
5808: fprintf(ficrespij,"\n");
5809: for (h=0; h<=nhstepm; h++){
5810: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5811: for(i=1; i<=nlstate;i++)
5812: for(j=1; j<=nlstate+ndeath;j++)
5813: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5814: fprintf(ficrespij,"\n");
5815: }
5816: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5817: fprintf(ficrespij,"\n");
5818: }
5819: }
5820: }
5821:
5822: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5823:
5824: fclose(ficrespij);
5825:
5826: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5827: for(i=1;i<=AGESUP;i++)
5828: for(j=1;j<=NCOVMAX;j++)
5829: for(k=1;k<=NCOVMAX;k++)
5830: probs[i][j][k]=0.;
5831:
5832: /*---------- Forecasting ------------------*/
5833: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5834: if(prevfcast==1){
5835: /* if(stepm ==1){*/
5836: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5837: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5838: /* } */
5839: /* else{ */
5840: /* erreur=108; */
5841: /* 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); */
5842: /* 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); */
5843: /* } */
5844: }
5845:
5846:
1.127 brouard 5847: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5848:
5849: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5850: /* 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",\
5851: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5852: */
1.126 brouard 5853:
1.127 brouard 5854: if (mobilav!=0) {
5855: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5856: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5857: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5858: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5859: }
1.126 brouard 5860: }
5861:
5862:
1.127 brouard 5863: /*---------- Health expectancies, no variances ------------*/
5864:
1.126 brouard 5865: strcpy(filerese,"e");
5866: strcat(filerese,fileres);
5867: if((ficreseij=fopen(filerese,"w"))==NULL) {
5868: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5869: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5870: }
5871: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5872: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.127 brouard 5873: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5874: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5875: k=k+1;
5876: fprintf(ficreseij,"\n#****** ");
5877: for(j=1;j<=cptcoveff;j++) {
5878: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5879: }
5880: fprintf(ficreseij,"******\n");
5881:
5882: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5883: oldm=oldms;savm=savms;
5884: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5885:
5886: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5887: }
5888: }
5889: fclose(ficreseij);
5890:
5891:
5892: /*---------- Health expectancies and variances ------------*/
5893:
5894:
5895: strcpy(filerest,"t");
5896: strcat(filerest,fileres);
5897: if((ficrest=fopen(filerest,"w"))==NULL) {
5898: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5899: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5900: }
5901: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5902: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5903:
1.126 brouard 5904:
5905: strcpy(fileresstde,"stde");
5906: strcat(fileresstde,fileres);
5907: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5908: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5909: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5910: }
5911: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5912: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5913:
5914: strcpy(filerescve,"cve");
5915: strcat(filerescve,fileres);
5916: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5917: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5918: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5919: }
5920: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5921: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5922:
5923: strcpy(fileresv,"v");
5924: strcat(fileresv,fileres);
5925: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5926: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5927: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5928: }
5929: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5930: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5931:
5932: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5933: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5934: k=k+1;
5935: fprintf(ficrest,"\n#****** ");
5936: for(j=1;j<=cptcoveff;j++)
5937: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5938: fprintf(ficrest,"******\n");
5939:
5940: fprintf(ficresstdeij,"\n#****** ");
5941: fprintf(ficrescveij,"\n#****** ");
5942: for(j=1;j<=cptcoveff;j++) {
5943: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5944: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5945: }
5946: fprintf(ficresstdeij,"******\n");
5947: fprintf(ficrescveij,"******\n");
5948:
5949: fprintf(ficresvij,"\n#****** ");
5950: for(j=1;j<=cptcoveff;j++)
5951: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5952: fprintf(ficresvij,"******\n");
5953:
5954: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5955: oldm=oldms;savm=savms;
1.127 brouard 5956: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.126 brouard 5957:
5958: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5959: pstamp(ficrest);
1.128 brouard 5960: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5961: oldm=oldms;savm=savms;
5962: 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 ");
5963: if(vpopbased==1)
5964: 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);
5965: else
5966: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
5967: fprintf(ficrest,"# Age e.. (std) ");
5968: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5969: fprintf(ficrest,"\n");
1.126 brouard 5970:
1.128 brouard 5971: epj=vector(1,nlstate+1);
5972: for(age=bage; age <=fage ;age++){
5973: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5974: if (vpopbased==1) {
5975: if(mobilav ==0){
5976: for(i=1; i<=nlstate;i++)
5977: prlim[i][i]=probs[(int)age][i][k];
5978: }else{ /* mobilav */
5979: for(i=1; i<=nlstate;i++)
5980: prlim[i][i]=mobaverage[(int)age][i][k];
5981: }
1.126 brouard 5982: }
5983:
1.128 brouard 5984: fprintf(ficrest," %4.0f",age);
5985: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5986: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5987: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5988: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5989: }
5990: epj[nlstate+1] +=epj[j];
1.126 brouard 5991: }
5992:
1.128 brouard 5993: for(i=1, vepp=0.;i <=nlstate;i++)
5994: for(j=1;j <=nlstate;j++)
5995: vepp += vareij[i][j][(int)age];
5996: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5997: for(j=1;j <=nlstate;j++){
5998: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5999: }
6000: fprintf(ficrest,"\n");
1.126 brouard 6001: }
6002: }
6003: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6004: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6005: free_vector(epj,1,nlstate+1);
6006: }
6007: }
6008: free_vector(weight,1,n);
6009: free_imatrix(Tvard,1,15,1,2);
6010: free_imatrix(s,1,maxwav+1,1,n);
6011: free_matrix(anint,1,maxwav,1,n);
6012: free_matrix(mint,1,maxwav,1,n);
6013: free_ivector(cod,1,n);
6014: free_ivector(tab,1,NCOVMAX);
6015: fclose(ficresstdeij);
6016: fclose(ficrescveij);
6017: fclose(ficresvij);
6018: fclose(ficrest);
6019: fclose(ficpar);
6020:
6021: /*------- Variance of period (stable) prevalence------*/
6022:
6023: strcpy(fileresvpl,"vpl");
6024: strcat(fileresvpl,fileres);
6025: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6026: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6027: exit(0);
6028: }
6029: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6030:
6031: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6032: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6033: k=k+1;
6034: fprintf(ficresvpl,"\n#****** ");
6035: for(j=1;j<=cptcoveff;j++)
6036: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6037: fprintf(ficresvpl,"******\n");
6038:
6039: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6040: oldm=oldms;savm=savms;
6041: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6042: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6043: }
6044: }
6045:
6046: fclose(ficresvpl);
6047:
6048: /*---------- End : free ----------------*/
6049: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6050: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6051:
6052: } /* mle==-3 arrives here for freeing */
1.131 brouard 6053: endfree:
1.126 brouard 6054: free_matrix(prlim,1,nlstate,1,nlstate);
6055: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6056: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6057: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6058: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6059: free_matrix(covar,0,NCOVMAX,1,n);
6060: free_matrix(matcov,1,npar,1,npar);
6061: /*free_vector(delti,1,npar);*/
6062: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6063: free_matrix(agev,1,maxwav,1,imx);
6064: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6065:
6066: free_ivector(ncodemax,1,8);
6067: free_ivector(Tvar,1,15);
6068: free_ivector(Tprod,1,15);
6069: free_ivector(Tvaraff,1,15);
6070: free_ivector(Tage,1,15);
6071:
6072: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6073: free_imatrix(codtab,1,100,1,10);
6074: fflush(fichtm);
6075: fflush(ficgp);
6076:
6077:
6078: if((nberr >0) || (nbwarn>0)){
6079: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6080: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6081: }else{
6082: printf("End of Imach\n");
6083: fprintf(ficlog,"End of Imach\n");
6084: }
6085: printf("See log file on %s\n",filelog);
6086: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6087: (void) gettimeofday(&end_time,&tzp);
6088: tm = *localtime(&end_time.tv_sec);
6089: tmg = *gmtime(&end_time.tv_sec);
6090: strcpy(strtend,asctime(&tm));
6091: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6092: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6093: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6094:
6095: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6096: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6097: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6098: /* printf("Total time was %d uSec.\n", total_usecs);*/
6099: /* if(fileappend(fichtm,optionfilehtm)){ */
6100: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6101: fclose(fichtm);
6102: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6103: fclose(fichtmcov);
6104: fclose(ficgp);
6105: fclose(ficlog);
6106: /*------ End -----------*/
6107:
6108:
6109: printf("Before Current directory %s!\n",pathcd);
6110: if(chdir(pathcd) != 0)
6111: printf("Can't move to directory %s!\n",path);
6112: if(getcwd(pathcd,MAXLINE) > 0)
6113: printf("Current directory %s!\n",pathcd);
6114: /*strcat(plotcmd,CHARSEPARATOR);*/
6115: sprintf(plotcmd,"gnuplot");
6116: #ifndef UNIX
6117: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6118: #endif
6119: if(!stat(plotcmd,&info)){
6120: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6121: if(!stat(getenv("GNUPLOTBIN"),&info)){
6122: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6123: }else
6124: strcpy(pplotcmd,plotcmd);
6125: #ifdef UNIX
6126: strcpy(plotcmd,GNUPLOTPROGRAM);
6127: if(!stat(plotcmd,&info)){
6128: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6129: }else
6130: strcpy(pplotcmd,plotcmd);
6131: #endif
6132: }else
6133: strcpy(pplotcmd,plotcmd);
6134:
6135: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6136: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6137:
6138: if((outcmd=system(plotcmd)) != 0){
6139: printf("\n Problem with gnuplot\n");
6140: }
6141: printf(" Wait...");
6142: while (z[0] != 'q') {
6143: /* chdir(path); */
6144: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6145: scanf("%s",z);
6146: /* if (z[0] == 'c') system("./imach"); */
6147: if (z[0] == 'e') {
6148: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6149: system(optionfilehtm);
6150: }
6151: else if (z[0] == 'g') system(plotcmd);
6152: else if (z[0] == 'q') exit(0);
6153: }
6154: end:
6155: while (z[0] != 'q') {
6156: printf("\nType q for exiting: ");
6157: scanf("%s",z);
6158: }
6159: }
6160:
6161:
6162:
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