1: /* $Id: imach.c,v 1.151 2014/06/18 16:43:30 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.151 2014/06/18 16:43:30 brouard
5: *** empty log message ***
6:
7: Revision 1.150 2014/06/18 16:42:35 brouard
8: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
9: Author: brouard
10:
11: Revision 1.149 2014/06/18 15:51:14 brouard
12: Summary: Some fixes in parameter files errors
13: Author: Nicolas Brouard
14:
15: Revision 1.148 2014/06/17 17:38:48 brouard
16: Summary: Nothing new
17: Author: Brouard
18:
19: Just a new packaging for OS/X version 0.98nS
20:
21: Revision 1.147 2014/06/16 10:33:11 brouard
22: *** empty log message ***
23:
24: Revision 1.146 2014/06/16 10:20:28 brouard
25: Summary: Merge
26: Author: Brouard
27:
28: Merge, before building revised version.
29:
30: Revision 1.145 2014/06/10 21:23:15 brouard
31: Summary: Debugging with valgrind
32: Author: Nicolas Brouard
33:
34: Lot of changes in order to output the results with some covariates
35: After the Edimburgh REVES conference 2014, it seems mandatory to
36: improve the code.
37: No more memory valgrind error but a lot has to be done in order to
38: continue the work of splitting the code into subroutines.
39: Also, decodemodel has been improved. Tricode is still not
40: optimal. nbcode should be improved. Documentation has been added in
41: the source code.
42:
43: Revision 1.143 2014/01/26 09:45:38 brouard
44: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
45:
46: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
47: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
48:
49: Revision 1.142 2014/01/26 03:57:36 brouard
50: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
51:
52: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
53:
54: Revision 1.141 2014/01/26 02:42:01 brouard
55: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
56:
57: Revision 1.140 2011/09/02 10:37:54 brouard
58: Summary: times.h is ok with mingw32 now.
59:
60: Revision 1.139 2010/06/14 07:50:17 brouard
61: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
62: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
63:
64: Revision 1.138 2010/04/30 18:19:40 brouard
65: *** empty log message ***
66:
67: Revision 1.137 2010/04/29 18:11:38 brouard
68: (Module): Checking covariates for more complex models
69: than V1+V2. A lot of change to be done. Unstable.
70:
71: Revision 1.136 2010/04/26 20:30:53 brouard
72: (Module): merging some libgsl code. Fixing computation
73: of likelione (using inter/intrapolation if mle = 0) in order to
74: get same likelihood as if mle=1.
75: Some cleaning of code and comments added.
76:
77: Revision 1.135 2009/10/29 15:33:14 brouard
78: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
79:
80: Revision 1.134 2009/10/29 13:18:53 brouard
81: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
82:
83: Revision 1.133 2009/07/06 10:21:25 brouard
84: just nforces
85:
86: Revision 1.132 2009/07/06 08:22:05 brouard
87: Many tings
88:
89: Revision 1.131 2009/06/20 16:22:47 brouard
90: Some dimensions resccaled
91:
92: Revision 1.130 2009/05/26 06:44:34 brouard
93: (Module): Max Covariate is now set to 20 instead of 8. A
94: lot of cleaning with variables initialized to 0. Trying to make
95: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
96:
97: Revision 1.129 2007/08/31 13:49:27 lievre
98: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
99:
100: Revision 1.128 2006/06/30 13:02:05 brouard
101: (Module): Clarifications on computing e.j
102:
103: Revision 1.127 2006/04/28 18:11:50 brouard
104: (Module): Yes the sum of survivors was wrong since
105: imach-114 because nhstepm was no more computed in the age
106: loop. Now we define nhstepma in the age loop.
107: (Module): In order to speed up (in case of numerous covariates) we
108: compute health expectancies (without variances) in a first step
109: and then all the health expectancies with variances or standard
110: deviation (needs data from the Hessian matrices) which slows the
111: computation.
112: In the future we should be able to stop the program is only health
113: expectancies and graph are needed without standard deviations.
114:
115: Revision 1.126 2006/04/28 17:23:28 brouard
116: (Module): Yes the sum of survivors was wrong since
117: imach-114 because nhstepm was no more computed in the age
118: loop. Now we define nhstepma in the age loop.
119: Version 0.98h
120:
121: Revision 1.125 2006/04/04 15:20:31 lievre
122: Errors in calculation of health expectancies. Age was not initialized.
123: Forecasting file added.
124:
125: Revision 1.124 2006/03/22 17:13:53 lievre
126: Parameters are printed with %lf instead of %f (more numbers after the comma).
127: The log-likelihood is printed in the log file
128:
129: Revision 1.123 2006/03/20 10:52:43 brouard
130: * imach.c (Module): <title> changed, corresponds to .htm file
131: name. <head> headers where missing.
132:
133: * imach.c (Module): Weights can have a decimal point as for
134: English (a comma might work with a correct LC_NUMERIC environment,
135: otherwise the weight is truncated).
136: Modification of warning when the covariates values are not 0 or
137: 1.
138: Version 0.98g
139:
140: Revision 1.122 2006/03/20 09:45:41 brouard
141: (Module): Weights can have a decimal point as for
142: English (a comma might work with a correct LC_NUMERIC environment,
143: otherwise the weight is truncated).
144: Modification of warning when the covariates values are not 0 or
145: 1.
146: Version 0.98g
147:
148: Revision 1.121 2006/03/16 17:45:01 lievre
149: * imach.c (Module): Comments concerning covariates added
150:
151: * imach.c (Module): refinements in the computation of lli if
152: status=-2 in order to have more reliable computation if stepm is
153: not 1 month. Version 0.98f
154:
155: Revision 1.120 2006/03/16 15:10:38 lievre
156: (Module): refinements in the computation of lli if
157: status=-2 in order to have more reliable computation if stepm is
158: not 1 month. Version 0.98f
159:
160: Revision 1.119 2006/03/15 17:42:26 brouard
161: (Module): Bug if status = -2, the loglikelihood was
162: computed as likelihood omitting the logarithm. Version O.98e
163:
164: Revision 1.118 2006/03/14 18:20:07 brouard
165: (Module): varevsij Comments added explaining the second
166: table of variances if popbased=1 .
167: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
168: (Module): Function pstamp added
169: (Module): Version 0.98d
170:
171: Revision 1.117 2006/03/14 17:16:22 brouard
172: (Module): varevsij Comments added explaining the second
173: table of variances if popbased=1 .
174: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
175: (Module): Function pstamp added
176: (Module): Version 0.98d
177:
178: Revision 1.116 2006/03/06 10:29:27 brouard
179: (Module): Variance-covariance wrong links and
180: varian-covariance of ej. is needed (Saito).
181:
182: Revision 1.115 2006/02/27 12:17:45 brouard
183: (Module): One freematrix added in mlikeli! 0.98c
184:
185: Revision 1.114 2006/02/26 12:57:58 brouard
186: (Module): Some improvements in processing parameter
187: filename with strsep.
188:
189: Revision 1.113 2006/02/24 14:20:24 brouard
190: (Module): Memory leaks checks with valgrind and:
191: datafile was not closed, some imatrix were not freed and on matrix
192: allocation too.
193:
194: Revision 1.112 2006/01/30 09:55:26 brouard
195: (Module): Back to gnuplot.exe instead of wgnuplot.exe
196:
197: Revision 1.111 2006/01/25 20:38:18 brouard
198: (Module): Lots of cleaning and bugs added (Gompertz)
199: (Module): Comments can be added in data file. Missing date values
200: can be a simple dot '.'.
201:
202: Revision 1.110 2006/01/25 00:51:50 brouard
203: (Module): Lots of cleaning and bugs added (Gompertz)
204:
205: Revision 1.109 2006/01/24 19:37:15 brouard
206: (Module): Comments (lines starting with a #) are allowed in data.
207:
208: Revision 1.108 2006/01/19 18:05:42 lievre
209: Gnuplot problem appeared...
210: To be fixed
211:
212: Revision 1.107 2006/01/19 16:20:37 brouard
213: Test existence of gnuplot in imach path
214:
215: Revision 1.106 2006/01/19 13:24:36 brouard
216: Some cleaning and links added in html output
217:
218: Revision 1.105 2006/01/05 20:23:19 lievre
219: *** empty log message ***
220:
221: Revision 1.104 2005/09/30 16:11:43 lievre
222: (Module): sump fixed, loop imx fixed, and simplifications.
223: (Module): If the status is missing at the last wave but we know
224: that the person is alive, then we can code his/her status as -2
225: (instead of missing=-1 in earlier versions) and his/her
226: contributions to the likelihood is 1 - Prob of dying from last
227: health status (= 1-p13= p11+p12 in the easiest case of somebody in
228: the healthy state at last known wave). Version is 0.98
229:
230: Revision 1.103 2005/09/30 15:54:49 lievre
231: (Module): sump fixed, loop imx fixed, and simplifications.
232:
233: Revision 1.102 2004/09/15 17:31:30 brouard
234: Add the possibility to read data file including tab characters.
235:
236: Revision 1.101 2004/09/15 10:38:38 brouard
237: Fix on curr_time
238:
239: Revision 1.100 2004/07/12 18:29:06 brouard
240: Add version for Mac OS X. Just define UNIX in Makefile
241:
242: Revision 1.99 2004/06/05 08:57:40 brouard
243: *** empty log message ***
244:
245: Revision 1.98 2004/05/16 15:05:56 brouard
246: New version 0.97 . First attempt to estimate force of mortality
247: directly from the data i.e. without the need of knowing the health
248: state at each age, but using a Gompertz model: log u =a + b*age .
249: This is the basic analysis of mortality and should be done before any
250: other analysis, in order to test if the mortality estimated from the
251: cross-longitudinal survey is different from the mortality estimated
252: from other sources like vital statistic data.
253:
254: The same imach parameter file can be used but the option for mle should be -3.
255:
256: Agnès, who wrote this part of the code, tried to keep most of the
257: former routines in order to include the new code within the former code.
258:
259: The output is very simple: only an estimate of the intercept and of
260: the slope with 95% confident intervals.
261:
262: Current limitations:
263: A) Even if you enter covariates, i.e. with the
264: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
265: B) There is no computation of Life Expectancy nor Life Table.
266:
267: Revision 1.97 2004/02/20 13:25:42 lievre
268: Version 0.96d. Population forecasting command line is (temporarily)
269: suppressed.
270:
271: Revision 1.96 2003/07/15 15:38:55 brouard
272: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
273: rewritten within the same printf. Workaround: many printfs.
274:
275: Revision 1.95 2003/07/08 07:54:34 brouard
276: * imach.c (Repository):
277: (Repository): Using imachwizard code to output a more meaningful covariance
278: matrix (cov(a12,c31) instead of numbers.
279:
280: Revision 1.94 2003/06/27 13:00:02 brouard
281: Just cleaning
282:
283: Revision 1.93 2003/06/25 16:33:55 brouard
284: (Module): On windows (cygwin) function asctime_r doesn't
285: exist so I changed back to asctime which exists.
286: (Module): Version 0.96b
287:
288: Revision 1.92 2003/06/25 16:30:45 brouard
289: (Module): On windows (cygwin) function asctime_r doesn't
290: exist so I changed back to asctime which exists.
291:
292: Revision 1.91 2003/06/25 15:30:29 brouard
293: * imach.c (Repository): Duplicated warning errors corrected.
294: (Repository): Elapsed time after each iteration is now output. It
295: helps to forecast when convergence will be reached. Elapsed time
296: is stamped in powell. We created a new html file for the graphs
297: concerning matrix of covariance. It has extension -cov.htm.
298:
299: Revision 1.90 2003/06/24 12:34:15 brouard
300: (Module): Some bugs corrected for windows. Also, when
301: mle=-1 a template is output in file "or"mypar.txt with the design
302: of the covariance matrix to be input.
303:
304: Revision 1.89 2003/06/24 12:30:52 brouard
305: (Module): Some bugs corrected for windows. Also, when
306: mle=-1 a template is output in file "or"mypar.txt with the design
307: of the covariance matrix to be input.
308:
309: Revision 1.88 2003/06/23 17:54:56 brouard
310: * 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.
311:
312: Revision 1.87 2003/06/18 12:26:01 brouard
313: Version 0.96
314:
315: Revision 1.86 2003/06/17 20:04:08 brouard
316: (Module): Change position of html and gnuplot routines and added
317: routine fileappend.
318:
319: Revision 1.85 2003/06/17 13:12:43 brouard
320: * imach.c (Repository): Check when date of death was earlier that
321: current date of interview. It may happen when the death was just
322: prior to the death. In this case, dh was negative and likelihood
323: was wrong (infinity). We still send an "Error" but patch by
324: assuming that the date of death was just one stepm after the
325: interview.
326: (Repository): Because some people have very long ID (first column)
327: we changed int to long in num[] and we added a new lvector for
328: memory allocation. But we also truncated to 8 characters (left
329: truncation)
330: (Repository): No more line truncation errors.
331:
332: Revision 1.84 2003/06/13 21:44:43 brouard
333: * imach.c (Repository): Replace "freqsummary" at a correct
334: place. It differs from routine "prevalence" which may be called
335: many times. Probs is memory consuming and must be used with
336: parcimony.
337: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
338:
339: Revision 1.83 2003/06/10 13:39:11 lievre
340: *** empty log message ***
341:
342: Revision 1.82 2003/06/05 15:57:20 brouard
343: Add log in imach.c and fullversion number is now printed.
344:
345: */
346: /*
347: Interpolated Markov Chain
348:
349: Short summary of the programme:
350:
351: This program computes Healthy Life Expectancies from
352: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
353: first survey ("cross") where individuals from different ages are
354: interviewed on their health status or degree of disability (in the
355: case of a health survey which is our main interest) -2- at least a
356: second wave of interviews ("longitudinal") which measure each change
357: (if any) in individual health status. Health expectancies are
358: computed from the time spent in each health state according to a
359: model. More health states you consider, more time is necessary to reach the
360: Maximum Likelihood of the parameters involved in the model. The
361: simplest model is the multinomial logistic model where pij is the
362: probability to be observed in state j at the second wave
363: conditional to be observed in state i at the first wave. Therefore
364: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
365: 'age' is age and 'sex' is a covariate. If you want to have a more
366: complex model than "constant and age", you should modify the program
367: where the markup *Covariates have to be included here again* invites
368: you to do it. More covariates you add, slower the
369: convergence.
370:
371: The advantage of this computer programme, compared to a simple
372: multinomial logistic model, is clear when the delay between waves is not
373: identical for each individual. Also, if a individual missed an
374: intermediate interview, the information is lost, but taken into
375: account using an interpolation or extrapolation.
376:
377: hPijx is the probability to be observed in state i at age x+h
378: conditional to the observed state i at age x. The delay 'h' can be
379: split into an exact number (nh*stepm) of unobserved intermediate
380: states. This elementary transition (by month, quarter,
381: semester or year) is modelled as a multinomial logistic. The hPx
382: matrix is simply the matrix product of nh*stepm elementary matrices
383: and the contribution of each individual to the likelihood is simply
384: hPijx.
385:
386: Also this programme outputs the covariance matrix of the parameters but also
387: of the life expectancies. It also computes the period (stable) prevalence.
388:
389: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
390: Institut national d'études démographiques, Paris.
391: This software have been partly granted by Euro-REVES, a concerted action
392: from the European Union.
393: It is copyrighted identically to a GNU software product, ie programme and
394: software can be distributed freely for non commercial use. Latest version
395: can be accessed at http://euroreves.ined.fr/imach .
396:
397: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
398: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
399:
400: **********************************************************************/
401: /*
402: main
403: read parameterfile
404: read datafile
405: concatwav
406: freqsummary
407: if (mle >= 1)
408: mlikeli
409: print results files
410: if mle==1
411: computes hessian
412: read end of parameter file: agemin, agemax, bage, fage, estepm
413: begin-prev-date,...
414: open gnuplot file
415: open html file
416: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
417: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
418: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
419: freexexit2 possible for memory heap.
420:
421: h Pij x | pij_nom ficrestpij
422: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
423: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
424: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
425:
426: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
427: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
428: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
429: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
430: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
431:
432: forecasting if prevfcast==1 prevforecast call prevalence()
433: health expectancies
434: Variance-covariance of DFLE
435: prevalence()
436: movingaverage()
437: varevsij()
438: if popbased==1 varevsij(,popbased)
439: total life expectancies
440: Variance of period (stable) prevalence
441: end
442: */
443:
444:
445:
446:
447: #include <math.h>
448: #include <stdio.h>
449: #include <stdlib.h>
450: #include <string.h>
451: #include <unistd.h>
452:
453: #include <limits.h>
454: #include <sys/types.h>
455: #include <sys/stat.h>
456: #include <errno.h>
457: extern int errno;
458:
459: #ifdef LINUX
460: #include <time.h>
461: #include "timeval.h"
462: #else
463: #include <sys/time.h>
464: #endif
465:
466: #ifdef GSL
467: #include <gsl/gsl_errno.h>
468: #include <gsl/gsl_multimin.h>
469: #endif
470:
471: /* #include <libintl.h> */
472: /* #define _(String) gettext (String) */
473:
474: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
475:
476: #define GNUPLOTPROGRAM "gnuplot"
477: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
478: #define FILENAMELENGTH 132
479:
480: #define GLOCK_ERROR_NOPATH -1 /* empty path */
481: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
482:
483: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
484: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
485:
486: #define NINTERVMAX 8
487: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
488: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
489: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
490: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
491: #define MAXN 20000
492: #define YEARM 12. /**< Number of months per year */
493: #define AGESUP 130
494: #define AGEBASE 40
495: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
496: #ifdef UNIX
497: #define DIRSEPARATOR '/'
498: #define CHARSEPARATOR "/"
499: #define ODIRSEPARATOR '\\'
500: #else
501: #define DIRSEPARATOR '\\'
502: #define CHARSEPARATOR "\\"
503: #define ODIRSEPARATOR '/'
504: #endif
505:
506: /* $Id: imach.c,v 1.151 2014/06/18 16:43:30 brouard Exp $ */
507: /* $State: Exp $ */
508:
509: char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
510: char fullversion[]="$Revision: 1.151 $ $Date: 2014/06/18 16:43:30 $";
511: char strstart[80];
512: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
513: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
514: int nvar=0, nforce=0; /* Number of variables, number of forces */
515: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
516: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
517: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
518: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
519: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
520: int cptcovprodnoage=0; /**< Number of covariate products without age */
521: int cptcoveff=0; /* Total number of covariates to vary for printing results */
522: int cptcov=0; /* Working variable */
523: int npar=NPARMAX;
524: int nlstate=2; /* Number of live states */
525: int ndeath=1; /* Number of dead states */
526: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
527: int popbased=0;
528:
529: int *wav; /* Number of waves for this individuual 0 is possible */
530: int maxwav=0; /* Maxim number of waves */
531: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
532: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
533: int gipmx=0, gsw=0; /* Global variables on the number of contributions
534: to the likelihood and the sum of weights (done by funcone)*/
535: int mle=1, weightopt=0;
536: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
537: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
538: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
539: * wave mi and wave mi+1 is not an exact multiple of stepm. */
540: double jmean=1; /* Mean space between 2 waves */
541: double **matprod2(); /* test */
542: double **oldm, **newm, **savm; /* Working pointers to matrices */
543: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
544: /*FILE *fic ; */ /* Used in readdata only */
545: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
546: FILE *ficlog, *ficrespow;
547: int globpr=0; /* Global variable for printing or not */
548: double fretone; /* Only one call to likelihood */
549: long ipmx=0; /* Number of contributions */
550: double sw; /* Sum of weights */
551: char filerespow[FILENAMELENGTH];
552: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
553: FILE *ficresilk;
554: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
555: FILE *ficresprobmorprev;
556: FILE *fichtm, *fichtmcov; /* Html File */
557: FILE *ficreseij;
558: char filerese[FILENAMELENGTH];
559: FILE *ficresstdeij;
560: char fileresstde[FILENAMELENGTH];
561: FILE *ficrescveij;
562: char filerescve[FILENAMELENGTH];
563: FILE *ficresvij;
564: char fileresv[FILENAMELENGTH];
565: FILE *ficresvpl;
566: char fileresvpl[FILENAMELENGTH];
567: char title[MAXLINE];
568: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
569: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
570: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
571: char command[FILENAMELENGTH];
572: int outcmd=0;
573:
574: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
575:
576: char filelog[FILENAMELENGTH]; /* Log file */
577: char filerest[FILENAMELENGTH];
578: char fileregp[FILENAMELENGTH];
579: char popfile[FILENAMELENGTH];
580:
581: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
582:
583: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
584: struct timezone tzp;
585: extern int gettimeofday();
586: struct tm tmg, tm, tmf, *gmtime(), *localtime();
587: long time_value;
588: extern long time();
589: char strcurr[80], strfor[80];
590:
591: char *endptr;
592: long lval;
593: double dval;
594:
595: #define NR_END 1
596: #define FREE_ARG char*
597: #define FTOL 1.0e-10
598:
599: #define NRANSI
600: #define ITMAX 200
601:
602: #define TOL 2.0e-4
603:
604: #define CGOLD 0.3819660
605: #define ZEPS 1.0e-10
606: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
607:
608: #define GOLD 1.618034
609: #define GLIMIT 100.0
610: #define TINY 1.0e-20
611:
612: static double maxarg1,maxarg2;
613: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
614: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
615:
616: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
617: #define rint(a) floor(a+0.5)
618:
619: static double sqrarg;
620: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
621: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
622: int agegomp= AGEGOMP;
623:
624: int imx;
625: int stepm=1;
626: /* Stepm, step in month: minimum step interpolation*/
627:
628: int estepm;
629: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
630:
631: int m,nb;
632: long *num;
633: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
634: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
635: double **pmmij, ***probs;
636: double *ageexmed,*agecens;
637: double dateintmean=0;
638:
639: double *weight;
640: int **s; /* Status */
641: double *agedc;
642: double **covar; /**< covar[j,i], value of jth covariate for individual i,
643: * covar=matrix(0,NCOVMAX,1,n);
644: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
645: double idx;
646: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
647: int *Ndum; /** Freq of modality (tricode */
648: int **codtab; /**< codtab=imatrix(1,100,1,10); */
649: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
650: double *lsurv, *lpop, *tpop;
651:
652: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
653: double ftolhess; /**< Tolerance for computing hessian */
654:
655: /**************** split *************************/
656: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
657: {
658: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
659: the name of the file (name), its extension only (ext) and its first part of the name (finame)
660: */
661: char *ss; /* pointer */
662: int l1, l2; /* length counters */
663:
664: l1 = strlen(path ); /* length of path */
665: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
666: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
667: if ( ss == NULL ) { /* no directory, so determine current directory */
668: strcpy( name, path ); /* we got the fullname name because no directory */
669: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
670: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
671: /* get current working directory */
672: /* extern char* getcwd ( char *buf , int len);*/
673: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
674: return( GLOCK_ERROR_GETCWD );
675: }
676: /* got dirc from getcwd*/
677: printf(" DIRC = %s \n",dirc);
678: } else { /* strip direcotry from path */
679: ss++; /* after this, the filename */
680: l2 = strlen( ss ); /* length of filename */
681: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
682: strcpy( name, ss ); /* save file name */
683: strncpy( dirc, path, l1 - l2 ); /* now the directory */
684: dirc[l1-l2] = 0; /* add zero */
685: printf(" DIRC2 = %s \n",dirc);
686: }
687: /* We add a separator at the end of dirc if not exists */
688: l1 = strlen( dirc ); /* length of directory */
689: if( dirc[l1-1] != DIRSEPARATOR ){
690: dirc[l1] = DIRSEPARATOR;
691: dirc[l1+1] = 0;
692: printf(" DIRC3 = %s \n",dirc);
693: }
694: ss = strrchr( name, '.' ); /* find last / */
695: if (ss >0){
696: ss++;
697: strcpy(ext,ss); /* save extension */
698: l1= strlen( name);
699: l2= strlen(ss)+1;
700: strncpy( finame, name, l1-l2);
701: finame[l1-l2]= 0;
702: }
703:
704: return( 0 ); /* we're done */
705: }
706:
707:
708: /******************************************/
709:
710: void replace_back_to_slash(char *s, char*t)
711: {
712: int i;
713: int lg=0;
714: i=0;
715: lg=strlen(t);
716: for(i=0; i<= lg; i++) {
717: (s[i] = t[i]);
718: if (t[i]== '\\') s[i]='/';
719: }
720: }
721:
722: char *trimbb(char *out, char *in)
723: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
724: char *s;
725: s=out;
726: while (*in != '\0'){
727: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
728: in++;
729: }
730: *out++ = *in++;
731: }
732: *out='\0';
733: return s;
734: }
735:
736: char *cutl(char *blocc, char *alocc, char *in, char occ)
737: {
738: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
739: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
740: gives blocc="abcdef2ghi" and alocc="j".
741: If occ is not found blocc is null and alocc is equal to in. Returns blocc
742: */
743: char *s, *t, *bl;
744: t=in;s=in;
745: while ((*in != occ) && (*in != '\0')){
746: *alocc++ = *in++;
747: }
748: if( *in == occ){
749: *(alocc)='\0';
750: s=++in;
751: }
752:
753: if (s == t) {/* occ not found */
754: *(alocc-(in-s))='\0';
755: in=s;
756: }
757: while ( *in != '\0'){
758: *blocc++ = *in++;
759: }
760:
761: *blocc='\0';
762: return t;
763: }
764: char *cutv(char *blocc, char *alocc, char *in, char occ)
765: {
766: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
767: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
768: gives blocc="abcdef2ghi" and alocc="j".
769: If occ is not found blocc is null and alocc is equal to in. Returns alocc
770: */
771: char *s, *t;
772: t=in;s=in;
773: while (*in != '\0'){
774: while( *in == occ){
775: *blocc++ = *in++;
776: s=in;
777: }
778: *blocc++ = *in++;
779: }
780: if (s == t) /* occ not found */
781: *(blocc-(in-s))='\0';
782: else
783: *(blocc-(in-s)-1)='\0';
784: in=s;
785: while ( *in != '\0'){
786: *alocc++ = *in++;
787: }
788:
789: *alocc='\0';
790: return s;
791: }
792:
793: int nbocc(char *s, char occ)
794: {
795: int i,j=0;
796: int lg=20;
797: i=0;
798: lg=strlen(s);
799: for(i=0; i<= lg; i++) {
800: if (s[i] == occ ) j++;
801: }
802: return j;
803: }
804:
805: /* void cutv(char *u,char *v, char*t, char occ) */
806: /* { */
807: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
808: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
809: /* gives u="abcdef2ghi" and v="j" *\/ */
810: /* int i,lg,j,p=0; */
811: /* i=0; */
812: /* lg=strlen(t); */
813: /* for(j=0; j<=lg-1; j++) { */
814: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
815: /* } */
816:
817: /* for(j=0; j<p; j++) { */
818: /* (u[j] = t[j]); */
819: /* } */
820: /* u[p]='\0'; */
821:
822: /* for(j=0; j<= lg; j++) { */
823: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
824: /* } */
825: /* } */
826:
827: /********************** nrerror ********************/
828:
829: void nrerror(char error_text[])
830: {
831: fprintf(stderr,"ERREUR ...\n");
832: fprintf(stderr,"%s\n",error_text);
833: exit(EXIT_FAILURE);
834: }
835: /*********************** vector *******************/
836: double *vector(int nl, int nh)
837: {
838: double *v;
839: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
840: if (!v) nrerror("allocation failure in vector");
841: return v-nl+NR_END;
842: }
843:
844: /************************ free vector ******************/
845: void free_vector(double*v, int nl, int nh)
846: {
847: free((FREE_ARG)(v+nl-NR_END));
848: }
849:
850: /************************ivector *******************************/
851: int *ivector(long nl,long nh)
852: {
853: int *v;
854: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
855: if (!v) nrerror("allocation failure in ivector");
856: return v-nl+NR_END;
857: }
858:
859: /******************free ivector **************************/
860: void free_ivector(int *v, long nl, long nh)
861: {
862: free((FREE_ARG)(v+nl-NR_END));
863: }
864:
865: /************************lvector *******************************/
866: long *lvector(long nl,long nh)
867: {
868: long *v;
869: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
870: if (!v) nrerror("allocation failure in ivector");
871: return v-nl+NR_END;
872: }
873:
874: /******************free lvector **************************/
875: void free_lvector(long *v, long nl, long nh)
876: {
877: free((FREE_ARG)(v+nl-NR_END));
878: }
879:
880: /******************* imatrix *******************************/
881: int **imatrix(long nrl, long nrh, long ncl, long nch)
882: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
883: {
884: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
885: int **m;
886:
887: /* allocate pointers to rows */
888: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
889: if (!m) nrerror("allocation failure 1 in matrix()");
890: m += NR_END;
891: m -= nrl;
892:
893:
894: /* allocate rows and set pointers to them */
895: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
896: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
897: m[nrl] += NR_END;
898: m[nrl] -= ncl;
899:
900: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
901:
902: /* return pointer to array of pointers to rows */
903: return m;
904: }
905:
906: /****************** free_imatrix *************************/
907: void free_imatrix(m,nrl,nrh,ncl,nch)
908: int **m;
909: long nch,ncl,nrh,nrl;
910: /* free an int matrix allocated by imatrix() */
911: {
912: free((FREE_ARG) (m[nrl]+ncl-NR_END));
913: free((FREE_ARG) (m+nrl-NR_END));
914: }
915:
916: /******************* matrix *******************************/
917: double **matrix(long nrl, long nrh, long ncl, long nch)
918: {
919: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
920: double **m;
921:
922: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
923: if (!m) nrerror("allocation failure 1 in matrix()");
924: m += NR_END;
925: m -= nrl;
926:
927: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
928: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
929: m[nrl] += NR_END;
930: m[nrl] -= ncl;
931:
932: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
933: return m;
934: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
935: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
936: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
937: */
938: }
939:
940: /*************************free matrix ************************/
941: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
942: {
943: free((FREE_ARG)(m[nrl]+ncl-NR_END));
944: free((FREE_ARG)(m+nrl-NR_END));
945: }
946:
947: /******************* ma3x *******************************/
948: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
949: {
950: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
951: double ***m;
952:
953: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
954: if (!m) nrerror("allocation failure 1 in matrix()");
955: m += NR_END;
956: m -= nrl;
957:
958: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
959: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
960: m[nrl] += NR_END;
961: m[nrl] -= ncl;
962:
963: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
964:
965: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
966: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
967: m[nrl][ncl] += NR_END;
968: m[nrl][ncl] -= nll;
969: for (j=ncl+1; j<=nch; j++)
970: m[nrl][j]=m[nrl][j-1]+nlay;
971:
972: for (i=nrl+1; i<=nrh; i++) {
973: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
974: for (j=ncl+1; j<=nch; j++)
975: m[i][j]=m[i][j-1]+nlay;
976: }
977: return m;
978: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
979: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
980: */
981: }
982:
983: /*************************free ma3x ************************/
984: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
985: {
986: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
987: free((FREE_ARG)(m[nrl]+ncl-NR_END));
988: free((FREE_ARG)(m+nrl-NR_END));
989: }
990:
991: /*************** function subdirf ***********/
992: char *subdirf(char fileres[])
993: {
994: /* Caution optionfilefiname is hidden */
995: strcpy(tmpout,optionfilefiname);
996: strcat(tmpout,"/"); /* Add to the right */
997: strcat(tmpout,fileres);
998: return tmpout;
999: }
1000:
1001: /*************** function subdirf2 ***********/
1002: char *subdirf2(char fileres[], char *preop)
1003: {
1004:
1005: /* Caution optionfilefiname is hidden */
1006: strcpy(tmpout,optionfilefiname);
1007: strcat(tmpout,"/");
1008: strcat(tmpout,preop);
1009: strcat(tmpout,fileres);
1010: return tmpout;
1011: }
1012:
1013: /*************** function subdirf3 ***********/
1014: char *subdirf3(char fileres[], char *preop, char *preop2)
1015: {
1016:
1017: /* Caution optionfilefiname is hidden */
1018: strcpy(tmpout,optionfilefiname);
1019: strcat(tmpout,"/");
1020: strcat(tmpout,preop);
1021: strcat(tmpout,preop2);
1022: strcat(tmpout,fileres);
1023: return tmpout;
1024: }
1025:
1026: /***************** f1dim *************************/
1027: extern int ncom;
1028: extern double *pcom,*xicom;
1029: extern double (*nrfunc)(double []);
1030:
1031: double f1dim(double x)
1032: {
1033: int j;
1034: double f;
1035: double *xt;
1036:
1037: xt=vector(1,ncom);
1038: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1039: f=(*nrfunc)(xt);
1040: free_vector(xt,1,ncom);
1041: return f;
1042: }
1043:
1044: /*****************brent *************************/
1045: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1046: {
1047: int iter;
1048: double a,b,d,etemp;
1049: double fu,fv,fw,fx;
1050: double ftemp;
1051: double p,q,r,tol1,tol2,u,v,w,x,xm;
1052: double e=0.0;
1053:
1054: a=(ax < cx ? ax : cx);
1055: b=(ax > cx ? ax : cx);
1056: x=w=v=bx;
1057: fw=fv=fx=(*f)(x);
1058: for (iter=1;iter<=ITMAX;iter++) {
1059: xm=0.5*(a+b);
1060: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1061: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1062: printf(".");fflush(stdout);
1063: fprintf(ficlog,".");fflush(ficlog);
1064: #ifdef DEBUG
1065: 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);
1066: 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);
1067: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1068: #endif
1069: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1070: *xmin=x;
1071: return fx;
1072: }
1073: ftemp=fu;
1074: if (fabs(e) > tol1) {
1075: r=(x-w)*(fx-fv);
1076: q=(x-v)*(fx-fw);
1077: p=(x-v)*q-(x-w)*r;
1078: q=2.0*(q-r);
1079: if (q > 0.0) p = -p;
1080: q=fabs(q);
1081: etemp=e;
1082: e=d;
1083: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1084: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1085: else {
1086: d=p/q;
1087: u=x+d;
1088: if (u-a < tol2 || b-u < tol2)
1089: d=SIGN(tol1,xm-x);
1090: }
1091: } else {
1092: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1093: }
1094: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1095: fu=(*f)(u);
1096: if (fu <= fx) {
1097: if (u >= x) a=x; else b=x;
1098: SHFT(v,w,x,u)
1099: SHFT(fv,fw,fx,fu)
1100: } else {
1101: if (u < x) a=u; else b=u;
1102: if (fu <= fw || w == x) {
1103: v=w;
1104: w=u;
1105: fv=fw;
1106: fw=fu;
1107: } else if (fu <= fv || v == x || v == w) {
1108: v=u;
1109: fv=fu;
1110: }
1111: }
1112: }
1113: nrerror("Too many iterations in brent");
1114: *xmin=x;
1115: return fx;
1116: }
1117:
1118: /****************** mnbrak ***********************/
1119:
1120: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1121: double (*func)(double))
1122: {
1123: double ulim,u,r,q, dum;
1124: double fu;
1125:
1126: *fa=(*func)(*ax);
1127: *fb=(*func)(*bx);
1128: if (*fb > *fa) {
1129: SHFT(dum,*ax,*bx,dum)
1130: SHFT(dum,*fb,*fa,dum)
1131: }
1132: *cx=(*bx)+GOLD*(*bx-*ax);
1133: *fc=(*func)(*cx);
1134: while (*fb > *fc) {
1135: r=(*bx-*ax)*(*fb-*fc);
1136: q=(*bx-*cx)*(*fb-*fa);
1137: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1138: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1139: ulim=(*bx)+GLIMIT*(*cx-*bx);
1140: if ((*bx-u)*(u-*cx) > 0.0) {
1141: fu=(*func)(u);
1142: } else if ((*cx-u)*(u-ulim) > 0.0) {
1143: fu=(*func)(u);
1144: if (fu < *fc) {
1145: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1146: SHFT(*fb,*fc,fu,(*func)(u))
1147: }
1148: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1149: u=ulim;
1150: fu=(*func)(u);
1151: } else {
1152: u=(*cx)+GOLD*(*cx-*bx);
1153: fu=(*func)(u);
1154: }
1155: SHFT(*ax,*bx,*cx,u)
1156: SHFT(*fa,*fb,*fc,fu)
1157: }
1158: }
1159:
1160: /*************** linmin ************************/
1161:
1162: int ncom;
1163: double *pcom,*xicom;
1164: double (*nrfunc)(double []);
1165:
1166: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1167: {
1168: double brent(double ax, double bx, double cx,
1169: double (*f)(double), double tol, double *xmin);
1170: double f1dim(double x);
1171: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1172: double *fc, double (*func)(double));
1173: int j;
1174: double xx,xmin,bx,ax;
1175: double fx,fb,fa;
1176:
1177: ncom=n;
1178: pcom=vector(1,n);
1179: xicom=vector(1,n);
1180: nrfunc=func;
1181: for (j=1;j<=n;j++) {
1182: pcom[j]=p[j];
1183: xicom[j]=xi[j];
1184: }
1185: ax=0.0;
1186: xx=1.0;
1187: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1188: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1189: #ifdef DEBUG
1190: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1191: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1192: #endif
1193: for (j=1;j<=n;j++) {
1194: xi[j] *= xmin;
1195: p[j] += xi[j];
1196: }
1197: free_vector(xicom,1,n);
1198: free_vector(pcom,1,n);
1199: }
1200:
1201: char *asc_diff_time(long time_sec, char ascdiff[])
1202: {
1203: long sec_left, days, hours, minutes;
1204: days = (time_sec) / (60*60*24);
1205: sec_left = (time_sec) % (60*60*24);
1206: hours = (sec_left) / (60*60) ;
1207: sec_left = (sec_left) %(60*60);
1208: minutes = (sec_left) /60;
1209: sec_left = (sec_left) % (60);
1210: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1211: return ascdiff;
1212: }
1213:
1214: /*************** powell ************************/
1215: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1216: double (*func)(double []))
1217: {
1218: void linmin(double p[], double xi[], int n, double *fret,
1219: double (*func)(double []));
1220: int i,ibig,j;
1221: double del,t,*pt,*ptt,*xit;
1222: double fp,fptt;
1223: double *xits;
1224: int niterf, itmp;
1225:
1226: pt=vector(1,n);
1227: ptt=vector(1,n);
1228: xit=vector(1,n);
1229: xits=vector(1,n);
1230: *fret=(*func)(p);
1231: for (j=1;j<=n;j++) pt[j]=p[j];
1232: for (*iter=1;;++(*iter)) {
1233: fp=(*fret);
1234: ibig=0;
1235: del=0.0;
1236: last_time=curr_time;
1237: (void) gettimeofday(&curr_time,&tzp);
1238: 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);
1239: 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);
1240: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1241: for (i=1;i<=n;i++) {
1242: printf(" %d %.12f",i, p[i]);
1243: fprintf(ficlog," %d %.12lf",i, p[i]);
1244: fprintf(ficrespow," %.12lf", p[i]);
1245: }
1246: printf("\n");
1247: fprintf(ficlog,"\n");
1248: fprintf(ficrespow,"\n");fflush(ficrespow);
1249: if(*iter <=3){
1250: tm = *localtime(&curr_time.tv_sec);
1251: strcpy(strcurr,asctime(&tm));
1252: /* asctime_r(&tm,strcurr); */
1253: forecast_time=curr_time;
1254: itmp = strlen(strcurr);
1255: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1256: strcurr[itmp-1]='\0';
1257: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1258: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1259: for(niterf=10;niterf<=30;niterf+=10){
1260: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1261: tmf = *localtime(&forecast_time.tv_sec);
1262: /* asctime_r(&tmf,strfor); */
1263: strcpy(strfor,asctime(&tmf));
1264: itmp = strlen(strfor);
1265: if(strfor[itmp-1]=='\n')
1266: strfor[itmp-1]='\0';
1267: 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);
1268: 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);
1269: }
1270: }
1271: for (i=1;i<=n;i++) {
1272: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1273: fptt=(*fret);
1274: #ifdef DEBUG
1275: printf("fret=%lf \n",*fret);
1276: fprintf(ficlog,"fret=%lf \n",*fret);
1277: #endif
1278: printf("%d",i);fflush(stdout);
1279: fprintf(ficlog,"%d",i);fflush(ficlog);
1280: linmin(p,xit,n,fret,func);
1281: if (fabs(fptt-(*fret)) > del) {
1282: del=fabs(fptt-(*fret));
1283: ibig=i;
1284: }
1285: #ifdef DEBUG
1286: printf("%d %.12e",i,(*fret));
1287: fprintf(ficlog,"%d %.12e",i,(*fret));
1288: for (j=1;j<=n;j++) {
1289: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1290: printf(" x(%d)=%.12e",j,xit[j]);
1291: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1292: }
1293: for(j=1;j<=n;j++) {
1294: printf(" p=%.12e",p[j]);
1295: fprintf(ficlog," p=%.12e",p[j]);
1296: }
1297: printf("\n");
1298: fprintf(ficlog,"\n");
1299: #endif
1300: }
1301: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1302: #ifdef DEBUG
1303: int k[2],l;
1304: k[0]=1;
1305: k[1]=-1;
1306: printf("Max: %.12e",(*func)(p));
1307: fprintf(ficlog,"Max: %.12e",(*func)(p));
1308: for (j=1;j<=n;j++) {
1309: printf(" %.12e",p[j]);
1310: fprintf(ficlog," %.12e",p[j]);
1311: }
1312: printf("\n");
1313: fprintf(ficlog,"\n");
1314: for(l=0;l<=1;l++) {
1315: for (j=1;j<=n;j++) {
1316: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1317: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1318: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1319: }
1320: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1321: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1322: }
1323: #endif
1324:
1325:
1326: free_vector(xit,1,n);
1327: free_vector(xits,1,n);
1328: free_vector(ptt,1,n);
1329: free_vector(pt,1,n);
1330: return;
1331: }
1332: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1333: for (j=1;j<=n;j++) {
1334: ptt[j]=2.0*p[j]-pt[j];
1335: xit[j]=p[j]-pt[j];
1336: pt[j]=p[j];
1337: }
1338: fptt=(*func)(ptt);
1339: if (fptt < fp) {
1340: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1341: if (t < 0.0) {
1342: linmin(p,xit,n,fret,func);
1343: for (j=1;j<=n;j++) {
1344: xi[j][ibig]=xi[j][n];
1345: xi[j][n]=xit[j];
1346: }
1347: #ifdef DEBUG
1348: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1349: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1350: for(j=1;j<=n;j++){
1351: printf(" %.12e",xit[j]);
1352: fprintf(ficlog," %.12e",xit[j]);
1353: }
1354: printf("\n");
1355: fprintf(ficlog,"\n");
1356: #endif
1357: }
1358: }
1359: }
1360: }
1361:
1362: /**** Prevalence limit (stable or period prevalence) ****************/
1363:
1364: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1365: {
1366: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1367: matrix by transitions matrix until convergence is reached */
1368:
1369: int i, ii,j,k;
1370: double min, max, maxmin, maxmax,sumnew=0.;
1371: /* double **matprod2(); */ /* test */
1372: double **out, cov[NCOVMAX+1], **pmij();
1373: double **newm;
1374: double agefin, delaymax=50 ; /* Max number of years to converge */
1375:
1376: for (ii=1;ii<=nlstate+ndeath;ii++)
1377: for (j=1;j<=nlstate+ndeath;j++){
1378: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1379: }
1380:
1381: cov[1]=1.;
1382:
1383: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1384: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1385: newm=savm;
1386: /* Covariates have to be included here again */
1387: cov[2]=agefin;
1388:
1389: for (k=1; k<=cptcovn;k++) {
1390: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1391: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1392: }
1393: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1394: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1395: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1396:
1397: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1398: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1399: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1400: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1401: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1402: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1403:
1404: savm=oldm;
1405: oldm=newm;
1406: maxmax=0.;
1407: for(j=1;j<=nlstate;j++){
1408: min=1.;
1409: max=0.;
1410: for(i=1; i<=nlstate; i++) {
1411: sumnew=0;
1412: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1413: prlim[i][j]= newm[i][j]/(1-sumnew);
1414: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1415: max=FMAX(max,prlim[i][j]);
1416: min=FMIN(min,prlim[i][j]);
1417: }
1418: maxmin=max-min;
1419: maxmax=FMAX(maxmax,maxmin);
1420: }
1421: if(maxmax < ftolpl){
1422: return prlim;
1423: }
1424: }
1425: }
1426:
1427: /*************** transition probabilities ***************/
1428:
1429: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1430: {
1431: /* According to parameters values stored in x and the covariate's values stored in cov,
1432: computes the probability to be observed in state j being in state i by appying the
1433: model to the ncovmodel covariates (including constant and age).
1434: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1435: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1436: ncth covariate in the global vector x is given by the formula:
1437: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1438: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1439: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1440: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1441: Outputs ps[i][j] the probability to be observed in j being in j according to
1442: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1443: */
1444: double s1, lnpijopii;
1445: /*double t34;*/
1446: int i,j,j1, nc, ii, jj;
1447:
1448: for(i=1; i<= nlstate; i++){
1449: for(j=1; j<i;j++){
1450: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1451: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1452: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1453: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1454: }
1455: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1456: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1457: }
1458: for(j=i+1; j<=nlstate+ndeath;j++){
1459: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1460: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1461: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1462: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1463: }
1464: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1465: }
1466: }
1467:
1468: for(i=1; i<= nlstate; i++){
1469: s1=0;
1470: for(j=1; j<i; j++){
1471: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1472: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1473: }
1474: for(j=i+1; j<=nlstate+ndeath; j++){
1475: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1476: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1477: }
1478: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1479: ps[i][i]=1./(s1+1.);
1480: /* Computing other pijs */
1481: for(j=1; j<i; j++)
1482: ps[i][j]= exp(ps[i][j])*ps[i][i];
1483: for(j=i+1; j<=nlstate+ndeath; j++)
1484: ps[i][j]= exp(ps[i][j])*ps[i][i];
1485: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1486: } /* end i */
1487:
1488: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1489: for(jj=1; jj<= nlstate+ndeath; jj++){
1490: ps[ii][jj]=0;
1491: ps[ii][ii]=1;
1492: }
1493: }
1494:
1495:
1496: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1497: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1498: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1499: /* } */
1500: /* printf("\n "); */
1501: /* } */
1502: /* printf("\n ");printf("%lf ",cov[2]);*/
1503: /*
1504: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1505: goto end;*/
1506: return ps;
1507: }
1508:
1509: /**************** Product of 2 matrices ******************/
1510:
1511: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1512: {
1513: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1514: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1515: /* in, b, out are matrice of pointers which should have been initialized
1516: before: only the contents of out is modified. The function returns
1517: a pointer to pointers identical to out */
1518: int i, j, k;
1519: for(i=nrl; i<= nrh; i++)
1520: for(k=ncolol; k<=ncoloh; k++){
1521: out[i][k]=0.;
1522: for(j=ncl; j<=nch; j++)
1523: out[i][k] +=in[i][j]*b[j][k];
1524: }
1525: return out;
1526: }
1527:
1528:
1529: /************* Higher Matrix Product ***************/
1530:
1531: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1532: {
1533: /* Computes the transition matrix starting at age 'age' over
1534: 'nhstepm*hstepm*stepm' months (i.e. until
1535: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1536: nhstepm*hstepm matrices.
1537: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1538: (typically every 2 years instead of every month which is too big
1539: for the memory).
1540: Model is determined by parameters x and covariates have to be
1541: included manually here.
1542:
1543: */
1544:
1545: int i, j, d, h, k;
1546: double **out, cov[NCOVMAX+1];
1547: double **newm;
1548:
1549: /* Hstepm could be zero and should return the unit matrix */
1550: for (i=1;i<=nlstate+ndeath;i++)
1551: for (j=1;j<=nlstate+ndeath;j++){
1552: oldm[i][j]=(i==j ? 1.0 : 0.0);
1553: po[i][j][0]=(i==j ? 1.0 : 0.0);
1554: }
1555: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1556: for(h=1; h <=nhstepm; h++){
1557: for(d=1; d <=hstepm; d++){
1558: newm=savm;
1559: /* Covariates have to be included here again */
1560: cov[1]=1.;
1561: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1562: for (k=1; k<=cptcovn;k++)
1563: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1564: for (k=1; k<=cptcovage;k++)
1565: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1566: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1567: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1568:
1569:
1570: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1571: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1572: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1573: pmij(pmmij,cov,ncovmodel,x,nlstate));
1574: savm=oldm;
1575: oldm=newm;
1576: }
1577: for(i=1; i<=nlstate+ndeath; i++)
1578: for(j=1;j<=nlstate+ndeath;j++) {
1579: po[i][j][h]=newm[i][j];
1580: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1581: }
1582: /*printf("h=%d ",h);*/
1583: } /* end h */
1584: /* printf("\n H=%d \n",h); */
1585: return po;
1586: }
1587:
1588:
1589: /*************** log-likelihood *************/
1590: double func( double *x)
1591: {
1592: int i, ii, j, k, mi, d, kk;
1593: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1594: double **out;
1595: double sw; /* Sum of weights */
1596: double lli; /* Individual log likelihood */
1597: int s1, s2;
1598: double bbh, survp;
1599: long ipmx;
1600: /*extern weight */
1601: /* We are differentiating ll according to initial status */
1602: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1603: /*for(i=1;i<imx;i++)
1604: printf(" %d\n",s[4][i]);
1605: */
1606: cov[1]=1.;
1607:
1608: for(k=1; k<=nlstate; k++) ll[k]=0.;
1609:
1610: if(mle==1){
1611: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1612: /* Computes the values of the ncovmodel covariates of the model
1613: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1614: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1615: to be observed in j being in i according to the model.
1616: */
1617: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1618: cov[2+k]=covar[Tvar[k]][i];
1619: }
1620: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1621: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1622: has been calculated etc */
1623: for(mi=1; mi<= wav[i]-1; mi++){
1624: for (ii=1;ii<=nlstate+ndeath;ii++)
1625: for (j=1;j<=nlstate+ndeath;j++){
1626: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1627: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1628: }
1629: for(d=0; d<dh[mi][i]; d++){
1630: newm=savm;
1631: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1632: for (kk=1; kk<=cptcovage;kk++) {
1633: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1634: }
1635: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1636: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1637: savm=oldm;
1638: oldm=newm;
1639: } /* end mult */
1640:
1641: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1642: /* But now since version 0.9 we anticipate for bias at large stepm.
1643: * If stepm is larger than one month (smallest stepm) and if the exact delay
1644: * (in months) between two waves is not a multiple of stepm, we rounded to
1645: * the nearest (and in case of equal distance, to the lowest) interval but now
1646: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1647: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1648: * probability in order to take into account the bias as a fraction of the way
1649: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1650: * -stepm/2 to stepm/2 .
1651: * For stepm=1 the results are the same as for previous versions of Imach.
1652: * For stepm > 1 the results are less biased than in previous versions.
1653: */
1654: s1=s[mw[mi][i]][i];
1655: s2=s[mw[mi+1][i]][i];
1656: bbh=(double)bh[mi][i]/(double)stepm;
1657: /* bias bh is positive if real duration
1658: * is higher than the multiple of stepm and negative otherwise.
1659: */
1660: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1661: if( s2 > nlstate){
1662: /* i.e. if s2 is a death state and if the date of death is known
1663: then the contribution to the likelihood is the probability to
1664: die between last step unit time and current step unit time,
1665: which is also equal to probability to die before dh
1666: minus probability to die before dh-stepm .
1667: In version up to 0.92 likelihood was computed
1668: as if date of death was unknown. Death was treated as any other
1669: health state: the date of the interview describes the actual state
1670: and not the date of a change in health state. The former idea was
1671: to consider that at each interview the state was recorded
1672: (healthy, disable or death) and IMaCh was corrected; but when we
1673: introduced the exact date of death then we should have modified
1674: the contribution of an exact death to the likelihood. This new
1675: contribution is smaller and very dependent of the step unit
1676: stepm. It is no more the probability to die between last interview
1677: and month of death but the probability to survive from last
1678: interview up to one month before death multiplied by the
1679: probability to die within a month. Thanks to Chris
1680: Jackson for correcting this bug. Former versions increased
1681: mortality artificially. The bad side is that we add another loop
1682: which slows down the processing. The difference can be up to 10%
1683: lower mortality.
1684: */
1685: lli=log(out[s1][s2] - savm[s1][s2]);
1686:
1687:
1688: } else if (s2==-2) {
1689: for (j=1,survp=0. ; j<=nlstate; j++)
1690: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1691: /*survp += out[s1][j]; */
1692: lli= log(survp);
1693: }
1694:
1695: else if (s2==-4) {
1696: for (j=3,survp=0. ; j<=nlstate; j++)
1697: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1698: lli= log(survp);
1699: }
1700:
1701: else if (s2==-5) {
1702: for (j=1,survp=0. ; j<=2; j++)
1703: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1704: lli= log(survp);
1705: }
1706:
1707: else{
1708: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1709: /* 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 */
1710: }
1711: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1712: /*if(lli ==000.0)*/
1713: /*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); */
1714: ipmx +=1;
1715: sw += weight[i];
1716: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1717: } /* end of wave */
1718: } /* end of individual */
1719: } else if(mle==2){
1720: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1721: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1722: for(mi=1; mi<= wav[i]-1; mi++){
1723: for (ii=1;ii<=nlstate+ndeath;ii++)
1724: for (j=1;j<=nlstate+ndeath;j++){
1725: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1726: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1727: }
1728: for(d=0; d<=dh[mi][i]; d++){
1729: newm=savm;
1730: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1731: for (kk=1; kk<=cptcovage;kk++) {
1732: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1733: }
1734: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1735: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1736: savm=oldm;
1737: oldm=newm;
1738: } /* end mult */
1739:
1740: s1=s[mw[mi][i]][i];
1741: s2=s[mw[mi+1][i]][i];
1742: bbh=(double)bh[mi][i]/(double)stepm;
1743: 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 */
1744: ipmx +=1;
1745: sw += weight[i];
1746: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1747: } /* end of wave */
1748: } /* end of individual */
1749: } else if(mle==3){ /* exponential inter-extrapolation */
1750: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1751: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1752: for(mi=1; mi<= wav[i]-1; mi++){
1753: for (ii=1;ii<=nlstate+ndeath;ii++)
1754: for (j=1;j<=nlstate+ndeath;j++){
1755: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1756: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1757: }
1758: for(d=0; d<dh[mi][i]; d++){
1759: newm=savm;
1760: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1761: for (kk=1; kk<=cptcovage;kk++) {
1762: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1763: }
1764: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1765: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1766: savm=oldm;
1767: oldm=newm;
1768: } /* end mult */
1769:
1770: s1=s[mw[mi][i]][i];
1771: s2=s[mw[mi+1][i]][i];
1772: bbh=(double)bh[mi][i]/(double)stepm;
1773: 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 */
1774: ipmx +=1;
1775: sw += weight[i];
1776: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1777: } /* end of wave */
1778: } /* end of individual */
1779: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1780: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1781: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1782: for(mi=1; mi<= wav[i]-1; mi++){
1783: for (ii=1;ii<=nlstate+ndeath;ii++)
1784: for (j=1;j<=nlstate+ndeath;j++){
1785: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1786: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1787: }
1788: for(d=0; d<dh[mi][i]; d++){
1789: newm=savm;
1790: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1791: for (kk=1; kk<=cptcovage;kk++) {
1792: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1793: }
1794:
1795: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1796: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1797: savm=oldm;
1798: oldm=newm;
1799: } /* end mult */
1800:
1801: s1=s[mw[mi][i]][i];
1802: s2=s[mw[mi+1][i]][i];
1803: if( s2 > nlstate){
1804: lli=log(out[s1][s2] - savm[s1][s2]);
1805: }else{
1806: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1807: }
1808: ipmx +=1;
1809: sw += weight[i];
1810: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1811: /* 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]); */
1812: } /* end of wave */
1813: } /* end of individual */
1814: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1815: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1816: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1817: for(mi=1; mi<= wav[i]-1; mi++){
1818: for (ii=1;ii<=nlstate+ndeath;ii++)
1819: for (j=1;j<=nlstate+ndeath;j++){
1820: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1821: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1822: }
1823: for(d=0; d<dh[mi][i]; d++){
1824: newm=savm;
1825: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1826: for (kk=1; kk<=cptcovage;kk++) {
1827: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1828: }
1829:
1830: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1831: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1832: savm=oldm;
1833: oldm=newm;
1834: } /* end mult */
1835:
1836: s1=s[mw[mi][i]][i];
1837: s2=s[mw[mi+1][i]][i];
1838: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1839: ipmx +=1;
1840: sw += weight[i];
1841: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1842: /*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]);*/
1843: } /* end of wave */
1844: } /* end of individual */
1845: } /* End of if */
1846: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1847: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1848: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1849: return -l;
1850: }
1851:
1852: /*************** log-likelihood *************/
1853: double funcone( double *x)
1854: {
1855: /* Same as likeli but slower because of a lot of printf and if */
1856: int i, ii, j, k, mi, d, kk;
1857: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1858: double **out;
1859: double lli; /* Individual log likelihood */
1860: double llt;
1861: int s1, s2;
1862: double bbh, survp;
1863: /*extern weight */
1864: /* We are differentiating ll according to initial status */
1865: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1866: /*for(i=1;i<imx;i++)
1867: printf(" %d\n",s[4][i]);
1868: */
1869: cov[1]=1.;
1870:
1871: for(k=1; k<=nlstate; k++) ll[k]=0.;
1872:
1873: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1874: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1875: for(mi=1; mi<= wav[i]-1; mi++){
1876: for (ii=1;ii<=nlstate+ndeath;ii++)
1877: for (j=1;j<=nlstate+ndeath;j++){
1878: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1879: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1880: }
1881: for(d=0; d<dh[mi][i]; d++){
1882: newm=savm;
1883: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1884: for (kk=1; kk<=cptcovage;kk++) {
1885: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1886: }
1887: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1888: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1889: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1890: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
1891: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1892: savm=oldm;
1893: oldm=newm;
1894: } /* end mult */
1895:
1896: s1=s[mw[mi][i]][i];
1897: s2=s[mw[mi+1][i]][i];
1898: bbh=(double)bh[mi][i]/(double)stepm;
1899: /* bias is positive if real duration
1900: * is higher than the multiple of stepm and negative otherwise.
1901: */
1902: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1903: lli=log(out[s1][s2] - savm[s1][s2]);
1904: } else if (s2==-2) {
1905: for (j=1,survp=0. ; j<=nlstate; j++)
1906: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1907: lli= log(survp);
1908: }else if (mle==1){
1909: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1910: } else if(mle==2){
1911: 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 */
1912: } else if(mle==3){ /* exponential inter-extrapolation */
1913: 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 */
1914: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1915: lli=log(out[s1][s2]); /* Original formula */
1916: } else{ /* mle=0 back to 1 */
1917: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1918: /*lli=log(out[s1][s2]); */ /* Original formula */
1919: } /* End of if */
1920: ipmx +=1;
1921: sw += weight[i];
1922: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1923: /*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]); */
1924: if(globpr){
1925: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1926: %11.6f %11.6f %11.6f ", \
1927: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1928: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1929: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1930: llt +=ll[k]*gipmx/gsw;
1931: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1932: }
1933: fprintf(ficresilk," %10.6f\n", -llt);
1934: }
1935: } /* end of wave */
1936: } /* end of individual */
1937: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1938: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1939: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1940: if(globpr==0){ /* First time we count the contributions and weights */
1941: gipmx=ipmx;
1942: gsw=sw;
1943: }
1944: return -l;
1945: }
1946:
1947:
1948: /*************** function likelione ***********/
1949: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1950: {
1951: /* This routine should help understanding what is done with
1952: the selection of individuals/waves and
1953: to check the exact contribution to the likelihood.
1954: Plotting could be done.
1955: */
1956: int k;
1957:
1958: if(*globpri !=0){ /* Just counts and sums, no printings */
1959: strcpy(fileresilk,"ilk");
1960: strcat(fileresilk,fileres);
1961: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1962: printf("Problem with resultfile: %s\n", fileresilk);
1963: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1964: }
1965: 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");
1966: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1967: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1968: for(k=1; k<=nlstate; k++)
1969: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1970: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1971: }
1972:
1973: *fretone=(*funcone)(p);
1974: if(*globpri !=0){
1975: fclose(ficresilk);
1976: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1977: fflush(fichtm);
1978: }
1979: return;
1980: }
1981:
1982:
1983: /*********** Maximum Likelihood Estimation ***************/
1984:
1985: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1986: {
1987: int i,j, iter;
1988: double **xi;
1989: double fret;
1990: double fretone; /* Only one call to likelihood */
1991: /* char filerespow[FILENAMELENGTH];*/
1992: xi=matrix(1,npar,1,npar);
1993: for (i=1;i<=npar;i++)
1994: for (j=1;j<=npar;j++)
1995: xi[i][j]=(i==j ? 1.0 : 0.0);
1996: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1997: strcpy(filerespow,"pow");
1998: strcat(filerespow,fileres);
1999: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2000: printf("Problem with resultfile: %s\n", filerespow);
2001: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2002: }
2003: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2004: for (i=1;i<=nlstate;i++)
2005: for(j=1;j<=nlstate+ndeath;j++)
2006: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2007: fprintf(ficrespow,"\n");
2008:
2009: powell(p,xi,npar,ftol,&iter,&fret,func);
2010:
2011: free_matrix(xi,1,npar,1,npar);
2012: fclose(ficrespow);
2013: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
2014: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2015: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2016:
2017: }
2018:
2019: /**** Computes Hessian and covariance matrix ***/
2020: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2021: {
2022: double **a,**y,*x,pd;
2023: double **hess;
2024: int i, j,jk;
2025: int *indx;
2026:
2027: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2028: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2029: void lubksb(double **a, int npar, int *indx, double b[]) ;
2030: void ludcmp(double **a, int npar, int *indx, double *d) ;
2031: double gompertz(double p[]);
2032: hess=matrix(1,npar,1,npar);
2033:
2034: printf("\nCalculation of the hessian matrix. Wait...\n");
2035: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2036: for (i=1;i<=npar;i++){
2037: printf("%d",i);fflush(stdout);
2038: fprintf(ficlog,"%d",i);fflush(ficlog);
2039:
2040: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2041:
2042: /* printf(" %f ",p[i]);
2043: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2044: }
2045:
2046: for (i=1;i<=npar;i++) {
2047: for (j=1;j<=npar;j++) {
2048: if (j>i) {
2049: printf(".%d%d",i,j);fflush(stdout);
2050: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2051: hess[i][j]=hessij(p,delti,i,j,func,npar);
2052:
2053: hess[j][i]=hess[i][j];
2054: /*printf(" %lf ",hess[i][j]);*/
2055: }
2056: }
2057: }
2058: printf("\n");
2059: fprintf(ficlog,"\n");
2060:
2061: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2062: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2063:
2064: a=matrix(1,npar,1,npar);
2065: y=matrix(1,npar,1,npar);
2066: x=vector(1,npar);
2067: indx=ivector(1,npar);
2068: for (i=1;i<=npar;i++)
2069: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2070: ludcmp(a,npar,indx,&pd);
2071:
2072: for (j=1;j<=npar;j++) {
2073: for (i=1;i<=npar;i++) x[i]=0;
2074: x[j]=1;
2075: lubksb(a,npar,indx,x);
2076: for (i=1;i<=npar;i++){
2077: matcov[i][j]=x[i];
2078: }
2079: }
2080:
2081: printf("\n#Hessian matrix#\n");
2082: fprintf(ficlog,"\n#Hessian matrix#\n");
2083: for (i=1;i<=npar;i++) {
2084: for (j=1;j<=npar;j++) {
2085: printf("%.3e ",hess[i][j]);
2086: fprintf(ficlog,"%.3e ",hess[i][j]);
2087: }
2088: printf("\n");
2089: fprintf(ficlog,"\n");
2090: }
2091:
2092: /* Recompute Inverse */
2093: for (i=1;i<=npar;i++)
2094: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2095: ludcmp(a,npar,indx,&pd);
2096:
2097: /* printf("\n#Hessian matrix recomputed#\n");
2098:
2099: for (j=1;j<=npar;j++) {
2100: for (i=1;i<=npar;i++) x[i]=0;
2101: x[j]=1;
2102: lubksb(a,npar,indx,x);
2103: for (i=1;i<=npar;i++){
2104: y[i][j]=x[i];
2105: printf("%.3e ",y[i][j]);
2106: fprintf(ficlog,"%.3e ",y[i][j]);
2107: }
2108: printf("\n");
2109: fprintf(ficlog,"\n");
2110: }
2111: */
2112:
2113: free_matrix(a,1,npar,1,npar);
2114: free_matrix(y,1,npar,1,npar);
2115: free_vector(x,1,npar);
2116: free_ivector(indx,1,npar);
2117: free_matrix(hess,1,npar,1,npar);
2118:
2119:
2120: }
2121:
2122: /*************** hessian matrix ****************/
2123: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2124: {
2125: int i;
2126: int l=1, lmax=20;
2127: double k1,k2;
2128: double p2[MAXPARM+1]; /* identical to x */
2129: double res;
2130: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2131: double fx;
2132: int k=0,kmax=10;
2133: double l1;
2134:
2135: fx=func(x);
2136: for (i=1;i<=npar;i++) p2[i]=x[i];
2137: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2138: l1=pow(10,l);
2139: delts=delt;
2140: for(k=1 ; k <kmax; k=k+1){
2141: delt = delta*(l1*k);
2142: p2[theta]=x[theta] +delt;
2143: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2144: p2[theta]=x[theta]-delt;
2145: k2=func(p2)-fx;
2146: /*res= (k1-2.0*fx+k2)/delt/delt; */
2147: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2148:
2149: #ifdef DEBUGHESS
2150: 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);
2151: 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);
2152: #endif
2153: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2154: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2155: k=kmax;
2156: }
2157: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2158: k=kmax; l=lmax*10.;
2159: }
2160: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2161: delts=delt;
2162: }
2163: }
2164: }
2165: delti[theta]=delts;
2166: return res;
2167:
2168: }
2169:
2170: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2171: {
2172: int i;
2173: int l=1, l1, lmax=20;
2174: double k1,k2,k3,k4,res,fx;
2175: double p2[MAXPARM+1];
2176: int k;
2177:
2178: fx=func(x);
2179: for (k=1; k<=2; k++) {
2180: for (i=1;i<=npar;i++) p2[i]=x[i];
2181: p2[thetai]=x[thetai]+delti[thetai]/k;
2182: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2183: k1=func(p2)-fx;
2184:
2185: p2[thetai]=x[thetai]+delti[thetai]/k;
2186: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2187: k2=func(p2)-fx;
2188:
2189: p2[thetai]=x[thetai]-delti[thetai]/k;
2190: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2191: k3=func(p2)-fx;
2192:
2193: p2[thetai]=x[thetai]-delti[thetai]/k;
2194: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2195: k4=func(p2)-fx;
2196: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2197: #ifdef DEBUG
2198: 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);
2199: 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);
2200: #endif
2201: }
2202: return res;
2203: }
2204:
2205: /************** Inverse of matrix **************/
2206: void ludcmp(double **a, int n, int *indx, double *d)
2207: {
2208: int i,imax,j,k;
2209: double big,dum,sum,temp;
2210: double *vv;
2211:
2212: vv=vector(1,n);
2213: *d=1.0;
2214: for (i=1;i<=n;i++) {
2215: big=0.0;
2216: for (j=1;j<=n;j++)
2217: if ((temp=fabs(a[i][j])) > big) big=temp;
2218: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2219: vv[i]=1.0/big;
2220: }
2221: for (j=1;j<=n;j++) {
2222: for (i=1;i<j;i++) {
2223: sum=a[i][j];
2224: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2225: a[i][j]=sum;
2226: }
2227: big=0.0;
2228: for (i=j;i<=n;i++) {
2229: sum=a[i][j];
2230: for (k=1;k<j;k++)
2231: sum -= a[i][k]*a[k][j];
2232: a[i][j]=sum;
2233: if ( (dum=vv[i]*fabs(sum)) >= big) {
2234: big=dum;
2235: imax=i;
2236: }
2237: }
2238: if (j != imax) {
2239: for (k=1;k<=n;k++) {
2240: dum=a[imax][k];
2241: a[imax][k]=a[j][k];
2242: a[j][k]=dum;
2243: }
2244: *d = -(*d);
2245: vv[imax]=vv[j];
2246: }
2247: indx[j]=imax;
2248: if (a[j][j] == 0.0) a[j][j]=TINY;
2249: if (j != n) {
2250: dum=1.0/(a[j][j]);
2251: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2252: }
2253: }
2254: free_vector(vv,1,n); /* Doesn't work */
2255: ;
2256: }
2257:
2258: void lubksb(double **a, int n, int *indx, double b[])
2259: {
2260: int i,ii=0,ip,j;
2261: double sum;
2262:
2263: for (i=1;i<=n;i++) {
2264: ip=indx[i];
2265: sum=b[ip];
2266: b[ip]=b[i];
2267: if (ii)
2268: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2269: else if (sum) ii=i;
2270: b[i]=sum;
2271: }
2272: for (i=n;i>=1;i--) {
2273: sum=b[i];
2274: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2275: b[i]=sum/a[i][i];
2276: }
2277: }
2278:
2279: void pstamp(FILE *fichier)
2280: {
2281: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2282: }
2283:
2284: /************ Frequencies ********************/
2285: 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[])
2286: { /* Some frequencies */
2287:
2288: int i, m, jk, k1,i1, j1, bool, z1,j;
2289: int first;
2290: double ***freq; /* Frequencies */
2291: double *pp, **prop;
2292: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2293: char fileresp[FILENAMELENGTH];
2294:
2295: pp=vector(1,nlstate);
2296: prop=matrix(1,nlstate,iagemin,iagemax+3);
2297: strcpy(fileresp,"p");
2298: strcat(fileresp,fileres);
2299: if((ficresp=fopen(fileresp,"w"))==NULL) {
2300: printf("Problem with prevalence resultfile: %s\n", fileresp);
2301: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2302: exit(0);
2303: }
2304: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2305: j1=0;
2306:
2307: j=cptcoveff;
2308: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2309:
2310: first=1;
2311:
2312: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2313: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2314: /* j1++;
2315: */
2316: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2317: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2318: scanf("%d", i);*/
2319: for (i=-5; i<=nlstate+ndeath; i++)
2320: for (jk=-5; jk<=nlstate+ndeath; jk++)
2321: for(m=iagemin; m <= iagemax+3; m++)
2322: freq[i][jk][m]=0;
2323:
2324: for (i=1; i<=nlstate; i++)
2325: for(m=iagemin; m <= iagemax+3; m++)
2326: prop[i][m]=0;
2327:
2328: dateintsum=0;
2329: k2cpt=0;
2330: for (i=1; i<=imx; i++) {
2331: bool=1;
2332: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2333: for (z1=1; z1<=cptcoveff; z1++)
2334: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2335: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2336: bool=0;
2337: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2338: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2339: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2340: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2341: }
2342: }
2343:
2344: if (bool==1){
2345: for(m=firstpass; m<=lastpass; m++){
2346: k2=anint[m][i]+(mint[m][i]/12.);
2347: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2348: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2349: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2350: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2351: if (m<lastpass) {
2352: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2353: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2354: }
2355:
2356: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2357: dateintsum=dateintsum+k2;
2358: k2cpt++;
2359: }
2360: /*}*/
2361: }
2362: }
2363: } /* end i */
2364:
2365: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2366: pstamp(ficresp);
2367: if (cptcovn>0) {
2368: fprintf(ficresp, "\n#********** Variable ");
2369: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2370: fprintf(ficresp, "**********\n#");
2371: fprintf(ficlog, "\n#********** Variable ");
2372: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2373: fprintf(ficlog, "**********\n#");
2374: }
2375: for(i=1; i<=nlstate;i++)
2376: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2377: fprintf(ficresp, "\n");
2378:
2379: for(i=iagemin; i <= iagemax+3; i++){
2380: if(i==iagemax+3){
2381: fprintf(ficlog,"Total");
2382: }else{
2383: if(first==1){
2384: first=0;
2385: printf("See log file for details...\n");
2386: }
2387: fprintf(ficlog,"Age %d", i);
2388: }
2389: for(jk=1; jk <=nlstate ; jk++){
2390: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2391: pp[jk] += freq[jk][m][i];
2392: }
2393: for(jk=1; jk <=nlstate ; jk++){
2394: for(m=-1, pos=0; m <=0 ; m++)
2395: pos += freq[jk][m][i];
2396: if(pp[jk]>=1.e-10){
2397: if(first==1){
2398: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2399: }
2400: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2401: }else{
2402: if(first==1)
2403: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2404: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2405: }
2406: }
2407:
2408: for(jk=1; jk <=nlstate ; jk++){
2409: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2410: pp[jk] += freq[jk][m][i];
2411: }
2412: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2413: pos += pp[jk];
2414: posprop += prop[jk][i];
2415: }
2416: for(jk=1; jk <=nlstate ; jk++){
2417: if(pos>=1.e-5){
2418: if(first==1)
2419: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2420: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2421: }else{
2422: if(first==1)
2423: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2424: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2425: }
2426: if( i <= iagemax){
2427: if(pos>=1.e-5){
2428: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2429: /*probs[i][jk][j1]= pp[jk]/pos;*/
2430: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2431: }
2432: else
2433: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2434: }
2435: }
2436:
2437: for(jk=-1; jk <=nlstate+ndeath; jk++)
2438: for(m=-1; m <=nlstate+ndeath; m++)
2439: if(freq[jk][m][i] !=0 ) {
2440: if(first==1)
2441: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2442: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2443: }
2444: if(i <= iagemax)
2445: fprintf(ficresp,"\n");
2446: if(first==1)
2447: printf("Others in log...\n");
2448: fprintf(ficlog,"\n");
2449: }
2450: /*}*/
2451: }
2452: dateintmean=dateintsum/k2cpt;
2453:
2454: fclose(ficresp);
2455: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2456: free_vector(pp,1,nlstate);
2457: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2458: /* End of Freq */
2459: }
2460:
2461: /************ Prevalence ********************/
2462: 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)
2463: {
2464: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2465: in each health status at the date of interview (if between dateprev1 and dateprev2).
2466: We still use firstpass and lastpass as another selection.
2467: */
2468:
2469: int i, m, jk, k1, i1, j1, bool, z1,j;
2470: double ***freq; /* Frequencies */
2471: double *pp, **prop;
2472: double pos,posprop;
2473: double y2; /* in fractional years */
2474: int iagemin, iagemax;
2475: int first; /** to stop verbosity which is redirected to log file */
2476:
2477: iagemin= (int) agemin;
2478: iagemax= (int) agemax;
2479: /*pp=vector(1,nlstate);*/
2480: prop=matrix(1,nlstate,iagemin,iagemax+3);
2481: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2482: j1=0;
2483:
2484: /*j=cptcoveff;*/
2485: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2486:
2487: first=1;
2488: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2489: /*for(i1=1; i1<=ncodemax[k1];i1++){
2490: j1++;*/
2491:
2492: for (i=1; i<=nlstate; i++)
2493: for(m=iagemin; m <= iagemax+3; m++)
2494: prop[i][m]=0.0;
2495:
2496: for (i=1; i<=imx; i++) { /* Each individual */
2497: bool=1;
2498: if (cptcovn>0) {
2499: for (z1=1; z1<=cptcoveff; z1++)
2500: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2501: bool=0;
2502: }
2503: if (bool==1) {
2504: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2505: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2506: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2507: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2508: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2509: 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);
2510: if (s[m][i]>0 && s[m][i]<=nlstate) {
2511: /*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]]);*/
2512: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2513: prop[s[m][i]][iagemax+3] += weight[i];
2514: }
2515: }
2516: } /* end selection of waves */
2517: }
2518: }
2519: for(i=iagemin; i <= iagemax+3; i++){
2520: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2521: posprop += prop[jk][i];
2522: }
2523:
2524: for(jk=1; jk <=nlstate ; jk++){
2525: if( i <= iagemax){
2526: if(posprop>=1.e-5){
2527: probs[i][jk][j1]= prop[jk][i]/posprop;
2528: } else{
2529: if(first==1){
2530: first=0;
2531: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
2532: }
2533: }
2534: }
2535: }/* end jk */
2536: }/* end i */
2537: /*} *//* end i1 */
2538: } /* end j1 */
2539:
2540: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2541: /*free_vector(pp,1,nlstate);*/
2542: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2543: } /* End of prevalence */
2544:
2545: /************* Waves Concatenation ***************/
2546:
2547: 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)
2548: {
2549: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2550: Death is a valid wave (if date is known).
2551: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2552: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2553: and mw[mi+1][i]. dh depends on stepm.
2554: */
2555:
2556: int i, mi, m;
2557: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2558: double sum=0., jmean=0.;*/
2559: int first;
2560: int j, k=0,jk, ju, jl;
2561: double sum=0.;
2562: first=0;
2563: jmin=1e+5;
2564: jmax=-1;
2565: jmean=0.;
2566: for(i=1; i<=imx; i++){
2567: mi=0;
2568: m=firstpass;
2569: while(s[m][i] <= nlstate){
2570: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2571: mw[++mi][i]=m;
2572: if(m >=lastpass)
2573: break;
2574: else
2575: m++;
2576: }/* end while */
2577: if (s[m][i] > nlstate){
2578: mi++; /* Death is another wave */
2579: /* if(mi==0) never been interviewed correctly before death */
2580: /* Only death is a correct wave */
2581: mw[mi][i]=m;
2582: }
2583:
2584: wav[i]=mi;
2585: if(mi==0){
2586: nbwarn++;
2587: if(first==0){
2588: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2589: first=1;
2590: }
2591: if(first==1){
2592: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2593: }
2594: } /* end mi==0 */
2595: } /* End individuals */
2596:
2597: for(i=1; i<=imx; i++){
2598: for(mi=1; mi<wav[i];mi++){
2599: if (stepm <=0)
2600: dh[mi][i]=1;
2601: else{
2602: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2603: if (agedc[i] < 2*AGESUP) {
2604: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2605: if(j==0) j=1; /* Survives at least one month after exam */
2606: else if(j<0){
2607: nberr++;
2608: 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]);
2609: j=1; /* Temporary Dangerous patch */
2610: 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);
2611: 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]);
2612: 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);
2613: }
2614: k=k+1;
2615: if (j >= jmax){
2616: jmax=j;
2617: ijmax=i;
2618: }
2619: if (j <= jmin){
2620: jmin=j;
2621: ijmin=i;
2622: }
2623: sum=sum+j;
2624: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2625: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2626: }
2627: }
2628: else{
2629: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2630: /* 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]); */
2631:
2632: k=k+1;
2633: if (j >= jmax) {
2634: jmax=j;
2635: ijmax=i;
2636: }
2637: else if (j <= jmin){
2638: jmin=j;
2639: ijmin=i;
2640: }
2641: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2642: /*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]);*/
2643: if(j<0){
2644: nberr++;
2645: 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]);
2646: 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]);
2647: }
2648: sum=sum+j;
2649: }
2650: jk= j/stepm;
2651: jl= j -jk*stepm;
2652: ju= j -(jk+1)*stepm;
2653: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2654: if(jl==0){
2655: dh[mi][i]=jk;
2656: bh[mi][i]=0;
2657: }else{ /* We want a negative bias in order to only have interpolation ie
2658: * to avoid the price of an extra matrix product in likelihood */
2659: dh[mi][i]=jk+1;
2660: bh[mi][i]=ju;
2661: }
2662: }else{
2663: if(jl <= -ju){
2664: dh[mi][i]=jk;
2665: bh[mi][i]=jl; /* bias is positive if real duration
2666: * is higher than the multiple of stepm and negative otherwise.
2667: */
2668: }
2669: else{
2670: dh[mi][i]=jk+1;
2671: bh[mi][i]=ju;
2672: }
2673: if(dh[mi][i]==0){
2674: dh[mi][i]=1; /* At least one step */
2675: bh[mi][i]=ju; /* At least one step */
2676: /* 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);*/
2677: }
2678: } /* end if mle */
2679: }
2680: } /* end wave */
2681: }
2682: jmean=sum/k;
2683: 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);
2684: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2685: }
2686:
2687: /*********** Tricode ****************************/
2688: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2689: {
2690: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2691: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2692: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2693: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2694: /* nbcode[Tvar[j]][1]=
2695: */
2696:
2697: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2698: int modmaxcovj=0; /* Modality max of covariates j */
2699: int cptcode=0; /* Modality max of covariates j */
2700: int modmincovj=0; /* Modality min of covariates j */
2701:
2702:
2703: cptcoveff=0;
2704:
2705: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2706: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2707:
2708: /* Loop on covariates without age and products */
2709: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2710: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2711: modality of this covariate Vj*/
2712: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2713: * If product of Vn*Vm, still boolean *:
2714: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2715: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2716: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2717: modality of the nth covariate of individual i. */
2718: if (ij > modmaxcovj)
2719: modmaxcovj=ij;
2720: else if (ij < modmincovj)
2721: modmincovj=ij;
2722: if ((ij < -1) && (ij > NCOVMAX)){
2723: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2724: exit(1);
2725: }else
2726: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2727: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2728: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2729: /* getting the maximum value of the modality of the covariate
2730: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2731: female is 1, then modmaxcovj=1.*/
2732: }
2733: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2734: cptcode=modmaxcovj;
2735: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2736: /*for (i=0; i<=cptcode; i++) {*/
2737: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2738: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2739: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2740: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2741: }
2742: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2743: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2744: } /* Ndum[-1] number of undefined modalities */
2745:
2746: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2747: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2748: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2749: modmincovj=3; modmaxcovj = 7;
2750: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2751: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2752: variables V1_1 and V1_2.
2753: nbcode[Tvar[j]][ij]=k;
2754: nbcode[Tvar[j]][1]=0;
2755: nbcode[Tvar[j]][2]=1;
2756: nbcode[Tvar[j]][3]=2;
2757: */
2758: ij=1; /* ij is similar to i but can jumps over null modalities */
2759: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2760: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2761: /*recode from 0 */
2762: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2763: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2764: k is a modality. If we have model=V1+V1*sex
2765: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2766: ij++;
2767: }
2768: if (ij > ncodemax[j]) break;
2769: } /* end of loop on */
2770: } /* end of loop on modality */
2771: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2772:
2773: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2774:
2775: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2776: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2777: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2778: Ndum[ij]++;
2779: }
2780:
2781: ij=1;
2782: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2783: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2784: if((Ndum[i]!=0) && (i<=ncovcol)){
2785: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2786: Tvaraff[ij]=i; /*For printing (unclear) */
2787: ij++;
2788: }else
2789: Tvaraff[ij]=0;
2790: }
2791: ij--;
2792: cptcoveff=ij; /*Number of total covariates*/
2793:
2794: }
2795:
2796:
2797: /*********** Health Expectancies ****************/
2798:
2799: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2800:
2801: {
2802: /* Health expectancies, no variances */
2803: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2804: int nhstepma, nstepma; /* Decreasing with age */
2805: double age, agelim, hf;
2806: double ***p3mat;
2807: double eip;
2808:
2809: pstamp(ficreseij);
2810: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2811: fprintf(ficreseij,"# Age");
2812: for(i=1; i<=nlstate;i++){
2813: for(j=1; j<=nlstate;j++){
2814: fprintf(ficreseij," e%1d%1d ",i,j);
2815: }
2816: fprintf(ficreseij," e%1d. ",i);
2817: }
2818: fprintf(ficreseij,"\n");
2819:
2820:
2821: if(estepm < stepm){
2822: printf ("Problem %d lower than %d\n",estepm, stepm);
2823: }
2824: else hstepm=estepm;
2825: /* We compute the life expectancy from trapezoids spaced every estepm months
2826: * This is mainly to measure the difference between two models: for example
2827: * if stepm=24 months pijx are given only every 2 years and by summing them
2828: * we are calculating an estimate of the Life Expectancy assuming a linear
2829: * progression in between and thus overestimating or underestimating according
2830: * to the curvature of the survival function. If, for the same date, we
2831: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2832: * to compare the new estimate of Life expectancy with the same linear
2833: * hypothesis. A more precise result, taking into account a more precise
2834: * curvature will be obtained if estepm is as small as stepm. */
2835:
2836: /* For example we decided to compute the life expectancy with the smallest unit */
2837: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2838: nhstepm is the number of hstepm from age to agelim
2839: nstepm is the number of stepm from age to agelin.
2840: Look at hpijx to understand the reason of that which relies in memory size
2841: and note for a fixed period like estepm months */
2842: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2843: survival function given by stepm (the optimization length). Unfortunately it
2844: means that if the survival funtion is printed only each two years of age and if
2845: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2846: results. So we changed our mind and took the option of the best precision.
2847: */
2848: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2849:
2850: agelim=AGESUP;
2851: /* If stepm=6 months */
2852: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2853: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2854:
2855: /* nhstepm age range expressed in number of stepm */
2856: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2857: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2858: /* if (stepm >= YEARM) hstepm=1;*/
2859: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2860: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2861:
2862: for (age=bage; age<=fage; age ++){
2863: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2864: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2865: /* if (stepm >= YEARM) hstepm=1;*/
2866: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2867:
2868: /* If stepm=6 months */
2869: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2870: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2871:
2872: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2873:
2874: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2875:
2876: printf("%d|",(int)age);fflush(stdout);
2877: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2878:
2879: /* Computing expectancies */
2880: for(i=1; i<=nlstate;i++)
2881: for(j=1; j<=nlstate;j++)
2882: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2883: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2884:
2885: /* 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]);*/
2886:
2887: }
2888:
2889: fprintf(ficreseij,"%3.0f",age );
2890: for(i=1; i<=nlstate;i++){
2891: eip=0;
2892: for(j=1; j<=nlstate;j++){
2893: eip +=eij[i][j][(int)age];
2894: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2895: }
2896: fprintf(ficreseij,"%9.4f", eip );
2897: }
2898: fprintf(ficreseij,"\n");
2899:
2900: }
2901: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2902: printf("\n");
2903: fprintf(ficlog,"\n");
2904:
2905: }
2906:
2907: 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[] )
2908:
2909: {
2910: /* Covariances of health expectancies eij and of total life expectancies according
2911: to initial status i, ei. .
2912: */
2913: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2914: int nhstepma, nstepma; /* Decreasing with age */
2915: double age, agelim, hf;
2916: double ***p3matp, ***p3matm, ***varhe;
2917: double **dnewm,**doldm;
2918: double *xp, *xm;
2919: double **gp, **gm;
2920: double ***gradg, ***trgradg;
2921: int theta;
2922:
2923: double eip, vip;
2924:
2925: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2926: xp=vector(1,npar);
2927: xm=vector(1,npar);
2928: dnewm=matrix(1,nlstate*nlstate,1,npar);
2929: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2930:
2931: pstamp(ficresstdeij);
2932: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2933: fprintf(ficresstdeij,"# Age");
2934: for(i=1; i<=nlstate;i++){
2935: for(j=1; j<=nlstate;j++)
2936: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2937: fprintf(ficresstdeij," e%1d. ",i);
2938: }
2939: fprintf(ficresstdeij,"\n");
2940:
2941: pstamp(ficrescveij);
2942: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2943: fprintf(ficrescveij,"# Age");
2944: for(i=1; i<=nlstate;i++)
2945: for(j=1; j<=nlstate;j++){
2946: cptj= (j-1)*nlstate+i;
2947: for(i2=1; i2<=nlstate;i2++)
2948: for(j2=1; j2<=nlstate;j2++){
2949: cptj2= (j2-1)*nlstate+i2;
2950: if(cptj2 <= cptj)
2951: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2952: }
2953: }
2954: fprintf(ficrescveij,"\n");
2955:
2956: if(estepm < stepm){
2957: printf ("Problem %d lower than %d\n",estepm, stepm);
2958: }
2959: else hstepm=estepm;
2960: /* We compute the life expectancy from trapezoids spaced every estepm months
2961: * This is mainly to measure the difference between two models: for example
2962: * if stepm=24 months pijx are given only every 2 years and by summing them
2963: * we are calculating an estimate of the Life Expectancy assuming a linear
2964: * progression in between and thus overestimating or underestimating according
2965: * to the curvature of the survival function. If, for the same date, we
2966: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2967: * to compare the new estimate of Life expectancy with the same linear
2968: * hypothesis. A more precise result, taking into account a more precise
2969: * curvature will be obtained if estepm is as small as stepm. */
2970:
2971: /* For example we decided to compute the life expectancy with the smallest unit */
2972: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2973: nhstepm is the number of hstepm from age to agelim
2974: nstepm is the number of stepm from age to agelin.
2975: Look at hpijx to understand the reason of that which relies in memory size
2976: and note for a fixed period like estepm months */
2977: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2978: survival function given by stepm (the optimization length). Unfortunately it
2979: means that if the survival funtion is printed only each two years of age and if
2980: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2981: results. So we changed our mind and took the option of the best precision.
2982: */
2983: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2984:
2985: /* If stepm=6 months */
2986: /* nhstepm age range expressed in number of stepm */
2987: agelim=AGESUP;
2988: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2989: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2990: /* if (stepm >= YEARM) hstepm=1;*/
2991: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2992:
2993: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2994: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2995: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2996: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2997: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2998: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2999:
3000: for (age=bage; age<=fage; age ++){
3001: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3002: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3003: /* if (stepm >= YEARM) hstepm=1;*/
3004: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3005:
3006: /* If stepm=6 months */
3007: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3008: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3009:
3010: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3011:
3012: /* Computing Variances of health expectancies */
3013: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3014: decrease memory allocation */
3015: for(theta=1; theta <=npar; theta++){
3016: for(i=1; i<=npar; i++){
3017: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3018: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3019: }
3020: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3021: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3022:
3023: for(j=1; j<= nlstate; j++){
3024: for(i=1; i<=nlstate; i++){
3025: for(h=0; h<=nhstepm-1; h++){
3026: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3027: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3028: }
3029: }
3030: }
3031:
3032: for(ij=1; ij<= nlstate*nlstate; ij++)
3033: for(h=0; h<=nhstepm-1; h++){
3034: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3035: }
3036: }/* End theta */
3037:
3038:
3039: for(h=0; h<=nhstepm-1; h++)
3040: for(j=1; j<=nlstate*nlstate;j++)
3041: for(theta=1; theta <=npar; theta++)
3042: trgradg[h][j][theta]=gradg[h][theta][j];
3043:
3044:
3045: for(ij=1;ij<=nlstate*nlstate;ij++)
3046: for(ji=1;ji<=nlstate*nlstate;ji++)
3047: varhe[ij][ji][(int)age] =0.;
3048:
3049: printf("%d|",(int)age);fflush(stdout);
3050: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3051: for(h=0;h<=nhstepm-1;h++){
3052: for(k=0;k<=nhstepm-1;k++){
3053: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3054: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3055: for(ij=1;ij<=nlstate*nlstate;ij++)
3056: for(ji=1;ji<=nlstate*nlstate;ji++)
3057: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3058: }
3059: }
3060:
3061: /* Computing expectancies */
3062: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3063: for(i=1; i<=nlstate;i++)
3064: for(j=1; j<=nlstate;j++)
3065: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3066: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3067:
3068: /* 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]);*/
3069:
3070: }
3071:
3072: fprintf(ficresstdeij,"%3.0f",age );
3073: for(i=1; i<=nlstate;i++){
3074: eip=0.;
3075: vip=0.;
3076: for(j=1; j<=nlstate;j++){
3077: eip += eij[i][j][(int)age];
3078: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3079: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3080: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3081: }
3082: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3083: }
3084: fprintf(ficresstdeij,"\n");
3085:
3086: fprintf(ficrescveij,"%3.0f",age );
3087: for(i=1; i<=nlstate;i++)
3088: for(j=1; j<=nlstate;j++){
3089: cptj= (j-1)*nlstate+i;
3090: for(i2=1; i2<=nlstate;i2++)
3091: for(j2=1; j2<=nlstate;j2++){
3092: cptj2= (j2-1)*nlstate+i2;
3093: if(cptj2 <= cptj)
3094: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3095: }
3096: }
3097: fprintf(ficrescveij,"\n");
3098:
3099: }
3100: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3101: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3102: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3103: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3104: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3105: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3106: printf("\n");
3107: fprintf(ficlog,"\n");
3108:
3109: free_vector(xm,1,npar);
3110: free_vector(xp,1,npar);
3111: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3112: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3113: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3114: }
3115:
3116: /************ Variance ******************/
3117: 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[])
3118: {
3119: /* Variance of health expectancies */
3120: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3121: /* double **newm;*/
3122: double **dnewm,**doldm;
3123: double **dnewmp,**doldmp;
3124: int i, j, nhstepm, hstepm, h, nstepm ;
3125: int k, cptcode;
3126: double *xp;
3127: double **gp, **gm; /* for var eij */
3128: double ***gradg, ***trgradg; /*for var eij */
3129: double **gradgp, **trgradgp; /* for var p point j */
3130: double *gpp, *gmp; /* for var p point j */
3131: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3132: double ***p3mat;
3133: double age,agelim, hf;
3134: double ***mobaverage;
3135: int theta;
3136: char digit[4];
3137: char digitp[25];
3138:
3139: char fileresprobmorprev[FILENAMELENGTH];
3140:
3141: if(popbased==1){
3142: if(mobilav!=0)
3143: strcpy(digitp,"-populbased-mobilav-");
3144: else strcpy(digitp,"-populbased-nomobil-");
3145: }
3146: else
3147: strcpy(digitp,"-stablbased-");
3148:
3149: if (mobilav!=0) {
3150: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3151: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3152: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3153: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3154: }
3155: }
3156:
3157: strcpy(fileresprobmorprev,"prmorprev");
3158: sprintf(digit,"%-d",ij);
3159: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3160: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3161: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3162: strcat(fileresprobmorprev,fileres);
3163: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3164: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3165: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3166: }
3167: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3168:
3169: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3170: pstamp(ficresprobmorprev);
3171: 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);
3172: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3173: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3174: fprintf(ficresprobmorprev," p.%-d SE",j);
3175: for(i=1; i<=nlstate;i++)
3176: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3177: }
3178: fprintf(ficresprobmorprev,"\n");
3179: fprintf(ficgp,"\n# Routine varevsij");
3180: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3181: 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");
3182: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3183: /* } */
3184: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3185: pstamp(ficresvij);
3186: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3187: if(popbased==1)
3188: 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);
3189: else
3190: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3191: fprintf(ficresvij,"# Age");
3192: for(i=1; i<=nlstate;i++)
3193: for(j=1; j<=nlstate;j++)
3194: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3195: fprintf(ficresvij,"\n");
3196:
3197: xp=vector(1,npar);
3198: dnewm=matrix(1,nlstate,1,npar);
3199: doldm=matrix(1,nlstate,1,nlstate);
3200: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3201: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3202:
3203: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3204: gpp=vector(nlstate+1,nlstate+ndeath);
3205: gmp=vector(nlstate+1,nlstate+ndeath);
3206: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3207:
3208: if(estepm < stepm){
3209: printf ("Problem %d lower than %d\n",estepm, stepm);
3210: }
3211: else hstepm=estepm;
3212: /* For example we decided to compute the life expectancy with the smallest unit */
3213: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3214: nhstepm is the number of hstepm from age to agelim
3215: nstepm is the number of stepm from age to agelin.
3216: Look at function hpijx to understand why (it is linked to memory size questions) */
3217: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3218: survival function given by stepm (the optimization length). Unfortunately it
3219: means that if the survival funtion is printed every two years of age and if
3220: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3221: results. So we changed our mind and took the option of the best precision.
3222: */
3223: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3224: agelim = AGESUP;
3225: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3226: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3227: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3228: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3229: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3230: gp=matrix(0,nhstepm,1,nlstate);
3231: gm=matrix(0,nhstepm,1,nlstate);
3232:
3233:
3234: for(theta=1; theta <=npar; theta++){
3235: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3236: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3237: }
3238: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3239: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3240:
3241: if (popbased==1) {
3242: if(mobilav ==0){
3243: for(i=1; i<=nlstate;i++)
3244: prlim[i][i]=probs[(int)age][i][ij];
3245: }else{ /* mobilav */
3246: for(i=1; i<=nlstate;i++)
3247: prlim[i][i]=mobaverage[(int)age][i][ij];
3248: }
3249: }
3250:
3251: for(j=1; j<= nlstate; j++){
3252: for(h=0; h<=nhstepm; h++){
3253: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3254: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3255: }
3256: }
3257: /* This for computing probability of death (h=1 means
3258: computed over hstepm matrices product = hstepm*stepm months)
3259: as a weighted average of prlim.
3260: */
3261: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3262: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3263: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3264: }
3265: /* end probability of death */
3266:
3267: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3268: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3269: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3270: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3271:
3272: if (popbased==1) {
3273: if(mobilav ==0){
3274: for(i=1; i<=nlstate;i++)
3275: prlim[i][i]=probs[(int)age][i][ij];
3276: }else{ /* mobilav */
3277: for(i=1; i<=nlstate;i++)
3278: prlim[i][i]=mobaverage[(int)age][i][ij];
3279: }
3280: }
3281:
3282: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3283: for(h=0; h<=nhstepm; h++){
3284: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3285: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3286: }
3287: }
3288: /* This for computing probability of death (h=1 means
3289: computed over hstepm matrices product = hstepm*stepm months)
3290: as a weighted average of prlim.
3291: */
3292: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3293: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3294: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3295: }
3296: /* end probability of death */
3297:
3298: for(j=1; j<= nlstate; j++) /* vareij */
3299: for(h=0; h<=nhstepm; h++){
3300: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3301: }
3302:
3303: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3304: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3305: }
3306:
3307: } /* End theta */
3308:
3309: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3310:
3311: for(h=0; h<=nhstepm; h++) /* veij */
3312: for(j=1; j<=nlstate;j++)
3313: for(theta=1; theta <=npar; theta++)
3314: trgradg[h][j][theta]=gradg[h][theta][j];
3315:
3316: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3317: for(theta=1; theta <=npar; theta++)
3318: trgradgp[j][theta]=gradgp[theta][j];
3319:
3320:
3321: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3322: for(i=1;i<=nlstate;i++)
3323: for(j=1;j<=nlstate;j++)
3324: vareij[i][j][(int)age] =0.;
3325:
3326: for(h=0;h<=nhstepm;h++){
3327: for(k=0;k<=nhstepm;k++){
3328: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3329: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3330: for(i=1;i<=nlstate;i++)
3331: for(j=1;j<=nlstate;j++)
3332: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3333: }
3334: }
3335:
3336: /* pptj */
3337: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3338: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3339: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3340: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3341: varppt[j][i]=doldmp[j][i];
3342: /* end ppptj */
3343: /* x centered again */
3344: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3345: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3346:
3347: if (popbased==1) {
3348: if(mobilav ==0){
3349: for(i=1; i<=nlstate;i++)
3350: prlim[i][i]=probs[(int)age][i][ij];
3351: }else{ /* mobilav */
3352: for(i=1; i<=nlstate;i++)
3353: prlim[i][i]=mobaverage[(int)age][i][ij];
3354: }
3355: }
3356:
3357: /* This for computing probability of death (h=1 means
3358: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3359: as a weighted average of prlim.
3360: */
3361: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3362: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3363: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3364: }
3365: /* end probability of death */
3366:
3367: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3368: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3369: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3370: for(i=1; i<=nlstate;i++){
3371: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3372: }
3373: }
3374: fprintf(ficresprobmorprev,"\n");
3375:
3376: fprintf(ficresvij,"%.0f ",age );
3377: for(i=1; i<=nlstate;i++)
3378: for(j=1; j<=nlstate;j++){
3379: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3380: }
3381: fprintf(ficresvij,"\n");
3382: free_matrix(gp,0,nhstepm,1,nlstate);
3383: free_matrix(gm,0,nhstepm,1,nlstate);
3384: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3385: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3386: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3387: } /* End age */
3388: free_vector(gpp,nlstate+1,nlstate+ndeath);
3389: free_vector(gmp,nlstate+1,nlstate+ndeath);
3390: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3391: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3392: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3393: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3394: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3395: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3396: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3397: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3398: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3399: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3400: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3401: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3402: 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);
3403: /* 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);
3404: */
3405: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3406: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3407:
3408: free_vector(xp,1,npar);
3409: free_matrix(doldm,1,nlstate,1,nlstate);
3410: free_matrix(dnewm,1,nlstate,1,npar);
3411: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3412: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3413: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3414: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3415: fclose(ficresprobmorprev);
3416: fflush(ficgp);
3417: fflush(fichtm);
3418: } /* end varevsij */
3419:
3420: /************ Variance of prevlim ******************/
3421: 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[])
3422: {
3423: /* Variance of prevalence limit */
3424: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3425: double **newm;
3426: double **dnewm,**doldm;
3427: int i, j, nhstepm, hstepm;
3428: int k, cptcode;
3429: double *xp;
3430: double *gp, *gm;
3431: double **gradg, **trgradg;
3432: double age,agelim;
3433: int theta;
3434:
3435: pstamp(ficresvpl);
3436: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3437: fprintf(ficresvpl,"# Age");
3438: for(i=1; i<=nlstate;i++)
3439: fprintf(ficresvpl," %1d-%1d",i,i);
3440: fprintf(ficresvpl,"\n");
3441:
3442: xp=vector(1,npar);
3443: dnewm=matrix(1,nlstate,1,npar);
3444: doldm=matrix(1,nlstate,1,nlstate);
3445:
3446: hstepm=1*YEARM; /* Every year of age */
3447: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3448: agelim = AGESUP;
3449: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3450: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3451: if (stepm >= YEARM) hstepm=1;
3452: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3453: gradg=matrix(1,npar,1,nlstate);
3454: gp=vector(1,nlstate);
3455: gm=vector(1,nlstate);
3456:
3457: for(theta=1; theta <=npar; theta++){
3458: for(i=1; i<=npar; i++){ /* Computes gradient */
3459: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3460: }
3461: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3462: for(i=1;i<=nlstate;i++)
3463: gp[i] = prlim[i][i];
3464:
3465: for(i=1; i<=npar; i++) /* Computes gradient */
3466: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3467: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3468: for(i=1;i<=nlstate;i++)
3469: gm[i] = prlim[i][i];
3470:
3471: for(i=1;i<=nlstate;i++)
3472: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3473: } /* End theta */
3474:
3475: trgradg =matrix(1,nlstate,1,npar);
3476:
3477: for(j=1; j<=nlstate;j++)
3478: for(theta=1; theta <=npar; theta++)
3479: trgradg[j][theta]=gradg[theta][j];
3480:
3481: for(i=1;i<=nlstate;i++)
3482: varpl[i][(int)age] =0.;
3483: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3484: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3485: for(i=1;i<=nlstate;i++)
3486: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3487:
3488: fprintf(ficresvpl,"%.0f ",age );
3489: for(i=1; i<=nlstate;i++)
3490: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3491: fprintf(ficresvpl,"\n");
3492: free_vector(gp,1,nlstate);
3493: free_vector(gm,1,nlstate);
3494: free_matrix(gradg,1,npar,1,nlstate);
3495: free_matrix(trgradg,1,nlstate,1,npar);
3496: } /* End age */
3497:
3498: free_vector(xp,1,npar);
3499: free_matrix(doldm,1,nlstate,1,npar);
3500: free_matrix(dnewm,1,nlstate,1,nlstate);
3501:
3502: }
3503:
3504: /************ Variance of one-step probabilities ******************/
3505: 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[])
3506: {
3507: int i, j=0, i1, k1, l1, t, tj;
3508: int k2, l2, j1, z1;
3509: int k=0,l, cptcode;
3510: int first=1, first1, first2;
3511: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3512: double **dnewm,**doldm;
3513: double *xp;
3514: double *gp, *gm;
3515: double **gradg, **trgradg;
3516: double **mu;
3517: double age,agelim, cov[NCOVMAX+1];
3518: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3519: int theta;
3520: char fileresprob[FILENAMELENGTH];
3521: char fileresprobcov[FILENAMELENGTH];
3522: char fileresprobcor[FILENAMELENGTH];
3523: double ***varpij;
3524:
3525: strcpy(fileresprob,"prob");
3526: strcat(fileresprob,fileres);
3527: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3528: printf("Problem with resultfile: %s\n", fileresprob);
3529: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3530: }
3531: strcpy(fileresprobcov,"probcov");
3532: strcat(fileresprobcov,fileres);
3533: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3534: printf("Problem with resultfile: %s\n", fileresprobcov);
3535: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3536: }
3537: strcpy(fileresprobcor,"probcor");
3538: strcat(fileresprobcor,fileres);
3539: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3540: printf("Problem with resultfile: %s\n", fileresprobcor);
3541: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3542: }
3543: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3544: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3545: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3546: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3547: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3548: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3549: pstamp(ficresprob);
3550: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3551: fprintf(ficresprob,"# Age");
3552: pstamp(ficresprobcov);
3553: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3554: fprintf(ficresprobcov,"# Age");
3555: pstamp(ficresprobcor);
3556: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3557: fprintf(ficresprobcor,"# Age");
3558:
3559:
3560: for(i=1; i<=nlstate;i++)
3561: for(j=1; j<=(nlstate+ndeath);j++){
3562: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3563: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3564: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3565: }
3566: /* fprintf(ficresprob,"\n");
3567: fprintf(ficresprobcov,"\n");
3568: fprintf(ficresprobcor,"\n");
3569: */
3570: xp=vector(1,npar);
3571: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3572: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3573: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3574: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3575: first=1;
3576: fprintf(ficgp,"\n# Routine varprob");
3577: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3578: fprintf(fichtm,"\n");
3579:
3580: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3581: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3582: file %s<br>\n",optionfilehtmcov);
3583: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3584: and drawn. It helps understanding how is the covariance between two incidences.\
3585: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3586: 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. \
3587: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3588: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3589: standard deviations wide on each axis. <br>\
3590: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3591: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3592: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3593:
3594: cov[1]=1;
3595: /* tj=cptcoveff; */
3596: tj = (int) pow(2,cptcoveff);
3597: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3598: j1=0;
3599: for(j1=1; j1<=tj;j1++){
3600: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3601: /*j1++;*/
3602: if (cptcovn>0) {
3603: fprintf(ficresprob, "\n#********** Variable ");
3604: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3605: fprintf(ficresprob, "**********\n#\n");
3606: fprintf(ficresprobcov, "\n#********** Variable ");
3607: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3608: fprintf(ficresprobcov, "**********\n#\n");
3609:
3610: fprintf(ficgp, "\n#********** Variable ");
3611: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3612: fprintf(ficgp, "**********\n#\n");
3613:
3614:
3615: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3616: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3617: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3618:
3619: fprintf(ficresprobcor, "\n#********** Variable ");
3620: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3621: fprintf(ficresprobcor, "**********\n#");
3622: }
3623:
3624: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3625: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3626: gp=vector(1,(nlstate)*(nlstate+ndeath));
3627: gm=vector(1,(nlstate)*(nlstate+ndeath));
3628: for (age=bage; age<=fage; age ++){
3629: cov[2]=age;
3630: for (k=1; k<=cptcovn;k++) {
3631: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3632: * 1 1 1 1 1
3633: * 2 2 1 1 1
3634: * 3 1 2 1 1
3635: */
3636: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3637: }
3638: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3639: for (k=1; k<=cptcovprod;k++)
3640: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3641:
3642:
3643: for(theta=1; theta <=npar; theta++){
3644: for(i=1; i<=npar; i++)
3645: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3646:
3647: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3648:
3649: k=0;
3650: for(i=1; i<= (nlstate); i++){
3651: for(j=1; j<=(nlstate+ndeath);j++){
3652: k=k+1;
3653: gp[k]=pmmij[i][j];
3654: }
3655: }
3656:
3657: for(i=1; i<=npar; i++)
3658: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3659:
3660: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3661: k=0;
3662: for(i=1; i<=(nlstate); i++){
3663: for(j=1; j<=(nlstate+ndeath);j++){
3664: k=k+1;
3665: gm[k]=pmmij[i][j];
3666: }
3667: }
3668:
3669: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3670: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3671: }
3672:
3673: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3674: for(theta=1; theta <=npar; theta++)
3675: trgradg[j][theta]=gradg[theta][j];
3676:
3677: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3678: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3679:
3680: pmij(pmmij,cov,ncovmodel,x,nlstate);
3681:
3682: k=0;
3683: for(i=1; i<=(nlstate); i++){
3684: for(j=1; j<=(nlstate+ndeath);j++){
3685: k=k+1;
3686: mu[k][(int) age]=pmmij[i][j];
3687: }
3688: }
3689: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3690: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3691: varpij[i][j][(int)age] = doldm[i][j];
3692:
3693: /*printf("\n%d ",(int)age);
3694: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3695: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3696: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3697: }*/
3698:
3699: fprintf(ficresprob,"\n%d ",(int)age);
3700: fprintf(ficresprobcov,"\n%d ",(int)age);
3701: fprintf(ficresprobcor,"\n%d ",(int)age);
3702:
3703: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3704: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3705: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3706: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3707: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3708: }
3709: i=0;
3710: for (k=1; k<=(nlstate);k++){
3711: for (l=1; l<=(nlstate+ndeath);l++){
3712: i++;
3713: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3714: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3715: for (j=1; j<=i;j++){
3716: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3717: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3718: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3719: }
3720: }
3721: }/* end of loop for state */
3722: } /* end of loop for age */
3723: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3724: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3725: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3726: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3727:
3728: /* Confidence intervalle of pij */
3729: /*
3730: fprintf(ficgp,"\nunset parametric;unset label");
3731: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3732: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3733: 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);
3734: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3735: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3736: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3737: */
3738:
3739: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3740: first1=1;first2=2;
3741: for (k2=1; k2<=(nlstate);k2++){
3742: for (l2=1; l2<=(nlstate+ndeath);l2++){
3743: if(l2==k2) continue;
3744: j=(k2-1)*(nlstate+ndeath)+l2;
3745: for (k1=1; k1<=(nlstate);k1++){
3746: for (l1=1; l1<=(nlstate+ndeath);l1++){
3747: if(l1==k1) continue;
3748: i=(k1-1)*(nlstate+ndeath)+l1;
3749: if(i<=j) continue;
3750: for (age=bage; age<=fage; age ++){
3751: if ((int)age %5==0){
3752: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3753: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3754: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3755: mu1=mu[i][(int) age]/stepm*YEARM ;
3756: mu2=mu[j][(int) age]/stepm*YEARM;
3757: c12=cv12/sqrt(v1*v2);
3758: /* Computing eigen value of matrix of covariance */
3759: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3760: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3761: if ((lc2 <0) || (lc1 <0) ){
3762: if(first2==1){
3763: first1=0;
3764: printf("Strange: j1=%d 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. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
3765: }
3766: fprintf(ficlog,"Strange: j1=%d 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. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
3767: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3768: /* lc2=fabs(lc2); */
3769: }
3770:
3771: /* Eigen vectors */
3772: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3773: /*v21=sqrt(1.-v11*v11); *//* error */
3774: v21=(lc1-v1)/cv12*v11;
3775: v12=-v21;
3776: v22=v11;
3777: tnalp=v21/v11;
3778: if(first1==1){
3779: first1=0;
3780: 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);
3781: }
3782: 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);
3783: /*printf(fignu*/
3784: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3785: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3786: if(first==1){
3787: first=0;
3788: fprintf(ficgp,"\nset parametric;unset label");
3789: 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);
3790: fprintf(ficgp,"\nset ter png small size 320, 240");
3791: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3792: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3793: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3794: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3795: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3796: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3797: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3798: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3799: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3800: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3801: 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",\
3802: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3803: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3804: }else{
3805: first=0;
3806: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3807: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3808: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3809: 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",\
3810: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3811: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3812: }/* if first */
3813: } /* age mod 5 */
3814: } /* end loop age */
3815: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3816: first=1;
3817: } /*l12 */
3818: } /* k12 */
3819: } /*l1 */
3820: }/* k1 */
3821: /* } /* loop covariates */
3822: }
3823: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3824: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3825: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3826: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3827: free_vector(xp,1,npar);
3828: fclose(ficresprob);
3829: fclose(ficresprobcov);
3830: fclose(ficresprobcor);
3831: fflush(ficgp);
3832: fflush(fichtmcov);
3833: }
3834:
3835:
3836: /******************* Printing html file ***********/
3837: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3838: int lastpass, int stepm, int weightopt, char model[],\
3839: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3840: int popforecast, int estepm ,\
3841: double jprev1, double mprev1,double anprev1, \
3842: double jprev2, double mprev2,double anprev2){
3843: int jj1, k1, i1, cpt;
3844:
3845: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3846: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3847: </ul>");
3848: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3849: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3850: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3851: fprintf(fichtm,"\
3852: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3853: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3854: fprintf(fichtm,"\
3855: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3856: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3857: fprintf(fichtm,"\
3858: - (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): \
3859: <a href=\"%s\">%s</a> <br>\n",
3860: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3861: fprintf(fichtm,"\
3862: - Population projections by age and states: \
3863: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3864:
3865: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3866:
3867: m=pow(2,cptcoveff);
3868: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3869:
3870: jj1=0;
3871: for(k1=1; k1<=m;k1++){
3872: for(i1=1; i1<=ncodemax[k1];i1++){
3873: jj1++;
3874: if (cptcovn > 0) {
3875: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3876: for (cpt=1; cpt<=cptcoveff;cpt++)
3877: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3878: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3879: }
3880: /* Pij */
3881: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
3882: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3883: /* Quasi-incidences */
3884: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3885: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
3886: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3887: /* Period (stable) prevalence in each health state */
3888: for(cpt=1; cpt<nlstate;cpt++){
3889: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
3890: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3891: }
3892: for(cpt=1; cpt<=nlstate;cpt++) {
3893: 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> \
3894: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3895: }
3896: } /* end i1 */
3897: }/* End k1 */
3898: fprintf(fichtm,"</ul>");
3899:
3900:
3901: fprintf(fichtm,"\
3902: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3903: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3904:
3905: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3906: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3907: fprintf(fichtm,"\
3908: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3909: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3910:
3911: fprintf(fichtm,"\
3912: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3913: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3914: fprintf(fichtm,"\
3915: - 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): \
3916: <a href=\"%s\">%s</a> <br>\n</li>",
3917: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3918: fprintf(fichtm,"\
3919: - (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): \
3920: <a href=\"%s\">%s</a> <br>\n</li>",
3921: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3922: fprintf(fichtm,"\
3923: - 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",
3924: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3925: fprintf(fichtm,"\
3926: - 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",
3927: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3928: fprintf(fichtm,"\
3929: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3930: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3931:
3932: /* if(popforecast==1) fprintf(fichtm,"\n */
3933: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3934: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3935: /* <br>",fileres,fileres,fileres,fileres); */
3936: /* else */
3937: /* 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); */
3938: fflush(fichtm);
3939: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3940:
3941: m=pow(2,cptcoveff);
3942: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3943:
3944: jj1=0;
3945: for(k1=1; k1<=m;k1++){
3946: for(i1=1; i1<=ncodemax[k1];i1++){
3947: jj1++;
3948: if (cptcovn > 0) {
3949: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3950: for (cpt=1; cpt<=cptcoveff;cpt++)
3951: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3952: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3953: }
3954: for(cpt=1; cpt<=nlstate;cpt++) {
3955: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3956: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
3957: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3958: }
3959: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3960: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3961: true period expectancies (those weighted with period prevalences are also\
3962: drawn in addition to the population based expectancies computed using\
3963: observed and cahotic prevalences: %s%d.png<br>\
3964: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3965: } /* end i1 */
3966: }/* End k1 */
3967: fprintf(fichtm,"</ul>");
3968: fflush(fichtm);
3969: }
3970:
3971: /******************* Gnuplot file **************/
3972: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3973:
3974: char dirfileres[132],optfileres[132];
3975: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3976: int ng=0;
3977: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3978: /* printf("Problem with file %s",optionfilegnuplot); */
3979: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3980: /* } */
3981:
3982: /*#ifdef windows */
3983: fprintf(ficgp,"cd \"%s\" \n",pathc);
3984: /*#endif */
3985: m=pow(2,cptcoveff);
3986:
3987: strcpy(dirfileres,optionfilefiname);
3988: strcpy(optfileres,"vpl");
3989: /* 1eme*/
3990: for (cpt=1; cpt<= nlstate ; cpt ++) {
3991: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
3992: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3993: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
3994: fprintf(ficgp,"set xlabel \"Age\" \n\
3995: set ylabel \"Probability\" \n\
3996: set ter png small size 320, 240\n\
3997: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3998:
3999: for (i=1; i<= nlstate ; i ++) {
4000: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4001: else fprintf(ficgp," \%%*lf (\%%*lf)");
4002: }
4003: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4004: for (i=1; i<= nlstate ; i ++) {
4005: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4006: else fprintf(ficgp," \%%*lf (\%%*lf)");
4007: }
4008: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4009: for (i=1; i<= nlstate ; i ++) {
4010: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4011: else fprintf(ficgp," \%%*lf (\%%*lf)");
4012: }
4013: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4014: }
4015: }
4016: /*2 eme*/
4017:
4018: for (k1=1; k1<= m ; k1 ++) {
4019: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4020: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4021:
4022: for (i=1; i<= nlstate+1 ; i ++) {
4023: k=2*i;
4024: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4025: for (j=1; j<= nlstate+1 ; j ++) {
4026: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4027: else fprintf(ficgp," \%%*lf (\%%*lf)");
4028: }
4029: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4030: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4031: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4032: for (j=1; j<= nlstate+1 ; j ++) {
4033: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4034: else fprintf(ficgp," \%%*lf (\%%*lf)");
4035: }
4036: fprintf(ficgp,"\" t\"\" w l lt 0,");
4037: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4038: for (j=1; j<= nlstate+1 ; j ++) {
4039: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4040: else fprintf(ficgp," \%%*lf (\%%*lf)");
4041: }
4042: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4043: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4044: }
4045: }
4046:
4047: /*3eme*/
4048:
4049: for (k1=1; k1<= m ; k1 ++) {
4050: for (cpt=1; cpt<= nlstate ; cpt ++) {
4051: /* k=2+nlstate*(2*cpt-2); */
4052: k=2+(nlstate+1)*(cpt-1);
4053: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4054: fprintf(ficgp,"set ter png small size 320, 240\n\
4055: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4056: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4057: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4058: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4059: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4060: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4061: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4062:
4063: */
4064: for (i=1; i< nlstate ; i ++) {
4065: 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);
4066: /* 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);*/
4067:
4068: }
4069: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4070: }
4071: }
4072:
4073: /* CV preval stable (period) */
4074: for (k1=1; k1<= m ; k1 ++) {
4075: for (cpt=1; cpt<=nlstate ; cpt ++) {
4076: k=3;
4077: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4078: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4079: set ter png small size 320, 240\n\
4080: unset log y\n\
4081: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
4082:
4083: for (i=1; i< nlstate ; i ++)
4084: fprintf(ficgp,"+$%d",k+i+1);
4085: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
4086:
4087: l=3+(nlstate+ndeath)*cpt;
4088: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
4089: for (i=1; i< nlstate ; i ++) {
4090: l=3+(nlstate+ndeath)*cpt;
4091: fprintf(ficgp,"+$%d",l+i+1);
4092: }
4093: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
4094: }
4095: }
4096:
4097: /* proba elementaires */
4098: for(i=1,jk=1; i <=nlstate; i++){
4099: for(k=1; k <=(nlstate+ndeath); k++){
4100: if (k != i) {
4101: for(j=1; j <=ncovmodel; j++){
4102: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4103: jk++;
4104: fprintf(ficgp,"\n");
4105: }
4106: }
4107: }
4108: }
4109: /*goto avoid;*/
4110: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4111: for(jk=1; jk <=m; jk++) {
4112: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4113: if (ng==2)
4114: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4115: else
4116: fprintf(ficgp,"\nset title \"Probability\"\n");
4117: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4118: i=1;
4119: for(k2=1; k2<=nlstate; k2++) {
4120: k3=i;
4121: for(k=1; k<=(nlstate+ndeath); k++) {
4122: if (k != k2){
4123: if(ng==2)
4124: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4125: else
4126: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4127: ij=1;/* To be checked else nbcode[0][0] wrong */
4128: for(j=3; j <=ncovmodel; j++) {
4129: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4130: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4131: /* ij++; */
4132: /* } */
4133: /* else */
4134: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4135: }
4136: fprintf(ficgp,")/(1");
4137:
4138: for(k1=1; k1 <=nlstate; k1++){
4139: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4140: ij=1;
4141: for(j=3; j <=ncovmodel; j++){
4142: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4143: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4144: /* ij++; */
4145: /* } */
4146: /* else */
4147: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4148: }
4149: fprintf(ficgp,")");
4150: }
4151: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4152: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4153: i=i+ncovmodel;
4154: }
4155: } /* end k */
4156: } /* end k2 */
4157: } /* end jk */
4158: } /* end ng */
4159: avoid:
4160: fflush(ficgp);
4161: } /* end gnuplot */
4162:
4163:
4164: /*************** Moving average **************/
4165: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4166:
4167: int i, cpt, cptcod;
4168: int modcovmax =1;
4169: int mobilavrange, mob;
4170: double age;
4171:
4172: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4173: a covariate has 2 modalities */
4174: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4175:
4176: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4177: if(mobilav==1) mobilavrange=5; /* default */
4178: else mobilavrange=mobilav;
4179: for (age=bage; age<=fage; age++)
4180: for (i=1; i<=nlstate;i++)
4181: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4182: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4183: /* We keep the original values on the extreme ages bage, fage and for
4184: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4185: we use a 5 terms etc. until the borders are no more concerned.
4186: */
4187: for (mob=3;mob <=mobilavrange;mob=mob+2){
4188: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4189: for (i=1; i<=nlstate;i++){
4190: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4191: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4192: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4193: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4194: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4195: }
4196: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4197: }
4198: }
4199: }/* end age */
4200: }/* end mob */
4201: }else return -1;
4202: return 0;
4203: }/* End movingaverage */
4204:
4205:
4206: /************** Forecasting ******************/
4207: 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){
4208: /* proj1, year, month, day of starting projection
4209: agemin, agemax range of age
4210: dateprev1 dateprev2 range of dates during which prevalence is computed
4211: anproj2 year of en of projection (same day and month as proj1).
4212: */
4213: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4214: int *popage;
4215: double agec; /* generic age */
4216: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4217: double *popeffectif,*popcount;
4218: double ***p3mat;
4219: double ***mobaverage;
4220: char fileresf[FILENAMELENGTH];
4221:
4222: agelim=AGESUP;
4223: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4224:
4225: strcpy(fileresf,"f");
4226: strcat(fileresf,fileres);
4227: if((ficresf=fopen(fileresf,"w"))==NULL) {
4228: printf("Problem with forecast resultfile: %s\n", fileresf);
4229: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4230: }
4231: printf("Computing forecasting: result on file '%s' \n", fileresf);
4232: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4233:
4234: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4235:
4236: if (mobilav!=0) {
4237: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4238: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4239: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4240: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4241: }
4242: }
4243:
4244: stepsize=(int) (stepm+YEARM-1)/YEARM;
4245: if (stepm<=12) stepsize=1;
4246: if(estepm < stepm){
4247: printf ("Problem %d lower than %d\n",estepm, stepm);
4248: }
4249: else hstepm=estepm;
4250:
4251: hstepm=hstepm/stepm;
4252: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4253: fractional in yp1 */
4254: anprojmean=yp;
4255: yp2=modf((yp1*12),&yp);
4256: mprojmean=yp;
4257: yp1=modf((yp2*30.5),&yp);
4258: jprojmean=yp;
4259: if(jprojmean==0) jprojmean=1;
4260: if(mprojmean==0) jprojmean=1;
4261:
4262: i1=cptcoveff;
4263: if (cptcovn < 1){i1=1;}
4264:
4265: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4266:
4267: fprintf(ficresf,"#****** Routine prevforecast **\n");
4268:
4269: /* if (h==(int)(YEARM*yearp)){ */
4270: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4271: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4272: k=k+1;
4273: fprintf(ficresf,"\n#******");
4274: for(j=1;j<=cptcoveff;j++) {
4275: 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]]);
4276: }
4277: fprintf(ficresf,"******\n");
4278: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4279: for(j=1; j<=nlstate+ndeath;j++){
4280: for(i=1; i<=nlstate;i++)
4281: fprintf(ficresf," p%d%d",i,j);
4282: fprintf(ficresf," p.%d",j);
4283: }
4284: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4285: fprintf(ficresf,"\n");
4286: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4287:
4288: for (agec=fage; agec>=(ageminpar-1); agec--){
4289: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4290: nhstepm = nhstepm/hstepm;
4291: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4292: oldm=oldms;savm=savms;
4293: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4294:
4295: for (h=0; h<=nhstepm; h++){
4296: if (h*hstepm/YEARM*stepm ==yearp) {
4297: fprintf(ficresf,"\n");
4298: for(j=1;j<=cptcoveff;j++)
4299: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4300: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4301: }
4302: for(j=1; j<=nlstate+ndeath;j++) {
4303: ppij=0.;
4304: for(i=1; i<=nlstate;i++) {
4305: if (mobilav==1)
4306: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4307: else {
4308: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4309: }
4310: if (h*hstepm/YEARM*stepm== yearp) {
4311: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4312: }
4313: } /* end i */
4314: if (h*hstepm/YEARM*stepm==yearp) {
4315: fprintf(ficresf," %.3f", ppij);
4316: }
4317: }/* end j */
4318: } /* end h */
4319: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4320: } /* end agec */
4321: } /* end yearp */
4322: } /* end cptcod */
4323: } /* end cptcov */
4324:
4325: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4326:
4327: fclose(ficresf);
4328: }
4329:
4330: /************** Forecasting *****not tested NB*************/
4331: 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){
4332:
4333: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4334: int *popage;
4335: double calagedatem, agelim, kk1, kk2;
4336: double *popeffectif,*popcount;
4337: double ***p3mat,***tabpop,***tabpopprev;
4338: double ***mobaverage;
4339: char filerespop[FILENAMELENGTH];
4340:
4341: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4342: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4343: agelim=AGESUP;
4344: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4345:
4346: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4347:
4348:
4349: strcpy(filerespop,"pop");
4350: strcat(filerespop,fileres);
4351: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4352: printf("Problem with forecast resultfile: %s\n", filerespop);
4353: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4354: }
4355: printf("Computing forecasting: result on file '%s' \n", filerespop);
4356: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4357:
4358: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4359:
4360: if (mobilav!=0) {
4361: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4362: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4363: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4364: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4365: }
4366: }
4367:
4368: stepsize=(int) (stepm+YEARM-1)/YEARM;
4369: if (stepm<=12) stepsize=1;
4370:
4371: agelim=AGESUP;
4372:
4373: hstepm=1;
4374: hstepm=hstepm/stepm;
4375:
4376: if (popforecast==1) {
4377: if((ficpop=fopen(popfile,"r"))==NULL) {
4378: printf("Problem with population file : %s\n",popfile);exit(0);
4379: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4380: }
4381: popage=ivector(0,AGESUP);
4382: popeffectif=vector(0,AGESUP);
4383: popcount=vector(0,AGESUP);
4384:
4385: i=1;
4386: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4387:
4388: imx=i;
4389: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4390: }
4391:
4392: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4393: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4394: k=k+1;
4395: fprintf(ficrespop,"\n#******");
4396: for(j=1;j<=cptcoveff;j++) {
4397: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4398: }
4399: fprintf(ficrespop,"******\n");
4400: fprintf(ficrespop,"# Age");
4401: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4402: if (popforecast==1) fprintf(ficrespop," [Population]");
4403:
4404: for (cpt=0; cpt<=0;cpt++) {
4405: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4406:
4407: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4408: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4409: nhstepm = nhstepm/hstepm;
4410:
4411: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4412: oldm=oldms;savm=savms;
4413: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4414:
4415: for (h=0; h<=nhstepm; h++){
4416: if (h==(int) (calagedatem+YEARM*cpt)) {
4417: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4418: }
4419: for(j=1; j<=nlstate+ndeath;j++) {
4420: kk1=0.;kk2=0;
4421: for(i=1; i<=nlstate;i++) {
4422: if (mobilav==1)
4423: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4424: else {
4425: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4426: }
4427: }
4428: if (h==(int)(calagedatem+12*cpt)){
4429: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4430: /*fprintf(ficrespop," %.3f", kk1);
4431: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4432: }
4433: }
4434: for(i=1; i<=nlstate;i++){
4435: kk1=0.;
4436: for(j=1; j<=nlstate;j++){
4437: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4438: }
4439: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4440: }
4441:
4442: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4443: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4444: }
4445: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4446: }
4447: }
4448:
4449: /******/
4450:
4451: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4452: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4453: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4454: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4455: nhstepm = nhstepm/hstepm;
4456:
4457: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4458: oldm=oldms;savm=savms;
4459: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4460: for (h=0; h<=nhstepm; h++){
4461: if (h==(int) (calagedatem+YEARM*cpt)) {
4462: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4463: }
4464: for(j=1; j<=nlstate+ndeath;j++) {
4465: kk1=0.;kk2=0;
4466: for(i=1; i<=nlstate;i++) {
4467: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4468: }
4469: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4470: }
4471: }
4472: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4473: }
4474: }
4475: }
4476: }
4477:
4478: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4479:
4480: if (popforecast==1) {
4481: free_ivector(popage,0,AGESUP);
4482: free_vector(popeffectif,0,AGESUP);
4483: free_vector(popcount,0,AGESUP);
4484: }
4485: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4486: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4487: fclose(ficrespop);
4488: } /* End of popforecast */
4489:
4490: int fileappend(FILE *fichier, char *optionfich)
4491: {
4492: if((fichier=fopen(optionfich,"a"))==NULL) {
4493: printf("Problem with file: %s\n", optionfich);
4494: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4495: return (0);
4496: }
4497: fflush(fichier);
4498: return (1);
4499: }
4500:
4501:
4502: /**************** function prwizard **********************/
4503: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4504: {
4505:
4506: /* Wizard to print covariance matrix template */
4507:
4508: char ca[32], cb[32], cc[32];
4509: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4510: int numlinepar;
4511:
4512: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4513: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4514: for(i=1; i <=nlstate; i++){
4515: jj=0;
4516: for(j=1; j <=nlstate+ndeath; j++){
4517: if(j==i) continue;
4518: jj++;
4519: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4520: printf("%1d%1d",i,j);
4521: fprintf(ficparo,"%1d%1d",i,j);
4522: for(k=1; k<=ncovmodel;k++){
4523: /* printf(" %lf",param[i][j][k]); */
4524: /* fprintf(ficparo," %lf",param[i][j][k]); */
4525: printf(" 0.");
4526: fprintf(ficparo," 0.");
4527: }
4528: printf("\n");
4529: fprintf(ficparo,"\n");
4530: }
4531: }
4532: printf("# Scales (for hessian or gradient estimation)\n");
4533: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4534: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4535: for(i=1; i <=nlstate; i++){
4536: jj=0;
4537: for(j=1; j <=nlstate+ndeath; j++){
4538: if(j==i) continue;
4539: jj++;
4540: fprintf(ficparo,"%1d%1d",i,j);
4541: printf("%1d%1d",i,j);
4542: fflush(stdout);
4543: for(k=1; k<=ncovmodel;k++){
4544: /* printf(" %le",delti3[i][j][k]); */
4545: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4546: printf(" 0.");
4547: fprintf(ficparo," 0.");
4548: }
4549: numlinepar++;
4550: printf("\n");
4551: fprintf(ficparo,"\n");
4552: }
4553: }
4554: printf("# Covariance matrix\n");
4555: /* # 121 Var(a12)\n\ */
4556: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4557: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4558: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4559: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4560: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4561: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4562: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4563: fflush(stdout);
4564: fprintf(ficparo,"# Covariance matrix\n");
4565: /* # 121 Var(a12)\n\ */
4566: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4567: /* # ...\n\ */
4568: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4569:
4570: for(itimes=1;itimes<=2;itimes++){
4571: jj=0;
4572: for(i=1; i <=nlstate; i++){
4573: for(j=1; j <=nlstate+ndeath; j++){
4574: if(j==i) continue;
4575: for(k=1; k<=ncovmodel;k++){
4576: jj++;
4577: ca[0]= k+'a'-1;ca[1]='\0';
4578: if(itimes==1){
4579: printf("#%1d%1d%d",i,j,k);
4580: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4581: }else{
4582: printf("%1d%1d%d",i,j,k);
4583: fprintf(ficparo,"%1d%1d%d",i,j,k);
4584: /* printf(" %.5le",matcov[i][j]); */
4585: }
4586: ll=0;
4587: for(li=1;li <=nlstate; li++){
4588: for(lj=1;lj <=nlstate+ndeath; lj++){
4589: if(lj==li) continue;
4590: for(lk=1;lk<=ncovmodel;lk++){
4591: ll++;
4592: if(ll<=jj){
4593: cb[0]= lk +'a'-1;cb[1]='\0';
4594: if(ll<jj){
4595: if(itimes==1){
4596: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4597: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4598: }else{
4599: printf(" 0.");
4600: fprintf(ficparo," 0.");
4601: }
4602: }else{
4603: if(itimes==1){
4604: printf(" Var(%s%1d%1d)",ca,i,j);
4605: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4606: }else{
4607: printf(" 0.");
4608: fprintf(ficparo," 0.");
4609: }
4610: }
4611: }
4612: } /* end lk */
4613: } /* end lj */
4614: } /* end li */
4615: printf("\n");
4616: fprintf(ficparo,"\n");
4617: numlinepar++;
4618: } /* end k*/
4619: } /*end j */
4620: } /* end i */
4621: } /* end itimes */
4622:
4623: } /* end of prwizard */
4624: /******************* Gompertz Likelihood ******************************/
4625: double gompertz(double x[])
4626: {
4627: double A,B,L=0.0,sump=0.,num=0.;
4628: int i,n=0; /* n is the size of the sample */
4629:
4630: for (i=0;i<=imx-1 ; i++) {
4631: sump=sump+weight[i];
4632: /* sump=sump+1;*/
4633: num=num+1;
4634: }
4635:
4636:
4637: /* for (i=0; i<=imx; i++)
4638: 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]);*/
4639:
4640: for (i=1;i<=imx ; i++)
4641: {
4642: if (cens[i] == 1 && wav[i]>1)
4643: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4644:
4645: if (cens[i] == 0 && wav[i]>1)
4646: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4647: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4648:
4649: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4650: if (wav[i] > 1 ) { /* ??? */
4651: L=L+A*weight[i];
4652: /* 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]);*/
4653: }
4654: }
4655:
4656: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4657:
4658: return -2*L*num/sump;
4659: }
4660:
4661: #ifdef GSL
4662: /******************* Gompertz_f Likelihood ******************************/
4663: double gompertz_f(const gsl_vector *v, void *params)
4664: {
4665: double A,B,LL=0.0,sump=0.,num=0.;
4666: double *x= (double *) v->data;
4667: int i,n=0; /* n is the size of the sample */
4668:
4669: for (i=0;i<=imx-1 ; i++) {
4670: sump=sump+weight[i];
4671: /* sump=sump+1;*/
4672: num=num+1;
4673: }
4674:
4675:
4676: /* for (i=0; i<=imx; i++)
4677: 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]);*/
4678: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4679: for (i=1;i<=imx ; i++)
4680: {
4681: if (cens[i] == 1 && wav[i]>1)
4682: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4683:
4684: if (cens[i] == 0 && wav[i]>1)
4685: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4686: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4687:
4688: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4689: if (wav[i] > 1 ) { /* ??? */
4690: LL=LL+A*weight[i];
4691: /* 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]);*/
4692: }
4693: }
4694:
4695: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4696: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4697:
4698: return -2*LL*num/sump;
4699: }
4700: #endif
4701:
4702: /******************* Printing html file ***********/
4703: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4704: int lastpass, int stepm, int weightopt, char model[],\
4705: int imx, double p[],double **matcov,double agemortsup){
4706: int i,k;
4707:
4708: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4709: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4710: for (i=1;i<=2;i++)
4711: 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]));
4712: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4713: fprintf(fichtm,"</ul>");
4714:
4715: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4716:
4717: 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>");
4718:
4719: for (k=agegomp;k<(agemortsup-2);k++)
4720: 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]);
4721:
4722:
4723: fflush(fichtm);
4724: }
4725:
4726: /******************* Gnuplot file **************/
4727: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4728:
4729: char dirfileres[132],optfileres[132];
4730: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4731: int ng;
4732:
4733:
4734: /*#ifdef windows */
4735: fprintf(ficgp,"cd \"%s\" \n",pathc);
4736: /*#endif */
4737:
4738:
4739: strcpy(dirfileres,optionfilefiname);
4740: strcpy(optfileres,"vpl");
4741: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4742: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4743: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4744: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4745: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4746:
4747: }
4748:
4749: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4750: {
4751:
4752: /*-------- data file ----------*/
4753: FILE *fic;
4754: char dummy[]=" ";
4755: int i, j, n;
4756: int linei, month, year,iout;
4757: char line[MAXLINE], linetmp[MAXLINE];
4758: char stra[80], strb[80];
4759: char *stratrunc;
4760: int lstra;
4761:
4762:
4763: if((fic=fopen(datafile,"r"))==NULL) {
4764: printf("Problem while opening datafile: %s\n", datafile);return 1;
4765: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4766: }
4767:
4768: i=1;
4769: linei=0;
4770: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4771: linei=linei+1;
4772: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4773: if(line[j] == '\t')
4774: line[j] = ' ';
4775: }
4776: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4777: ;
4778: };
4779: line[j+1]=0; /* Trims blanks at end of line */
4780: if(line[0]=='#'){
4781: fprintf(ficlog,"Comment line\n%s\n",line);
4782: printf("Comment line\n%s\n",line);
4783: continue;
4784: }
4785: trimbb(linetmp,line); /* Trims multiple blanks in line */
4786: for (j=0; line[j]!='\0';j++){
4787: line[j]=linetmp[j];
4788: }
4789:
4790:
4791: for (j=maxwav;j>=1;j--){
4792: cutv(stra, strb, line, ' ');
4793: if(strb[0]=='.') { /* Missing status */
4794: lval=-1;
4795: }else{
4796: errno=0;
4797: lval=strtol(strb,&endptr,10);
4798: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4799: if( strb[0]=='\0' || (*endptr != '\0')){
4800: printf("Error reading data around '%s' at line number %d 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);
4801: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);
4802: return 1;
4803: }
4804: }
4805: s[j][i]=lval;
4806:
4807: strcpy(line,stra);
4808: cutv(stra, strb,line,' ');
4809: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4810: }
4811: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4812: month=99;
4813: year=9999;
4814: }else{
4815: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4816: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);
4817: return 1;
4818: }
4819: anint[j][i]= (double) year;
4820: mint[j][i]= (double)month;
4821: strcpy(line,stra);
4822: } /* ENd Waves */
4823:
4824: cutv(stra, strb,line,' ');
4825: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4826: }
4827: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4828: month=99;
4829: year=9999;
4830: }else{
4831: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4832: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4833: return 1;
4834: }
4835: andc[i]=(double) year;
4836: moisdc[i]=(double) month;
4837: strcpy(line,stra);
4838:
4839: cutv(stra, strb,line,' ');
4840: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4841: }
4842: else if(iout=sscanf(strb,"%s.", dummy) != 0){
4843: month=99;
4844: year=9999;
4845: }else{
4846: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4847: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4848: return 1;
4849: }
4850: if (year==9999) {
4851: printf("Error reading data around '%s' at line number %d 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);
4852: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);
4853: return 1;
4854:
4855: }
4856: annais[i]=(double)(year);
4857: moisnais[i]=(double)(month);
4858: strcpy(line,stra);
4859:
4860: cutv(stra, strb,line,' ');
4861: errno=0;
4862: dval=strtod(strb,&endptr);
4863: if( strb[0]=='\0' || (*endptr != '\0')){
4864: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4865: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4866: fflush(ficlog);
4867: return 1;
4868: }
4869: weight[i]=dval;
4870: strcpy(line,stra);
4871:
4872: for (j=ncovcol;j>=1;j--){
4873: cutv(stra, strb,line,' ');
4874: if(strb[0]=='.') { /* Missing status */
4875: lval=-1;
4876: }else{
4877: errno=0;
4878: lval=strtol(strb,&endptr,10);
4879: if( strb[0]=='\0' || (*endptr != '\0')){
4880: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
4881: fprintf(ficlog,"Error reading data around '%ld' at line number %d 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);
4882: return 1;
4883: }
4884: }
4885: if(lval <-1 || lval >1){
4886: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4887: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4888: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4889: For example, for multinomial values like 1, 2 and 3,\n \
4890: build V1=0 V2=0 for the reference value (1),\n \
4891: V1=1 V2=0 for (2) \n \
4892: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4893: output of IMaCh is often meaningless.\n \
4894: Exiting.\n",lval,linei, i,line,j);
4895: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4896: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4897: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4898: For example, for multinomial values like 1, 2 and 3,\n \
4899: build V1=0 V2=0 for the reference value (1),\n \
4900: V1=1 V2=0 for (2) \n \
4901: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4902: output of IMaCh is often meaningless.\n \
4903: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4904: return 1;
4905: }
4906: covar[j][i]=(double)(lval);
4907: strcpy(line,stra);
4908: }
4909: lstra=strlen(stra);
4910:
4911: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4912: stratrunc = &(stra[lstra-9]);
4913: num[i]=atol(stratrunc);
4914: }
4915: else
4916: num[i]=atol(stra);
4917: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4918: 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;}*/
4919:
4920: i=i+1;
4921: } /* End loop reading data */
4922:
4923: *imax=i-1; /* Number of individuals */
4924: fclose(fic);
4925:
4926: return (0);
4927: endread:
4928: printf("Exiting readdata: ");
4929: fclose(fic);
4930: return (1);
4931:
4932:
4933:
4934: }
4935: void removespace(char *str) {
4936: char *p1 = str, *p2 = str;
4937: do
4938: while (*p2 == ' ')
4939: p2++;
4940: while (*p1++ = *p2++);
4941: }
4942:
4943: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
4944: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
4945: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
4946: * - cptcovn or number of covariates k of the models excluding age*products =6
4947: * - cptcovage number of covariates with age*products =2
4948: * - cptcovs number of simple covariates
4949: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
4950: * which is a new column after the 9 (ncovcol) variables.
4951: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
4952: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
4953: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
4954: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
4955: */
4956: {
4957: int i, j, k, ks;
4958: int i1, j1, k1, k2;
4959: char modelsav[80];
4960: char stra[80], strb[80], strc[80], strd[80],stre[80];
4961:
4962: /*removespace(model);*/
4963: if (strlen(model) >1){ /* If there is at least 1 covariate */
4964: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
4965: j=nbocc(model,'+'); /**< j=Number of '+' */
4966: j1=nbocc(model,'*'); /**< j1=Number of '*' */
4967: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
4968: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
4969: /* including age products which are counted in cptcovage.
4970: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
4971: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
4972: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
4973: strcpy(modelsav,model);
4974: if (strstr(model,"AGE") !=0){
4975: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4976: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
4977: return 1;
4978: }
4979: if (strstr(model,"v") !=0){
4980: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4981: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4982: return 1;
4983: }
4984:
4985: /* Design
4986: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
4987: * < ncovcol=8 >
4988: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
4989: * k= 1 2 3 4 5 6 7 8
4990: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
4991: * covar[k,i], value of kth covariate if not including age for individual i:
4992: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
4993: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
4994: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
4995: * Tage[++cptcovage]=k
4996: * if products, new covar are created after ncovcol with k1
4997: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
4998: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
4999: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
5000: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5001: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5002: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5003: * < ncovcol=8 >
5004: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5005: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5006: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5007: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5008: * p Tprod[1]@2={ 6, 5}
5009: *p Tvard[1][1]@4= {7, 8, 5, 6}
5010: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5011: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5012: *How to reorganize?
5013: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5014: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5015: * {2, 1, 4, 8, 5, 6, 3, 7}
5016: * Struct []
5017: */
5018:
5019: /* This loop fills the array Tvar from the string 'model'.*/
5020: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5021: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5022: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5023: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5024: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5025: /* k=1 Tvar[1]=2 (from V2) */
5026: /* k=5 Tvar[5] */
5027: /* for (k=1; k<=cptcovn;k++) { */
5028: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5029: /* } */
5030: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5031: /*
5032: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5033: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5034: Tvar[k]=0;
5035: cptcovage=0;
5036: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5037: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5038: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5039: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5040: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5041: /*scanf("%d",i);*/
5042: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5043: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5044: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5045: /* covar is not filled and then is empty */
5046: cptcovprod--;
5047: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5048: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5049: cptcovage++; /* Sums the number of covariates which include age as a product */
5050: Tage[cptcovage]=k; /* Tage[1] = 4 */
5051: /*printf("stre=%s ", stre);*/
5052: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5053: cptcovprod--;
5054: cutl(stre,strb,strc,'V');
5055: Tvar[k]=atoi(stre);
5056: cptcovage++;
5057: Tage[cptcovage]=k;
5058: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5059: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5060: cptcovn++;
5061: cptcovprodnoage++;k1++;
5062: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5063: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5064: because this model-covariate is a construction we invent a new column
5065: ncovcol + k1
5066: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5067: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5068: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5069: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5070: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5071: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5072: k2=k2+2;
5073: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5074: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5075: for (i=1; i<=lastobs;i++){
5076: /* Computes the new covariate which is a product of
5077: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5078: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5079: }
5080: } /* End age is not in the model */
5081: } /* End if model includes a product */
5082: else { /* no more sum */
5083: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5084: /* scanf("%d",i);*/
5085: cutl(strd,strc,strb,'V');
5086: ks++; /**< Number of simple covariates */
5087: cptcovn++;
5088: Tvar[k]=atoi(strd);
5089: }
5090: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5091: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5092: scanf("%d",i);*/
5093: } /* end of loop + */
5094: } /* end model */
5095:
5096: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5097: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5098:
5099: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5100: printf("cptcovprod=%d ", cptcovprod);
5101: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5102:
5103: scanf("%d ",i);*/
5104:
5105:
5106: return (0); /* with covar[new additional covariate if product] and Tage if age */
5107: endread:
5108: printf("Exiting decodemodel: ");
5109: return (1);
5110: }
5111:
5112: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5113: {
5114: int i, m;
5115:
5116: for (i=1; i<=imx; i++) {
5117: for(m=2; (m<= maxwav); m++) {
5118: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5119: anint[m][i]=9999;
5120: s[m][i]=-1;
5121: }
5122: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5123: *nberr++;
5124: 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);
5125: 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);
5126: s[m][i]=-1;
5127: }
5128: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5129: *nberr++;
5130: 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]);
5131: 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]);
5132: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5133: }
5134: }
5135: }
5136:
5137: for (i=1; i<=imx; i++) {
5138: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5139: for(m=firstpass; (m<= lastpass); m++){
5140: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5141: if (s[m][i] >= nlstate+1) {
5142: if(agedc[i]>0)
5143: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5144: agev[m][i]=agedc[i];
5145: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5146: else {
5147: if ((int)andc[i]!=9999){
5148: nbwarn++;
5149: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5150: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5151: agev[m][i]=-1;
5152: }
5153: }
5154: }
5155: else if(s[m][i] !=9){ /* Standard case, age in fractional
5156: years but with the precision of a month */
5157: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5158: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5159: agev[m][i]=1;
5160: else if(agev[m][i] < *agemin){
5161: *agemin=agev[m][i];
5162: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5163: }
5164: else if(agev[m][i] >*agemax){
5165: *agemax=agev[m][i];
5166: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
5167: }
5168: /*agev[m][i]=anint[m][i]-annais[i];*/
5169: /* agev[m][i] = age[i]+2*m;*/
5170: }
5171: else { /* =9 */
5172: agev[m][i]=1;
5173: s[m][i]=-1;
5174: }
5175: }
5176: else /*= 0 Unknown */
5177: agev[m][i]=1;
5178: }
5179:
5180: }
5181: for (i=1; i<=imx; i++) {
5182: for(m=firstpass; (m<=lastpass); m++){
5183: if (s[m][i] > (nlstate+ndeath)) {
5184: *nberr++;
5185: 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);
5186: 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);
5187: return 1;
5188: }
5189: }
5190: }
5191:
5192: /*for (i=1; i<=imx; i++){
5193: for (m=firstpass; (m<lastpass); m++){
5194: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5195: }
5196:
5197: }*/
5198:
5199:
5200: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5201: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5202:
5203: return (0);
5204: endread:
5205: printf("Exiting calandcheckages: ");
5206: return (1);
5207: }
5208:
5209:
5210: /***********************************************/
5211: /**************** Main Program *****************/
5212: /***********************************************/
5213:
5214: int main(int argc, char *argv[])
5215: {
5216: #ifdef GSL
5217: const gsl_multimin_fminimizer_type *T;
5218: size_t iteri = 0, it;
5219: int rval = GSL_CONTINUE;
5220: int status = GSL_SUCCESS;
5221: double ssval;
5222: #endif
5223: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5224: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5225: int linei, month, year,iout;
5226: int jj, ll, li, lj, lk, imk;
5227: int numlinepar=0; /* Current linenumber of parameter file */
5228: int itimes;
5229: int NDIM=2;
5230: int vpopbased=0;
5231:
5232: char ca[32], cb[32], cc[32];
5233: /* FILE *fichtm; *//* Html File */
5234: /* FILE *ficgp;*/ /*Gnuplot File */
5235: struct stat info;
5236: double agedeb, agefin,hf;
5237: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5238:
5239: double fret;
5240: double **xi,tmp,delta;
5241:
5242: double dum; /* Dummy variable */
5243: double ***p3mat;
5244: double ***mobaverage;
5245: int *indx;
5246: char line[MAXLINE], linepar[MAXLINE];
5247: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5248: char pathr[MAXLINE], pathimach[MAXLINE];
5249: char **bp, *tok, *val; /* pathtot */
5250: int firstobs=1, lastobs=10;
5251: int sdeb, sfin; /* Status at beginning and end */
5252: int c, h , cpt,l;
5253: int ju,jl, mi;
5254: int i1,j1, jk,aa,bb, stepsize, ij;
5255: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5256: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5257: int mobilav=0,popforecast=0;
5258: int hstepm, nhstepm;
5259: int agemortsup;
5260: float sumlpop=0.;
5261: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5262: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5263:
5264: double bage, fage, age, agelim, agebase;
5265: double ftolpl=FTOL;
5266: double **prlim;
5267: double ***param; /* Matrix of parameters */
5268: double *p;
5269: double **matcov; /* Matrix of covariance */
5270: double ***delti3; /* Scale */
5271: double *delti; /* Scale */
5272: double ***eij, ***vareij;
5273: double **varpl; /* Variances of prevalence limits by age */
5274: double *epj, vepp;
5275: double kk1, kk2;
5276: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5277: double **ximort;
5278: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5279: int *dcwave;
5280:
5281: char z[1]="c", occ;
5282:
5283: /*char *strt;*/
5284: char strtend[80];
5285:
5286: long total_usecs;
5287:
5288: /* setlocale (LC_ALL, ""); */
5289: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5290: /* textdomain (PACKAGE); */
5291: /* setlocale (LC_CTYPE, ""); */
5292: /* setlocale (LC_MESSAGES, ""); */
5293:
5294: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5295: (void) gettimeofday(&start_time,&tzp);
5296: curr_time=start_time;
5297: tm = *localtime(&start_time.tv_sec);
5298: tmg = *gmtime(&start_time.tv_sec);
5299: strcpy(strstart,asctime(&tm));
5300:
5301: /* printf("Localtime (at start)=%s",strstart); */
5302: /* tp.tv_sec = tp.tv_sec +86400; */
5303: /* tm = *localtime(&start_time.tv_sec); */
5304: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5305: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5306: /* tmg.tm_hour=tmg.tm_hour + 1; */
5307: /* tp.tv_sec = mktime(&tmg); */
5308: /* strt=asctime(&tmg); */
5309: /* printf("Time(after) =%s",strstart); */
5310: /* (void) time (&time_value);
5311: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5312: * tm = *localtime(&time_value);
5313: * strstart=asctime(&tm);
5314: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5315: */
5316:
5317: nberr=0; /* Number of errors and warnings */
5318: nbwarn=0;
5319: getcwd(pathcd, size);
5320:
5321: printf("\n%s\n%s",version,fullversion);
5322: if(argc <=1){
5323: printf("\nEnter the parameter file name: ");
5324: fgets(pathr,FILENAMELENGTH,stdin);
5325: i=strlen(pathr);
5326: if(pathr[i-1]=='\n')
5327: pathr[i-1]='\0';
5328: for (tok = pathr; tok != NULL; ){
5329: printf("Pathr |%s|\n",pathr);
5330: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5331: printf("val= |%s| pathr=%s\n",val,pathr);
5332: strcpy (pathtot, val);
5333: if(pathr[0] == '\0') break; /* Dirty */
5334: }
5335: }
5336: else{
5337: strcpy(pathtot,argv[1]);
5338: }
5339: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5340: /*cygwin_split_path(pathtot,path,optionfile);
5341: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5342: /* cutv(path,optionfile,pathtot,'\\');*/
5343:
5344: /* Split argv[0], imach program to get pathimach */
5345: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5346: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5347: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5348: /* strcpy(pathimach,argv[0]); */
5349: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5350: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5351: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5352: chdir(path); /* Can be a relative path */
5353: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5354: printf("Current directory %s!\n",pathcd);
5355: strcpy(command,"mkdir ");
5356: strcat(command,optionfilefiname);
5357: if((outcmd=system(command)) != 0){
5358: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5359: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5360: /* fclose(ficlog); */
5361: /* exit(1); */
5362: }
5363: /* if((imk=mkdir(optionfilefiname))<0){ */
5364: /* perror("mkdir"); */
5365: /* } */
5366:
5367: /*-------- arguments in the command line --------*/
5368:
5369: /* Log file */
5370: strcat(filelog, optionfilefiname);
5371: strcat(filelog,".log"); /* */
5372: if((ficlog=fopen(filelog,"w"))==NULL) {
5373: printf("Problem with logfile %s\n",filelog);
5374: goto end;
5375: }
5376: fprintf(ficlog,"Log filename:%s\n",filelog);
5377: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5378: fprintf(ficlog,"\nEnter the parameter file name: \n");
5379: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5380: path=%s \n\
5381: optionfile=%s\n\
5382: optionfilext=%s\n\
5383: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5384:
5385: printf("Local time (at start):%s",strstart);
5386: fprintf(ficlog,"Local time (at start): %s",strstart);
5387: fflush(ficlog);
5388: /* (void) gettimeofday(&curr_time,&tzp); */
5389: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5390:
5391: /* */
5392: strcpy(fileres,"r");
5393: strcat(fileres, optionfilefiname);
5394: strcat(fileres,".txt"); /* Other files have txt extension */
5395:
5396: /*---------arguments file --------*/
5397:
5398: if((ficpar=fopen(optionfile,"r"))==NULL) {
5399: printf("Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
5400: fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
5401: fflush(ficlog);
5402: /* goto end; */
5403: exit(70);
5404: }
5405:
5406:
5407:
5408: strcpy(filereso,"o");
5409: strcat(filereso,fileres);
5410: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5411: printf("Problem with Output resultfile: %s\n", filereso);
5412: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5413: fflush(ficlog);
5414: goto end;
5415: }
5416:
5417: /* Reads comments: lines beginning with '#' */
5418: numlinepar=0;
5419: while((c=getc(ficpar))=='#' && c!= EOF){
5420: ungetc(c,ficpar);
5421: fgets(line, MAXLINE, ficpar);
5422: numlinepar++;
5423: fputs(line,stdout);
5424: fputs(line,ficparo);
5425: fputs(line,ficlog);
5426: }
5427: ungetc(c,ficpar);
5428:
5429: 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);
5430: numlinepar++;
5431: 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);
5432: 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);
5433: 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);
5434: fflush(ficlog);
5435: while((c=getc(ficpar))=='#' && c!= EOF){
5436: ungetc(c,ficpar);
5437: fgets(line, MAXLINE, ficpar);
5438: numlinepar++;
5439: fputs(line, stdout);
5440: //puts(line);
5441: fputs(line,ficparo);
5442: fputs(line,ficlog);
5443: }
5444: ungetc(c,ficpar);
5445:
5446:
5447: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5448: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5449: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5450: v1+v2*age+v2*v3 makes cptcovn = 3
5451: */
5452: if (strlen(model)>1)
5453: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
5454: else
5455: ncovmodel=2;
5456: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5457: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5458: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5459: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5460: 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);
5461: 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);
5462: fflush(stdout);
5463: fclose (ficlog);
5464: goto end;
5465: }
5466: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5467: delti=delti3[1][1];
5468: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5469: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5470: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5471: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5472: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5473: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5474: fclose (ficparo);
5475: fclose (ficlog);
5476: goto end;
5477: exit(0);
5478: }
5479: else if(mle==-3) {
5480: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5481: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5482: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5483: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5484: matcov=matrix(1,npar,1,npar);
5485: }
5486: else{
5487: /* Read guessed parameters */
5488: /* Reads comments: lines beginning with '#' */
5489: while((c=getc(ficpar))=='#' && c!= EOF){
5490: ungetc(c,ficpar);
5491: fgets(line, MAXLINE, ficpar);
5492: numlinepar++;
5493: fputs(line,stdout);
5494: fputs(line,ficparo);
5495: fputs(line,ficlog);
5496: }
5497: ungetc(c,ficpar);
5498:
5499: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5500: for(i=1; i <=nlstate; i++){
5501: j=0;
5502: for(jj=1; jj <=nlstate+ndeath; jj++){
5503: if(jj==i) continue;
5504: j++;
5505: fscanf(ficpar,"%1d%1d",&i1,&j1);
5506: if ((i1 != i) && (j1 != j)){
5507: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5508: It might be a problem of design; if ncovcol and the model are correct\n \
5509: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5510: exit(1);
5511: }
5512: fprintf(ficparo,"%1d%1d",i1,j1);
5513: if(mle==1)
5514: printf("%1d%1d",i,j);
5515: fprintf(ficlog,"%1d%1d",i,j);
5516: for(k=1; k<=ncovmodel;k++){
5517: fscanf(ficpar," %lf",¶m[i][j][k]);
5518: if(mle==1){
5519: printf(" %lf",param[i][j][k]);
5520: fprintf(ficlog," %lf",param[i][j][k]);
5521: }
5522: else
5523: fprintf(ficlog," %lf",param[i][j][k]);
5524: fprintf(ficparo," %lf",param[i][j][k]);
5525: }
5526: fscanf(ficpar,"\n");
5527: numlinepar++;
5528: if(mle==1)
5529: printf("\n");
5530: fprintf(ficlog,"\n");
5531: fprintf(ficparo,"\n");
5532: }
5533: }
5534: fflush(ficlog);
5535:
5536: /* Reads scales values */
5537: p=param[1][1];
5538:
5539: /* Reads comments: lines beginning with '#' */
5540: while((c=getc(ficpar))=='#' && c!= EOF){
5541: ungetc(c,ficpar);
5542: fgets(line, MAXLINE, ficpar);
5543: numlinepar++;
5544: fputs(line,stdout);
5545: fputs(line,ficparo);
5546: fputs(line,ficlog);
5547: }
5548: ungetc(c,ficpar);
5549:
5550: for(i=1; i <=nlstate; i++){
5551: for(j=1; j <=nlstate+ndeath-1; j++){
5552: fscanf(ficpar,"%1d%1d",&i1,&j1);
5553: if ((i1-i)*(j1-j)!=0){
5554: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5555: exit(1);
5556: }
5557: printf("%1d%1d",i,j);
5558: fprintf(ficparo,"%1d%1d",i1,j1);
5559: fprintf(ficlog,"%1d%1d",i1,j1);
5560: for(k=1; k<=ncovmodel;k++){
5561: fscanf(ficpar,"%le",&delti3[i][j][k]);
5562: printf(" %le",delti3[i][j][k]);
5563: fprintf(ficparo," %le",delti3[i][j][k]);
5564: fprintf(ficlog," %le",delti3[i][j][k]);
5565: }
5566: fscanf(ficpar,"\n");
5567: numlinepar++;
5568: printf("\n");
5569: fprintf(ficparo,"\n");
5570: fprintf(ficlog,"\n");
5571: }
5572: }
5573: fflush(ficlog);
5574:
5575: /* Reads covariance matrix */
5576: delti=delti3[1][1];
5577:
5578:
5579: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5580:
5581: /* Reads comments: lines beginning with '#' */
5582: while((c=getc(ficpar))=='#' && c!= EOF){
5583: ungetc(c,ficpar);
5584: fgets(line, MAXLINE, ficpar);
5585: numlinepar++;
5586: fputs(line,stdout);
5587: fputs(line,ficparo);
5588: fputs(line,ficlog);
5589: }
5590: ungetc(c,ficpar);
5591:
5592: matcov=matrix(1,npar,1,npar);
5593: for(i=1; i <=npar; i++)
5594: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5595:
5596: for(i=1; i <=npar; i++){
5597: fscanf(ficpar,"%s",str);
5598: if(mle==1)
5599: printf("%s",str);
5600: fprintf(ficlog,"%s",str);
5601: fprintf(ficparo,"%s",str);
5602: for(j=1; j <=i; j++){
5603: fscanf(ficpar," %le",&matcov[i][j]);
5604: if(mle==1){
5605: printf(" %.5le",matcov[i][j]);
5606: }
5607: fprintf(ficlog," %.5le",matcov[i][j]);
5608: fprintf(ficparo," %.5le",matcov[i][j]);
5609: }
5610: fscanf(ficpar,"\n");
5611: numlinepar++;
5612: if(mle==1)
5613: printf("\n");
5614: fprintf(ficlog,"\n");
5615: fprintf(ficparo,"\n");
5616: }
5617: for(i=1; i <=npar; i++)
5618: for(j=i+1;j<=npar;j++)
5619: matcov[i][j]=matcov[j][i];
5620:
5621: if(mle==1)
5622: printf("\n");
5623: fprintf(ficlog,"\n");
5624:
5625: fflush(ficlog);
5626:
5627: /*-------- Rewriting parameter file ----------*/
5628: strcpy(rfileres,"r"); /* "Rparameterfile */
5629: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5630: strcat(rfileres,"."); /* */
5631: strcat(rfileres,optionfilext); /* Other files have txt extension */
5632: if((ficres =fopen(rfileres,"w"))==NULL) {
5633: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5634: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5635: }
5636: fprintf(ficres,"#%s\n",version);
5637: } /* End of mle != -3 */
5638:
5639:
5640: n= lastobs;
5641: num=lvector(1,n);
5642: moisnais=vector(1,n);
5643: annais=vector(1,n);
5644: moisdc=vector(1,n);
5645: andc=vector(1,n);
5646: agedc=vector(1,n);
5647: cod=ivector(1,n);
5648: weight=vector(1,n);
5649: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5650: mint=matrix(1,maxwav,1,n);
5651: anint=matrix(1,maxwav,1,n);
5652: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5653: tab=ivector(1,NCOVMAX);
5654: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5655:
5656: /* Reads data from file datafile */
5657: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5658: goto end;
5659:
5660: /* Calculation of the number of parameters from char model */
5661: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5662: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5663: k=3 V4 Tvar[k=3]= 4 (from V4)
5664: k=2 V1 Tvar[k=2]= 1 (from V1)
5665: k=1 Tvar[1]=2 (from V2)
5666: */
5667: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5668: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5669: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5670: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5671: */
5672: /* For model-covariate k tells which data-covariate to use but
5673: because this model-covariate is a construction we invent a new column
5674: ncovcol + k1
5675: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5676: Tvar[3=V1*V4]=4+1 etc */
5677: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5678: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5679: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5680: */
5681: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5682: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
5683: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5684: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5685: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5686: 4 covariates (3 plus signs)
5687: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5688: */
5689:
5690: if(decodemodel(model, lastobs) == 1)
5691: goto end;
5692:
5693: if((double)(lastobs-imx)/(double)imx > 1.10){
5694: nbwarn++;
5695: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5696: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5697: }
5698: /* if(mle==1){*/
5699: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5700: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5701: }
5702:
5703: /*-calculation of age at interview from date of interview and age at death -*/
5704: agev=matrix(1,maxwav,1,imx);
5705:
5706: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5707: goto end;
5708:
5709:
5710: agegomp=(int)agemin;
5711: free_vector(moisnais,1,n);
5712: free_vector(annais,1,n);
5713: /* free_matrix(mint,1,maxwav,1,n);
5714: free_matrix(anint,1,maxwav,1,n);*/
5715: free_vector(moisdc,1,n);
5716: free_vector(andc,1,n);
5717: /* */
5718:
5719: wav=ivector(1,imx);
5720: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5721: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5722: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5723:
5724: /* Concatenates waves */
5725: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5726: /* */
5727:
5728: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5729:
5730: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5731: ncodemax[1]=1;
5732: Ndum =ivector(-1,NCOVMAX);
5733: if (ncovmodel > 2)
5734: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5735:
5736: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5737: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5738: h=0;
5739:
5740:
5741: /*if (cptcovn > 0) */
5742:
5743:
5744: m=pow(2,cptcoveff);
5745:
5746: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5747: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5748: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5749: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5750: h++;
5751: if (h>m)
5752: h=1;
5753: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5754: * h 1 2 3 4
5755: *______________________________
5756: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5757: * 2 2 1 1 1
5758: * 3 i=2 1 2 1 1
5759: * 4 2 2 1 1
5760: * 5 i=3 1 i=2 1 2 1
5761: * 6 2 1 2 1
5762: * 7 i=4 1 2 2 1
5763: * 8 2 2 2 1
5764: * 9 i=5 1 i=3 1 i=2 1 1
5765: * 10 2 1 1 1
5766: * 11 i=6 1 2 1 1
5767: * 12 2 2 1 1
5768: * 13 i=7 1 i=4 1 2 1
5769: * 14 2 1 2 1
5770: * 15 i=8 1 2 2 1
5771: * 16 2 2 2 1
5772: */
5773: codtab[h][k]=j;
5774: /*codtab[h][Tvar[k]]=j;*/
5775: 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]]);
5776: }
5777: }
5778: }
5779: }
5780: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5781: codtab[1][2]=1;codtab[2][2]=2; */
5782: /* for(i=1; i <=m ;i++){
5783: for(k=1; k <=cptcovn; k++){
5784: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5785: }
5786: printf("\n");
5787: }
5788: scanf("%d",i);*/
5789:
5790: free_ivector(Ndum,-1,NCOVMAX);
5791:
5792:
5793:
5794: /*------------ gnuplot -------------*/
5795: strcpy(optionfilegnuplot,optionfilefiname);
5796: if(mle==-3)
5797: strcat(optionfilegnuplot,"-mort");
5798: strcat(optionfilegnuplot,".gp");
5799:
5800: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5801: printf("Problem with file %s",optionfilegnuplot);
5802: }
5803: else{
5804: fprintf(ficgp,"\n# %s\n", version);
5805: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5806: //fprintf(ficgp,"set missing 'NaNq'\n");
5807: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5808: }
5809: /* fclose(ficgp);*/
5810: /*--------- index.htm --------*/
5811:
5812: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5813: if(mle==-3)
5814: strcat(optionfilehtm,"-mort");
5815: strcat(optionfilehtm,".htm");
5816: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5817: printf("Problem with %s \n",optionfilehtm);
5818: exit(0);
5819: }
5820:
5821: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5822: strcat(optionfilehtmcov,"-cov.htm");
5823: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5824: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5825: }
5826: else{
5827: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5828: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5829: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5830: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5831: }
5832:
5833: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5834: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5835: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5836: \n\
5837: <hr size=\"2\" color=\"#EC5E5E\">\
5838: <ul><li><h4>Parameter files</h4>\n\
5839: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5840: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5841: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5842: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5843: - Date and time at start: %s</ul>\n",\
5844: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5845: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5846: fileres,fileres,\
5847: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5848: fflush(fichtm);
5849:
5850: strcpy(pathr,path);
5851: strcat(pathr,optionfilefiname);
5852: chdir(optionfilefiname); /* Move to directory named optionfile */
5853:
5854: /* Calculates basic frequencies. Computes observed prevalence at single age
5855: and prints on file fileres'p'. */
5856: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5857:
5858: fprintf(fichtm,"\n");
5859: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5860: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5861: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5862: imx,agemin,agemax,jmin,jmax,jmean);
5863: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5864: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5865: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5866: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5867: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5868:
5869:
5870: /* For Powell, parameters are in a vector p[] starting at p[1]
5871: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5872: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5873:
5874: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5875:
5876: if (mle==-3){
5877: ximort=matrix(1,NDIM,1,NDIM);
5878: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5879: cens=ivector(1,n);
5880: ageexmed=vector(1,n);
5881: agecens=vector(1,n);
5882: dcwave=ivector(1,n);
5883:
5884: for (i=1; i<=imx; i++){
5885: dcwave[i]=-1;
5886: for (m=firstpass; m<=lastpass; m++)
5887: if (s[m][i]>nlstate) {
5888: dcwave[i]=m;
5889: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5890: break;
5891: }
5892: }
5893:
5894: for (i=1; i<=imx; i++) {
5895: if (wav[i]>0){
5896: ageexmed[i]=agev[mw[1][i]][i];
5897: j=wav[i];
5898: agecens[i]=1.;
5899:
5900: if (ageexmed[i]> 1 && wav[i] > 0){
5901: agecens[i]=agev[mw[j][i]][i];
5902: cens[i]= 1;
5903: }else if (ageexmed[i]< 1)
5904: cens[i]= -1;
5905: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5906: cens[i]=0 ;
5907: }
5908: else cens[i]=-1;
5909: }
5910:
5911: for (i=1;i<=NDIM;i++) {
5912: for (j=1;j<=NDIM;j++)
5913: ximort[i][j]=(i == j ? 1.0 : 0.0);
5914: }
5915:
5916: /*p[1]=0.0268; p[NDIM]=0.083;*/
5917: /*printf("%lf %lf", p[1], p[2]);*/
5918:
5919:
5920: #ifdef GSL
5921: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5922: #elsedef
5923: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5924: #endif
5925: strcpy(filerespow,"pow-mort");
5926: strcat(filerespow,fileres);
5927: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5928: printf("Problem with resultfile: %s\n", filerespow);
5929: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5930: }
5931: #ifdef GSL
5932: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5933: #elsedef
5934: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5935: #endif
5936: /* for (i=1;i<=nlstate;i++)
5937: for(j=1;j<=nlstate+ndeath;j++)
5938: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5939: */
5940: fprintf(ficrespow,"\n");
5941: #ifdef GSL
5942: /* gsl starts here */
5943: T = gsl_multimin_fminimizer_nmsimplex;
5944: gsl_multimin_fminimizer *sfm = NULL;
5945: gsl_vector *ss, *x;
5946: gsl_multimin_function minex_func;
5947:
5948: /* Initial vertex size vector */
5949: ss = gsl_vector_alloc (NDIM);
5950:
5951: if (ss == NULL){
5952: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5953: }
5954: /* Set all step sizes to 1 */
5955: gsl_vector_set_all (ss, 0.001);
5956:
5957: /* Starting point */
5958:
5959: x = gsl_vector_alloc (NDIM);
5960:
5961: if (x == NULL){
5962: gsl_vector_free(ss);
5963: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5964: }
5965:
5966: /* Initialize method and iterate */
5967: /* p[1]=0.0268; p[NDIM]=0.083; */
5968: /* gsl_vector_set(x, 0, 0.0268); */
5969: /* gsl_vector_set(x, 1, 0.083); */
5970: gsl_vector_set(x, 0, p[1]);
5971: gsl_vector_set(x, 1, p[2]);
5972:
5973: minex_func.f = &gompertz_f;
5974: minex_func.n = NDIM;
5975: minex_func.params = (void *)&p; /* ??? */
5976:
5977: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5978: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5979:
5980: printf("Iterations beginning .....\n\n");
5981: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5982:
5983: iteri=0;
5984: while (rval == GSL_CONTINUE){
5985: iteri++;
5986: status = gsl_multimin_fminimizer_iterate(sfm);
5987:
5988: if (status) printf("error: %s\n", gsl_strerror (status));
5989: fflush(0);
5990:
5991: if (status)
5992: break;
5993:
5994: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5995: ssval = gsl_multimin_fminimizer_size (sfm);
5996:
5997: if (rval == GSL_SUCCESS)
5998: printf ("converged to a local maximum at\n");
5999:
6000: printf("%5d ", iteri);
6001: for (it = 0; it < NDIM; it++){
6002: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6003: }
6004: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6005: }
6006:
6007: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6008:
6009: gsl_vector_free(x); /* initial values */
6010: gsl_vector_free(ss); /* inital step size */
6011: for (it=0; it<NDIM; it++){
6012: p[it+1]=gsl_vector_get(sfm->x,it);
6013: fprintf(ficrespow," %.12lf", p[it]);
6014: }
6015: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6016: #endif
6017: #ifdef POWELL
6018: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6019: #endif
6020: fclose(ficrespow);
6021:
6022: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6023:
6024: for(i=1; i <=NDIM; i++)
6025: for(j=i+1;j<=NDIM;j++)
6026: matcov[i][j]=matcov[j][i];
6027:
6028: printf("\nCovariance matrix\n ");
6029: for(i=1; i <=NDIM; i++) {
6030: for(j=1;j<=NDIM;j++){
6031: printf("%f ",matcov[i][j]);
6032: }
6033: printf("\n ");
6034: }
6035:
6036: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6037: for (i=1;i<=NDIM;i++)
6038: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6039:
6040: lsurv=vector(1,AGESUP);
6041: lpop=vector(1,AGESUP);
6042: tpop=vector(1,AGESUP);
6043: lsurv[agegomp]=100000;
6044:
6045: for (k=agegomp;k<=AGESUP;k++) {
6046: agemortsup=k;
6047: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6048: }
6049:
6050: for (k=agegomp;k<agemortsup;k++)
6051: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6052:
6053: for (k=agegomp;k<agemortsup;k++){
6054: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6055: sumlpop=sumlpop+lpop[k];
6056: }
6057:
6058: tpop[agegomp]=sumlpop;
6059: for (k=agegomp;k<(agemortsup-3);k++){
6060: /* tpop[k+1]=2;*/
6061: tpop[k+1]=tpop[k]-lpop[k];
6062: }
6063:
6064:
6065: printf("\nAge lx qx dx Lx Tx e(x)\n");
6066: for (k=agegomp;k<(agemortsup-2);k++)
6067: 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]);
6068:
6069:
6070: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6071: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6072:
6073: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6074: stepm, weightopt,\
6075: model,imx,p,matcov,agemortsup);
6076:
6077: free_vector(lsurv,1,AGESUP);
6078: free_vector(lpop,1,AGESUP);
6079: free_vector(tpop,1,AGESUP);
6080: #ifdef GSL
6081: free_ivector(cens,1,n);
6082: free_vector(agecens,1,n);
6083: free_ivector(dcwave,1,n);
6084: free_matrix(ximort,1,NDIM,1,NDIM);
6085: #endif
6086: } /* Endof if mle==-3 */
6087:
6088: else{ /* For mle >=1 */
6089: globpr=0;/* debug */
6090: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6091: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6092: for (k=1; k<=npar;k++)
6093: printf(" %d %8.5f",k,p[k]);
6094: printf("\n");
6095: globpr=1; /* to print the contributions */
6096: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6097: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6098: for (k=1; k<=npar;k++)
6099: printf(" %d %8.5f",k,p[k]);
6100: printf("\n");
6101: if(mle>=1){ /* Could be 1 or 2 */
6102: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6103: }
6104:
6105: /*--------- results files --------------*/
6106: 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);
6107:
6108:
6109: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6110: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6111: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6112: for(i=1,jk=1; i <=nlstate; i++){
6113: for(k=1; k <=(nlstate+ndeath); k++){
6114: if (k != i) {
6115: printf("%d%d ",i,k);
6116: fprintf(ficlog,"%d%d ",i,k);
6117: fprintf(ficres,"%1d%1d ",i,k);
6118: for(j=1; j <=ncovmodel; j++){
6119: printf("%lf ",p[jk]);
6120: fprintf(ficlog,"%lf ",p[jk]);
6121: fprintf(ficres,"%lf ",p[jk]);
6122: jk++;
6123: }
6124: printf("\n");
6125: fprintf(ficlog,"\n");
6126: fprintf(ficres,"\n");
6127: }
6128: }
6129: }
6130: if(mle!=0){
6131: /* Computing hessian and covariance matrix */
6132: ftolhess=ftol; /* Usually correct */
6133: hesscov(matcov, p, npar, delti, ftolhess, func);
6134: }
6135: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6136: printf("# Scales (for hessian or gradient estimation)\n");
6137: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6138: for(i=1,jk=1; i <=nlstate; i++){
6139: for(j=1; j <=nlstate+ndeath; j++){
6140: if (j!=i) {
6141: fprintf(ficres,"%1d%1d",i,j);
6142: printf("%1d%1d",i,j);
6143: fprintf(ficlog,"%1d%1d",i,j);
6144: for(k=1; k<=ncovmodel;k++){
6145: printf(" %.5e",delti[jk]);
6146: fprintf(ficlog," %.5e",delti[jk]);
6147: fprintf(ficres," %.5e",delti[jk]);
6148: jk++;
6149: }
6150: printf("\n");
6151: fprintf(ficlog,"\n");
6152: fprintf(ficres,"\n");
6153: }
6154: }
6155: }
6156:
6157: 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");
6158: if(mle>=1)
6159: 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");
6160: 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");
6161: /* # 121 Var(a12)\n\ */
6162: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6163: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6164: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6165: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6166: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6167: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6168: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6169:
6170:
6171: /* Just to have a covariance matrix which will be more understandable
6172: even is we still don't want to manage dictionary of variables
6173: */
6174: for(itimes=1;itimes<=2;itimes++){
6175: jj=0;
6176: for(i=1; i <=nlstate; i++){
6177: for(j=1; j <=nlstate+ndeath; j++){
6178: if(j==i) continue;
6179: for(k=1; k<=ncovmodel;k++){
6180: jj++;
6181: ca[0]= k+'a'-1;ca[1]='\0';
6182: if(itimes==1){
6183: if(mle>=1)
6184: printf("#%1d%1d%d",i,j,k);
6185: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6186: fprintf(ficres,"#%1d%1d%d",i,j,k);
6187: }else{
6188: if(mle>=1)
6189: printf("%1d%1d%d",i,j,k);
6190: fprintf(ficlog,"%1d%1d%d",i,j,k);
6191: fprintf(ficres,"%1d%1d%d",i,j,k);
6192: }
6193: ll=0;
6194: for(li=1;li <=nlstate; li++){
6195: for(lj=1;lj <=nlstate+ndeath; lj++){
6196: if(lj==li) continue;
6197: for(lk=1;lk<=ncovmodel;lk++){
6198: ll++;
6199: if(ll<=jj){
6200: cb[0]= lk +'a'-1;cb[1]='\0';
6201: if(ll<jj){
6202: if(itimes==1){
6203: if(mle>=1)
6204: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6205: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6206: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6207: }else{
6208: if(mle>=1)
6209: printf(" %.5e",matcov[jj][ll]);
6210: fprintf(ficlog," %.5e",matcov[jj][ll]);
6211: fprintf(ficres," %.5e",matcov[jj][ll]);
6212: }
6213: }else{
6214: if(itimes==1){
6215: if(mle>=1)
6216: printf(" Var(%s%1d%1d)",ca,i,j);
6217: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6218: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6219: }else{
6220: if(mle>=1)
6221: printf(" %.5e",matcov[jj][ll]);
6222: fprintf(ficlog," %.5e",matcov[jj][ll]);
6223: fprintf(ficres," %.5e",matcov[jj][ll]);
6224: }
6225: }
6226: }
6227: } /* end lk */
6228: } /* end lj */
6229: } /* end li */
6230: if(mle>=1)
6231: printf("\n");
6232: fprintf(ficlog,"\n");
6233: fprintf(ficres,"\n");
6234: numlinepar++;
6235: } /* end k*/
6236: } /*end j */
6237: } /* end i */
6238: } /* end itimes */
6239:
6240: fflush(ficlog);
6241: fflush(ficres);
6242:
6243: while((c=getc(ficpar))=='#' && c!= EOF){
6244: ungetc(c,ficpar);
6245: fgets(line, MAXLINE, ficpar);
6246: fputs(line,stdout);
6247: fputs(line,ficparo);
6248: }
6249: ungetc(c,ficpar);
6250:
6251: estepm=0;
6252: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6253: if (estepm==0 || estepm < stepm) estepm=stepm;
6254: if (fage <= 2) {
6255: bage = ageminpar;
6256: fage = agemaxpar;
6257: }
6258:
6259: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6260: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6261: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6262:
6263: while((c=getc(ficpar))=='#' && c!= EOF){
6264: ungetc(c,ficpar);
6265: fgets(line, MAXLINE, ficpar);
6266: fputs(line,stdout);
6267: fputs(line,ficparo);
6268: }
6269: ungetc(c,ficpar);
6270:
6271: 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);
6272: 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);
6273: 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);
6274: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6275: 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);
6276:
6277: while((c=getc(ficpar))=='#' && c!= EOF){
6278: ungetc(c,ficpar);
6279: fgets(line, MAXLINE, ficpar);
6280: fputs(line,stdout);
6281: fputs(line,ficparo);
6282: }
6283: ungetc(c,ficpar);
6284:
6285:
6286: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6287: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6288:
6289: fscanf(ficpar,"pop_based=%d\n",&popbased);
6290: fprintf(ficparo,"pop_based=%d\n",popbased);
6291: fprintf(ficres,"pop_based=%d\n",popbased);
6292:
6293: while((c=getc(ficpar))=='#' && c!= EOF){
6294: ungetc(c,ficpar);
6295: fgets(line, MAXLINE, ficpar);
6296: fputs(line,stdout);
6297: fputs(line,ficparo);
6298: }
6299: ungetc(c,ficpar);
6300:
6301: 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);
6302: 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);
6303: 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);
6304: 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);
6305: 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);
6306: /* day and month of proj2 are not used but only year anproj2.*/
6307:
6308:
6309:
6310: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6311: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6312:
6313: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6314: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6315:
6316: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6317: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6318: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6319:
6320: /*------------ free_vector -------------*/
6321: /* chdir(path); */
6322:
6323: free_ivector(wav,1,imx);
6324: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6325: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6326: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6327: free_lvector(num,1,n);
6328: free_vector(agedc,1,n);
6329: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6330: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6331: fclose(ficparo);
6332: fclose(ficres);
6333:
6334:
6335: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6336: #include "prevlim.h" /* Use ficrespl, ficlog */
6337: fclose(ficrespl);
6338:
6339: #ifdef FREEEXIT2
6340: #include "freeexit2.h"
6341: #endif
6342:
6343: /*------------- h Pij x at various ages ------------*/
6344: #include "hpijx.h"
6345: fclose(ficrespij);
6346:
6347: /*-------------- Variance of one-step probabilities---*/
6348: k=1;
6349: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6350:
6351:
6352: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6353: for(i=1;i<=AGESUP;i++)
6354: for(j=1;j<=NCOVMAX;j++)
6355: for(k=1;k<=NCOVMAX;k++)
6356: probs[i][j][k]=0.;
6357:
6358: /*---------- Forecasting ------------------*/
6359: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6360: if(prevfcast==1){
6361: /* if(stepm ==1){*/
6362: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6363: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6364: /* } */
6365: /* else{ */
6366: /* erreur=108; */
6367: /* 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); */
6368: /* 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); */
6369: /* } */
6370: }
6371:
6372:
6373: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6374:
6375: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6376: /* 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",\
6377: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6378: */
6379:
6380: if (mobilav!=0) {
6381: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6382: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6383: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6384: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6385: }
6386: }
6387:
6388:
6389: /*---------- Health expectancies, no variances ------------*/
6390:
6391: strcpy(filerese,"e");
6392: strcat(filerese,fileres);
6393: if((ficreseij=fopen(filerese,"w"))==NULL) {
6394: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6395: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6396: }
6397: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6398: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6399: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6400: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6401:
6402: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6403: fprintf(ficreseij,"\n#****** ");
6404: for(j=1;j<=cptcoveff;j++) {
6405: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6406: }
6407: fprintf(ficreseij,"******\n");
6408:
6409: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6410: oldm=oldms;savm=savms;
6411: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6412:
6413: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6414: /*}*/
6415: }
6416: fclose(ficreseij);
6417:
6418:
6419: /*---------- Health expectancies and variances ------------*/
6420:
6421:
6422: strcpy(filerest,"t");
6423: strcat(filerest,fileres);
6424: if((ficrest=fopen(filerest,"w"))==NULL) {
6425: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6426: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6427: }
6428: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6429: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6430:
6431:
6432: strcpy(fileresstde,"stde");
6433: strcat(fileresstde,fileres);
6434: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6435: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6436: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6437: }
6438: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6439: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6440:
6441: strcpy(filerescve,"cve");
6442: strcat(filerescve,fileres);
6443: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6444: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6445: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6446: }
6447: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6448: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6449:
6450: strcpy(fileresv,"v");
6451: strcat(fileresv,fileres);
6452: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6453: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6454: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6455: }
6456: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6457: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6458:
6459: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6460: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6461:
6462: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6463: fprintf(ficrest,"\n#****** ");
6464: for(j=1;j<=cptcoveff;j++)
6465: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6466: fprintf(ficrest,"******\n");
6467:
6468: fprintf(ficresstdeij,"\n#****** ");
6469: fprintf(ficrescveij,"\n#****** ");
6470: for(j=1;j<=cptcoveff;j++) {
6471: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6472: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6473: }
6474: fprintf(ficresstdeij,"******\n");
6475: fprintf(ficrescveij,"******\n");
6476:
6477: fprintf(ficresvij,"\n#****** ");
6478: for(j=1;j<=cptcoveff;j++)
6479: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6480: fprintf(ficresvij,"******\n");
6481:
6482: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6483: oldm=oldms;savm=savms;
6484: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6485: /*
6486: */
6487: /* goto endfree; */
6488:
6489: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6490: pstamp(ficrest);
6491:
6492:
6493: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6494: oldm=oldms;savm=savms; /* Segmentation fault */
6495: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
6496: 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 ");
6497: if(vpopbased==1)
6498: 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);
6499: else
6500: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6501: fprintf(ficrest,"# Age e.. (std) ");
6502: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6503: fprintf(ficrest,"\n");
6504:
6505: epj=vector(1,nlstate+1);
6506: for(age=bage; age <=fage ;age++){
6507: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6508: if (vpopbased==1) {
6509: if(mobilav ==0){
6510: for(i=1; i<=nlstate;i++)
6511: prlim[i][i]=probs[(int)age][i][k];
6512: }else{ /* mobilav */
6513: for(i=1; i<=nlstate;i++)
6514: prlim[i][i]=mobaverage[(int)age][i][k];
6515: }
6516: }
6517:
6518: fprintf(ficrest," %4.0f",age);
6519: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6520: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6521: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6522: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6523: }
6524: epj[nlstate+1] +=epj[j];
6525: }
6526:
6527: for(i=1, vepp=0.;i <=nlstate;i++)
6528: for(j=1;j <=nlstate;j++)
6529: vepp += vareij[i][j][(int)age];
6530: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6531: for(j=1;j <=nlstate;j++){
6532: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6533: }
6534: fprintf(ficrest,"\n");
6535: }
6536: }
6537: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6538: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6539: free_vector(epj,1,nlstate+1);
6540: /*}*/
6541: }
6542: free_vector(weight,1,n);
6543: free_imatrix(Tvard,1,NCOVMAX,1,2);
6544: free_imatrix(s,1,maxwav+1,1,n);
6545: free_matrix(anint,1,maxwav,1,n);
6546: free_matrix(mint,1,maxwav,1,n);
6547: free_ivector(cod,1,n);
6548: free_ivector(tab,1,NCOVMAX);
6549: fclose(ficresstdeij);
6550: fclose(ficrescveij);
6551: fclose(ficresvij);
6552: fclose(ficrest);
6553: fclose(ficpar);
6554:
6555: /*------- Variance of period (stable) prevalence------*/
6556:
6557: strcpy(fileresvpl,"vpl");
6558: strcat(fileresvpl,fileres);
6559: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6560: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6561: exit(0);
6562: }
6563: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6564:
6565: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6566: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6567:
6568: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6569: fprintf(ficresvpl,"\n#****** ");
6570: for(j=1;j<=cptcoveff;j++)
6571: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6572: fprintf(ficresvpl,"******\n");
6573:
6574: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6575: oldm=oldms;savm=savms;
6576: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6577: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6578: /*}*/
6579: }
6580:
6581: fclose(ficresvpl);
6582:
6583: /*---------- End : free ----------------*/
6584: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6585: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6586: } /* mle==-3 arrives here for freeing */
6587: endfree:
6588: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6589: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6590: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6591: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6592: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6593: free_matrix(covar,0,NCOVMAX,1,n);
6594: free_matrix(matcov,1,npar,1,npar);
6595: /*free_vector(delti,1,npar);*/
6596: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6597: free_matrix(agev,1,maxwav,1,imx);
6598: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6599:
6600: free_ivector(ncodemax,1,NCOVMAX);
6601: free_ivector(Tvar,1,NCOVMAX);
6602: free_ivector(Tprod,1,NCOVMAX);
6603: free_ivector(Tvaraff,1,NCOVMAX);
6604: free_ivector(Tage,1,NCOVMAX);
6605:
6606: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6607: free_imatrix(codtab,1,100,1,10);
6608: fflush(fichtm);
6609: fflush(ficgp);
6610:
6611:
6612: if((nberr >0) || (nbwarn>0)){
6613: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6614: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6615: }else{
6616: printf("End of Imach\n");
6617: fprintf(ficlog,"End of Imach\n");
6618: }
6619: printf("See log file on %s\n",filelog);
6620: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6621: (void) gettimeofday(&end_time,&tzp);
6622: tm = *localtime(&end_time.tv_sec);
6623: tmg = *gmtime(&end_time.tv_sec);
6624: strcpy(strtend,asctime(&tm));
6625: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6626: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6627: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6628:
6629: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6630: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6631: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6632: /* printf("Total time was %d uSec.\n", total_usecs);*/
6633: /* if(fileappend(fichtm,optionfilehtm)){ */
6634: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6635: fclose(fichtm);
6636: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6637: fclose(fichtmcov);
6638: fclose(ficgp);
6639: fclose(ficlog);
6640: /*------ End -----------*/
6641:
6642:
6643: printf("Before Current directory %s!\n",pathcd);
6644: if(chdir(pathcd) != 0)
6645: printf("Can't move to directory %s!\n",path);
6646: if(getcwd(pathcd,MAXLINE) > 0)
6647: printf("Current directory %s!\n",pathcd);
6648: /*strcat(plotcmd,CHARSEPARATOR);*/
6649: sprintf(plotcmd,"gnuplot");
6650: #ifndef UNIX
6651: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6652: #endif
6653: if(!stat(plotcmd,&info)){
6654: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6655: if(!stat(getenv("GNUPLOTBIN"),&info)){
6656: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6657: }else
6658: strcpy(pplotcmd,plotcmd);
6659: #ifdef UNIX
6660: strcpy(plotcmd,GNUPLOTPROGRAM);
6661: if(!stat(plotcmd,&info)){
6662: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6663: }else
6664: strcpy(pplotcmd,plotcmd);
6665: #endif
6666: }else
6667: strcpy(pplotcmd,plotcmd);
6668:
6669: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6670: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6671:
6672: if((outcmd=system(plotcmd)) != 0){
6673: printf("\n Problem with gnuplot command %s\n", plotcmd);
6674: printf("\n Trying on same directory\n");
6675: sprintf(plotcmd,"./gnuplot %s", optionfilegnuplot);
6676: if((outcmd=system(plotcmd)) != 0)
6677: printf("\n Still a problem with gnuplot command %s\n", plotcmd);
6678: }
6679: printf(" Wait...");
6680: while (z[0] != 'q') {
6681: /* chdir(path); */
6682: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6683: scanf("%s",z);
6684: /* if (z[0] == 'c') system("./imach"); */
6685: if (z[0] == 'e') {
6686: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6687: system(optionfilehtm);
6688: }
6689: else if (z[0] == 'g') system(plotcmd);
6690: else if (z[0] == 'q') exit(0);
6691: }
6692: end:
6693: while (z[0] != 'q') {
6694: printf("\nType q for exiting: ");
6695: scanf("%s",z);
6696: }
6697: }
6698:
6699:
6700:
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