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Mon Apr 26 20:30:53 2010 UTC (14 years, 1 month ago) by
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(Module): merging some libgsl code. Fixing computation
of likelione (using inter/intrapolation if mle = 0) in order to
get same likelihood as if mle=1.
Some cleaning of code and comments added.
1: /* $Id: imach.c,v 1.136 2010/04/26 20:30:53 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.136 2010/04/26 20:30:53 brouard
5: (Module): merging some libgsl code. Fixing computation
6: of likelione (using inter/intrapolation if mle = 0) in order to
7: get same likelihood as if mle=1.
8: Some cleaning of code and comments added.
9:
10: Revision 1.135 2009/10/29 15:33:14 brouard
11: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
12:
13: Revision 1.134 2009/10/29 13:18:53 brouard
14: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
15:
16: Revision 1.133 2009/07/06 10:21:25 brouard
17: just nforces
18:
19: Revision 1.132 2009/07/06 08:22:05 brouard
20: Many tings
21:
22: Revision 1.131 2009/06/20 16:22:47 brouard
23: Some dimensions resccaled
24:
25: Revision 1.130 2009/05/26 06:44:34 brouard
26: (Module): Max Covariate is now set to 20 instead of 8. A
27: lot of cleaning with variables initialized to 0. Trying to make
28: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
29:
30: Revision 1.129 2007/08/31 13:49:27 lievre
31: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
32:
33: Revision 1.128 2006/06/30 13:02:05 brouard
34: (Module): Clarifications on computing e.j
35:
36: Revision 1.127 2006/04/28 18:11:50 brouard
37: (Module): Yes the sum of survivors was wrong since
38: imach-114 because nhstepm was no more computed in the age
39: loop. Now we define nhstepma in the age loop.
40: (Module): In order to speed up (in case of numerous covariates) we
41: compute health expectancies (without variances) in a first step
42: and then all the health expectancies with variances or standard
43: deviation (needs data from the Hessian matrices) which slows the
44: computation.
45: In the future we should be able to stop the program is only health
46: expectancies and graph are needed without standard deviations.
47:
48: Revision 1.126 2006/04/28 17:23:28 brouard
49: (Module): Yes the sum of survivors was wrong since
50: imach-114 because nhstepm was no more computed in the age
51: loop. Now we define nhstepma in the age loop.
52: Version 0.98h
53:
54: Revision 1.125 2006/04/04 15:20:31 lievre
55: Errors in calculation of health expectancies. Age was not initialized.
56: Forecasting file added.
57:
58: Revision 1.124 2006/03/22 17:13:53 lievre
59: Parameters are printed with %lf instead of %f (more numbers after the comma).
60: The log-likelihood is printed in the log file
61:
62: Revision 1.123 2006/03/20 10:52:43 brouard
63: * imach.c (Module): <title> changed, corresponds to .htm file
64: name. <head> headers where missing.
65:
66: * imach.c (Module): Weights can have a decimal point as for
67: English (a comma might work with a correct LC_NUMERIC environment,
68: otherwise the weight is truncated).
69: Modification of warning when the covariates values are not 0 or
70: 1.
71: Version 0.98g
72:
73: Revision 1.122 2006/03/20 09:45:41 brouard
74: (Module): Weights can have a decimal point as for
75: English (a comma might work with a correct LC_NUMERIC environment,
76: otherwise the weight is truncated).
77: Modification of warning when the covariates values are not 0 or
78: 1.
79: Version 0.98g
80:
81: Revision 1.121 2006/03/16 17:45:01 lievre
82: * imach.c (Module): Comments concerning covariates added
83:
84: * imach.c (Module): refinements in the computation of lli if
85: status=-2 in order to have more reliable computation if stepm is
86: not 1 month. Version 0.98f
87:
88: Revision 1.120 2006/03/16 15:10:38 lievre
89: (Module): refinements in the computation of lli if
90: status=-2 in order to have more reliable computation if stepm is
91: not 1 month. Version 0.98f
92:
93: Revision 1.119 2006/03/15 17:42:26 brouard
94: (Module): Bug if status = -2, the loglikelihood was
95: computed as likelihood omitting the logarithm. Version O.98e
96:
97: Revision 1.118 2006/03/14 18:20:07 brouard
98: (Module): varevsij Comments added explaining the second
99: table of variances if popbased=1 .
100: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
101: (Module): Function pstamp added
102: (Module): Version 0.98d
103:
104: Revision 1.117 2006/03/14 17:16:22 brouard
105: (Module): varevsij Comments added explaining the second
106: table of variances if popbased=1 .
107: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
108: (Module): Function pstamp added
109: (Module): Version 0.98d
110:
111: Revision 1.116 2006/03/06 10:29:27 brouard
112: (Module): Variance-covariance wrong links and
113: varian-covariance of ej. is needed (Saito).
114:
115: Revision 1.115 2006/02/27 12:17:45 brouard
116: (Module): One freematrix added in mlikeli! 0.98c
117:
118: Revision 1.114 2006/02/26 12:57:58 brouard
119: (Module): Some improvements in processing parameter
120: filename with strsep.
121:
122: Revision 1.113 2006/02/24 14:20:24 brouard
123: (Module): Memory leaks checks with valgrind and:
124: datafile was not closed, some imatrix were not freed and on matrix
125: allocation too.
126:
127: Revision 1.112 2006/01/30 09:55:26 brouard
128: (Module): Back to gnuplot.exe instead of wgnuplot.exe
129:
130: Revision 1.111 2006/01/25 20:38:18 brouard
131: (Module): Lots of cleaning and bugs added (Gompertz)
132: (Module): Comments can be added in data file. Missing date values
133: can be a simple dot '.'.
134:
135: Revision 1.110 2006/01/25 00:51:50 brouard
136: (Module): Lots of cleaning and bugs added (Gompertz)
137:
138: Revision 1.109 2006/01/24 19:37:15 brouard
139: (Module): Comments (lines starting with a #) are allowed in data.
140:
141: Revision 1.108 2006/01/19 18:05:42 lievre
142: Gnuplot problem appeared...
143: To be fixed
144:
145: Revision 1.107 2006/01/19 16:20:37 brouard
146: Test existence of gnuplot in imach path
147:
148: Revision 1.106 2006/01/19 13:24:36 brouard
149: Some cleaning and links added in html output
150:
151: Revision 1.105 2006/01/05 20:23:19 lievre
152: *** empty log message ***
153:
154: Revision 1.104 2005/09/30 16:11:43 lievre
155: (Module): sump fixed, loop imx fixed, and simplifications.
156: (Module): If the status is missing at the last wave but we know
157: that the person is alive, then we can code his/her status as -2
158: (instead of missing=-1 in earlier versions) and his/her
159: contributions to the likelihood is 1 - Prob of dying from last
160: health status (= 1-p13= p11+p12 in the easiest case of somebody in
161: the healthy state at last known wave). Version is 0.98
162:
163: Revision 1.103 2005/09/30 15:54:49 lievre
164: (Module): sump fixed, loop imx fixed, and simplifications.
165:
166: Revision 1.102 2004/09/15 17:31:30 brouard
167: Add the possibility to read data file including tab characters.
168:
169: Revision 1.101 2004/09/15 10:38:38 brouard
170: Fix on curr_time
171:
172: Revision 1.100 2004/07/12 18:29:06 brouard
173: Add version for Mac OS X. Just define UNIX in Makefile
174:
175: Revision 1.99 2004/06/05 08:57:40 brouard
176: *** empty log message ***
177:
178: Revision 1.98 2004/05/16 15:05:56 brouard
179: New version 0.97 . First attempt to estimate force of mortality
180: directly from the data i.e. without the need of knowing the health
181: state at each age, but using a Gompertz model: log u =a + b*age .
182: This is the basic analysis of mortality and should be done before any
183: other analysis, in order to test if the mortality estimated from the
184: cross-longitudinal survey is different from the mortality estimated
185: from other sources like vital statistic data.
186:
187: The same imach parameter file can be used but the option for mle should be -3.
188:
189: Agnès, who wrote this part of the code, tried to keep most of the
190: former routines in order to include the new code within the former code.
191:
192: The output is very simple: only an estimate of the intercept and of
193: the slope with 95% confident intervals.
194:
195: Current limitations:
196: A) Even if you enter covariates, i.e. with the
197: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
198: B) There is no computation of Life Expectancy nor Life Table.
199:
200: Revision 1.97 2004/02/20 13:25:42 lievre
201: Version 0.96d. Population forecasting command line is (temporarily)
202: suppressed.
203:
204: Revision 1.96 2003/07/15 15:38:55 brouard
205: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
206: rewritten within the same printf. Workaround: many printfs.
207:
208: Revision 1.95 2003/07/08 07:54:34 brouard
209: * imach.c (Repository):
210: (Repository): Using imachwizard code to output a more meaningful covariance
211: matrix (cov(a12,c31) instead of numbers.
212:
213: Revision 1.94 2003/06/27 13:00:02 brouard
214: Just cleaning
215:
216: Revision 1.93 2003/06/25 16:33:55 brouard
217: (Module): On windows (cygwin) function asctime_r doesn't
218: exist so I changed back to asctime which exists.
219: (Module): Version 0.96b
220:
221: Revision 1.92 2003/06/25 16:30:45 brouard
222: (Module): On windows (cygwin) function asctime_r doesn't
223: exist so I changed back to asctime which exists.
224:
225: Revision 1.91 2003/06/25 15:30:29 brouard
226: * imach.c (Repository): Duplicated warning errors corrected.
227: (Repository): Elapsed time after each iteration is now output. It
228: helps to forecast when convergence will be reached. Elapsed time
229: is stamped in powell. We created a new html file for the graphs
230: concerning matrix of covariance. It has extension -cov.htm.
231:
232: Revision 1.90 2003/06/24 12:34:15 brouard
233: (Module): Some bugs corrected for windows. Also, when
234: mle=-1 a template is output in file "or"mypar.txt with the design
235: of the covariance matrix to be input.
236:
237: Revision 1.89 2003/06/24 12:30:52 brouard
238: (Module): Some bugs corrected for windows. Also, when
239: mle=-1 a template is output in file "or"mypar.txt with the design
240: of the covariance matrix to be input.
241:
242: Revision 1.88 2003/06/23 17:54:56 brouard
243: * 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.
244:
245: Revision 1.87 2003/06/18 12:26:01 brouard
246: Version 0.96
247:
248: Revision 1.86 2003/06/17 20:04:08 brouard
249: (Module): Change position of html and gnuplot routines and added
250: routine fileappend.
251:
252: Revision 1.85 2003/06/17 13:12:43 brouard
253: * imach.c (Repository): Check when date of death was earlier that
254: current date of interview. It may happen when the death was just
255: prior to the death. In this case, dh was negative and likelihood
256: was wrong (infinity). We still send an "Error" but patch by
257: assuming that the date of death was just one stepm after the
258: interview.
259: (Repository): Because some people have very long ID (first column)
260: we changed int to long in num[] and we added a new lvector for
261: memory allocation. But we also truncated to 8 characters (left
262: truncation)
263: (Repository): No more line truncation errors.
264:
265: Revision 1.84 2003/06/13 21:44:43 brouard
266: * imach.c (Repository): Replace "freqsummary" at a correct
267: place. It differs from routine "prevalence" which may be called
268: many times. Probs is memory consuming and must be used with
269: parcimony.
270: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
271:
272: Revision 1.83 2003/06/10 13:39:11 lievre
273: *** empty log message ***
274:
275: Revision 1.82 2003/06/05 15:57:20 brouard
276: Add log in imach.c and fullversion number is now printed.
277:
278: */
279: /*
280: Interpolated Markov Chain
281:
282: Short summary of the programme:
283:
284: This program computes Healthy Life Expectancies from
285: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
286: first survey ("cross") where individuals from different ages are
287: interviewed on their health status or degree of disability (in the
288: case of a health survey which is our main interest) -2- at least a
289: second wave of interviews ("longitudinal") which measure each change
290: (if any) in individual health status. Health expectancies are
291: computed from the time spent in each health state according to a
292: model. More health states you consider, more time is necessary to reach the
293: Maximum Likelihood of the parameters involved in the model. The
294: simplest model is the multinomial logistic model where pij is the
295: probability to be observed in state j at the second wave
296: conditional to be observed in state i at the first wave. Therefore
297: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
298: 'age' is age and 'sex' is a covariate. If you want to have a more
299: complex model than "constant and age", you should modify the program
300: where the markup *Covariates have to be included here again* invites
301: you to do it. More covariates you add, slower the
302: convergence.
303:
304: The advantage of this computer programme, compared to a simple
305: multinomial logistic model, is clear when the delay between waves is not
306: identical for each individual. Also, if a individual missed an
307: intermediate interview, the information is lost, but taken into
308: account using an interpolation or extrapolation.
309:
310: hPijx is the probability to be observed in state i at age x+h
311: conditional to the observed state i at age x. The delay 'h' can be
312: split into an exact number (nh*stepm) of unobserved intermediate
313: states. This elementary transition (by month, quarter,
314: semester or year) is modelled as a multinomial logistic. The hPx
315: matrix is simply the matrix product of nh*stepm elementary matrices
316: and the contribution of each individual to the likelihood is simply
317: hPijx.
318:
319: Also this programme outputs the covariance matrix of the parameters but also
320: of the life expectancies. It also computes the period (stable) prevalence.
321:
322: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
323: Institut national d'études démographiques, Paris.
324: This software have been partly granted by Euro-REVES, a concerted action
325: from the European Union.
326: It is copyrighted identically to a GNU software product, ie programme and
327: software can be distributed freely for non commercial use. Latest version
328: can be accessed at http://euroreves.ined.fr/imach .
329:
330: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
331: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
332:
333: **********************************************************************/
334: /*
335: main
336: read parameterfile
337: read datafile
338: concatwav
339: freqsummary
340: if (mle >= 1)
341: mlikeli
342: print results files
343: if mle==1
344: computes hessian
345: read end of parameter file: agemin, agemax, bage, fage, estepm
346: begin-prev-date,...
347: open gnuplot file
348: open html file
349: period (stable) prevalence
350: for age prevalim()
351: h Pij x
352: variance of p varprob
353: forecasting if prevfcast==1 prevforecast call prevalence()
354: health expectancies
355: Variance-covariance of DFLE
356: prevalence()
357: movingaverage()
358: varevsij()
359: if popbased==1 varevsij(,popbased)
360: total life expectancies
361: Variance of period (stable) prevalence
362: end
363: */
364:
365:
366:
367:
368: #include <math.h>
369: #include <stdio.h>
370: #include <stdlib.h>
371: #include <string.h>
372: #include <unistd.h>
373:
374: #include <limits.h>
375: #include <sys/types.h>
376: #include <sys/stat.h>
377: #include <errno.h>
378: extern int errno;
379:
380: /* #include <sys/time.h> */
381: #include <time.h>
382: #include "timeval.h"
383:
384: #ifdef GSL
385: #include <gsl/gsl_errno.h>
386: #include <gsl/gsl_multimin.h>
387: #endif
388:
389: /* #include <libintl.h> */
390: /* #define _(String) gettext (String) */
391:
392: #define MAXLINE 256
393:
394: #define GNUPLOTPROGRAM "gnuplot"
395: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
396: #define FILENAMELENGTH 132
397:
398: #define GLOCK_ERROR_NOPATH -1 /* empty path */
399: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
400:
401: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
402: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
403:
404: #define NINTERVMAX 8
405: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
406: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
407: #define NCOVMAX 20 /* Maximum number of covariates */
408: #define MAXN 20000
409: #define YEARM 12. /* Number of months per year */
410: #define AGESUP 130
411: #define AGEBASE 40
412: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
413: #ifdef UNIX
414: #define DIRSEPARATOR '/'
415: #define CHARSEPARATOR "/"
416: #define ODIRSEPARATOR '\\'
417: #else
418: #define DIRSEPARATOR '\\'
419: #define CHARSEPARATOR "\\"
420: #define ODIRSEPARATOR '/'
421: #endif
422:
423: /* $Id: imach.c,v 1.136 2010/04/26 20:30:53 brouard Exp $ */
424: /* $State: Exp $ */
425:
426: char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
427: char fullversion[]="$Revision: 1.136 $ $Date: 2010/04/26 20:30:53 $";
428: char strstart[80];
429: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
430: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
431: int nvar=0, nforce=0; /* Number of variables, number of forces */
432: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
433: int npar=NPARMAX;
434: int nlstate=2; /* Number of live states */
435: int ndeath=1; /* Number of dead states */
436: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
437: int popbased=0;
438:
439: int *wav; /* Number of waves for this individuual 0 is possible */
440: int maxwav=0; /* Maxim number of waves */
441: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
442: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
443: int gipmx=0, gsw=0; /* Global variables on the number of contributions
444: to the likelihood and the sum of weights (done by funcone)*/
445: int mle=1, weightopt=0;
446: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
447: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
448: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
449: * wave mi and wave mi+1 is not an exact multiple of stepm. */
450: double jmean=1; /* Mean space between 2 waves */
451: double **oldm, **newm, **savm; /* Working pointers to matrices */
452: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
453: /*FILE *fic ; */ /* Used in readdata only */
454: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
455: FILE *ficlog, *ficrespow;
456: int globpr=0; /* Global variable for printing or not */
457: double fretone; /* Only one call to likelihood */
458: long ipmx=0; /* Number of contributions */
459: double sw; /* Sum of weights */
460: char filerespow[FILENAMELENGTH];
461: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
462: FILE *ficresilk;
463: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
464: FILE *ficresprobmorprev;
465: FILE *fichtm, *fichtmcov; /* Html File */
466: FILE *ficreseij;
467: char filerese[FILENAMELENGTH];
468: FILE *ficresstdeij;
469: char fileresstde[FILENAMELENGTH];
470: FILE *ficrescveij;
471: char filerescve[FILENAMELENGTH];
472: FILE *ficresvij;
473: char fileresv[FILENAMELENGTH];
474: FILE *ficresvpl;
475: char fileresvpl[FILENAMELENGTH];
476: char title[MAXLINE];
477: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
478: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
479: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
480: char command[FILENAMELENGTH];
481: int outcmd=0;
482:
483: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
484:
485: char filelog[FILENAMELENGTH]; /* Log file */
486: char filerest[FILENAMELENGTH];
487: char fileregp[FILENAMELENGTH];
488: char popfile[FILENAMELENGTH];
489:
490: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
491:
492: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
493: struct timezone tzp;
494: extern int gettimeofday();
495: struct tm tmg, tm, tmf, *gmtime(), *localtime();
496: long time_value;
497: extern long time();
498: char strcurr[80], strfor[80];
499:
500: char *endptr;
501: long lval;
502: double dval;
503:
504: #define NR_END 1
505: #define FREE_ARG char*
506: #define FTOL 1.0e-10
507:
508: #define NRANSI
509: #define ITMAX 200
510:
511: #define TOL 2.0e-4
512:
513: #define CGOLD 0.3819660
514: #define ZEPS 1.0e-10
515: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
516:
517: #define GOLD 1.618034
518: #define GLIMIT 100.0
519: #define TINY 1.0e-20
520:
521: static double maxarg1,maxarg2;
522: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
523: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
524:
525: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
526: #define rint(a) floor(a+0.5)
527:
528: static double sqrarg;
529: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
530: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
531: int agegomp= AGEGOMP;
532:
533: int imx;
534: int stepm=1;
535: /* Stepm, step in month: minimum step interpolation*/
536:
537: int estepm;
538: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
539:
540: int m,nb;
541: long *num;
542: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
543: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
544: double **pmmij, ***probs;
545: double *ageexmed,*agecens;
546: double dateintmean=0;
547:
548: double *weight;
549: int **s; /* Status */
550: double *agedc, **covar, idx;
551: int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
552: double *lsurv, *lpop, *tpop;
553:
554: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
555: double ftolhess; /* Tolerance for computing hessian */
556:
557: /**************** split *************************/
558: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
559: {
560: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
561: the name of the file (name), its extension only (ext) and its first part of the name (finame)
562: */
563: char *ss; /* pointer */
564: int l1, l2; /* length counters */
565:
566: l1 = strlen(path ); /* length of path */
567: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
568: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
569: if ( ss == NULL ) { /* no directory, so determine current directory */
570: strcpy( name, path ); /* we got the fullname name because no directory */
571: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
572: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
573: /* get current working directory */
574: /* extern char* getcwd ( char *buf , int len);*/
575: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
576: return( GLOCK_ERROR_GETCWD );
577: }
578: /* got dirc from getcwd*/
579: printf(" DIRC = %s \n",dirc);
580: } else { /* strip direcotry from path */
581: ss++; /* after this, the filename */
582: l2 = strlen( ss ); /* length of filename */
583: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
584: strcpy( name, ss ); /* save file name */
585: strncpy( dirc, path, l1 - l2 ); /* now the directory */
586: dirc[l1-l2] = 0; /* add zero */
587: printf(" DIRC2 = %s \n",dirc);
588: }
589: /* We add a separator at the end of dirc if not exists */
590: l1 = strlen( dirc ); /* length of directory */
591: if( dirc[l1-1] != DIRSEPARATOR ){
592: dirc[l1] = DIRSEPARATOR;
593: dirc[l1+1] = 0;
594: printf(" DIRC3 = %s \n",dirc);
595: }
596: ss = strrchr( name, '.' ); /* find last / */
597: if (ss >0){
598: ss++;
599: strcpy(ext,ss); /* save extension */
600: l1= strlen( name);
601: l2= strlen(ss)+1;
602: strncpy( finame, name, l1-l2);
603: finame[l1-l2]= 0;
604: }
605:
606: return( 0 ); /* we're done */
607: }
608:
609:
610: /******************************************/
611:
612: void replace_back_to_slash(char *s, char*t)
613: {
614: int i;
615: int lg=0;
616: i=0;
617: lg=strlen(t);
618: for(i=0; i<= lg; i++) {
619: (s[i] = t[i]);
620: if (t[i]== '\\') s[i]='/';
621: }
622: }
623:
624: char *trimbb(char *out, char *in)
625: { /* Trim multiple blanks in line */
626: char *s;
627: s=out;
628: while (*in != '\0'){
629: while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
630: in++;
631: }
632: *out++ = *in++;
633: }
634: *out='\0';
635: return s;
636: }
637:
638: int nbocc(char *s, char occ)
639: {
640: int i,j=0;
641: int lg=20;
642: i=0;
643: lg=strlen(s);
644: for(i=0; i<= lg; i++) {
645: if (s[i] == occ ) j++;
646: }
647: return j;
648: }
649:
650: void cutv(char *u,char *v, char*t, char occ)
651: {
652: /* cuts string t into u and v where u ends before first occurence of char 'occ'
653: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
654: gives u="abcedf" and v="ghi2j" */
655: int i,lg,j,p=0;
656: i=0;
657: for(j=0; j<=strlen(t)-1; j++) {
658: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
659: }
660:
661: lg=strlen(t);
662: for(j=0; j<p; j++) {
663: (u[j] = t[j]);
664: }
665: u[p]='\0';
666:
667: for(j=0; j<= lg; j++) {
668: if (j>=(p+1))(v[j-p-1] = t[j]);
669: }
670: }
671:
672: /********************** nrerror ********************/
673:
674: void nrerror(char error_text[])
675: {
676: fprintf(stderr,"ERREUR ...\n");
677: fprintf(stderr,"%s\n",error_text);
678: exit(EXIT_FAILURE);
679: }
680: /*********************** vector *******************/
681: double *vector(int nl, int nh)
682: {
683: double *v;
684: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
685: if (!v) nrerror("allocation failure in vector");
686: return v-nl+NR_END;
687: }
688:
689: /************************ free vector ******************/
690: void free_vector(double*v, int nl, int nh)
691: {
692: free((FREE_ARG)(v+nl-NR_END));
693: }
694:
695: /************************ivector *******************************/
696: int *ivector(long nl,long nh)
697: {
698: int *v;
699: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
700: if (!v) nrerror("allocation failure in ivector");
701: return v-nl+NR_END;
702: }
703:
704: /******************free ivector **************************/
705: void free_ivector(int *v, long nl, long nh)
706: {
707: free((FREE_ARG)(v+nl-NR_END));
708: }
709:
710: /************************lvector *******************************/
711: long *lvector(long nl,long nh)
712: {
713: long *v;
714: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
715: if (!v) nrerror("allocation failure in ivector");
716: return v-nl+NR_END;
717: }
718:
719: /******************free lvector **************************/
720: void free_lvector(long *v, long nl, long nh)
721: {
722: free((FREE_ARG)(v+nl-NR_END));
723: }
724:
725: /******************* imatrix *******************************/
726: int **imatrix(long nrl, long nrh, long ncl, long nch)
727: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
728: {
729: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
730: int **m;
731:
732: /* allocate pointers to rows */
733: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
734: if (!m) nrerror("allocation failure 1 in matrix()");
735: m += NR_END;
736: m -= nrl;
737:
738:
739: /* allocate rows and set pointers to them */
740: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
741: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
742: m[nrl] += NR_END;
743: m[nrl] -= ncl;
744:
745: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
746:
747: /* return pointer to array of pointers to rows */
748: return m;
749: }
750:
751: /****************** free_imatrix *************************/
752: void free_imatrix(m,nrl,nrh,ncl,nch)
753: int **m;
754: long nch,ncl,nrh,nrl;
755: /* free an int matrix allocated by imatrix() */
756: {
757: free((FREE_ARG) (m[nrl]+ncl-NR_END));
758: free((FREE_ARG) (m+nrl-NR_END));
759: }
760:
761: /******************* matrix *******************************/
762: double **matrix(long nrl, long nrh, long ncl, long nch)
763: {
764: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
765: double **m;
766:
767: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
768: if (!m) nrerror("allocation failure 1 in matrix()");
769: m += NR_END;
770: m -= nrl;
771:
772: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
773: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
774: m[nrl] += NR_END;
775: m[nrl] -= ncl;
776:
777: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
778: return m;
779: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
780: */
781: }
782:
783: /*************************free matrix ************************/
784: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
785: {
786: free((FREE_ARG)(m[nrl]+ncl-NR_END));
787: free((FREE_ARG)(m+nrl-NR_END));
788: }
789:
790: /******************* ma3x *******************************/
791: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
792: {
793: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
794: double ***m;
795:
796: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
797: if (!m) nrerror("allocation failure 1 in matrix()");
798: m += NR_END;
799: m -= nrl;
800:
801: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
802: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
803: m[nrl] += NR_END;
804: m[nrl] -= ncl;
805:
806: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
807:
808: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
809: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
810: m[nrl][ncl] += NR_END;
811: m[nrl][ncl] -= nll;
812: for (j=ncl+1; j<=nch; j++)
813: m[nrl][j]=m[nrl][j-1]+nlay;
814:
815: for (i=nrl+1; i<=nrh; i++) {
816: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
817: for (j=ncl+1; j<=nch; j++)
818: m[i][j]=m[i][j-1]+nlay;
819: }
820: return m;
821: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
822: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
823: */
824: }
825:
826: /*************************free ma3x ************************/
827: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
828: {
829: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
830: free((FREE_ARG)(m[nrl]+ncl-NR_END));
831: free((FREE_ARG)(m+nrl-NR_END));
832: }
833:
834: /*************** function subdirf ***********/
835: char *subdirf(char fileres[])
836: {
837: /* Caution optionfilefiname is hidden */
838: strcpy(tmpout,optionfilefiname);
839: strcat(tmpout,"/"); /* Add to the right */
840: strcat(tmpout,fileres);
841: return tmpout;
842: }
843:
844: /*************** function subdirf2 ***********/
845: char *subdirf2(char fileres[], char *preop)
846: {
847:
848: /* Caution optionfilefiname is hidden */
849: strcpy(tmpout,optionfilefiname);
850: strcat(tmpout,"/");
851: strcat(tmpout,preop);
852: strcat(tmpout,fileres);
853: return tmpout;
854: }
855:
856: /*************** function subdirf3 ***********/
857: char *subdirf3(char fileres[], char *preop, char *preop2)
858: {
859:
860: /* Caution optionfilefiname is hidden */
861: strcpy(tmpout,optionfilefiname);
862: strcat(tmpout,"/");
863: strcat(tmpout,preop);
864: strcat(tmpout,preop2);
865: strcat(tmpout,fileres);
866: return tmpout;
867: }
868:
869: /***************** f1dim *************************/
870: extern int ncom;
871: extern double *pcom,*xicom;
872: extern double (*nrfunc)(double []);
873:
874: double f1dim(double x)
875: {
876: int j;
877: double f;
878: double *xt;
879:
880: xt=vector(1,ncom);
881: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
882: f=(*nrfunc)(xt);
883: free_vector(xt,1,ncom);
884: return f;
885: }
886:
887: /*****************brent *************************/
888: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
889: {
890: int iter;
891: double a,b,d,etemp;
892: double fu,fv,fw,fx;
893: double ftemp;
894: double p,q,r,tol1,tol2,u,v,w,x,xm;
895: double e=0.0;
896:
897: a=(ax < cx ? ax : cx);
898: b=(ax > cx ? ax : cx);
899: x=w=v=bx;
900: fw=fv=fx=(*f)(x);
901: for (iter=1;iter<=ITMAX;iter++) {
902: xm=0.5*(a+b);
903: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
904: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
905: printf(".");fflush(stdout);
906: fprintf(ficlog,".");fflush(ficlog);
907: #ifdef DEBUG
908: 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);
909: 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);
910: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
911: #endif
912: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
913: *xmin=x;
914: return fx;
915: }
916: ftemp=fu;
917: if (fabs(e) > tol1) {
918: r=(x-w)*(fx-fv);
919: q=(x-v)*(fx-fw);
920: p=(x-v)*q-(x-w)*r;
921: q=2.0*(q-r);
922: if (q > 0.0) p = -p;
923: q=fabs(q);
924: etemp=e;
925: e=d;
926: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
927: d=CGOLD*(e=(x >= xm ? a-x : b-x));
928: else {
929: d=p/q;
930: u=x+d;
931: if (u-a < tol2 || b-u < tol2)
932: d=SIGN(tol1,xm-x);
933: }
934: } else {
935: d=CGOLD*(e=(x >= xm ? a-x : b-x));
936: }
937: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
938: fu=(*f)(u);
939: if (fu <= fx) {
940: if (u >= x) a=x; else b=x;
941: SHFT(v,w,x,u)
942: SHFT(fv,fw,fx,fu)
943: } else {
944: if (u < x) a=u; else b=u;
945: if (fu <= fw || w == x) {
946: v=w;
947: w=u;
948: fv=fw;
949: fw=fu;
950: } else if (fu <= fv || v == x || v == w) {
951: v=u;
952: fv=fu;
953: }
954: }
955: }
956: nrerror("Too many iterations in brent");
957: *xmin=x;
958: return fx;
959: }
960:
961: /****************** mnbrak ***********************/
962:
963: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
964: double (*func)(double))
965: {
966: double ulim,u,r,q, dum;
967: double fu;
968:
969: *fa=(*func)(*ax);
970: *fb=(*func)(*bx);
971: if (*fb > *fa) {
972: SHFT(dum,*ax,*bx,dum)
973: SHFT(dum,*fb,*fa,dum)
974: }
975: *cx=(*bx)+GOLD*(*bx-*ax);
976: *fc=(*func)(*cx);
977: while (*fb > *fc) {
978: r=(*bx-*ax)*(*fb-*fc);
979: q=(*bx-*cx)*(*fb-*fa);
980: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
981: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
982: ulim=(*bx)+GLIMIT*(*cx-*bx);
983: if ((*bx-u)*(u-*cx) > 0.0) {
984: fu=(*func)(u);
985: } else if ((*cx-u)*(u-ulim) > 0.0) {
986: fu=(*func)(u);
987: if (fu < *fc) {
988: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
989: SHFT(*fb,*fc,fu,(*func)(u))
990: }
991: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
992: u=ulim;
993: fu=(*func)(u);
994: } else {
995: u=(*cx)+GOLD*(*cx-*bx);
996: fu=(*func)(u);
997: }
998: SHFT(*ax,*bx,*cx,u)
999: SHFT(*fa,*fb,*fc,fu)
1000: }
1001: }
1002:
1003: /*************** linmin ************************/
1004:
1005: int ncom;
1006: double *pcom,*xicom;
1007: double (*nrfunc)(double []);
1008:
1009: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1010: {
1011: double brent(double ax, double bx, double cx,
1012: double (*f)(double), double tol, double *xmin);
1013: double f1dim(double x);
1014: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1015: double *fc, double (*func)(double));
1016: int j;
1017: double xx,xmin,bx,ax;
1018: double fx,fb,fa;
1019:
1020: ncom=n;
1021: pcom=vector(1,n);
1022: xicom=vector(1,n);
1023: nrfunc=func;
1024: for (j=1;j<=n;j++) {
1025: pcom[j]=p[j];
1026: xicom[j]=xi[j];
1027: }
1028: ax=0.0;
1029: xx=1.0;
1030: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1031: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1032: #ifdef DEBUG
1033: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1034: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1035: #endif
1036: for (j=1;j<=n;j++) {
1037: xi[j] *= xmin;
1038: p[j] += xi[j];
1039: }
1040: free_vector(xicom,1,n);
1041: free_vector(pcom,1,n);
1042: }
1043:
1044: char *asc_diff_time(long time_sec, char ascdiff[])
1045: {
1046: long sec_left, days, hours, minutes;
1047: days = (time_sec) / (60*60*24);
1048: sec_left = (time_sec) % (60*60*24);
1049: hours = (sec_left) / (60*60) ;
1050: sec_left = (sec_left) %(60*60);
1051: minutes = (sec_left) /60;
1052: sec_left = (sec_left) % (60);
1053: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1054: return ascdiff;
1055: }
1056:
1057: /*************** powell ************************/
1058: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1059: double (*func)(double []))
1060: {
1061: void linmin(double p[], double xi[], int n, double *fret,
1062: double (*func)(double []));
1063: int i,ibig,j;
1064: double del,t,*pt,*ptt,*xit;
1065: double fp,fptt;
1066: double *xits;
1067: int niterf, itmp;
1068:
1069: pt=vector(1,n);
1070: ptt=vector(1,n);
1071: xit=vector(1,n);
1072: xits=vector(1,n);
1073: *fret=(*func)(p);
1074: for (j=1;j<=n;j++) pt[j]=p[j];
1075: for (*iter=1;;++(*iter)) {
1076: fp=(*fret);
1077: ibig=0;
1078: del=0.0;
1079: last_time=curr_time;
1080: (void) gettimeofday(&curr_time,&tzp);
1081: 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);
1082: 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);
1083: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1084: for (i=1;i<=n;i++) {
1085: printf(" %d %.12f",i, p[i]);
1086: fprintf(ficlog," %d %.12lf",i, p[i]);
1087: fprintf(ficrespow," %.12lf", p[i]);
1088: }
1089: printf("\n");
1090: fprintf(ficlog,"\n");
1091: fprintf(ficrespow,"\n");fflush(ficrespow);
1092: if(*iter <=3){
1093: tm = *localtime(&curr_time.tv_sec);
1094: strcpy(strcurr,asctime(&tm));
1095: /* asctime_r(&tm,strcurr); */
1096: forecast_time=curr_time;
1097: itmp = strlen(strcurr);
1098: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1099: strcurr[itmp-1]='\0';
1100: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1101: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1102: for(niterf=10;niterf<=30;niterf+=10){
1103: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1104: tmf = *localtime(&forecast_time.tv_sec);
1105: /* asctime_r(&tmf,strfor); */
1106: strcpy(strfor,asctime(&tmf));
1107: itmp = strlen(strfor);
1108: if(strfor[itmp-1]=='\n')
1109: strfor[itmp-1]='\0';
1110: 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);
1111: 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);
1112: }
1113: }
1114: for (i=1;i<=n;i++) {
1115: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1116: fptt=(*fret);
1117: #ifdef DEBUG
1118: printf("fret=%lf \n",*fret);
1119: fprintf(ficlog,"fret=%lf \n",*fret);
1120: #endif
1121: printf("%d",i);fflush(stdout);
1122: fprintf(ficlog,"%d",i);fflush(ficlog);
1123: linmin(p,xit,n,fret,func);
1124: if (fabs(fptt-(*fret)) > del) {
1125: del=fabs(fptt-(*fret));
1126: ibig=i;
1127: }
1128: #ifdef DEBUG
1129: printf("%d %.12e",i,(*fret));
1130: fprintf(ficlog,"%d %.12e",i,(*fret));
1131: for (j=1;j<=n;j++) {
1132: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1133: printf(" x(%d)=%.12e",j,xit[j]);
1134: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1135: }
1136: for(j=1;j<=n;j++) {
1137: printf(" p=%.12e",p[j]);
1138: fprintf(ficlog," p=%.12e",p[j]);
1139: }
1140: printf("\n");
1141: fprintf(ficlog,"\n");
1142: #endif
1143: }
1144: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1145: #ifdef DEBUG
1146: int k[2],l;
1147: k[0]=1;
1148: k[1]=-1;
1149: printf("Max: %.12e",(*func)(p));
1150: fprintf(ficlog,"Max: %.12e",(*func)(p));
1151: for (j=1;j<=n;j++) {
1152: printf(" %.12e",p[j]);
1153: fprintf(ficlog," %.12e",p[j]);
1154: }
1155: printf("\n");
1156: fprintf(ficlog,"\n");
1157: for(l=0;l<=1;l++) {
1158: for (j=1;j<=n;j++) {
1159: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1160: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1161: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1162: }
1163: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1164: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1165: }
1166: #endif
1167:
1168:
1169: free_vector(xit,1,n);
1170: free_vector(xits,1,n);
1171: free_vector(ptt,1,n);
1172: free_vector(pt,1,n);
1173: return;
1174: }
1175: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1176: for (j=1;j<=n;j++) {
1177: ptt[j]=2.0*p[j]-pt[j];
1178: xit[j]=p[j]-pt[j];
1179: pt[j]=p[j];
1180: }
1181: fptt=(*func)(ptt);
1182: if (fptt < fp) {
1183: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1184: if (t < 0.0) {
1185: linmin(p,xit,n,fret,func);
1186: for (j=1;j<=n;j++) {
1187: xi[j][ibig]=xi[j][n];
1188: xi[j][n]=xit[j];
1189: }
1190: #ifdef DEBUG
1191: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1192: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1193: for(j=1;j<=n;j++){
1194: printf(" %.12e",xit[j]);
1195: fprintf(ficlog," %.12e",xit[j]);
1196: }
1197: printf("\n");
1198: fprintf(ficlog,"\n");
1199: #endif
1200: }
1201: }
1202: }
1203: }
1204:
1205: /**** Prevalence limit (stable or period prevalence) ****************/
1206:
1207: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1208: {
1209: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1210: matrix by transitions matrix until convergence is reached */
1211:
1212: int i, ii,j,k;
1213: double min, max, maxmin, maxmax,sumnew=0.;
1214: double **matprod2();
1215: double **out, cov[NCOVMAX+1], **pmij();
1216: double **newm;
1217: double agefin, delaymax=50 ; /* Max number of years to converge */
1218:
1219: for (ii=1;ii<=nlstate+ndeath;ii++)
1220: for (j=1;j<=nlstate+ndeath;j++){
1221: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1222: }
1223:
1224: cov[1]=1.;
1225:
1226: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1227: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1228: newm=savm;
1229: /* Covariates have to be included here again */
1230: cov[2]=agefin;
1231:
1232: for (k=1; k<=cptcovn;k++) {
1233: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1234: /* 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]]);*/
1235: }
1236: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1237: for (k=1; k<=cptcovprod;k++)
1238: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1239:
1240: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1241: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1242: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1243: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1244:
1245: savm=oldm;
1246: oldm=newm;
1247: maxmax=0.;
1248: for(j=1;j<=nlstate;j++){
1249: min=1.;
1250: max=0.;
1251: for(i=1; i<=nlstate; i++) {
1252: sumnew=0;
1253: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1254: prlim[i][j]= newm[i][j]/(1-sumnew);
1255: max=FMAX(max,prlim[i][j]);
1256: min=FMIN(min,prlim[i][j]);
1257: }
1258: maxmin=max-min;
1259: maxmax=FMAX(maxmax,maxmin);
1260: }
1261: if(maxmax < ftolpl){
1262: return prlim;
1263: }
1264: }
1265: }
1266:
1267: /*************** transition probabilities ***************/
1268:
1269: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1270: {
1271: double s1, s2;
1272: /*double t34;*/
1273: int i,j,j1, nc, ii, jj;
1274:
1275: for(i=1; i<= nlstate; i++){
1276: for(j=1; j<i;j++){
1277: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1278: /*s2 += param[i][j][nc]*cov[nc];*/
1279: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1280: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1281: }
1282: ps[i][j]=s2;
1283: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1284: }
1285: for(j=i+1; j<=nlstate+ndeath;j++){
1286: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1287: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1288: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1289: }
1290: ps[i][j]=s2;
1291: }
1292: }
1293: /*ps[3][2]=1;*/
1294:
1295: for(i=1; i<= nlstate; i++){
1296: s1=0;
1297: for(j=1; j<i; j++){
1298: s1+=exp(ps[i][j]);
1299: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1300: }
1301: for(j=i+1; j<=nlstate+ndeath; j++){
1302: s1+=exp(ps[i][j]);
1303: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1304: }
1305: ps[i][i]=1./(s1+1.);
1306: for(j=1; j<i; j++)
1307: ps[i][j]= exp(ps[i][j])*ps[i][i];
1308: for(j=i+1; j<=nlstate+ndeath; j++)
1309: ps[i][j]= exp(ps[i][j])*ps[i][i];
1310: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1311: } /* end i */
1312:
1313: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1314: for(jj=1; jj<= nlstate+ndeath; jj++){
1315: ps[ii][jj]=0;
1316: ps[ii][ii]=1;
1317: }
1318: }
1319:
1320:
1321: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1322: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1323: /* printf("ddd %lf ",ps[ii][jj]); */
1324: /* } */
1325: /* printf("\n "); */
1326: /* } */
1327: /* printf("\n ");printf("%lf ",cov[2]); */
1328: /*
1329: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1330: goto end;*/
1331: return ps;
1332: }
1333:
1334: /**************** Product of 2 matrices ******************/
1335:
1336: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1337: {
1338: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1339: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1340: /* in, b, out are matrice of pointers which should have been initialized
1341: before: only the contents of out is modified. The function returns
1342: a pointer to pointers identical to out */
1343: long i, j, k;
1344: for(i=nrl; i<= nrh; i++)
1345: for(k=ncolol; k<=ncoloh; k++)
1346: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1347: out[i][k] +=in[i][j]*b[j][k];
1348:
1349: return out;
1350: }
1351:
1352:
1353: /************* Higher Matrix Product ***************/
1354:
1355: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1356: {
1357: /* Computes the transition matrix starting at age 'age' over
1358: 'nhstepm*hstepm*stepm' months (i.e. until
1359: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1360: nhstepm*hstepm matrices.
1361: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1362: (typically every 2 years instead of every month which is too big
1363: for the memory).
1364: Model is determined by parameters x and covariates have to be
1365: included manually here.
1366:
1367: */
1368:
1369: int i, j, d, h, k;
1370: double **out, cov[NCOVMAX+1];
1371: double **newm;
1372:
1373: /* Hstepm could be zero and should return the unit matrix */
1374: for (i=1;i<=nlstate+ndeath;i++)
1375: for (j=1;j<=nlstate+ndeath;j++){
1376: oldm[i][j]=(i==j ? 1.0 : 0.0);
1377: po[i][j][0]=(i==j ? 1.0 : 0.0);
1378: }
1379: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1380: for(h=1; h <=nhstepm; h++){
1381: for(d=1; d <=hstepm; d++){
1382: newm=savm;
1383: /* Covariates have to be included here again */
1384: cov[1]=1.;
1385: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1386: for (k=1; k<=cptcovn;k++)
1387: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1388: for (k=1; k<=cptcovage;k++)
1389: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1390: for (k=1; k<=cptcovprod;k++)
1391: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1392:
1393:
1394: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1395: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1396: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1397: pmij(pmmij,cov,ncovmodel,x,nlstate));
1398: savm=oldm;
1399: oldm=newm;
1400: }
1401: for(i=1; i<=nlstate+ndeath; i++)
1402: for(j=1;j<=nlstate+ndeath;j++) {
1403: po[i][j][h]=newm[i][j];
1404: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1405: }
1406: /*printf("h=%d ",h);*/
1407: } /* end h */
1408: /* printf("\n H=%d \n",h); */
1409: return po;
1410: }
1411:
1412:
1413: /*************** log-likelihood *************/
1414: double func( double *x)
1415: {
1416: int i, ii, j, k, mi, d, kk;
1417: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1418: double **out;
1419: double sw; /* Sum of weights */
1420: double lli; /* Individual log likelihood */
1421: int s1, s2;
1422: double bbh, survp;
1423: long ipmx;
1424: /*extern weight */
1425: /* We are differentiating ll according to initial status */
1426: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1427: /*for(i=1;i<imx;i++)
1428: printf(" %d\n",s[4][i]);
1429: */
1430: cov[1]=1.;
1431:
1432: for(k=1; k<=nlstate; k++) ll[k]=0.;
1433:
1434: if(mle==1){
1435: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1436: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1437: for(mi=1; mi<= wav[i]-1; mi++){
1438: for (ii=1;ii<=nlstate+ndeath;ii++)
1439: for (j=1;j<=nlstate+ndeath;j++){
1440: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1441: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1442: }
1443: for(d=0; d<dh[mi][i]; d++){
1444: newm=savm;
1445: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1446: for (kk=1; kk<=cptcovage;kk++) {
1447: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1448: }
1449: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1450: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1451: savm=oldm;
1452: oldm=newm;
1453: } /* end mult */
1454:
1455: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1456: /* But now since version 0.9 we anticipate for bias at large stepm.
1457: * If stepm is larger than one month (smallest stepm) and if the exact delay
1458: * (in months) between two waves is not a multiple of stepm, we rounded to
1459: * the nearest (and in case of equal distance, to the lowest) interval but now
1460: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1461: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1462: * probability in order to take into account the bias as a fraction of the way
1463: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1464: * -stepm/2 to stepm/2 .
1465: * For stepm=1 the results are the same as for previous versions of Imach.
1466: * For stepm > 1 the results are less biased than in previous versions.
1467: */
1468: s1=s[mw[mi][i]][i];
1469: s2=s[mw[mi+1][i]][i];
1470: bbh=(double)bh[mi][i]/(double)stepm;
1471: /* bias bh is positive if real duration
1472: * is higher than the multiple of stepm and negative otherwise.
1473: */
1474: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1475: if( s2 > nlstate){
1476: /* i.e. if s2 is a death state and if the date of death is known
1477: then the contribution to the likelihood is the probability to
1478: die between last step unit time and current step unit time,
1479: which is also equal to probability to die before dh
1480: minus probability to die before dh-stepm .
1481: In version up to 0.92 likelihood was computed
1482: as if date of death was unknown. Death was treated as any other
1483: health state: the date of the interview describes the actual state
1484: and not the date of a change in health state. The former idea was
1485: to consider that at each interview the state was recorded
1486: (healthy, disable or death) and IMaCh was corrected; but when we
1487: introduced the exact date of death then we should have modified
1488: the contribution of an exact death to the likelihood. This new
1489: contribution is smaller and very dependent of the step unit
1490: stepm. It is no more the probability to die between last interview
1491: and month of death but the probability to survive from last
1492: interview up to one month before death multiplied by the
1493: probability to die within a month. Thanks to Chris
1494: Jackson for correcting this bug. Former versions increased
1495: mortality artificially. The bad side is that we add another loop
1496: which slows down the processing. The difference can be up to 10%
1497: lower mortality.
1498: */
1499: lli=log(out[s1][s2] - savm[s1][s2]);
1500:
1501:
1502: } else if (s2==-2) {
1503: for (j=1,survp=0. ; j<=nlstate; j++)
1504: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1505: /*survp += out[s1][j]; */
1506: lli= log(survp);
1507: }
1508:
1509: else if (s2==-4) {
1510: for (j=3,survp=0. ; j<=nlstate; j++)
1511: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1512: lli= log(survp);
1513: }
1514:
1515: else if (s2==-5) {
1516: for (j=1,survp=0. ; j<=2; j++)
1517: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1518: lli= log(survp);
1519: }
1520:
1521: else{
1522: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1523: /* 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 */
1524: }
1525: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1526: /*if(lli ==000.0)*/
1527: /*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); */
1528: ipmx +=1;
1529: sw += weight[i];
1530: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1531: } /* end of wave */
1532: } /* end of individual */
1533: } else if(mle==2){
1534: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1535: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1536: for(mi=1; mi<= wav[i]-1; mi++){
1537: for (ii=1;ii<=nlstate+ndeath;ii++)
1538: for (j=1;j<=nlstate+ndeath;j++){
1539: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1540: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1541: }
1542: for(d=0; d<=dh[mi][i]; d++){
1543: newm=savm;
1544: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1545: for (kk=1; kk<=cptcovage;kk++) {
1546: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1547: }
1548: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1549: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1550: savm=oldm;
1551: oldm=newm;
1552: } /* end mult */
1553:
1554: s1=s[mw[mi][i]][i];
1555: s2=s[mw[mi+1][i]][i];
1556: bbh=(double)bh[mi][i]/(double)stepm;
1557: 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 */
1558: ipmx +=1;
1559: sw += weight[i];
1560: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1561: } /* end of wave */
1562: } /* end of individual */
1563: } else if(mle==3){ /* exponential inter-extrapolation */
1564: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1565: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1566: for(mi=1; mi<= wav[i]-1; mi++){
1567: for (ii=1;ii<=nlstate+ndeath;ii++)
1568: for (j=1;j<=nlstate+ndeath;j++){
1569: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1570: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1571: }
1572: for(d=0; d<dh[mi][i]; d++){
1573: newm=savm;
1574: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1575: for (kk=1; kk<=cptcovage;kk++) {
1576: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1577: }
1578: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1579: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1580: savm=oldm;
1581: oldm=newm;
1582: } /* end mult */
1583:
1584: s1=s[mw[mi][i]][i];
1585: s2=s[mw[mi+1][i]][i];
1586: bbh=(double)bh[mi][i]/(double)stepm;
1587: 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 */
1588: ipmx +=1;
1589: sw += weight[i];
1590: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1591: } /* end of wave */
1592: } /* end of individual */
1593: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1594: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1595: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1596: for(mi=1; mi<= wav[i]-1; mi++){
1597: for (ii=1;ii<=nlstate+ndeath;ii++)
1598: for (j=1;j<=nlstate+ndeath;j++){
1599: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1600: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1601: }
1602: for(d=0; d<dh[mi][i]; d++){
1603: newm=savm;
1604: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1605: for (kk=1; kk<=cptcovage;kk++) {
1606: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1607: }
1608:
1609: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1610: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1611: savm=oldm;
1612: oldm=newm;
1613: } /* end mult */
1614:
1615: s1=s[mw[mi][i]][i];
1616: s2=s[mw[mi+1][i]][i];
1617: if( s2 > nlstate){
1618: lli=log(out[s1][s2] - savm[s1][s2]);
1619: }else{
1620: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1621: }
1622: ipmx +=1;
1623: sw += weight[i];
1624: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1625: /* 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]); */
1626: } /* end of wave */
1627: } /* end of individual */
1628: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1629: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1630: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1631: for(mi=1; mi<= wav[i]-1; mi++){
1632: for (ii=1;ii<=nlstate+ndeath;ii++)
1633: for (j=1;j<=nlstate+ndeath;j++){
1634: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1635: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1636: }
1637: for(d=0; d<dh[mi][i]; d++){
1638: newm=savm;
1639: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1640: for (kk=1; kk<=cptcovage;kk++) {
1641: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1642: }
1643:
1644: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1645: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1646: savm=oldm;
1647: oldm=newm;
1648: } /* end mult */
1649:
1650: s1=s[mw[mi][i]][i];
1651: s2=s[mw[mi+1][i]][i];
1652: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1653: ipmx +=1;
1654: sw += weight[i];
1655: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1656: /*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]);*/
1657: } /* end of wave */
1658: } /* end of individual */
1659: } /* End of if */
1660: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1661: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1662: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1663: return -l;
1664: }
1665:
1666: /*************** log-likelihood *************/
1667: double funcone( double *x)
1668: {
1669: /* Same as likeli but slower because of a lot of printf and if */
1670: int i, ii, j, k, mi, d, kk;
1671: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1672: double **out;
1673: double lli; /* Individual log likelihood */
1674: double llt;
1675: int s1, s2;
1676: double bbh, survp;
1677: /*extern weight */
1678: /* We are differentiating ll according to initial status */
1679: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1680: /*for(i=1;i<imx;i++)
1681: printf(" %d\n",s[4][i]);
1682: */
1683: cov[1]=1.;
1684:
1685: for(k=1; k<=nlstate; k++) ll[k]=0.;
1686:
1687: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1688: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1689: for(mi=1; mi<= wav[i]-1; mi++){
1690: for (ii=1;ii<=nlstate+ndeath;ii++)
1691: for (j=1;j<=nlstate+ndeath;j++){
1692: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1693: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1694: }
1695: for(d=0; d<dh[mi][i]; d++){
1696: newm=savm;
1697: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1698: for (kk=1; kk<=cptcovage;kk++) {
1699: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1700: }
1701: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1702: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1703: savm=oldm;
1704: oldm=newm;
1705: } /* end mult */
1706:
1707: s1=s[mw[mi][i]][i];
1708: s2=s[mw[mi+1][i]][i];
1709: bbh=(double)bh[mi][i]/(double)stepm;
1710: /* bias is positive if real duration
1711: * is higher than the multiple of stepm and negative otherwise.
1712: */
1713: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1714: lli=log(out[s1][s2] - savm[s1][s2]);
1715: } else if (s2==-2) {
1716: for (j=1,survp=0. ; j<=nlstate; j++)
1717: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1718: lli= log(survp);
1719: }else if (mle==1){
1720: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1721: } else if(mle==2){
1722: 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 */
1723: } else if(mle==3){ /* exponential inter-extrapolation */
1724: 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 */
1725: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1726: lli=log(out[s1][s2]); /* Original formula */
1727: } else{ /* mle=0 back to 1 */
1728: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1729: /*lli=log(out[s1][s2]); */ /* Original formula */
1730: } /* End of if */
1731: ipmx +=1;
1732: sw += weight[i];
1733: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1734: /*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]); */
1735: if(globpr){
1736: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1737: %11.6f %11.6f %11.6f ", \
1738: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1739: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1740: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1741: llt +=ll[k]*gipmx/gsw;
1742: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1743: }
1744: fprintf(ficresilk," %10.6f\n", -llt);
1745: }
1746: } /* end of wave */
1747: } /* end of individual */
1748: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1749: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1750: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1751: if(globpr==0){ /* First time we count the contributions and weights */
1752: gipmx=ipmx;
1753: gsw=sw;
1754: }
1755: return -l;
1756: }
1757:
1758:
1759: /*************** function likelione ***********/
1760: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1761: {
1762: /* This routine should help understanding what is done with
1763: the selection of individuals/waves and
1764: to check the exact contribution to the likelihood.
1765: Plotting could be done.
1766: */
1767: int k;
1768:
1769: if(*globpri !=0){ /* Just counts and sums, no printings */
1770: strcpy(fileresilk,"ilk");
1771: strcat(fileresilk,fileres);
1772: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1773: printf("Problem with resultfile: %s\n", fileresilk);
1774: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1775: }
1776: 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");
1777: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1778: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1779: for(k=1; k<=nlstate; k++)
1780: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1781: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1782: }
1783:
1784: *fretone=(*funcone)(p);
1785: if(*globpri !=0){
1786: fclose(ficresilk);
1787: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1788: fflush(fichtm);
1789: }
1790: return;
1791: }
1792:
1793:
1794: /*********** Maximum Likelihood Estimation ***************/
1795:
1796: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1797: {
1798: int i,j, iter;
1799: double **xi;
1800: double fret;
1801: double fretone; /* Only one call to likelihood */
1802: /* char filerespow[FILENAMELENGTH];*/
1803: xi=matrix(1,npar,1,npar);
1804: for (i=1;i<=npar;i++)
1805: for (j=1;j<=npar;j++)
1806: xi[i][j]=(i==j ? 1.0 : 0.0);
1807: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1808: strcpy(filerespow,"pow");
1809: strcat(filerespow,fileres);
1810: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1811: printf("Problem with resultfile: %s\n", filerespow);
1812: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1813: }
1814: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1815: for (i=1;i<=nlstate;i++)
1816: for(j=1;j<=nlstate+ndeath;j++)
1817: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1818: fprintf(ficrespow,"\n");
1819:
1820: powell(p,xi,npar,ftol,&iter,&fret,func);
1821:
1822: free_matrix(xi,1,npar,1,npar);
1823: fclose(ficrespow);
1824: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1825: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1826: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1827:
1828: }
1829:
1830: /**** Computes Hessian and covariance matrix ***/
1831: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1832: {
1833: double **a,**y,*x,pd;
1834: double **hess;
1835: int i, j,jk;
1836: int *indx;
1837:
1838: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1839: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1840: void lubksb(double **a, int npar, int *indx, double b[]) ;
1841: void ludcmp(double **a, int npar, int *indx, double *d) ;
1842: double gompertz(double p[]);
1843: hess=matrix(1,npar,1,npar);
1844:
1845: printf("\nCalculation of the hessian matrix. Wait...\n");
1846: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1847: for (i=1;i<=npar;i++){
1848: printf("%d",i);fflush(stdout);
1849: fprintf(ficlog,"%d",i);fflush(ficlog);
1850:
1851: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1852:
1853: /* printf(" %f ",p[i]);
1854: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1855: }
1856:
1857: for (i=1;i<=npar;i++) {
1858: for (j=1;j<=npar;j++) {
1859: if (j>i) {
1860: printf(".%d%d",i,j);fflush(stdout);
1861: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1862: hess[i][j]=hessij(p,delti,i,j,func,npar);
1863:
1864: hess[j][i]=hess[i][j];
1865: /*printf(" %lf ",hess[i][j]);*/
1866: }
1867: }
1868: }
1869: printf("\n");
1870: fprintf(ficlog,"\n");
1871:
1872: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1873: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1874:
1875: a=matrix(1,npar,1,npar);
1876: y=matrix(1,npar,1,npar);
1877: x=vector(1,npar);
1878: indx=ivector(1,npar);
1879: for (i=1;i<=npar;i++)
1880: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1881: ludcmp(a,npar,indx,&pd);
1882:
1883: for (j=1;j<=npar;j++) {
1884: for (i=1;i<=npar;i++) x[i]=0;
1885: x[j]=1;
1886: lubksb(a,npar,indx,x);
1887: for (i=1;i<=npar;i++){
1888: matcov[i][j]=x[i];
1889: }
1890: }
1891:
1892: printf("\n#Hessian matrix#\n");
1893: fprintf(ficlog,"\n#Hessian matrix#\n");
1894: for (i=1;i<=npar;i++) {
1895: for (j=1;j<=npar;j++) {
1896: printf("%.3e ",hess[i][j]);
1897: fprintf(ficlog,"%.3e ",hess[i][j]);
1898: }
1899: printf("\n");
1900: fprintf(ficlog,"\n");
1901: }
1902:
1903: /* Recompute Inverse */
1904: for (i=1;i<=npar;i++)
1905: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1906: ludcmp(a,npar,indx,&pd);
1907:
1908: /* printf("\n#Hessian matrix recomputed#\n");
1909:
1910: for (j=1;j<=npar;j++) {
1911: for (i=1;i<=npar;i++) x[i]=0;
1912: x[j]=1;
1913: lubksb(a,npar,indx,x);
1914: for (i=1;i<=npar;i++){
1915: y[i][j]=x[i];
1916: printf("%.3e ",y[i][j]);
1917: fprintf(ficlog,"%.3e ",y[i][j]);
1918: }
1919: printf("\n");
1920: fprintf(ficlog,"\n");
1921: }
1922: */
1923:
1924: free_matrix(a,1,npar,1,npar);
1925: free_matrix(y,1,npar,1,npar);
1926: free_vector(x,1,npar);
1927: free_ivector(indx,1,npar);
1928: free_matrix(hess,1,npar,1,npar);
1929:
1930:
1931: }
1932:
1933: /*************** hessian matrix ****************/
1934: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1935: {
1936: int i;
1937: int l=1, lmax=20;
1938: double k1,k2;
1939: double p2[MAXPARM+1]; /* identical to x */
1940: double res;
1941: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1942: double fx;
1943: int k=0,kmax=10;
1944: double l1;
1945:
1946: fx=func(x);
1947: for (i=1;i<=npar;i++) p2[i]=x[i];
1948: for(l=0 ; l <=lmax; l++){
1949: l1=pow(10,l);
1950: delts=delt;
1951: for(k=1 ; k <kmax; k=k+1){
1952: delt = delta*(l1*k);
1953: p2[theta]=x[theta] +delt;
1954: k1=func(p2)-fx;
1955: p2[theta]=x[theta]-delt;
1956: k2=func(p2)-fx;
1957: /*res= (k1-2.0*fx+k2)/delt/delt; */
1958: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1959:
1960: #ifdef DEBUGHESS
1961: 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);
1962: 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);
1963: #endif
1964: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1965: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1966: k=kmax;
1967: }
1968: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1969: k=kmax; l=lmax*10.;
1970: }
1971: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1972: delts=delt;
1973: }
1974: }
1975: }
1976: delti[theta]=delts;
1977: return res;
1978:
1979: }
1980:
1981: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1982: {
1983: int i;
1984: int l=1, l1, lmax=20;
1985: double k1,k2,k3,k4,res,fx;
1986: double p2[MAXPARM+1];
1987: int k;
1988:
1989: fx=func(x);
1990: for (k=1; k<=2; k++) {
1991: for (i=1;i<=npar;i++) p2[i]=x[i];
1992: p2[thetai]=x[thetai]+delti[thetai]/k;
1993: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1994: k1=func(p2)-fx;
1995:
1996: p2[thetai]=x[thetai]+delti[thetai]/k;
1997: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1998: k2=func(p2)-fx;
1999:
2000: p2[thetai]=x[thetai]-delti[thetai]/k;
2001: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2002: k3=func(p2)-fx;
2003:
2004: p2[thetai]=x[thetai]-delti[thetai]/k;
2005: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2006: k4=func(p2)-fx;
2007: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2008: #ifdef DEBUG
2009: 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);
2010: 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);
2011: #endif
2012: }
2013: return res;
2014: }
2015:
2016: /************** Inverse of matrix **************/
2017: void ludcmp(double **a, int n, int *indx, double *d)
2018: {
2019: int i,imax,j,k;
2020: double big,dum,sum,temp;
2021: double *vv;
2022:
2023: vv=vector(1,n);
2024: *d=1.0;
2025: for (i=1;i<=n;i++) {
2026: big=0.0;
2027: for (j=1;j<=n;j++)
2028: if ((temp=fabs(a[i][j])) > big) big=temp;
2029: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2030: vv[i]=1.0/big;
2031: }
2032: for (j=1;j<=n;j++) {
2033: for (i=1;i<j;i++) {
2034: sum=a[i][j];
2035: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2036: a[i][j]=sum;
2037: }
2038: big=0.0;
2039: for (i=j;i<=n;i++) {
2040: sum=a[i][j];
2041: for (k=1;k<j;k++)
2042: sum -= a[i][k]*a[k][j];
2043: a[i][j]=sum;
2044: if ( (dum=vv[i]*fabs(sum)) >= big) {
2045: big=dum;
2046: imax=i;
2047: }
2048: }
2049: if (j != imax) {
2050: for (k=1;k<=n;k++) {
2051: dum=a[imax][k];
2052: a[imax][k]=a[j][k];
2053: a[j][k]=dum;
2054: }
2055: *d = -(*d);
2056: vv[imax]=vv[j];
2057: }
2058: indx[j]=imax;
2059: if (a[j][j] == 0.0) a[j][j]=TINY;
2060: if (j != n) {
2061: dum=1.0/(a[j][j]);
2062: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2063: }
2064: }
2065: free_vector(vv,1,n); /* Doesn't work */
2066: ;
2067: }
2068:
2069: void lubksb(double **a, int n, int *indx, double b[])
2070: {
2071: int i,ii=0,ip,j;
2072: double sum;
2073:
2074: for (i=1;i<=n;i++) {
2075: ip=indx[i];
2076: sum=b[ip];
2077: b[ip]=b[i];
2078: if (ii)
2079: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2080: else if (sum) ii=i;
2081: b[i]=sum;
2082: }
2083: for (i=n;i>=1;i--) {
2084: sum=b[i];
2085: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2086: b[i]=sum/a[i][i];
2087: }
2088: }
2089:
2090: void pstamp(FILE *fichier)
2091: {
2092: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2093: }
2094:
2095: /************ Frequencies ********************/
2096: 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[])
2097: { /* Some frequencies */
2098:
2099: int i, m, jk, k1,i1, j1, bool, z1,j;
2100: int first;
2101: double ***freq; /* Frequencies */
2102: double *pp, **prop;
2103: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2104: char fileresp[FILENAMELENGTH];
2105:
2106: pp=vector(1,nlstate);
2107: prop=matrix(1,nlstate,iagemin,iagemax+3);
2108: strcpy(fileresp,"p");
2109: strcat(fileresp,fileres);
2110: if((ficresp=fopen(fileresp,"w"))==NULL) {
2111: printf("Problem with prevalence resultfile: %s\n", fileresp);
2112: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2113: exit(0);
2114: }
2115: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2116: j1=0;
2117:
2118: j=cptcoveff;
2119: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2120:
2121: first=1;
2122:
2123: for(k1=1; k1<=j;k1++){
2124: for(i1=1; i1<=ncodemax[k1];i1++){
2125: j1++;
2126: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2127: scanf("%d", i);*/
2128: for (i=-5; i<=nlstate+ndeath; i++)
2129: for (jk=-5; jk<=nlstate+ndeath; jk++)
2130: for(m=iagemin; m <= iagemax+3; m++)
2131: freq[i][jk][m]=0;
2132:
2133: for (i=1; i<=nlstate; i++)
2134: for(m=iagemin; m <= iagemax+3; m++)
2135: prop[i][m]=0;
2136:
2137: dateintsum=0;
2138: k2cpt=0;
2139: for (i=1; i<=imx; i++) {
2140: bool=1;
2141: if (cptcovn>0) {
2142: for (z1=1; z1<=cptcoveff; z1++)
2143: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2144: bool=0;
2145: }
2146: if (bool==1){
2147: for(m=firstpass; m<=lastpass; m++){
2148: k2=anint[m][i]+(mint[m][i]/12.);
2149: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2150: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2151: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2152: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2153: if (m<lastpass) {
2154: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2155: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2156: }
2157:
2158: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2159: dateintsum=dateintsum+k2;
2160: k2cpt++;
2161: }
2162: /*}*/
2163: }
2164: }
2165: }
2166:
2167: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2168: pstamp(ficresp);
2169: if (cptcovn>0) {
2170: fprintf(ficresp, "\n#********** Variable ");
2171: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2172: fprintf(ficresp, "**********\n#");
2173: }
2174: for(i=1; i<=nlstate;i++)
2175: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2176: fprintf(ficresp, "\n");
2177:
2178: for(i=iagemin; i <= iagemax+3; i++){
2179: if(i==iagemax+3){
2180: fprintf(ficlog,"Total");
2181: }else{
2182: if(first==1){
2183: first=0;
2184: printf("See log file for details...\n");
2185: }
2186: fprintf(ficlog,"Age %d", i);
2187: }
2188: for(jk=1; jk <=nlstate ; jk++){
2189: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2190: pp[jk] += freq[jk][m][i];
2191: }
2192: for(jk=1; jk <=nlstate ; jk++){
2193: for(m=-1, pos=0; m <=0 ; m++)
2194: pos += freq[jk][m][i];
2195: if(pp[jk]>=1.e-10){
2196: if(first==1){
2197: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2198: }
2199: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2200: }else{
2201: if(first==1)
2202: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2203: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2204: }
2205: }
2206:
2207: for(jk=1; jk <=nlstate ; jk++){
2208: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2209: pp[jk] += freq[jk][m][i];
2210: }
2211: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2212: pos += pp[jk];
2213: posprop += prop[jk][i];
2214: }
2215: for(jk=1; jk <=nlstate ; jk++){
2216: if(pos>=1.e-5){
2217: if(first==1)
2218: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2219: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2220: }else{
2221: if(first==1)
2222: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2223: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2224: }
2225: if( i <= iagemax){
2226: if(pos>=1.e-5){
2227: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2228: /*probs[i][jk][j1]= pp[jk]/pos;*/
2229: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2230: }
2231: else
2232: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2233: }
2234: }
2235:
2236: for(jk=-1; jk <=nlstate+ndeath; jk++)
2237: for(m=-1; m <=nlstate+ndeath; m++)
2238: if(freq[jk][m][i] !=0 ) {
2239: if(first==1)
2240: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2241: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2242: }
2243: if(i <= iagemax)
2244: fprintf(ficresp,"\n");
2245: if(first==1)
2246: printf("Others in log...\n");
2247: fprintf(ficlog,"\n");
2248: }
2249: }
2250: }
2251: dateintmean=dateintsum/k2cpt;
2252:
2253: fclose(ficresp);
2254: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2255: free_vector(pp,1,nlstate);
2256: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2257: /* End of Freq */
2258: }
2259:
2260: /************ Prevalence ********************/
2261: 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)
2262: {
2263: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2264: in each health status at the date of interview (if between dateprev1 and dateprev2).
2265: We still use firstpass and lastpass as another selection.
2266: */
2267:
2268: int i, m, jk, k1, i1, j1, bool, z1,j;
2269: double ***freq; /* Frequencies */
2270: double *pp, **prop;
2271: double pos,posprop;
2272: double y2; /* in fractional years */
2273: int iagemin, iagemax;
2274:
2275: iagemin= (int) agemin;
2276: iagemax= (int) agemax;
2277: /*pp=vector(1,nlstate);*/
2278: prop=matrix(1,nlstate,iagemin,iagemax+3);
2279: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2280: j1=0;
2281:
2282: j=cptcoveff;
2283: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2284:
2285: for(k1=1; k1<=j;k1++){
2286: for(i1=1; i1<=ncodemax[k1];i1++){
2287: j1++;
2288:
2289: for (i=1; i<=nlstate; i++)
2290: for(m=iagemin; m <= iagemax+3; m++)
2291: prop[i][m]=0.0;
2292:
2293: for (i=1; i<=imx; i++) { /* Each individual */
2294: bool=1;
2295: if (cptcovn>0) {
2296: for (z1=1; z1<=cptcoveff; z1++)
2297: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2298: bool=0;
2299: }
2300: if (bool==1) {
2301: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2302: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2303: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2304: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2305: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2306: 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);
2307: if (s[m][i]>0 && s[m][i]<=nlstate) {
2308: /*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]]);*/
2309: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2310: prop[s[m][i]][iagemax+3] += weight[i];
2311: }
2312: }
2313: } /* end selection of waves */
2314: }
2315: }
2316: for(i=iagemin; i <= iagemax+3; i++){
2317:
2318: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2319: posprop += prop[jk][i];
2320: }
2321:
2322: for(jk=1; jk <=nlstate ; jk++){
2323: if( i <= iagemax){
2324: if(posprop>=1.e-5){
2325: probs[i][jk][j1]= prop[jk][i]/posprop;
2326: } else
2327: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
2328: }
2329: }/* end jk */
2330: }/* end i */
2331: } /* end i1 */
2332: } /* end k1 */
2333:
2334: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2335: /*free_vector(pp,1,nlstate);*/
2336: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2337: } /* End of prevalence */
2338:
2339: /************* Waves Concatenation ***************/
2340:
2341: 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)
2342: {
2343: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2344: Death is a valid wave (if date is known).
2345: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2346: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2347: and mw[mi+1][i]. dh depends on stepm.
2348: */
2349:
2350: int i, mi, m;
2351: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2352: double sum=0., jmean=0.;*/
2353: int first;
2354: int j, k=0,jk, ju, jl;
2355: double sum=0.;
2356: first=0;
2357: jmin=1e+5;
2358: jmax=-1;
2359: jmean=0.;
2360: for(i=1; i<=imx; i++){
2361: mi=0;
2362: m=firstpass;
2363: while(s[m][i] <= nlstate){
2364: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2365: mw[++mi][i]=m;
2366: if(m >=lastpass)
2367: break;
2368: else
2369: m++;
2370: }/* end while */
2371: if (s[m][i] > nlstate){
2372: mi++; /* Death is another wave */
2373: /* if(mi==0) never been interviewed correctly before death */
2374: /* Only death is a correct wave */
2375: mw[mi][i]=m;
2376: }
2377:
2378: wav[i]=mi;
2379: if(mi==0){
2380: nbwarn++;
2381: if(first==0){
2382: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2383: first=1;
2384: }
2385: if(first==1){
2386: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2387: }
2388: } /* end mi==0 */
2389: } /* End individuals */
2390:
2391: for(i=1; i<=imx; i++){
2392: for(mi=1; mi<wav[i];mi++){
2393: if (stepm <=0)
2394: dh[mi][i]=1;
2395: else{
2396: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2397: if (agedc[i] < 2*AGESUP) {
2398: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2399: if(j==0) j=1; /* Survives at least one month after exam */
2400: else if(j<0){
2401: nberr++;
2402: 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]);
2403: j=1; /* Temporary Dangerous patch */
2404: 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);
2405: 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]);
2406: 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);
2407: }
2408: k=k+1;
2409: if (j >= jmax){
2410: jmax=j;
2411: ijmax=i;
2412: }
2413: if (j <= jmin){
2414: jmin=j;
2415: ijmin=i;
2416: }
2417: sum=sum+j;
2418: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2419: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2420: }
2421: }
2422: else{
2423: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2424: /* 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]); */
2425:
2426: k=k+1;
2427: if (j >= jmax) {
2428: jmax=j;
2429: ijmax=i;
2430: }
2431: else if (j <= jmin){
2432: jmin=j;
2433: ijmin=i;
2434: }
2435: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2436: /*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]);*/
2437: if(j<0){
2438: nberr++;
2439: 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]);
2440: 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]);
2441: }
2442: sum=sum+j;
2443: }
2444: jk= j/stepm;
2445: jl= j -jk*stepm;
2446: ju= j -(jk+1)*stepm;
2447: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2448: if(jl==0){
2449: dh[mi][i]=jk;
2450: bh[mi][i]=0;
2451: }else{ /* We want a negative bias in order to only have interpolation ie
2452: * to avoid the price of an extra matrix product in likelihood */
2453: dh[mi][i]=jk+1;
2454: bh[mi][i]=ju;
2455: }
2456: }else{
2457: if(jl <= -ju){
2458: dh[mi][i]=jk;
2459: bh[mi][i]=jl; /* bias is positive if real duration
2460: * is higher than the multiple of stepm and negative otherwise.
2461: */
2462: }
2463: else{
2464: dh[mi][i]=jk+1;
2465: bh[mi][i]=ju;
2466: }
2467: if(dh[mi][i]==0){
2468: dh[mi][i]=1; /* At least one step */
2469: bh[mi][i]=ju; /* At least one step */
2470: /* 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);*/
2471: }
2472: } /* end if mle */
2473: }
2474: } /* end wave */
2475: }
2476: jmean=sum/k;
2477: 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);
2478: 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);
2479: }
2480:
2481: /*********** Tricode ****************************/
2482: void tricode(int *Tvar, int **nbcode, int imx)
2483: {
2484: /* Uses cptcovn+2*cptcovprod as the number of covariates */
2485: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2486:
2487: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2488: int modmaxcovj=0; /* Modality max of covariates j */
2489: cptcoveff=0;
2490:
2491: for (k=0; k<maxncov; k++) Ndum[k]=0;
2492: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
2493:
2494: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
2495: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
2496: modality of this covariate Vj*/
2497: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
2498: modality of the nth covariate of individual i. */
2499: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2500: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2501: if (ij > modmaxcovj) modmaxcovj=ij;
2502: /* getting the maximum value of the modality of the covariate
2503: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2504: female is 1, then modmaxcovj=1.*/
2505: }
2506:
2507: for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*/
2508: if( Ndum[i] != 0 )
2509: ncodemax[j]++;
2510: /* Number of modalities of the j th covariate. In fact
2511: ncodemax[j]=2 (dichotom. variables only) but it could be more for
2512: historical reasons */
2513: } /* Ndum[-1] number of undefined modalities */
2514:
2515: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2516: ij=1;
2517: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
2518: for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
2519: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2520: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2521: k is a modality. If we have model=V1+V1*sex
2522: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2523: ij++;
2524: }
2525: if (ij > ncodemax[j]) break;
2526: }
2527: }
2528: }
2529:
2530: for (k=0; k< maxncov; k++) Ndum[k]=0;
2531:
2532: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2533: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2534: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2535: Ndum[ij]++;
2536: }
2537:
2538: ij=1;
2539: for (i=1; i<= maxncov; i++) {
2540: if((Ndum[i]!=0) && (i<=ncovcol)){
2541: Tvaraff[ij]=i; /*For printing */
2542: ij++;
2543: }
2544: }
2545: ij--;
2546: cptcoveff=ij; /*Number of simple covariates*/
2547: }
2548:
2549: /*********** Health Expectancies ****************/
2550:
2551: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2552:
2553: {
2554: /* Health expectancies, no variances */
2555: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2556: int nhstepma, nstepma; /* Decreasing with age */
2557: double age, agelim, hf;
2558: double ***p3mat;
2559: double eip;
2560:
2561: pstamp(ficreseij);
2562: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2563: fprintf(ficreseij,"# Age");
2564: for(i=1; i<=nlstate;i++){
2565: for(j=1; j<=nlstate;j++){
2566: fprintf(ficreseij," e%1d%1d ",i,j);
2567: }
2568: fprintf(ficreseij," e%1d. ",i);
2569: }
2570: fprintf(ficreseij,"\n");
2571:
2572:
2573: if(estepm < stepm){
2574: printf ("Problem %d lower than %d\n",estepm, stepm);
2575: }
2576: else hstepm=estepm;
2577: /* We compute the life expectancy from trapezoids spaced every estepm months
2578: * This is mainly to measure the difference between two models: for example
2579: * if stepm=24 months pijx are given only every 2 years and by summing them
2580: * we are calculating an estimate of the Life Expectancy assuming a linear
2581: * progression in between and thus overestimating or underestimating according
2582: * to the curvature of the survival function. If, for the same date, we
2583: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2584: * to compare the new estimate of Life expectancy with the same linear
2585: * hypothesis. A more precise result, taking into account a more precise
2586: * curvature will be obtained if estepm is as small as stepm. */
2587:
2588: /* For example we decided to compute the life expectancy with the smallest unit */
2589: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2590: nhstepm is the number of hstepm from age to agelim
2591: nstepm is the number of stepm from age to agelin.
2592: Look at hpijx to understand the reason of that which relies in memory size
2593: and note for a fixed period like estepm months */
2594: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2595: survival function given by stepm (the optimization length). Unfortunately it
2596: means that if the survival funtion is printed only each two years of age and if
2597: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2598: results. So we changed our mind and took the option of the best precision.
2599: */
2600: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2601:
2602: agelim=AGESUP;
2603: /* If stepm=6 months */
2604: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2605: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2606:
2607: /* nhstepm age range expressed in number of stepm */
2608: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2609: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2610: /* if (stepm >= YEARM) hstepm=1;*/
2611: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2612: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2613:
2614: for (age=bage; age<=fage; age ++){
2615: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2616: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2617: /* if (stepm >= YEARM) hstepm=1;*/
2618: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2619:
2620: /* If stepm=6 months */
2621: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2622: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2623:
2624: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2625:
2626: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2627:
2628: printf("%d|",(int)age);fflush(stdout);
2629: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2630:
2631: /* Computing expectancies */
2632: for(i=1; i<=nlstate;i++)
2633: for(j=1; j<=nlstate;j++)
2634: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2635: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2636:
2637: /* 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]);*/
2638:
2639: }
2640:
2641: fprintf(ficreseij,"%3.0f",age );
2642: for(i=1; i<=nlstate;i++){
2643: eip=0;
2644: for(j=1; j<=nlstate;j++){
2645: eip +=eij[i][j][(int)age];
2646: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2647: }
2648: fprintf(ficreseij,"%9.4f", eip );
2649: }
2650: fprintf(ficreseij,"\n");
2651:
2652: }
2653: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2654: printf("\n");
2655: fprintf(ficlog,"\n");
2656:
2657: }
2658:
2659: 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[] )
2660:
2661: {
2662: /* Covariances of health expectancies eij and of total life expectancies according
2663: to initial status i, ei. .
2664: */
2665: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2666: int nhstepma, nstepma; /* Decreasing with age */
2667: double age, agelim, hf;
2668: double ***p3matp, ***p3matm, ***varhe;
2669: double **dnewm,**doldm;
2670: double *xp, *xm;
2671: double **gp, **gm;
2672: double ***gradg, ***trgradg;
2673: int theta;
2674:
2675: double eip, vip;
2676:
2677: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2678: xp=vector(1,npar);
2679: xm=vector(1,npar);
2680: dnewm=matrix(1,nlstate*nlstate,1,npar);
2681: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2682:
2683: pstamp(ficresstdeij);
2684: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2685: fprintf(ficresstdeij,"# Age");
2686: for(i=1; i<=nlstate;i++){
2687: for(j=1; j<=nlstate;j++)
2688: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2689: fprintf(ficresstdeij," e%1d. ",i);
2690: }
2691: fprintf(ficresstdeij,"\n");
2692:
2693: pstamp(ficrescveij);
2694: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2695: fprintf(ficrescveij,"# Age");
2696: for(i=1; i<=nlstate;i++)
2697: for(j=1; j<=nlstate;j++){
2698: cptj= (j-1)*nlstate+i;
2699: for(i2=1; i2<=nlstate;i2++)
2700: for(j2=1; j2<=nlstate;j2++){
2701: cptj2= (j2-1)*nlstate+i2;
2702: if(cptj2 <= cptj)
2703: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2704: }
2705: }
2706: fprintf(ficrescveij,"\n");
2707:
2708: if(estepm < stepm){
2709: printf ("Problem %d lower than %d\n",estepm, stepm);
2710: }
2711: else hstepm=estepm;
2712: /* We compute the life expectancy from trapezoids spaced every estepm months
2713: * This is mainly to measure the difference between two models: for example
2714: * if stepm=24 months pijx are given only every 2 years and by summing them
2715: * we are calculating an estimate of the Life Expectancy assuming a linear
2716: * progression in between and thus overestimating or underestimating according
2717: * to the curvature of the survival function. If, for the same date, we
2718: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2719: * to compare the new estimate of Life expectancy with the same linear
2720: * hypothesis. A more precise result, taking into account a more precise
2721: * curvature will be obtained if estepm is as small as stepm. */
2722:
2723: /* For example we decided to compute the life expectancy with the smallest unit */
2724: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2725: nhstepm is the number of hstepm from age to agelim
2726: nstepm is the number of stepm from age to agelin.
2727: Look at hpijx to understand the reason of that which relies in memory size
2728: and note for a fixed period like estepm months */
2729: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2730: survival function given by stepm (the optimization length). Unfortunately it
2731: means that if the survival funtion is printed only each two years of age and if
2732: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2733: results. So we changed our mind and took the option of the best precision.
2734: */
2735: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2736:
2737: /* If stepm=6 months */
2738: /* nhstepm age range expressed in number of stepm */
2739: agelim=AGESUP;
2740: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2741: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2742: /* if (stepm >= YEARM) hstepm=1;*/
2743: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2744:
2745: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2746: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2747: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2748: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2749: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2750: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2751:
2752: for (age=bage; age<=fage; age ++){
2753: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2754: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2755: /* if (stepm >= YEARM) hstepm=1;*/
2756: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2757:
2758: /* If stepm=6 months */
2759: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2760: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2761:
2762: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2763:
2764: /* Computing Variances of health expectancies */
2765: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2766: decrease memory allocation */
2767: for(theta=1; theta <=npar; theta++){
2768: for(i=1; i<=npar; i++){
2769: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2770: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2771: }
2772: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2773: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2774:
2775: for(j=1; j<= nlstate; j++){
2776: for(i=1; i<=nlstate; i++){
2777: for(h=0; h<=nhstepm-1; h++){
2778: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2779: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2780: }
2781: }
2782: }
2783:
2784: for(ij=1; ij<= nlstate*nlstate; ij++)
2785: for(h=0; h<=nhstepm-1; h++){
2786: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2787: }
2788: }/* End theta */
2789:
2790:
2791: for(h=0; h<=nhstepm-1; h++)
2792: for(j=1; j<=nlstate*nlstate;j++)
2793: for(theta=1; theta <=npar; theta++)
2794: trgradg[h][j][theta]=gradg[h][theta][j];
2795:
2796:
2797: for(ij=1;ij<=nlstate*nlstate;ij++)
2798: for(ji=1;ji<=nlstate*nlstate;ji++)
2799: varhe[ij][ji][(int)age] =0.;
2800:
2801: printf("%d|",(int)age);fflush(stdout);
2802: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2803: for(h=0;h<=nhstepm-1;h++){
2804: for(k=0;k<=nhstepm-1;k++){
2805: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2806: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2807: for(ij=1;ij<=nlstate*nlstate;ij++)
2808: for(ji=1;ji<=nlstate*nlstate;ji++)
2809: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2810: }
2811: }
2812:
2813: /* Computing expectancies */
2814: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2815: for(i=1; i<=nlstate;i++)
2816: for(j=1; j<=nlstate;j++)
2817: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2818: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2819:
2820: /* 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]);*/
2821:
2822: }
2823:
2824: fprintf(ficresstdeij,"%3.0f",age );
2825: for(i=1; i<=nlstate;i++){
2826: eip=0.;
2827: vip=0.;
2828: for(j=1; j<=nlstate;j++){
2829: eip += eij[i][j][(int)age];
2830: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2831: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2832: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2833: }
2834: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2835: }
2836: fprintf(ficresstdeij,"\n");
2837:
2838: fprintf(ficrescveij,"%3.0f",age );
2839: for(i=1; i<=nlstate;i++)
2840: for(j=1; j<=nlstate;j++){
2841: cptj= (j-1)*nlstate+i;
2842: for(i2=1; i2<=nlstate;i2++)
2843: for(j2=1; j2<=nlstate;j2++){
2844: cptj2= (j2-1)*nlstate+i2;
2845: if(cptj2 <= cptj)
2846: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2847: }
2848: }
2849: fprintf(ficrescveij,"\n");
2850:
2851: }
2852: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2853: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2854: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2855: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2856: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2857: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2858: printf("\n");
2859: fprintf(ficlog,"\n");
2860:
2861: free_vector(xm,1,npar);
2862: free_vector(xp,1,npar);
2863: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2864: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2865: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2866: }
2867:
2868: /************ Variance ******************/
2869: 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[])
2870: {
2871: /* Variance of health expectancies */
2872: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2873: /* double **newm;*/
2874: double **dnewm,**doldm;
2875: double **dnewmp,**doldmp;
2876: int i, j, nhstepm, hstepm, h, nstepm ;
2877: int k, cptcode;
2878: double *xp;
2879: double **gp, **gm; /* for var eij */
2880: double ***gradg, ***trgradg; /*for var eij */
2881: double **gradgp, **trgradgp; /* for var p point j */
2882: double *gpp, *gmp; /* for var p point j */
2883: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2884: double ***p3mat;
2885: double age,agelim, hf;
2886: double ***mobaverage;
2887: int theta;
2888: char digit[4];
2889: char digitp[25];
2890:
2891: char fileresprobmorprev[FILENAMELENGTH];
2892:
2893: if(popbased==1){
2894: if(mobilav!=0)
2895: strcpy(digitp,"-populbased-mobilav-");
2896: else strcpy(digitp,"-populbased-nomobil-");
2897: }
2898: else
2899: strcpy(digitp,"-stablbased-");
2900:
2901: if (mobilav!=0) {
2902: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2903: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2904: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2905: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2906: }
2907: }
2908:
2909: strcpy(fileresprobmorprev,"prmorprev");
2910: sprintf(digit,"%-d",ij);
2911: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2912: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2913: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2914: strcat(fileresprobmorprev,fileres);
2915: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2916: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2917: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2918: }
2919: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2920:
2921: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2922: pstamp(ficresprobmorprev);
2923: 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);
2924: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2925: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2926: fprintf(ficresprobmorprev," p.%-d SE",j);
2927: for(i=1; i<=nlstate;i++)
2928: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2929: }
2930: fprintf(ficresprobmorprev,"\n");
2931: fprintf(ficgp,"\n# Routine varevsij");
2932: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2933: 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");
2934: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2935: /* } */
2936: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2937: pstamp(ficresvij);
2938: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2939: if(popbased==1)
2940: 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);
2941: else
2942: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2943: fprintf(ficresvij,"# Age");
2944: for(i=1; i<=nlstate;i++)
2945: for(j=1; j<=nlstate;j++)
2946: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2947: fprintf(ficresvij,"\n");
2948:
2949: xp=vector(1,npar);
2950: dnewm=matrix(1,nlstate,1,npar);
2951: doldm=matrix(1,nlstate,1,nlstate);
2952: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2953: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2954:
2955: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2956: gpp=vector(nlstate+1,nlstate+ndeath);
2957: gmp=vector(nlstate+1,nlstate+ndeath);
2958: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2959:
2960: if(estepm < stepm){
2961: printf ("Problem %d lower than %d\n",estepm, stepm);
2962: }
2963: else hstepm=estepm;
2964: /* For example we decided to compute the life expectancy with the smallest unit */
2965: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2966: nhstepm is the number of hstepm from age to agelim
2967: nstepm is the number of stepm from age to agelin.
2968: Look at function hpijx to understand why (it is linked to memory size questions) */
2969: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2970: survival function given by stepm (the optimization length). Unfortunately it
2971: means that if the survival funtion is printed every two years of age and if
2972: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2973: results. So we changed our mind and took the option of the best precision.
2974: */
2975: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2976: agelim = AGESUP;
2977: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2978: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2979: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2980: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2981: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2982: gp=matrix(0,nhstepm,1,nlstate);
2983: gm=matrix(0,nhstepm,1,nlstate);
2984:
2985:
2986: for(theta=1; theta <=npar; theta++){
2987: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2988: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2989: }
2990: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2991: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2992:
2993: if (popbased==1) {
2994: if(mobilav ==0){
2995: for(i=1; i<=nlstate;i++)
2996: prlim[i][i]=probs[(int)age][i][ij];
2997: }else{ /* mobilav */
2998: for(i=1; i<=nlstate;i++)
2999: prlim[i][i]=mobaverage[(int)age][i][ij];
3000: }
3001: }
3002:
3003: for(j=1; j<= nlstate; j++){
3004: for(h=0; h<=nhstepm; h++){
3005: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3006: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3007: }
3008: }
3009: /* This for computing probability of death (h=1 means
3010: computed over hstepm matrices product = hstepm*stepm months)
3011: as a weighted average of prlim.
3012: */
3013: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3014: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3015: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3016: }
3017: /* end probability of death */
3018:
3019: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3020: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3021: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3022: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3023:
3024: if (popbased==1) {
3025: if(mobilav ==0){
3026: for(i=1; i<=nlstate;i++)
3027: prlim[i][i]=probs[(int)age][i][ij];
3028: }else{ /* mobilav */
3029: for(i=1; i<=nlstate;i++)
3030: prlim[i][i]=mobaverage[(int)age][i][ij];
3031: }
3032: }
3033:
3034: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3035: for(h=0; h<=nhstepm; h++){
3036: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3037: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3038: }
3039: }
3040: /* This for computing probability of death (h=1 means
3041: computed over hstepm matrices product = hstepm*stepm months)
3042: as a weighted average of prlim.
3043: */
3044: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3045: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3046: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3047: }
3048: /* end probability of death */
3049:
3050: for(j=1; j<= nlstate; j++) /* vareij */
3051: for(h=0; h<=nhstepm; h++){
3052: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3053: }
3054:
3055: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3056: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3057: }
3058:
3059: } /* End theta */
3060:
3061: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3062:
3063: for(h=0; h<=nhstepm; h++) /* veij */
3064: for(j=1; j<=nlstate;j++)
3065: for(theta=1; theta <=npar; theta++)
3066: trgradg[h][j][theta]=gradg[h][theta][j];
3067:
3068: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3069: for(theta=1; theta <=npar; theta++)
3070: trgradgp[j][theta]=gradgp[theta][j];
3071:
3072:
3073: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3074: for(i=1;i<=nlstate;i++)
3075: for(j=1;j<=nlstate;j++)
3076: vareij[i][j][(int)age] =0.;
3077:
3078: for(h=0;h<=nhstepm;h++){
3079: for(k=0;k<=nhstepm;k++){
3080: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3081: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3082: for(i=1;i<=nlstate;i++)
3083: for(j=1;j<=nlstate;j++)
3084: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3085: }
3086: }
3087:
3088: /* pptj */
3089: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3090: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3091: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3092: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3093: varppt[j][i]=doldmp[j][i];
3094: /* end ppptj */
3095: /* x centered again */
3096: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3097: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3098:
3099: if (popbased==1) {
3100: if(mobilav ==0){
3101: for(i=1; i<=nlstate;i++)
3102: prlim[i][i]=probs[(int)age][i][ij];
3103: }else{ /* mobilav */
3104: for(i=1; i<=nlstate;i++)
3105: prlim[i][i]=mobaverage[(int)age][i][ij];
3106: }
3107: }
3108:
3109: /* This for computing probability of death (h=1 means
3110: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3111: as a weighted average of prlim.
3112: */
3113: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3114: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3115: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3116: }
3117: /* end probability of death */
3118:
3119: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3120: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3121: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3122: for(i=1; i<=nlstate;i++){
3123: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3124: }
3125: }
3126: fprintf(ficresprobmorprev,"\n");
3127:
3128: fprintf(ficresvij,"%.0f ",age );
3129: for(i=1; i<=nlstate;i++)
3130: for(j=1; j<=nlstate;j++){
3131: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3132: }
3133: fprintf(ficresvij,"\n");
3134: free_matrix(gp,0,nhstepm,1,nlstate);
3135: free_matrix(gm,0,nhstepm,1,nlstate);
3136: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3137: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3138: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3139: } /* End age */
3140: free_vector(gpp,nlstate+1,nlstate+ndeath);
3141: free_vector(gmp,nlstate+1,nlstate+ndeath);
3142: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3143: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3144: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
3145: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3146: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3147: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3148: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3149: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3150: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3151: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3152: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3153: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3154: 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);
3155: /* 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);
3156: */
3157: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3158: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3159:
3160: free_vector(xp,1,npar);
3161: free_matrix(doldm,1,nlstate,1,nlstate);
3162: free_matrix(dnewm,1,nlstate,1,npar);
3163: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3164: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3165: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3166: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3167: fclose(ficresprobmorprev);
3168: fflush(ficgp);
3169: fflush(fichtm);
3170: } /* end varevsij */
3171:
3172: /************ Variance of prevlim ******************/
3173: 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[])
3174: {
3175: /* Variance of prevalence limit */
3176: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3177: double **newm;
3178: double **dnewm,**doldm;
3179: int i, j, nhstepm, hstepm;
3180: int k, cptcode;
3181: double *xp;
3182: double *gp, *gm;
3183: double **gradg, **trgradg;
3184: double age,agelim;
3185: int theta;
3186:
3187: pstamp(ficresvpl);
3188: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3189: fprintf(ficresvpl,"# Age");
3190: for(i=1; i<=nlstate;i++)
3191: fprintf(ficresvpl," %1d-%1d",i,i);
3192: fprintf(ficresvpl,"\n");
3193:
3194: xp=vector(1,npar);
3195: dnewm=matrix(1,nlstate,1,npar);
3196: doldm=matrix(1,nlstate,1,nlstate);
3197:
3198: hstepm=1*YEARM; /* Every year of age */
3199: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3200: agelim = AGESUP;
3201: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3202: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3203: if (stepm >= YEARM) hstepm=1;
3204: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3205: gradg=matrix(1,npar,1,nlstate);
3206: gp=vector(1,nlstate);
3207: gm=vector(1,nlstate);
3208:
3209: for(theta=1; theta <=npar; theta++){
3210: for(i=1; i<=npar; i++){ /* Computes gradient */
3211: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3212: }
3213: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3214: for(i=1;i<=nlstate;i++)
3215: gp[i] = prlim[i][i];
3216:
3217: for(i=1; i<=npar; i++) /* Computes gradient */
3218: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3219: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3220: for(i=1;i<=nlstate;i++)
3221: gm[i] = prlim[i][i];
3222:
3223: for(i=1;i<=nlstate;i++)
3224: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3225: } /* End theta */
3226:
3227: trgradg =matrix(1,nlstate,1,npar);
3228:
3229: for(j=1; j<=nlstate;j++)
3230: for(theta=1; theta <=npar; theta++)
3231: trgradg[j][theta]=gradg[theta][j];
3232:
3233: for(i=1;i<=nlstate;i++)
3234: varpl[i][(int)age] =0.;
3235: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3236: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3237: for(i=1;i<=nlstate;i++)
3238: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3239:
3240: fprintf(ficresvpl,"%.0f ",age );
3241: for(i=1; i<=nlstate;i++)
3242: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3243: fprintf(ficresvpl,"\n");
3244: free_vector(gp,1,nlstate);
3245: free_vector(gm,1,nlstate);
3246: free_matrix(gradg,1,npar,1,nlstate);
3247: free_matrix(trgradg,1,nlstate,1,npar);
3248: } /* End age */
3249:
3250: free_vector(xp,1,npar);
3251: free_matrix(doldm,1,nlstate,1,npar);
3252: free_matrix(dnewm,1,nlstate,1,nlstate);
3253:
3254: }
3255:
3256: /************ Variance of one-step probabilities ******************/
3257: 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[])
3258: {
3259: int i, j=0, i1, k1, l1, t, tj;
3260: int k2, l2, j1, z1;
3261: int k=0,l, cptcode;
3262: int first=1, first1;
3263: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3264: double **dnewm,**doldm;
3265: double *xp;
3266: double *gp, *gm;
3267: double **gradg, **trgradg;
3268: double **mu;
3269: double age,agelim, cov[NCOVMAX];
3270: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3271: int theta;
3272: char fileresprob[FILENAMELENGTH];
3273: char fileresprobcov[FILENAMELENGTH];
3274: char fileresprobcor[FILENAMELENGTH];
3275:
3276: double ***varpij;
3277:
3278: strcpy(fileresprob,"prob");
3279: strcat(fileresprob,fileres);
3280: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3281: printf("Problem with resultfile: %s\n", fileresprob);
3282: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3283: }
3284: strcpy(fileresprobcov,"probcov");
3285: strcat(fileresprobcov,fileres);
3286: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3287: printf("Problem with resultfile: %s\n", fileresprobcov);
3288: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3289: }
3290: strcpy(fileresprobcor,"probcor");
3291: strcat(fileresprobcor,fileres);
3292: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3293: printf("Problem with resultfile: %s\n", fileresprobcor);
3294: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3295: }
3296: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3297: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3298: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3299: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3300: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3301: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3302: pstamp(ficresprob);
3303: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3304: fprintf(ficresprob,"# Age");
3305: pstamp(ficresprobcov);
3306: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3307: fprintf(ficresprobcov,"# Age");
3308: pstamp(ficresprobcor);
3309: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3310: fprintf(ficresprobcor,"# Age");
3311:
3312:
3313: for(i=1; i<=nlstate;i++)
3314: for(j=1; j<=(nlstate+ndeath);j++){
3315: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3316: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3317: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3318: }
3319: /* fprintf(ficresprob,"\n");
3320: fprintf(ficresprobcov,"\n");
3321: fprintf(ficresprobcor,"\n");
3322: */
3323: xp=vector(1,npar);
3324: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3325: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3326: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3327: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3328: first=1;
3329: fprintf(ficgp,"\n# Routine varprob");
3330: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3331: fprintf(fichtm,"\n");
3332:
3333: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3334: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3335: file %s<br>\n",optionfilehtmcov);
3336: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3337: and drawn. It helps understanding how is the covariance between two incidences.\
3338: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3339: 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. \
3340: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3341: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3342: standard deviations wide on each axis. <br>\
3343: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3344: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3345: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3346:
3347: cov[1]=1;
3348: tj=cptcoveff;
3349: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3350: j1=0;
3351: for(t=1; t<=tj;t++){
3352: for(i1=1; i1<=ncodemax[t];i1++){
3353: j1++;
3354: if (cptcovn>0) {
3355: fprintf(ficresprob, "\n#********** Variable ");
3356: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3357: fprintf(ficresprob, "**********\n#\n");
3358: fprintf(ficresprobcov, "\n#********** Variable ");
3359: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3360: fprintf(ficresprobcov, "**********\n#\n");
3361:
3362: fprintf(ficgp, "\n#********** Variable ");
3363: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3364: fprintf(ficgp, "**********\n#\n");
3365:
3366:
3367: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3368: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3369: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3370:
3371: fprintf(ficresprobcor, "\n#********** Variable ");
3372: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3373: fprintf(ficresprobcor, "**********\n#");
3374: }
3375:
3376: for (age=bage; age<=fage; age ++){
3377: cov[2]=age;
3378: for (k=1; k<=cptcovn;k++) {
3379: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3380: }
3381: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3382: for (k=1; k<=cptcovprod;k++)
3383: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3384:
3385: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3386: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3387: gp=vector(1,(nlstate)*(nlstate+ndeath));
3388: gm=vector(1,(nlstate)*(nlstate+ndeath));
3389:
3390: for(theta=1; theta <=npar; theta++){
3391: for(i=1; i<=npar; i++)
3392: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3393:
3394: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3395:
3396: k=0;
3397: for(i=1; i<= (nlstate); i++){
3398: for(j=1; j<=(nlstate+ndeath);j++){
3399: k=k+1;
3400: gp[k]=pmmij[i][j];
3401: }
3402: }
3403:
3404: for(i=1; i<=npar; i++)
3405: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3406:
3407: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3408: k=0;
3409: for(i=1; i<=(nlstate); i++){
3410: for(j=1; j<=(nlstate+ndeath);j++){
3411: k=k+1;
3412: gm[k]=pmmij[i][j];
3413: }
3414: }
3415:
3416: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3417: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3418: }
3419:
3420: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3421: for(theta=1; theta <=npar; theta++)
3422: trgradg[j][theta]=gradg[theta][j];
3423:
3424: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3425: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3426: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3427: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3428: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3429: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3430:
3431: pmij(pmmij,cov,ncovmodel,x,nlstate);
3432:
3433: k=0;
3434: for(i=1; i<=(nlstate); i++){
3435: for(j=1; j<=(nlstate+ndeath);j++){
3436: k=k+1;
3437: mu[k][(int) age]=pmmij[i][j];
3438: }
3439: }
3440: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3441: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3442: varpij[i][j][(int)age] = doldm[i][j];
3443:
3444: /*printf("\n%d ",(int)age);
3445: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3446: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3447: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3448: }*/
3449:
3450: fprintf(ficresprob,"\n%d ",(int)age);
3451: fprintf(ficresprobcov,"\n%d ",(int)age);
3452: fprintf(ficresprobcor,"\n%d ",(int)age);
3453:
3454: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3455: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3456: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3457: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3458: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3459: }
3460: i=0;
3461: for (k=1; k<=(nlstate);k++){
3462: for (l=1; l<=(nlstate+ndeath);l++){
3463: i=i++;
3464: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3465: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3466: for (j=1; j<=i;j++){
3467: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3468: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3469: }
3470: }
3471: }/* end of loop for state */
3472: } /* end of loop for age */
3473:
3474: /* Confidence intervalle of pij */
3475: /*
3476: fprintf(ficgp,"\nunset parametric;unset label");
3477: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3478: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3479: 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);
3480: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3481: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3482: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3483: */
3484:
3485: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3486: first1=1;
3487: for (k2=1; k2<=(nlstate);k2++){
3488: for (l2=1; l2<=(nlstate+ndeath);l2++){
3489: if(l2==k2) continue;
3490: j=(k2-1)*(nlstate+ndeath)+l2;
3491: for (k1=1; k1<=(nlstate);k1++){
3492: for (l1=1; l1<=(nlstate+ndeath);l1++){
3493: if(l1==k1) continue;
3494: i=(k1-1)*(nlstate+ndeath)+l1;
3495: if(i<=j) continue;
3496: for (age=bage; age<=fage; age ++){
3497: if ((int)age %5==0){
3498: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3499: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3500: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3501: mu1=mu[i][(int) age]/stepm*YEARM ;
3502: mu2=mu[j][(int) age]/stepm*YEARM;
3503: c12=cv12/sqrt(v1*v2);
3504: /* Computing eigen value of matrix of covariance */
3505: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3506: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3507: if ((lc2 <0) || (lc1 <0) ){
3508: printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
3509: fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
3510: lc1=fabs(lc1);
3511: lc2=fabs(lc2);
3512: }
3513:
3514: /* Eigen vectors */
3515: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3516: /*v21=sqrt(1.-v11*v11); *//* error */
3517: v21=(lc1-v1)/cv12*v11;
3518: v12=-v21;
3519: v22=v11;
3520: tnalp=v21/v11;
3521: if(first1==1){
3522: first1=0;
3523: 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);
3524: }
3525: 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);
3526: /*printf(fignu*/
3527: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3528: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3529: if(first==1){
3530: first=0;
3531: fprintf(ficgp,"\nset parametric;unset label");
3532: 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);
3533: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3534: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3535: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3536: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3537: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3538: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3539: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3540: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3541: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3542: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3543: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3544: 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",\
3545: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3546: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3547: }else{
3548: first=0;
3549: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3550: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3551: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3552: 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",\
3553: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3554: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3555: }/* if first */
3556: } /* age mod 5 */
3557: } /* end loop age */
3558: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3559: first=1;
3560: } /*l12 */
3561: } /* k12 */
3562: } /*l1 */
3563: }/* k1 */
3564: } /* loop covariates */
3565: }
3566: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3567: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3568: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3569: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3570: free_vector(xp,1,npar);
3571: fclose(ficresprob);
3572: fclose(ficresprobcov);
3573: fclose(ficresprobcor);
3574: fflush(ficgp);
3575: fflush(fichtmcov);
3576: }
3577:
3578:
3579: /******************* Printing html file ***********/
3580: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3581: int lastpass, int stepm, int weightopt, char model[],\
3582: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3583: int popforecast, int estepm ,\
3584: double jprev1, double mprev1,double anprev1, \
3585: double jprev2, double mprev2,double anprev2){
3586: int jj1, k1, i1, cpt;
3587:
3588: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3589: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3590: </ul>");
3591: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3592: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3593: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3594: fprintf(fichtm,"\
3595: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3596: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3597: fprintf(fichtm,"\
3598: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3599: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3600: fprintf(fichtm,"\
3601: - (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): \
3602: <a href=\"%s\">%s</a> <br>\n",
3603: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3604: fprintf(fichtm,"\
3605: - Population projections by age and states: \
3606: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3607:
3608: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3609:
3610: m=cptcoveff;
3611: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3612:
3613: jj1=0;
3614: for(k1=1; k1<=m;k1++){
3615: for(i1=1; i1<=ncodemax[k1];i1++){
3616: jj1++;
3617: if (cptcovn > 0) {
3618: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3619: for (cpt=1; cpt<=cptcoveff;cpt++)
3620: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3621: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3622: }
3623: /* Pij */
3624: 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> \
3625: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3626: /* Quasi-incidences */
3627: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3628: 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> \
3629: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3630: /* Period (stable) prevalence in each health state */
3631: for(cpt=1; cpt<nlstate;cpt++){
3632: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3633: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3634: }
3635: for(cpt=1; cpt<=nlstate;cpt++) {
3636: 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> \
3637: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3638: }
3639: } /* end i1 */
3640: }/* End k1 */
3641: fprintf(fichtm,"</ul>");
3642:
3643:
3644: fprintf(fichtm,"\
3645: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3646: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3647:
3648: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3649: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3650: fprintf(fichtm,"\
3651: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3652: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3653:
3654: fprintf(fichtm,"\
3655: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3656: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3657: fprintf(fichtm,"\
3658: - 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): \
3659: <a href=\"%s\">%s</a> <br>\n</li>",
3660: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3661: fprintf(fichtm,"\
3662: - (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): \
3663: <a href=\"%s\">%s</a> <br>\n</li>",
3664: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3665: fprintf(fichtm,"\
3666: - 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",
3667: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3668: fprintf(fichtm,"\
3669: - 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",
3670: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3671: fprintf(fichtm,"\
3672: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3673: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3674:
3675: /* if(popforecast==1) fprintf(fichtm,"\n */
3676: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3677: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3678: /* <br>",fileres,fileres,fileres,fileres); */
3679: /* else */
3680: /* 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); */
3681: fflush(fichtm);
3682: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3683:
3684: m=cptcoveff;
3685: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3686:
3687: jj1=0;
3688: for(k1=1; k1<=m;k1++){
3689: for(i1=1; i1<=ncodemax[k1];i1++){
3690: jj1++;
3691: if (cptcovn > 0) {
3692: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3693: for (cpt=1; cpt<=cptcoveff;cpt++)
3694: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3695: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3696: }
3697: for(cpt=1; cpt<=nlstate;cpt++) {
3698: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3699: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3700: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3701: }
3702: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3703: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3704: true period expectancies (those weighted with period prevalences are also\
3705: drawn in addition to the population based expectancies computed using\
3706: observed and cahotic prevalences: %s%d.png<br>\
3707: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3708: } /* end i1 */
3709: }/* End k1 */
3710: fprintf(fichtm,"</ul>");
3711: fflush(fichtm);
3712: }
3713:
3714: /******************* Gnuplot file **************/
3715: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3716:
3717: char dirfileres[132],optfileres[132];
3718: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3719: int ng=0;
3720: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3721: /* printf("Problem with file %s",optionfilegnuplot); */
3722: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3723: /* } */
3724:
3725: /*#ifdef windows */
3726: fprintf(ficgp,"cd \"%s\" \n",pathc);
3727: /*#endif */
3728: m=pow(2,cptcoveff);
3729:
3730: strcpy(dirfileres,optionfilefiname);
3731: strcpy(optfileres,"vpl");
3732: /* 1eme*/
3733: for (cpt=1; cpt<= nlstate ; cpt ++) {
3734: for (k1=1; k1<= m ; k1 ++) {
3735: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3736: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3737: fprintf(ficgp,"set xlabel \"Age\" \n\
3738: set ylabel \"Probability\" \n\
3739: set ter png small\n\
3740: set size 0.65,0.65\n\
3741: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3742:
3743: for (i=1; i<= nlstate ; i ++) {
3744: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3745: else fprintf(ficgp," \%%*lf (\%%*lf)");
3746: }
3747: 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);
3748: for (i=1; i<= nlstate ; i ++) {
3749: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3750: else fprintf(ficgp," \%%*lf (\%%*lf)");
3751: }
3752: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3753: for (i=1; i<= nlstate ; i ++) {
3754: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3755: else fprintf(ficgp," \%%*lf (\%%*lf)");
3756: }
3757: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3758: }
3759: }
3760: /*2 eme*/
3761:
3762: for (k1=1; k1<= m ; k1 ++) {
3763: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3764: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3765:
3766: for (i=1; i<= nlstate+1 ; i ++) {
3767: k=2*i;
3768: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3769: for (j=1; j<= nlstate+1 ; j ++) {
3770: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3771: else fprintf(ficgp," \%%*lf (\%%*lf)");
3772: }
3773: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3774: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3775: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3776: for (j=1; j<= nlstate+1 ; j ++) {
3777: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3778: else fprintf(ficgp," \%%*lf (\%%*lf)");
3779: }
3780: fprintf(ficgp,"\" t\"\" w l 0,");
3781: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3782: for (j=1; j<= nlstate+1 ; j ++) {
3783: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3784: else fprintf(ficgp," \%%*lf (\%%*lf)");
3785: }
3786: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3787: else fprintf(ficgp,"\" t\"\" w l 0,");
3788: }
3789: }
3790:
3791: /*3eme*/
3792:
3793: for (k1=1; k1<= m ; k1 ++) {
3794: for (cpt=1; cpt<= nlstate ; cpt ++) {
3795: /* k=2+nlstate*(2*cpt-2); */
3796: k=2+(nlstate+1)*(cpt-1);
3797: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3798: fprintf(ficgp,"set ter png small\n\
3799: set size 0.65,0.65\n\
3800: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3801: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3802: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3803: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3804: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3805: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3806: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3807:
3808: */
3809: for (i=1; i< nlstate ; i ++) {
3810: 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);
3811: /* 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);*/
3812:
3813: }
3814: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3815: }
3816: }
3817:
3818: /* CV preval stable (period) */
3819: for (k1=1; k1<= m ; k1 ++) {
3820: for (cpt=1; cpt<=nlstate ; cpt ++) {
3821: k=3;
3822: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3823: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3824: set ter png small\nset size 0.65,0.65\n\
3825: unset log y\n\
3826: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3827:
3828: for (i=1; i< nlstate ; i ++)
3829: fprintf(ficgp,"+$%d",k+i+1);
3830: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3831:
3832: l=3+(nlstate+ndeath)*cpt;
3833: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3834: for (i=1; i< nlstate ; i ++) {
3835: l=3+(nlstate+ndeath)*cpt;
3836: fprintf(ficgp,"+$%d",l+i+1);
3837: }
3838: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3839: }
3840: }
3841:
3842: /* proba elementaires */
3843: for(i=1,jk=1; i <=nlstate; i++){
3844: for(k=1; k <=(nlstate+ndeath); k++){
3845: if (k != i) {
3846: for(j=1; j <=ncovmodel; j++){
3847: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3848: jk++;
3849: fprintf(ficgp,"\n");
3850: }
3851: }
3852: }
3853: }
3854:
3855: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3856: for(jk=1; jk <=m; jk++) {
3857: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3858: if (ng==2)
3859: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3860: else
3861: fprintf(ficgp,"\nset title \"Probability\"\n");
3862: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3863: i=1;
3864: for(k2=1; k2<=nlstate; k2++) {
3865: k3=i;
3866: for(k=1; k<=(nlstate+ndeath); k++) {
3867: if (k != k2){
3868: if(ng==2)
3869: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3870: else
3871: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3872: ij=1;
3873: for(j=3; j <=ncovmodel; j++) {
3874: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3875: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3876: ij++;
3877: }
3878: else
3879: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3880: }
3881: fprintf(ficgp,")/(1");
3882:
3883: for(k1=1; k1 <=nlstate; k1++){
3884: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3885: ij=1;
3886: for(j=3; j <=ncovmodel; j++){
3887: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3888: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3889: ij++;
3890: }
3891: else
3892: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3893: }
3894: fprintf(ficgp,")");
3895: }
3896: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3897: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3898: i=i+ncovmodel;
3899: }
3900: } /* end k */
3901: } /* end k2 */
3902: } /* end jk */
3903: } /* end ng */
3904: fflush(ficgp);
3905: } /* end gnuplot */
3906:
3907:
3908: /*************** Moving average **************/
3909: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3910:
3911: int i, cpt, cptcod;
3912: int modcovmax =1;
3913: int mobilavrange, mob;
3914: double age;
3915:
3916: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3917: a covariate has 2 modalities */
3918: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3919:
3920: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3921: if(mobilav==1) mobilavrange=5; /* default */
3922: else mobilavrange=mobilav;
3923: for (age=bage; age<=fage; age++)
3924: for (i=1; i<=nlstate;i++)
3925: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3926: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3927: /* We keep the original values on the extreme ages bage, fage and for
3928: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3929: we use a 5 terms etc. until the borders are no more concerned.
3930: */
3931: for (mob=3;mob <=mobilavrange;mob=mob+2){
3932: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3933: for (i=1; i<=nlstate;i++){
3934: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3935: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3936: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3937: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3938: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3939: }
3940: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3941: }
3942: }
3943: }/* end age */
3944: }/* end mob */
3945: }else return -1;
3946: return 0;
3947: }/* End movingaverage */
3948:
3949:
3950: /************** Forecasting ******************/
3951: 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){
3952: /* proj1, year, month, day of starting projection
3953: agemin, agemax range of age
3954: dateprev1 dateprev2 range of dates during which prevalence is computed
3955: anproj2 year of en of projection (same day and month as proj1).
3956: */
3957: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3958: int *popage;
3959: double agec; /* generic age */
3960: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3961: double *popeffectif,*popcount;
3962: double ***p3mat;
3963: double ***mobaverage;
3964: char fileresf[FILENAMELENGTH];
3965:
3966: agelim=AGESUP;
3967: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3968:
3969: strcpy(fileresf,"f");
3970: strcat(fileresf,fileres);
3971: if((ficresf=fopen(fileresf,"w"))==NULL) {
3972: printf("Problem with forecast resultfile: %s\n", fileresf);
3973: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3974: }
3975: printf("Computing forecasting: result on file '%s' \n", fileresf);
3976: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3977:
3978: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3979:
3980: if (mobilav!=0) {
3981: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3982: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3983: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3984: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3985: }
3986: }
3987:
3988: stepsize=(int) (stepm+YEARM-1)/YEARM;
3989: if (stepm<=12) stepsize=1;
3990: if(estepm < stepm){
3991: printf ("Problem %d lower than %d\n",estepm, stepm);
3992: }
3993: else hstepm=estepm;
3994:
3995: hstepm=hstepm/stepm;
3996: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3997: fractional in yp1 */
3998: anprojmean=yp;
3999: yp2=modf((yp1*12),&yp);
4000: mprojmean=yp;
4001: yp1=modf((yp2*30.5),&yp);
4002: jprojmean=yp;
4003: if(jprojmean==0) jprojmean=1;
4004: if(mprojmean==0) jprojmean=1;
4005:
4006: i1=cptcoveff;
4007: if (cptcovn < 1){i1=1;}
4008:
4009: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4010:
4011: fprintf(ficresf,"#****** Routine prevforecast **\n");
4012:
4013: /* if (h==(int)(YEARM*yearp)){ */
4014: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4015: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4016: k=k+1;
4017: fprintf(ficresf,"\n#******");
4018: for(j=1;j<=cptcoveff;j++) {
4019: 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]]);
4020: }
4021: fprintf(ficresf,"******\n");
4022: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4023: for(j=1; j<=nlstate+ndeath;j++){
4024: for(i=1; i<=nlstate;i++)
4025: fprintf(ficresf," p%d%d",i,j);
4026: fprintf(ficresf," p.%d",j);
4027: }
4028: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4029: fprintf(ficresf,"\n");
4030: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4031:
4032: for (agec=fage; agec>=(ageminpar-1); agec--){
4033: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4034: nhstepm = nhstepm/hstepm;
4035: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4036: oldm=oldms;savm=savms;
4037: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4038:
4039: for (h=0; h<=nhstepm; h++){
4040: if (h*hstepm/YEARM*stepm ==yearp) {
4041: fprintf(ficresf,"\n");
4042: for(j=1;j<=cptcoveff;j++)
4043: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4044: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4045: }
4046: for(j=1; j<=nlstate+ndeath;j++) {
4047: ppij=0.;
4048: for(i=1; i<=nlstate;i++) {
4049: if (mobilav==1)
4050: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4051: else {
4052: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4053: }
4054: if (h*hstepm/YEARM*stepm== yearp) {
4055: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4056: }
4057: } /* end i */
4058: if (h*hstepm/YEARM*stepm==yearp) {
4059: fprintf(ficresf," %.3f", ppij);
4060: }
4061: }/* end j */
4062: } /* end h */
4063: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4064: } /* end agec */
4065: } /* end yearp */
4066: } /* end cptcod */
4067: } /* end cptcov */
4068:
4069: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4070:
4071: fclose(ficresf);
4072: }
4073:
4074: /************** Forecasting *****not tested NB*************/
4075: 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){
4076:
4077: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4078: int *popage;
4079: double calagedatem, agelim, kk1, kk2;
4080: double *popeffectif,*popcount;
4081: double ***p3mat,***tabpop,***tabpopprev;
4082: double ***mobaverage;
4083: char filerespop[FILENAMELENGTH];
4084:
4085: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4086: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4087: agelim=AGESUP;
4088: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4089:
4090: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4091:
4092:
4093: strcpy(filerespop,"pop");
4094: strcat(filerespop,fileres);
4095: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4096: printf("Problem with forecast resultfile: %s\n", filerespop);
4097: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4098: }
4099: printf("Computing forecasting: result on file '%s' \n", filerespop);
4100: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4101:
4102: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4103:
4104: if (mobilav!=0) {
4105: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4106: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4107: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4108: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4109: }
4110: }
4111:
4112: stepsize=(int) (stepm+YEARM-1)/YEARM;
4113: if (stepm<=12) stepsize=1;
4114:
4115: agelim=AGESUP;
4116:
4117: hstepm=1;
4118: hstepm=hstepm/stepm;
4119:
4120: if (popforecast==1) {
4121: if((ficpop=fopen(popfile,"r"))==NULL) {
4122: printf("Problem with population file : %s\n",popfile);exit(0);
4123: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4124: }
4125: popage=ivector(0,AGESUP);
4126: popeffectif=vector(0,AGESUP);
4127: popcount=vector(0,AGESUP);
4128:
4129: i=1;
4130: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4131:
4132: imx=i;
4133: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4134: }
4135:
4136: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4137: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4138: k=k+1;
4139: fprintf(ficrespop,"\n#******");
4140: for(j=1;j<=cptcoveff;j++) {
4141: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4142: }
4143: fprintf(ficrespop,"******\n");
4144: fprintf(ficrespop,"# Age");
4145: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4146: if (popforecast==1) fprintf(ficrespop," [Population]");
4147:
4148: for (cpt=0; cpt<=0;cpt++) {
4149: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4150:
4151: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4152: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4153: nhstepm = nhstepm/hstepm;
4154:
4155: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4156: oldm=oldms;savm=savms;
4157: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4158:
4159: for (h=0; h<=nhstepm; h++){
4160: if (h==(int) (calagedatem+YEARM*cpt)) {
4161: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4162: }
4163: for(j=1; j<=nlstate+ndeath;j++) {
4164: kk1=0.;kk2=0;
4165: for(i=1; i<=nlstate;i++) {
4166: if (mobilav==1)
4167: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4168: else {
4169: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4170: }
4171: }
4172: if (h==(int)(calagedatem+12*cpt)){
4173: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4174: /*fprintf(ficrespop," %.3f", kk1);
4175: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4176: }
4177: }
4178: for(i=1; i<=nlstate;i++){
4179: kk1=0.;
4180: for(j=1; j<=nlstate;j++){
4181: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4182: }
4183: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4184: }
4185:
4186: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4187: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4188: }
4189: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4190: }
4191: }
4192:
4193: /******/
4194:
4195: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4196: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4197: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4198: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4199: nhstepm = nhstepm/hstepm;
4200:
4201: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4202: oldm=oldms;savm=savms;
4203: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4204: for (h=0; h<=nhstepm; h++){
4205: if (h==(int) (calagedatem+YEARM*cpt)) {
4206: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4207: }
4208: for(j=1; j<=nlstate+ndeath;j++) {
4209: kk1=0.;kk2=0;
4210: for(i=1; i<=nlstate;i++) {
4211: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4212: }
4213: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4214: }
4215: }
4216: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4217: }
4218: }
4219: }
4220: }
4221:
4222: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4223:
4224: if (popforecast==1) {
4225: free_ivector(popage,0,AGESUP);
4226: free_vector(popeffectif,0,AGESUP);
4227: free_vector(popcount,0,AGESUP);
4228: }
4229: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4230: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4231: fclose(ficrespop);
4232: } /* End of popforecast */
4233:
4234: int fileappend(FILE *fichier, char *optionfich)
4235: {
4236: if((fichier=fopen(optionfich,"a"))==NULL) {
4237: printf("Problem with file: %s\n", optionfich);
4238: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4239: return (0);
4240: }
4241: fflush(fichier);
4242: return (1);
4243: }
4244:
4245:
4246: /**************** function prwizard **********************/
4247: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4248: {
4249:
4250: /* Wizard to print covariance matrix template */
4251:
4252: char ca[32], cb[32], cc[32];
4253: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4254: int numlinepar;
4255:
4256: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4257: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4258: for(i=1; i <=nlstate; i++){
4259: jj=0;
4260: for(j=1; j <=nlstate+ndeath; j++){
4261: if(j==i) continue;
4262: jj++;
4263: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4264: printf("%1d%1d",i,j);
4265: fprintf(ficparo,"%1d%1d",i,j);
4266: for(k=1; k<=ncovmodel;k++){
4267: /* printf(" %lf",param[i][j][k]); */
4268: /* fprintf(ficparo," %lf",param[i][j][k]); */
4269: printf(" 0.");
4270: fprintf(ficparo," 0.");
4271: }
4272: printf("\n");
4273: fprintf(ficparo,"\n");
4274: }
4275: }
4276: printf("# Scales (for hessian or gradient estimation)\n");
4277: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4278: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4279: for(i=1; i <=nlstate; i++){
4280: jj=0;
4281: for(j=1; j <=nlstate+ndeath; j++){
4282: if(j==i) continue;
4283: jj++;
4284: fprintf(ficparo,"%1d%1d",i,j);
4285: printf("%1d%1d",i,j);
4286: fflush(stdout);
4287: for(k=1; k<=ncovmodel;k++){
4288: /* printf(" %le",delti3[i][j][k]); */
4289: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4290: printf(" 0.");
4291: fprintf(ficparo," 0.");
4292: }
4293: numlinepar++;
4294: printf("\n");
4295: fprintf(ficparo,"\n");
4296: }
4297: }
4298: printf("# Covariance matrix\n");
4299: /* # 121 Var(a12)\n\ */
4300: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4301: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4302: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4303: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4304: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4305: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4306: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4307: fflush(stdout);
4308: fprintf(ficparo,"# Covariance matrix\n");
4309: /* # 121 Var(a12)\n\ */
4310: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4311: /* # ...\n\ */
4312: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4313:
4314: for(itimes=1;itimes<=2;itimes++){
4315: jj=0;
4316: for(i=1; i <=nlstate; i++){
4317: for(j=1; j <=nlstate+ndeath; j++){
4318: if(j==i) continue;
4319: for(k=1; k<=ncovmodel;k++){
4320: jj++;
4321: ca[0]= k+'a'-1;ca[1]='\0';
4322: if(itimes==1){
4323: printf("#%1d%1d%d",i,j,k);
4324: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4325: }else{
4326: printf("%1d%1d%d",i,j,k);
4327: fprintf(ficparo,"%1d%1d%d",i,j,k);
4328: /* printf(" %.5le",matcov[i][j]); */
4329: }
4330: ll=0;
4331: for(li=1;li <=nlstate; li++){
4332: for(lj=1;lj <=nlstate+ndeath; lj++){
4333: if(lj==li) continue;
4334: for(lk=1;lk<=ncovmodel;lk++){
4335: ll++;
4336: if(ll<=jj){
4337: cb[0]= lk +'a'-1;cb[1]='\0';
4338: if(ll<jj){
4339: if(itimes==1){
4340: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4341: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4342: }else{
4343: printf(" 0.");
4344: fprintf(ficparo," 0.");
4345: }
4346: }else{
4347: if(itimes==1){
4348: printf(" Var(%s%1d%1d)",ca,i,j);
4349: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4350: }else{
4351: printf(" 0.");
4352: fprintf(ficparo," 0.");
4353: }
4354: }
4355: }
4356: } /* end lk */
4357: } /* end lj */
4358: } /* end li */
4359: printf("\n");
4360: fprintf(ficparo,"\n");
4361: numlinepar++;
4362: } /* end k*/
4363: } /*end j */
4364: } /* end i */
4365: } /* end itimes */
4366:
4367: } /* end of prwizard */
4368: /******************* Gompertz Likelihood ******************************/
4369: double gompertz(double x[])
4370: {
4371: double A,B,L=0.0,sump=0.,num=0.;
4372: int i,n=0; /* n is the size of the sample */
4373:
4374: for (i=0;i<=imx-1 ; i++) {
4375: sump=sump+weight[i];
4376: /* sump=sump+1;*/
4377: num=num+1;
4378: }
4379:
4380:
4381: /* for (i=0; i<=imx; i++)
4382: 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]);*/
4383:
4384: for (i=1;i<=imx ; i++)
4385: {
4386: if (cens[i] == 1 && wav[i]>1)
4387: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4388:
4389: if (cens[i] == 0 && wav[i]>1)
4390: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4391: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4392:
4393: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4394: if (wav[i] > 1 ) { /* ??? */
4395: L=L+A*weight[i];
4396: /* 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]);*/
4397: }
4398: }
4399:
4400: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4401:
4402: return -2*L*num/sump;
4403: }
4404:
4405: #ifdef GSL
4406: /******************* Gompertz_f Likelihood ******************************/
4407: double gompertz_f(const gsl_vector *v, void *params)
4408: {
4409: double A,B,LL=0.0,sump=0.,num=0.;
4410: double *x= (double *) v->data;
4411: int i,n=0; /* n is the size of the sample */
4412:
4413: for (i=0;i<=imx-1 ; i++) {
4414: sump=sump+weight[i];
4415: /* sump=sump+1;*/
4416: num=num+1;
4417: }
4418:
4419:
4420: /* for (i=0; i<=imx; i++)
4421: 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]);*/
4422: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4423: for (i=1;i<=imx ; i++)
4424: {
4425: if (cens[i] == 1 && wav[i]>1)
4426: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4427:
4428: if (cens[i] == 0 && wav[i]>1)
4429: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4430: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4431:
4432: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4433: if (wav[i] > 1 ) { /* ??? */
4434: LL=LL+A*weight[i];
4435: /* 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]);*/
4436: }
4437: }
4438:
4439: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4440: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4441:
4442: return -2*LL*num/sump;
4443: }
4444: #endif
4445:
4446: /******************* Printing html file ***********/
4447: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4448: int lastpass, int stepm, int weightopt, char model[],\
4449: int imx, double p[],double **matcov,double agemortsup){
4450: int i,k;
4451:
4452: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4453: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4454: for (i=1;i<=2;i++)
4455: 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]));
4456: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4457: fprintf(fichtm,"</ul>");
4458:
4459: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4460:
4461: 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>");
4462:
4463: for (k=agegomp;k<(agemortsup-2);k++)
4464: 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]);
4465:
4466:
4467: fflush(fichtm);
4468: }
4469:
4470: /******************* Gnuplot file **************/
4471: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4472:
4473: char dirfileres[132],optfileres[132];
4474: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4475: int ng;
4476:
4477:
4478: /*#ifdef windows */
4479: fprintf(ficgp,"cd \"%s\" \n",pathc);
4480: /*#endif */
4481:
4482:
4483: strcpy(dirfileres,optionfilefiname);
4484: strcpy(optfileres,"vpl");
4485: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4486: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4487: fprintf(ficgp, "set ter png small\n set log y\n");
4488: fprintf(ficgp, "set size 0.65,0.65\n");
4489: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4490:
4491: }
4492:
4493: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4494: {
4495:
4496: /*-------- data file ----------*/
4497: FILE *fic;
4498: char dummy[]=" ";
4499: int i, j, n;
4500: int linei, month, year,iout;
4501: char line[MAXLINE], linetmp[MAXLINE];
4502: char stra[80], strb[80];
4503: char *stratrunc;
4504: int lstra;
4505:
4506:
4507: if((fic=fopen(datafile,"r"))==NULL) {
4508: printf("Problem while opening datafile: %s\n", datafile);return 1;
4509: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4510: }
4511:
4512: i=1;
4513: linei=0;
4514: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4515: linei=linei+1;
4516: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4517: if(line[j] == '\t')
4518: line[j] = ' ';
4519: }
4520: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4521: ;
4522: };
4523: line[j+1]=0; /* Trims blanks at end of line */
4524: if(line[0]=='#'){
4525: fprintf(ficlog,"Comment line\n%s\n",line);
4526: printf("Comment line\n%s\n",line);
4527: continue;
4528: }
4529: trimbb(linetmp,line); /* Trims multiple blanks in line */
4530: for (j=0; line[j]!='\0';j++){
4531: line[j]=linetmp[j];
4532: }
4533:
4534:
4535: for (j=maxwav;j>=1;j--){
4536: cutv(stra, strb,line,' ');
4537: if(strb[0]=='.') { /* Missing status */
4538: lval=-1;
4539: }else{
4540: errno=0;
4541: lval=strtol(strb,&endptr,10);
4542: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4543: if( strb[0]=='\0' || (*endptr != '\0')){
4544: 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);
4545: 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);
4546: return 1;
4547: }
4548: }
4549: s[j][i]=lval;
4550:
4551: strcpy(line,stra);
4552: cutv(stra, strb,line,' ');
4553: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4554: }
4555: else if(iout=sscanf(strb,"%s.") != 0){
4556: month=99;
4557: year=9999;
4558: }else{
4559: 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);
4560: 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);
4561: return 1;
4562: }
4563: anint[j][i]= (double) year;
4564: mint[j][i]= (double)month;
4565: strcpy(line,stra);
4566: } /* ENd Waves */
4567:
4568: cutv(stra, strb,line,' ');
4569: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4570: }
4571: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4572: month=99;
4573: year=9999;
4574: }else{
4575: 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);
4576: 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);
4577: return 1;
4578: }
4579: andc[i]=(double) year;
4580: moisdc[i]=(double) month;
4581: strcpy(line,stra);
4582:
4583: cutv(stra, strb,line,' ');
4584: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4585: }
4586: else if(iout=sscanf(strb,"%s.") != 0){
4587: month=99;
4588: year=9999;
4589: }else{
4590: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4591: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4592: return 1;
4593: }
4594: if (year==9999) {
4595: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
4596: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
4597: return 1;
4598:
4599: }
4600: annais[i]=(double)(year);
4601: moisnais[i]=(double)(month);
4602: strcpy(line,stra);
4603:
4604: cutv(stra, strb,line,' ');
4605: errno=0;
4606: dval=strtod(strb,&endptr);
4607: if( strb[0]=='\0' || (*endptr != '\0')){
4608: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4609: 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);
4610: fflush(ficlog);
4611: return 1;
4612: }
4613: weight[i]=dval;
4614: strcpy(line,stra);
4615:
4616: for (j=ncovcol;j>=1;j--){
4617: cutv(stra, strb,line,' ');
4618: if(strb[0]=='.') { /* Missing status */
4619: lval=-1;
4620: }else{
4621: errno=0;
4622: lval=strtol(strb,&endptr,10);
4623: if( strb[0]=='\0' || (*endptr != '\0')){
4624: 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);
4625: 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);
4626: return 1;
4627: }
4628: }
4629: if(lval <-1 || lval >1){
4630: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4631: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4632: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4633: For example, for multinomial values like 1, 2 and 3,\n \
4634: build V1=0 V2=0 for the reference value (1),\n \
4635: V1=1 V2=0 for (2) \n \
4636: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4637: output of IMaCh is often meaningless.\n \
4638: Exiting.\n",lval,linei, i,line,j);
4639: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4640: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4641: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4642: For example, for multinomial values like 1, 2 and 3,\n \
4643: build V1=0 V2=0 for the reference value (1),\n \
4644: V1=1 V2=0 for (2) \n \
4645: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4646: output of IMaCh is often meaningless.\n \
4647: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4648: return 1;
4649: }
4650: covar[j][i]=(double)(lval);
4651: strcpy(line,stra);
4652: }
4653: lstra=strlen(stra);
4654:
4655: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4656: stratrunc = &(stra[lstra-9]);
4657: num[i]=atol(stratrunc);
4658: }
4659: else
4660: num[i]=atol(stra);
4661: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4662: 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;}*/
4663:
4664: i=i+1;
4665: } /* End loop reading data */
4666:
4667: *imax=i-1; /* Number of individuals */
4668: fclose(fic);
4669:
4670: return (0);
4671: endread:
4672: printf("Exiting readdata: ");
4673: fclose(fic);
4674: return (1);
4675:
4676:
4677:
4678: }
4679:
4680: int decodemodel ( char model[], int lastobs)
4681: {
4682: int i, j, k;
4683: int i1, j1, k1, k2;
4684: char modelsav[80];
4685: char stra[80], strb[80], strc[80], strd[80],stre[80];
4686:
4687: if (strlen(model) >1){ /* If there is at least 1 covariate */
4688: j=0, j1=0, k1=1, k2=1;
4689: j=nbocc(model,'+'); /* j=Number of '+' */
4690: j1=nbocc(model,'*'); /* j1=Number of '*' */
4691: cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
4692: but the covariates which are product must be computed and stored. */
4693: cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
4694:
4695: strcpy(modelsav,model);
4696: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4697: printf("Error. Non available option model=%s ",model);
4698: fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
4699: return 1;
4700: }
4701:
4702: /* This loop fills the array Tvar from the string 'model'.*/
4703: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
4704: /* modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
4705: i=1 Tvar[1]=3 Tage[1]=1
4706: i=2 Tvar[2]=2
4707: i=3 Tvar[3]=1
4708: i=4 Tvar[4]= 4
4709: i=5 Tvar[5]
4710: for (k=1; k<=cptcovn;k++) {
4711: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
4712: */
4713: for(k=1; k<=(j+1);k++){
4714: cutv(strb,stra,modelsav,'+'); /* keeps in strb after the first '+'
4715: modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
4716: */
4717: /* if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);*/ /* and analyzes it */
4718: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4719: /*scanf("%d",i);*/
4720: if (strchr(strb,'*')) { /* Model includes a product V3*age+V2+V1+V4 strb=V3*age */
4721: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
4722: if (strcmp(strc,"age")==0) { /* Vn*age */
4723: cptcovprod--;
4724: cutv(strb,stre,strd,'V'); /* stre="V3" */
4725: Tvar[k]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3, and Tvar[3]=2 */
4726: cptcovage++; /* Sums the number of covariates which include age as a product */
4727: Tage[cptcovage]=k; /* Tage[1] =2 */
4728: /*printf("stre=%s ", stre);*/
4729: }
4730: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4731: cptcovprod--;
4732: cutv(strb,stre,strc,'V');
4733: Tvar[k]=atoi(stre);
4734: cptcovage++;
4735: Tage[cptcovage]=k;
4736: }
4737: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
4738: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
4739: Tvar[k]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
4740: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
4741: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4742: Tprod[k1]=k; /* Tprod[1] */
4743: Tvard[k1][1]=atoi(strc); /* m*/
4744: Tvard[k1][2]=atoi(stre); /* n */
4745: Tvar[cptcovn+k2]=Tvard[k1][1];
4746: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4747: for (i=1; i<=lastobs;i++) /* Computes the new covariate which is a product of covar[n][i]* covar[m][i]
4748: and is stored at ncovol+k1 */
4749: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
4750: k1++;
4751: k2=k2+2;
4752: }
4753: }
4754: else { /* no more sum */
4755: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4756: /* scanf("%d",i);*/
4757: cutv(strd,strc,strb,'V');
4758: Tvar[i]=atoi(strc);
4759: }
4760: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
4761: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4762: scanf("%d",i);*/
4763: } /* end of loop + */
4764: } /* end model */
4765:
4766: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4767: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4768:
4769: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4770: printf("cptcovprod=%d ", cptcovprod);
4771: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4772:
4773: scanf("%d ",i);*/
4774:
4775:
4776: return (0);
4777: endread:
4778: printf("Exiting decodemodel: ");
4779: return (1);
4780: }
4781:
4782: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
4783: {
4784: int i, m;
4785:
4786: for (i=1; i<=imx; i++) {
4787: for(m=2; (m<= maxwav); m++) {
4788: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4789: anint[m][i]=9999;
4790: s[m][i]=-1;
4791: }
4792: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4793: *nberr++;
4794: 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);
4795: 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);
4796: s[m][i]=-1;
4797: }
4798: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4799: *nberr++;
4800: 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]);
4801: 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]);
4802: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4803: }
4804: }
4805: }
4806:
4807: for (i=1; i<=imx; i++) {
4808: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4809: for(m=firstpass; (m<= lastpass); m++){
4810: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4811: if (s[m][i] >= nlstate+1) {
4812: if(agedc[i]>0)
4813: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4814: agev[m][i]=agedc[i];
4815: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4816: else {
4817: if ((int)andc[i]!=9999){
4818: nbwarn++;
4819: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4820: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4821: agev[m][i]=-1;
4822: }
4823: }
4824: }
4825: else if(s[m][i] !=9){ /* Standard case, age in fractional
4826: years but with the precision of a month */
4827: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4828: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4829: agev[m][i]=1;
4830: else if(agev[m][i] < *agemin){
4831: *agemin=agev[m][i];
4832: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
4833: }
4834: else if(agev[m][i] >*agemax){
4835: *agemax=agev[m][i];
4836: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4837: }
4838: /*agev[m][i]=anint[m][i]-annais[i];*/
4839: /* agev[m][i] = age[i]+2*m;*/
4840: }
4841: else { /* =9 */
4842: agev[m][i]=1;
4843: s[m][i]=-1;
4844: }
4845: }
4846: else /*= 0 Unknown */
4847: agev[m][i]=1;
4848: }
4849:
4850: }
4851: for (i=1; i<=imx; i++) {
4852: for(m=firstpass; (m<=lastpass); m++){
4853: if (s[m][i] > (nlstate+ndeath)) {
4854: *nberr++;
4855: 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);
4856: 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);
4857: return 1;
4858: }
4859: }
4860: }
4861:
4862: /*for (i=1; i<=imx; i++){
4863: for (m=firstpass; (m<lastpass); m++){
4864: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4865: }
4866:
4867: }*/
4868:
4869:
4870: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4871: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4872:
4873: return (0);
4874: endread:
4875: printf("Exiting calandcheckages: ");
4876: return (1);
4877: }
4878:
4879:
4880: /***********************************************/
4881: /**************** Main Program *****************/
4882: /***********************************************/
4883:
4884: int main(int argc, char *argv[])
4885: {
4886: #ifdef GSL
4887: const gsl_multimin_fminimizer_type *T;
4888: size_t iteri = 0, it;
4889: int rval = GSL_CONTINUE;
4890: int status = GSL_SUCCESS;
4891: double ssval;
4892: #endif
4893: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4894: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4895: int linei, month, year,iout;
4896: int jj, ll, li, lj, lk, imk;
4897: int numlinepar=0; /* Current linenumber of parameter file */
4898: int itimes;
4899: int NDIM=2;
4900: int vpopbased=0;
4901:
4902: char ca[32], cb[32], cc[32];
4903: /* FILE *fichtm; *//* Html File */
4904: /* FILE *ficgp;*/ /*Gnuplot File */
4905: struct stat info;
4906: double agedeb, agefin,hf;
4907: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4908:
4909: double fret;
4910: double **xi,tmp,delta;
4911:
4912: double dum; /* Dummy variable */
4913: double ***p3mat;
4914: double ***mobaverage;
4915: int *indx;
4916: char line[MAXLINE], linepar[MAXLINE];
4917: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4918: char pathr[MAXLINE], pathimach[MAXLINE];
4919: char **bp, *tok, *val; /* pathtot */
4920: int firstobs=1, lastobs=10;
4921: int sdeb, sfin; /* Status at beginning and end */
4922: int c, h , cpt,l;
4923: int ju,jl, mi;
4924: int i1,j1, jk,aa,bb, stepsize, ij;
4925: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
4926: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4927: int mobilav=0,popforecast=0;
4928: int hstepm, nhstepm;
4929: int agemortsup;
4930: float sumlpop=0.;
4931: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4932: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4933:
4934: double bage, fage, age, agelim, agebase;
4935: double ftolpl=FTOL;
4936: double **prlim;
4937: double ***param; /* Matrix of parameters */
4938: double *p;
4939: double **matcov; /* Matrix of covariance */
4940: double ***delti3; /* Scale */
4941: double *delti; /* Scale */
4942: double ***eij, ***vareij;
4943: double **varpl; /* Variances of prevalence limits by age */
4944: double *epj, vepp;
4945: double kk1, kk2;
4946: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4947: double **ximort;
4948: char *alph[]={"a","a","b","c","d","e"}, str[4];
4949: int *dcwave;
4950:
4951: char z[1]="c", occ;
4952:
4953: /*char *strt;*/
4954: char strtend[80];
4955:
4956: long total_usecs;
4957:
4958: /* setlocale (LC_ALL, ""); */
4959: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4960: /* textdomain (PACKAGE); */
4961: /* setlocale (LC_CTYPE, ""); */
4962: /* setlocale (LC_MESSAGES, ""); */
4963:
4964: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4965: (void) gettimeofday(&start_time,&tzp);
4966: curr_time=start_time;
4967: tm = *localtime(&start_time.tv_sec);
4968: tmg = *gmtime(&start_time.tv_sec);
4969: strcpy(strstart,asctime(&tm));
4970:
4971: /* printf("Localtime (at start)=%s",strstart); */
4972: /* tp.tv_sec = tp.tv_sec +86400; */
4973: /* tm = *localtime(&start_time.tv_sec); */
4974: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4975: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4976: /* tmg.tm_hour=tmg.tm_hour + 1; */
4977: /* tp.tv_sec = mktime(&tmg); */
4978: /* strt=asctime(&tmg); */
4979: /* printf("Time(after) =%s",strstart); */
4980: /* (void) time (&time_value);
4981: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4982: * tm = *localtime(&time_value);
4983: * strstart=asctime(&tm);
4984: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4985: */
4986:
4987: nberr=0; /* Number of errors and warnings */
4988: nbwarn=0;
4989: getcwd(pathcd, size);
4990:
4991: printf("\n%s\n%s",version,fullversion);
4992: if(argc <=1){
4993: printf("\nEnter the parameter file name: ");
4994: fgets(pathr,FILENAMELENGTH,stdin);
4995: i=strlen(pathr);
4996: if(pathr[i-1]=='\n')
4997: pathr[i-1]='\0';
4998: for (tok = pathr; tok != NULL; ){
4999: printf("Pathr |%s|\n",pathr);
5000: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5001: printf("val= |%s| pathr=%s\n",val,pathr);
5002: strcpy (pathtot, val);
5003: if(pathr[0] == '\0') break; /* Dirty */
5004: }
5005: }
5006: else{
5007: strcpy(pathtot,argv[1]);
5008: }
5009: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5010: /*cygwin_split_path(pathtot,path,optionfile);
5011: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5012: /* cutv(path,optionfile,pathtot,'\\');*/
5013:
5014: /* Split argv[0], imach program to get pathimach */
5015: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5016: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5017: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5018: /* strcpy(pathimach,argv[0]); */
5019: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5020: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5021: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5022: chdir(path); /* Can be a relative path */
5023: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5024: printf("Current directory %s!\n",pathcd);
5025: strcpy(command,"mkdir ");
5026: strcat(command,optionfilefiname);
5027: if((outcmd=system(command)) != 0){
5028: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5029: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5030: /* fclose(ficlog); */
5031: /* exit(1); */
5032: }
5033: /* if((imk=mkdir(optionfilefiname))<0){ */
5034: /* perror("mkdir"); */
5035: /* } */
5036:
5037: /*-------- arguments in the command line --------*/
5038:
5039: /* Log file */
5040: strcat(filelog, optionfilefiname);
5041: strcat(filelog,".log"); /* */
5042: if((ficlog=fopen(filelog,"w"))==NULL) {
5043: printf("Problem with logfile %s\n",filelog);
5044: goto end;
5045: }
5046: fprintf(ficlog,"Log filename:%s\n",filelog);
5047: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5048: fprintf(ficlog,"\nEnter the parameter file name: \n");
5049: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5050: path=%s \n\
5051: optionfile=%s\n\
5052: optionfilext=%s\n\
5053: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5054:
5055: printf("Local time (at start):%s",strstart);
5056: fprintf(ficlog,"Local time (at start): %s",strstart);
5057: fflush(ficlog);
5058: /* (void) gettimeofday(&curr_time,&tzp); */
5059: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5060:
5061: /* */
5062: strcpy(fileres,"r");
5063: strcat(fileres, optionfilefiname);
5064: strcat(fileres,".txt"); /* Other files have txt extension */
5065:
5066: /*---------arguments file --------*/
5067:
5068: if((ficpar=fopen(optionfile,"r"))==NULL) {
5069: printf("Problem with optionfile %s\n",optionfile);
5070: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
5071: fflush(ficlog);
5072: goto end;
5073: }
5074:
5075:
5076:
5077: strcpy(filereso,"o");
5078: strcat(filereso,fileres);
5079: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5080: printf("Problem with Output resultfile: %s\n", filereso);
5081: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5082: fflush(ficlog);
5083: goto end;
5084: }
5085:
5086: /* Reads comments: lines beginning with '#' */
5087: numlinepar=0;
5088: while((c=getc(ficpar))=='#' && c!= EOF){
5089: ungetc(c,ficpar);
5090: fgets(line, MAXLINE, ficpar);
5091: numlinepar++;
5092: puts(line);
5093: fputs(line,ficparo);
5094: fputs(line,ficlog);
5095: }
5096: ungetc(c,ficpar);
5097:
5098: 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);
5099: numlinepar++;
5100: 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);
5101: 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);
5102: 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);
5103: fflush(ficlog);
5104: while((c=getc(ficpar))=='#' && c!= EOF){
5105: ungetc(c,ficpar);
5106: fgets(line, MAXLINE, ficpar);
5107: numlinepar++;
5108: puts(line);
5109: fputs(line,ficparo);
5110: fputs(line,ficlog);
5111: }
5112: ungetc(c,ficpar);
5113:
5114:
5115: covar=matrix(0,NCOVMAX,1,n);
5116: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5117: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5118: v1+v2*age+v2*v3 makes cptcovn = 3
5119: */
5120: if (strlen(model)>1)
5121: cptcovn=nbocc(model,'+')+1;
5122: /* ncovprod */
5123: ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
5124: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5125: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5126: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5127: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5128: 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);
5129: 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);
5130: fflush(stdout);
5131: fclose (ficlog);
5132: goto end;
5133: }
5134: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5135: delti=delti3[1][1];
5136: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5137: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5138: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5139: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5140: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5141: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5142: fclose (ficparo);
5143: fclose (ficlog);
5144: goto end;
5145: exit(0);
5146: }
5147: else if(mle==-3) {
5148: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5149: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5150: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5151: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5152: matcov=matrix(1,npar,1,npar);
5153: }
5154: else{
5155: /* Read guess parameters */
5156: /* Reads comments: lines beginning with '#' */
5157: while((c=getc(ficpar))=='#' && c!= EOF){
5158: ungetc(c,ficpar);
5159: fgets(line, MAXLINE, ficpar);
5160: numlinepar++;
5161: puts(line);
5162: fputs(line,ficparo);
5163: fputs(line,ficlog);
5164: }
5165: ungetc(c,ficpar);
5166:
5167: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5168: for(i=1; i <=nlstate; i++){
5169: j=0;
5170: for(jj=1; jj <=nlstate+ndeath; jj++){
5171: if(jj==i) continue;
5172: j++;
5173: fscanf(ficpar,"%1d%1d",&i1,&j1);
5174: if ((i1 != i) && (j1 != j)){
5175: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5176: It might be a problem of design; if ncovcol and the model are correct\n \
5177: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5178: exit(1);
5179: }
5180: fprintf(ficparo,"%1d%1d",i1,j1);
5181: if(mle==1)
5182: printf("%1d%1d",i,j);
5183: fprintf(ficlog,"%1d%1d",i,j);
5184: for(k=1; k<=ncovmodel;k++){
5185: fscanf(ficpar," %lf",¶m[i][j][k]);
5186: if(mle==1){
5187: printf(" %lf",param[i][j][k]);
5188: fprintf(ficlog," %lf",param[i][j][k]);
5189: }
5190: else
5191: fprintf(ficlog," %lf",param[i][j][k]);
5192: fprintf(ficparo," %lf",param[i][j][k]);
5193: }
5194: fscanf(ficpar,"\n");
5195: numlinepar++;
5196: if(mle==1)
5197: printf("\n");
5198: fprintf(ficlog,"\n");
5199: fprintf(ficparo,"\n");
5200: }
5201: }
5202: fflush(ficlog);
5203:
5204: p=param[1][1];
5205:
5206: /* Reads comments: lines beginning with '#' */
5207: while((c=getc(ficpar))=='#' && c!= EOF){
5208: ungetc(c,ficpar);
5209: fgets(line, MAXLINE, ficpar);
5210: numlinepar++;
5211: puts(line);
5212: fputs(line,ficparo);
5213: fputs(line,ficlog);
5214: }
5215: ungetc(c,ficpar);
5216:
5217: for(i=1; i <=nlstate; i++){
5218: for(j=1; j <=nlstate+ndeath-1; j++){
5219: fscanf(ficpar,"%1d%1d",&i1,&j1);
5220: if ((i1-i)*(j1-j)!=0){
5221: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5222: exit(1);
5223: }
5224: printf("%1d%1d",i,j);
5225: fprintf(ficparo,"%1d%1d",i1,j1);
5226: fprintf(ficlog,"%1d%1d",i1,j1);
5227: for(k=1; k<=ncovmodel;k++){
5228: fscanf(ficpar,"%le",&delti3[i][j][k]);
5229: printf(" %le",delti3[i][j][k]);
5230: fprintf(ficparo," %le",delti3[i][j][k]);
5231: fprintf(ficlog," %le",delti3[i][j][k]);
5232: }
5233: fscanf(ficpar,"\n");
5234: numlinepar++;
5235: printf("\n");
5236: fprintf(ficparo,"\n");
5237: fprintf(ficlog,"\n");
5238: }
5239: }
5240: fflush(ficlog);
5241:
5242: delti=delti3[1][1];
5243:
5244:
5245: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5246:
5247: /* Reads comments: lines beginning with '#' */
5248: while((c=getc(ficpar))=='#' && c!= EOF){
5249: ungetc(c,ficpar);
5250: fgets(line, MAXLINE, ficpar);
5251: numlinepar++;
5252: puts(line);
5253: fputs(line,ficparo);
5254: fputs(line,ficlog);
5255: }
5256: ungetc(c,ficpar);
5257:
5258: matcov=matrix(1,npar,1,npar);
5259: for(i=1; i <=npar; i++)
5260: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5261:
5262: for(i=1; i <=npar; i++){
5263: fscanf(ficpar,"%s",&str);
5264: if(mle==1)
5265: printf("%s",str);
5266: fprintf(ficlog,"%s",str);
5267: fprintf(ficparo,"%s",str);
5268: for(j=1; j <=i; j++){
5269: fscanf(ficpar," %le",&matcov[i][j]);
5270: if(mle==1){
5271: printf(" %.5le",matcov[i][j]);
5272: }
5273: fprintf(ficlog," %.5le",matcov[i][j]);
5274: fprintf(ficparo," %.5le",matcov[i][j]);
5275: }
5276: fscanf(ficpar,"\n");
5277: numlinepar++;
5278: if(mle==1)
5279: printf("\n");
5280: fprintf(ficlog,"\n");
5281: fprintf(ficparo,"\n");
5282: }
5283: for(i=1; i <=npar; i++)
5284: for(j=i+1;j<=npar;j++)
5285: matcov[i][j]=matcov[j][i];
5286:
5287: if(mle==1)
5288: printf("\n");
5289: fprintf(ficlog,"\n");
5290:
5291: fflush(ficlog);
5292:
5293: /*-------- Rewriting parameter file ----------*/
5294: strcpy(rfileres,"r"); /* "Rparameterfile */
5295: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5296: strcat(rfileres,"."); /* */
5297: strcat(rfileres,optionfilext); /* Other files have txt extension */
5298: if((ficres =fopen(rfileres,"w"))==NULL) {
5299: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5300: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5301: }
5302: fprintf(ficres,"#%s\n",version);
5303: } /* End of mle != -3 */
5304:
5305:
5306: n= lastobs;
5307: num=lvector(1,n);
5308: moisnais=vector(1,n);
5309: annais=vector(1,n);
5310: moisdc=vector(1,n);
5311: andc=vector(1,n);
5312: agedc=vector(1,n);
5313: cod=ivector(1,n);
5314: weight=vector(1,n);
5315: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5316: mint=matrix(1,maxwav,1,n);
5317: anint=matrix(1,maxwav,1,n);
5318: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5319: tab=ivector(1,NCOVMAX);
5320: ncodemax=ivector(1,8);
5321:
5322: /* Reads data from file datafile */
5323: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5324: goto end;
5325:
5326: /* Calculation of the number of parameters from char model */
5327: 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 */
5328: Tprod=ivector(1,15);
5329: Tvaraff=ivector(1,15);
5330: Tvard=imatrix(1,15,1,2);
5331: Tage=ivector(1,15);
5332:
5333: if(decodemodel(model, lastobs) == 1)
5334: goto end;
5335:
5336: /* if(mle==1){*/
5337: if (weightopt != 1) { /* Maximisation without weights*/
5338: for(i=1;i<=n;i++) weight[i]=1.0;
5339: }
5340:
5341: /*-calculation of age at interview from date of interview and age at death -*/
5342: agev=matrix(1,maxwav,1,imx);
5343:
5344: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5345: goto end;
5346:
5347:
5348: agegomp=(int)agemin;
5349: free_vector(moisnais,1,n);
5350: free_vector(annais,1,n);
5351: /* free_matrix(mint,1,maxwav,1,n);
5352: free_matrix(anint,1,maxwav,1,n);*/
5353: free_vector(moisdc,1,n);
5354: free_vector(andc,1,n);
5355:
5356:
5357: wav=ivector(1,imx);
5358: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5359: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5360: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5361:
5362: /* Concatenates waves */
5363: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5364:
5365: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5366:
5367: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5368: ncodemax[1]=1;
5369: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5370:
5371: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5372: the estimations*/
5373: h=0;
5374: m=pow(2,cptcoveff);
5375:
5376: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5377: 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 */
5378: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
5379: 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 */
5380: h++;
5381: if (h>m) {
5382: h=1;
5383: codtab[h][k]=j;
5384: codtab[h][Tvar[k]]=j;
5385: }
5386: 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]]);
5387: }
5388: }
5389: }
5390: }
5391: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5392: codtab[1][2]=1;codtab[2][2]=2; */
5393: /* for(i=1; i <=m ;i++){
5394: for(k=1; k <=cptcovn; k++){
5395: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5396: }
5397: printf("\n");
5398: }
5399: scanf("%d",i);*/
5400:
5401: /*------------ gnuplot -------------*/
5402: strcpy(optionfilegnuplot,optionfilefiname);
5403: if(mle==-3)
5404: strcat(optionfilegnuplot,"-mort");
5405: strcat(optionfilegnuplot,".gp");
5406:
5407: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5408: printf("Problem with file %s",optionfilegnuplot);
5409: }
5410: else{
5411: fprintf(ficgp,"\n# %s\n", version);
5412: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5413: fprintf(ficgp,"set missing 'NaNq'\n");
5414: }
5415: /* fclose(ficgp);*/
5416: /*--------- index.htm --------*/
5417:
5418: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5419: if(mle==-3)
5420: strcat(optionfilehtm,"-mort");
5421: strcat(optionfilehtm,".htm");
5422: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5423: printf("Problem with %s \n",optionfilehtm);
5424: exit(0);
5425: }
5426:
5427: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5428: strcat(optionfilehtmcov,"-cov.htm");
5429: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5430: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5431: }
5432: else{
5433: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5434: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5435: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5436: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5437: }
5438:
5439: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5440: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5441: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5442: \n\
5443: <hr size=\"2\" color=\"#EC5E5E\">\
5444: <ul><li><h4>Parameter files</h4>\n\
5445: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5446: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5447: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5448: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5449: - Date and time at start: %s</ul>\n",\
5450: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5451: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5452: fileres,fileres,\
5453: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5454: fflush(fichtm);
5455:
5456: strcpy(pathr,path);
5457: strcat(pathr,optionfilefiname);
5458: chdir(optionfilefiname); /* Move to directory named optionfile */
5459:
5460: /* Calculates basic frequencies. Computes observed prevalence at single age
5461: and prints on file fileres'p'. */
5462: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5463:
5464: fprintf(fichtm,"\n");
5465: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5466: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5467: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5468: imx,agemin,agemax,jmin,jmax,jmean);
5469: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5470: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5471: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5472: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5473: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5474:
5475:
5476: /* For Powell, parameters are in a vector p[] starting at p[1]
5477: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5478: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5479:
5480: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5481:
5482: if (mle==-3){
5483: ximort=matrix(1,NDIM,1,NDIM);
5484: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5485: cens=ivector(1,n);
5486: ageexmed=vector(1,n);
5487: agecens=vector(1,n);
5488: dcwave=ivector(1,n);
5489:
5490: for (i=1; i<=imx; i++){
5491: dcwave[i]=-1;
5492: for (m=firstpass; m<=lastpass; m++)
5493: if (s[m][i]>nlstate) {
5494: dcwave[i]=m;
5495: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5496: break;
5497: }
5498: }
5499:
5500: for (i=1; i<=imx; i++) {
5501: if (wav[i]>0){
5502: ageexmed[i]=agev[mw[1][i]][i];
5503: j=wav[i];
5504: agecens[i]=1.;
5505:
5506: if (ageexmed[i]> 1 && wav[i] > 0){
5507: agecens[i]=agev[mw[j][i]][i];
5508: cens[i]= 1;
5509: }else if (ageexmed[i]< 1)
5510: cens[i]= -1;
5511: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5512: cens[i]=0 ;
5513: }
5514: else cens[i]=-1;
5515: }
5516:
5517: for (i=1;i<=NDIM;i++) {
5518: for (j=1;j<=NDIM;j++)
5519: ximort[i][j]=(i == j ? 1.0 : 0.0);
5520: }
5521:
5522: p[1]=0.0268; p[NDIM]=0.083;
5523: /*printf("%lf %lf", p[1], p[2]);*/
5524:
5525:
5526: #ifdef GSL
5527: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5528: #elsedef
5529: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5530: #endif
5531: strcpy(filerespow,"pow-mort");
5532: strcat(filerespow,fileres);
5533: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5534: printf("Problem with resultfile: %s\n", filerespow);
5535: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5536: }
5537: #ifdef GSL
5538: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5539: #elsedef
5540: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5541: #endif
5542: /* for (i=1;i<=nlstate;i++)
5543: for(j=1;j<=nlstate+ndeath;j++)
5544: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5545: */
5546: fprintf(ficrespow,"\n");
5547: #ifdef GSL
5548: /* gsl starts here */
5549: T = gsl_multimin_fminimizer_nmsimplex;
5550: gsl_multimin_fminimizer *sfm = NULL;
5551: gsl_vector *ss, *x;
5552: gsl_multimin_function minex_func;
5553:
5554: /* Initial vertex size vector */
5555: ss = gsl_vector_alloc (NDIM);
5556:
5557: if (ss == NULL){
5558: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5559: }
5560: /* Set all step sizes to 1 */
5561: gsl_vector_set_all (ss, 0.001);
5562:
5563: /* Starting point */
5564:
5565: x = gsl_vector_alloc (NDIM);
5566:
5567: if (x == NULL){
5568: gsl_vector_free(ss);
5569: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5570: }
5571:
5572: /* Initialize method and iterate */
5573: /* p[1]=0.0268; p[NDIM]=0.083; */
5574: /* gsl_vector_set(x, 0, 0.0268); */
5575: /* gsl_vector_set(x, 1, 0.083); */
5576: gsl_vector_set(x, 0, p[1]);
5577: gsl_vector_set(x, 1, p[2]);
5578:
5579: minex_func.f = &gompertz_f;
5580: minex_func.n = NDIM;
5581: minex_func.params = (void *)&p; /* ??? */
5582:
5583: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5584: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5585:
5586: printf("Iterations beginning .....\n\n");
5587: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5588:
5589: iteri=0;
5590: while (rval == GSL_CONTINUE){
5591: iteri++;
5592: status = gsl_multimin_fminimizer_iterate(sfm);
5593:
5594: if (status) printf("error: %s\n", gsl_strerror (status));
5595: fflush(0);
5596:
5597: if (status)
5598: break;
5599:
5600: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5601: ssval = gsl_multimin_fminimizer_size (sfm);
5602:
5603: if (rval == GSL_SUCCESS)
5604: printf ("converged to a local maximum at\n");
5605:
5606: printf("%5d ", iteri);
5607: for (it = 0; it < NDIM; it++){
5608: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
5609: }
5610: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
5611: }
5612:
5613: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
5614:
5615: gsl_vector_free(x); /* initial values */
5616: gsl_vector_free(ss); /* inital step size */
5617: for (it=0; it<NDIM; it++){
5618: p[it+1]=gsl_vector_get(sfm->x,it);
5619: fprintf(ficrespow," %.12lf", p[it]);
5620: }
5621: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
5622: #endif
5623: #ifdef POWELL
5624: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5625: #endif
5626: fclose(ficrespow);
5627:
5628: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5629:
5630: for(i=1; i <=NDIM; i++)
5631: for(j=i+1;j<=NDIM;j++)
5632: matcov[i][j]=matcov[j][i];
5633:
5634: printf("\nCovariance matrix\n ");
5635: for(i=1; i <=NDIM; i++) {
5636: for(j=1;j<=NDIM;j++){
5637: printf("%f ",matcov[i][j]);
5638: }
5639: printf("\n ");
5640: }
5641:
5642: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5643: for (i=1;i<=NDIM;i++)
5644: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5645:
5646: lsurv=vector(1,AGESUP);
5647: lpop=vector(1,AGESUP);
5648: tpop=vector(1,AGESUP);
5649: lsurv[agegomp]=100000;
5650:
5651: for (k=agegomp;k<=AGESUP;k++) {
5652: agemortsup=k;
5653: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5654: }
5655:
5656: for (k=agegomp;k<agemortsup;k++)
5657: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5658:
5659: for (k=agegomp;k<agemortsup;k++){
5660: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5661: sumlpop=sumlpop+lpop[k];
5662: }
5663:
5664: tpop[agegomp]=sumlpop;
5665: for (k=agegomp;k<(agemortsup-3);k++){
5666: /* tpop[k+1]=2;*/
5667: tpop[k+1]=tpop[k]-lpop[k];
5668: }
5669:
5670:
5671: printf("\nAge lx qx dx Lx Tx e(x)\n");
5672: for (k=agegomp;k<(agemortsup-2);k++)
5673: 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]);
5674:
5675:
5676: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5677: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5678:
5679: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5680: stepm, weightopt,\
5681: model,imx,p,matcov,agemortsup);
5682:
5683: free_vector(lsurv,1,AGESUP);
5684: free_vector(lpop,1,AGESUP);
5685: free_vector(tpop,1,AGESUP);
5686: #ifdef GSL
5687: free_ivector(cens,1,n);
5688: free_vector(agecens,1,n);
5689: free_ivector(dcwave,1,n);
5690: free_matrix(ximort,1,NDIM,1,NDIM);
5691: #endif
5692: } /* Endof if mle==-3 */
5693:
5694: else{ /* For mle >=1 */
5695: globpr=0;/* debug */
5696: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5697: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5698: for (k=1; k<=npar;k++)
5699: printf(" %d %8.5f",k,p[k]);
5700: printf("\n");
5701: globpr=1; /* to print the contributions */
5702: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5703: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5704: for (k=1; k<=npar;k++)
5705: printf(" %d %8.5f",k,p[k]);
5706: printf("\n");
5707: if(mle>=1){ /* Could be 1 or 2 */
5708: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5709: }
5710:
5711: /*--------- results files --------------*/
5712: 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);
5713:
5714:
5715: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5716: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5717: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5718: for(i=1,jk=1; i <=nlstate; i++){
5719: for(k=1; k <=(nlstate+ndeath); k++){
5720: if (k != i) {
5721: printf("%d%d ",i,k);
5722: fprintf(ficlog,"%d%d ",i,k);
5723: fprintf(ficres,"%1d%1d ",i,k);
5724: for(j=1; j <=ncovmodel; j++){
5725: printf("%lf ",p[jk]);
5726: fprintf(ficlog,"%lf ",p[jk]);
5727: fprintf(ficres,"%lf ",p[jk]);
5728: jk++;
5729: }
5730: printf("\n");
5731: fprintf(ficlog,"\n");
5732: fprintf(ficres,"\n");
5733: }
5734: }
5735: }
5736: if(mle!=0){
5737: /* Computing hessian and covariance matrix */
5738: ftolhess=ftol; /* Usually correct */
5739: hesscov(matcov, p, npar, delti, ftolhess, func);
5740: }
5741: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5742: printf("# Scales (for hessian or gradient estimation)\n");
5743: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5744: for(i=1,jk=1; i <=nlstate; i++){
5745: for(j=1; j <=nlstate+ndeath; j++){
5746: if (j!=i) {
5747: fprintf(ficres,"%1d%1d",i,j);
5748: printf("%1d%1d",i,j);
5749: fprintf(ficlog,"%1d%1d",i,j);
5750: for(k=1; k<=ncovmodel;k++){
5751: printf(" %.5e",delti[jk]);
5752: fprintf(ficlog," %.5e",delti[jk]);
5753: fprintf(ficres," %.5e",delti[jk]);
5754: jk++;
5755: }
5756: printf("\n");
5757: fprintf(ficlog,"\n");
5758: fprintf(ficres,"\n");
5759: }
5760: }
5761: }
5762:
5763: 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");
5764: if(mle>=1)
5765: 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");
5766: 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");
5767: /* # 121 Var(a12)\n\ */
5768: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5769: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5770: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5771: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5772: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5773: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5774: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5775:
5776:
5777: /* Just to have a covariance matrix which will be more understandable
5778: even is we still don't want to manage dictionary of variables
5779: */
5780: for(itimes=1;itimes<=2;itimes++){
5781: jj=0;
5782: for(i=1; i <=nlstate; i++){
5783: for(j=1; j <=nlstate+ndeath; j++){
5784: if(j==i) continue;
5785: for(k=1; k<=ncovmodel;k++){
5786: jj++;
5787: ca[0]= k+'a'-1;ca[1]='\0';
5788: if(itimes==1){
5789: if(mle>=1)
5790: printf("#%1d%1d%d",i,j,k);
5791: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5792: fprintf(ficres,"#%1d%1d%d",i,j,k);
5793: }else{
5794: if(mle>=1)
5795: printf("%1d%1d%d",i,j,k);
5796: fprintf(ficlog,"%1d%1d%d",i,j,k);
5797: fprintf(ficres,"%1d%1d%d",i,j,k);
5798: }
5799: ll=0;
5800: for(li=1;li <=nlstate; li++){
5801: for(lj=1;lj <=nlstate+ndeath; lj++){
5802: if(lj==li) continue;
5803: for(lk=1;lk<=ncovmodel;lk++){
5804: ll++;
5805: if(ll<=jj){
5806: cb[0]= lk +'a'-1;cb[1]='\0';
5807: if(ll<jj){
5808: if(itimes==1){
5809: if(mle>=1)
5810: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5811: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5812: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5813: }else{
5814: if(mle>=1)
5815: printf(" %.5e",matcov[jj][ll]);
5816: fprintf(ficlog," %.5e",matcov[jj][ll]);
5817: fprintf(ficres," %.5e",matcov[jj][ll]);
5818: }
5819: }else{
5820: if(itimes==1){
5821: if(mle>=1)
5822: printf(" Var(%s%1d%1d)",ca,i,j);
5823: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5824: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5825: }else{
5826: if(mle>=1)
5827: printf(" %.5e",matcov[jj][ll]);
5828: fprintf(ficlog," %.5e",matcov[jj][ll]);
5829: fprintf(ficres," %.5e",matcov[jj][ll]);
5830: }
5831: }
5832: }
5833: } /* end lk */
5834: } /* end lj */
5835: } /* end li */
5836: if(mle>=1)
5837: printf("\n");
5838: fprintf(ficlog,"\n");
5839: fprintf(ficres,"\n");
5840: numlinepar++;
5841: } /* end k*/
5842: } /*end j */
5843: } /* end i */
5844: } /* end itimes */
5845:
5846: fflush(ficlog);
5847: fflush(ficres);
5848:
5849: while((c=getc(ficpar))=='#' && c!= EOF){
5850: ungetc(c,ficpar);
5851: fgets(line, MAXLINE, ficpar);
5852: puts(line);
5853: fputs(line,ficparo);
5854: }
5855: ungetc(c,ficpar);
5856:
5857: estepm=0;
5858: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5859: if (estepm==0 || estepm < stepm) estepm=stepm;
5860: if (fage <= 2) {
5861: bage = ageminpar;
5862: fage = agemaxpar;
5863: }
5864:
5865: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5866: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5867: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5868:
5869: while((c=getc(ficpar))=='#' && c!= EOF){
5870: ungetc(c,ficpar);
5871: fgets(line, MAXLINE, ficpar);
5872: puts(line);
5873: fputs(line,ficparo);
5874: }
5875: ungetc(c,ficpar);
5876:
5877: 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);
5878: 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);
5879: 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);
5880: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5881: 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);
5882:
5883: while((c=getc(ficpar))=='#' && c!= EOF){
5884: ungetc(c,ficpar);
5885: fgets(line, MAXLINE, ficpar);
5886: puts(line);
5887: fputs(line,ficparo);
5888: }
5889: ungetc(c,ficpar);
5890:
5891:
5892: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5893: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5894:
5895: fscanf(ficpar,"pop_based=%d\n",&popbased);
5896: fprintf(ficparo,"pop_based=%d\n",popbased);
5897: fprintf(ficres,"pop_based=%d\n",popbased);
5898:
5899: while((c=getc(ficpar))=='#' && c!= EOF){
5900: ungetc(c,ficpar);
5901: fgets(line, MAXLINE, ficpar);
5902: puts(line);
5903: fputs(line,ficparo);
5904: }
5905: ungetc(c,ficpar);
5906:
5907: 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);
5908: 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);
5909: 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);
5910: 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);
5911: 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);
5912: /* day and month of proj2 are not used but only year anproj2.*/
5913:
5914:
5915:
5916: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5917: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5918:
5919: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5920: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5921:
5922: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5923: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5924: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5925:
5926: /*------------ free_vector -------------*/
5927: /* chdir(path); */
5928:
5929: free_ivector(wav,1,imx);
5930: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5931: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5932: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5933: free_lvector(num,1,n);
5934: free_vector(agedc,1,n);
5935: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5936: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5937: fclose(ficparo);
5938: fclose(ficres);
5939:
5940:
5941: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5942:
5943: strcpy(filerespl,"pl");
5944: strcat(filerespl,fileres);
5945: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5946: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5947: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5948: }
5949: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5950: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5951: pstamp(ficrespl);
5952: fprintf(ficrespl,"# Period (stable) prevalence \n");
5953: fprintf(ficrespl,"#Age ");
5954: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5955: fprintf(ficrespl,"\n");
5956:
5957: prlim=matrix(1,nlstate,1,nlstate);
5958:
5959: agebase=ageminpar;
5960: agelim=agemaxpar;
5961: ftolpl=1.e-10;
5962: i1=cptcoveff;
5963: if (cptcovn < 1){i1=1;}
5964:
5965: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5966: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5967: k=k+1;
5968: /* to clean */
5969: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
5970: fprintf(ficrespl,"\n#******");
5971: printf("\n#******");
5972: fprintf(ficlog,"\n#******");
5973: for(j=1;j<=cptcoveff;j++) {
5974: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5975: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5976: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5977: }
5978: fprintf(ficrespl,"******\n");
5979: printf("******\n");
5980: fprintf(ficlog,"******\n");
5981:
5982: for (age=agebase; age<=agelim; age++){
5983: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5984: fprintf(ficrespl,"%.0f ",age );
5985: for(j=1;j<=cptcoveff;j++)
5986: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5987: for(i=1; i<=nlstate;i++)
5988: fprintf(ficrespl," %.5f", prlim[i][i]);
5989: fprintf(ficrespl,"\n");
5990: }
5991: }
5992: }
5993: fclose(ficrespl);
5994:
5995: /*------------- h Pij x at various ages ------------*/
5996:
5997: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5998: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5999: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
6000: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
6001: }
6002: printf("Computing pij: result on file '%s' \n", filerespij);
6003: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6004:
6005: stepsize=(int) (stepm+YEARM-1)/YEARM;
6006: /*if (stepm<=24) stepsize=2;*/
6007:
6008: agelim=AGESUP;
6009: hstepm=stepsize*YEARM; /* Every year of age */
6010: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6011:
6012: /* hstepm=1; aff par mois*/
6013: pstamp(ficrespij);
6014: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6015: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6016: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6017: k=k+1;
6018: fprintf(ficrespij,"\n#****** ");
6019: for(j=1;j<=cptcoveff;j++)
6020: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6021: fprintf(ficrespij,"******\n");
6022:
6023: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6024: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6025: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6026:
6027: /* nhstepm=nhstepm*YEARM; aff par mois*/
6028:
6029: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6030: oldm=oldms;savm=savms;
6031: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6032: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6033: for(i=1; i<=nlstate;i++)
6034: for(j=1; j<=nlstate+ndeath;j++)
6035: fprintf(ficrespij," %1d-%1d",i,j);
6036: fprintf(ficrespij,"\n");
6037: for (h=0; h<=nhstepm; h++){
6038: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
6039: for(i=1; i<=nlstate;i++)
6040: for(j=1; j<=nlstate+ndeath;j++)
6041: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6042: fprintf(ficrespij,"\n");
6043: }
6044: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6045: fprintf(ficrespij,"\n");
6046: }
6047: }
6048: }
6049:
6050: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6051:
6052: fclose(ficrespij);
6053:
6054: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6055: for(i=1;i<=AGESUP;i++)
6056: for(j=1;j<=NCOVMAX;j++)
6057: for(k=1;k<=NCOVMAX;k++)
6058: probs[i][j][k]=0.;
6059:
6060: /*---------- Forecasting ------------------*/
6061: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6062: if(prevfcast==1){
6063: /* if(stepm ==1){*/
6064: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6065: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6066: /* } */
6067: /* else{ */
6068: /* erreur=108; */
6069: /* 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); */
6070: /* 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); */
6071: /* } */
6072: }
6073:
6074:
6075: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6076:
6077: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6078: /* 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",\
6079: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6080: */
6081:
6082: if (mobilav!=0) {
6083: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6084: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6085: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6086: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6087: }
6088: }
6089:
6090:
6091: /*---------- Health expectancies, no variances ------------*/
6092:
6093: strcpy(filerese,"e");
6094: strcat(filerese,fileres);
6095: if((ficreseij=fopen(filerese,"w"))==NULL) {
6096: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6097: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6098: }
6099: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6100: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6101: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6102: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6103: k=k+1;
6104: fprintf(ficreseij,"\n#****** ");
6105: for(j=1;j<=cptcoveff;j++) {
6106: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6107: }
6108: fprintf(ficreseij,"******\n");
6109:
6110: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6111: oldm=oldms;savm=savms;
6112: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6113:
6114: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6115: }
6116: }
6117: fclose(ficreseij);
6118:
6119:
6120: /*---------- Health expectancies and variances ------------*/
6121:
6122:
6123: strcpy(filerest,"t");
6124: strcat(filerest,fileres);
6125: if((ficrest=fopen(filerest,"w"))==NULL) {
6126: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6127: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6128: }
6129: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6130: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6131:
6132:
6133: strcpy(fileresstde,"stde");
6134: strcat(fileresstde,fileres);
6135: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6136: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6137: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6138: }
6139: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6140: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6141:
6142: strcpy(filerescve,"cve");
6143: strcat(filerescve,fileres);
6144: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6145: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6146: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6147: }
6148: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6149: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6150:
6151: strcpy(fileresv,"v");
6152: strcat(fileresv,fileres);
6153: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6154: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6155: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6156: }
6157: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6158: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6159:
6160: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6161: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6162: k=k+1;
6163: fprintf(ficrest,"\n#****** ");
6164: for(j=1;j<=cptcoveff;j++)
6165: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6166: fprintf(ficrest,"******\n");
6167:
6168: fprintf(ficresstdeij,"\n#****** ");
6169: fprintf(ficrescveij,"\n#****** ");
6170: for(j=1;j<=cptcoveff;j++) {
6171: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6172: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6173: }
6174: fprintf(ficresstdeij,"******\n");
6175: fprintf(ficrescveij,"******\n");
6176:
6177: fprintf(ficresvij,"\n#****** ");
6178: for(j=1;j<=cptcoveff;j++)
6179: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6180: fprintf(ficresvij,"******\n");
6181:
6182: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6183: oldm=oldms;savm=savms;
6184: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6185:
6186: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6187: pstamp(ficrest);
6188: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6189: oldm=oldms;savm=savms;
6190: 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 ");
6191: if(vpopbased==1)
6192: 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);
6193: else
6194: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6195: fprintf(ficrest,"# Age e.. (std) ");
6196: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6197: fprintf(ficrest,"\n");
6198:
6199: epj=vector(1,nlstate+1);
6200: for(age=bage; age <=fage ;age++){
6201: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6202: if (vpopbased==1) {
6203: if(mobilav ==0){
6204: for(i=1; i<=nlstate;i++)
6205: prlim[i][i]=probs[(int)age][i][k];
6206: }else{ /* mobilav */
6207: for(i=1; i<=nlstate;i++)
6208: prlim[i][i]=mobaverage[(int)age][i][k];
6209: }
6210: }
6211:
6212: fprintf(ficrest," %4.0f",age);
6213: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6214: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6215: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6216: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6217: }
6218: epj[nlstate+1] +=epj[j];
6219: }
6220:
6221: for(i=1, vepp=0.;i <=nlstate;i++)
6222: for(j=1;j <=nlstate;j++)
6223: vepp += vareij[i][j][(int)age];
6224: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6225: for(j=1;j <=nlstate;j++){
6226: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6227: }
6228: fprintf(ficrest,"\n");
6229: }
6230: }
6231: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6232: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6233: free_vector(epj,1,nlstate+1);
6234: }
6235: }
6236: free_vector(weight,1,n);
6237: free_imatrix(Tvard,1,15,1,2);
6238: free_imatrix(s,1,maxwav+1,1,n);
6239: free_matrix(anint,1,maxwav,1,n);
6240: free_matrix(mint,1,maxwav,1,n);
6241: free_ivector(cod,1,n);
6242: free_ivector(tab,1,NCOVMAX);
6243: fclose(ficresstdeij);
6244: fclose(ficrescveij);
6245: fclose(ficresvij);
6246: fclose(ficrest);
6247: fclose(ficpar);
6248:
6249: /*------- Variance of period (stable) prevalence------*/
6250:
6251: strcpy(fileresvpl,"vpl");
6252: strcat(fileresvpl,fileres);
6253: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6254: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6255: exit(0);
6256: }
6257: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6258:
6259: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6260: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6261: k=k+1;
6262: fprintf(ficresvpl,"\n#****** ");
6263: for(j=1;j<=cptcoveff;j++)
6264: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6265: fprintf(ficresvpl,"******\n");
6266:
6267: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6268: oldm=oldms;savm=savms;
6269: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6270: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6271: }
6272: }
6273:
6274: fclose(ficresvpl);
6275:
6276: /*---------- End : free ----------------*/
6277: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6278: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6279:
6280: } /* mle==-3 arrives here for freeing */
6281: endfree:
6282: free_matrix(prlim,1,nlstate,1,nlstate);
6283: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6284: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6285: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6286: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6287: free_matrix(covar,0,NCOVMAX,1,n);
6288: free_matrix(matcov,1,npar,1,npar);
6289: /*free_vector(delti,1,npar);*/
6290: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6291: free_matrix(agev,1,maxwav,1,imx);
6292: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6293:
6294: free_ivector(ncodemax,1,8);
6295: free_ivector(Tvar,1,15);
6296: free_ivector(Tprod,1,15);
6297: free_ivector(Tvaraff,1,15);
6298: free_ivector(Tage,1,15);
6299:
6300: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6301: free_imatrix(codtab,1,100,1,10);
6302: fflush(fichtm);
6303: fflush(ficgp);
6304:
6305:
6306: if((nberr >0) || (nbwarn>0)){
6307: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6308: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6309: }else{
6310: printf("End of Imach\n");
6311: fprintf(ficlog,"End of Imach\n");
6312: }
6313: printf("See log file on %s\n",filelog);
6314: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6315: (void) gettimeofday(&end_time,&tzp);
6316: tm = *localtime(&end_time.tv_sec);
6317: tmg = *gmtime(&end_time.tv_sec);
6318: strcpy(strtend,asctime(&tm));
6319: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6320: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6321: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6322:
6323: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6324: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6325: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6326: /* printf("Total time was %d uSec.\n", total_usecs);*/
6327: /* if(fileappend(fichtm,optionfilehtm)){ */
6328: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6329: fclose(fichtm);
6330: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6331: fclose(fichtmcov);
6332: fclose(ficgp);
6333: fclose(ficlog);
6334: /*------ End -----------*/
6335:
6336:
6337: printf("Before Current directory %s!\n",pathcd);
6338: if(chdir(pathcd) != 0)
6339: printf("Can't move to directory %s!\n",path);
6340: if(getcwd(pathcd,MAXLINE) > 0)
6341: printf("Current directory %s!\n",pathcd);
6342: /*strcat(plotcmd,CHARSEPARATOR);*/
6343: sprintf(plotcmd,"gnuplot");
6344: #ifndef UNIX
6345: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6346: #endif
6347: if(!stat(plotcmd,&info)){
6348: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6349: if(!stat(getenv("GNUPLOTBIN"),&info)){
6350: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6351: }else
6352: strcpy(pplotcmd,plotcmd);
6353: #ifdef UNIX
6354: strcpy(plotcmd,GNUPLOTPROGRAM);
6355: if(!stat(plotcmd,&info)){
6356: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6357: }else
6358: strcpy(pplotcmd,plotcmd);
6359: #endif
6360: }else
6361: strcpy(pplotcmd,plotcmd);
6362:
6363: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6364: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6365:
6366: if((outcmd=system(plotcmd)) != 0){
6367: printf("\n Problem with gnuplot\n");
6368: }
6369: printf(" Wait...");
6370: while (z[0] != 'q') {
6371: /* chdir(path); */
6372: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6373: scanf("%s",z);
6374: /* if (z[0] == 'c') system("./imach"); */
6375: if (z[0] == 'e') {
6376: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6377: system(optionfilehtm);
6378: }
6379: else if (z[0] == 'g') system(plotcmd);
6380: else if (z[0] == 'q') exit(0);
6381: }
6382: end:
6383: while (z[0] != 'q') {
6384: printf("\nType q for exiting: ");
6385: scanf("%s",z);
6386: }
6387: }
6388:
6389:
6390:
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