1: /* $Id: imach.c,v 1.156 2014/08/25 20:10:10 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.156 2014/08/25 20:10:10 brouard
5: *** empty log message ***
6:
7: Revision 1.155 2014/08/25 18:32:34 brouard
8: Summary: New compile, minor changes
9: Author: Brouard
10:
11: Revision 1.154 2014/06/20 17:32:08 brouard
12: Summary: Outputs now all graphs of convergence to period prevalence
13:
14: Revision 1.153 2014/06/20 16:45:46 brouard
15: Summary: If 3 live state, convergence to period prevalence on same graph
16: Author: Brouard
17:
18: Revision 1.152 2014/06/18 17:54:09 brouard
19: Summary: open browser, use gnuplot on same dir than imach if not found in the path
20:
21: Revision 1.151 2014/06/18 16:43:30 brouard
22: *** empty log message ***
23:
24: Revision 1.150 2014/06/18 16:42:35 brouard
25: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
26: Author: brouard
27:
28: Revision 1.149 2014/06/18 15:51:14 brouard
29: Summary: Some fixes in parameter files errors
30: Author: Nicolas Brouard
31:
32: Revision 1.148 2014/06/17 17:38:48 brouard
33: Summary: Nothing new
34: Author: Brouard
35:
36: Just a new packaging for OS/X version 0.98nS
37:
38: Revision 1.147 2014/06/16 10:33:11 brouard
39: *** empty log message ***
40:
41: Revision 1.146 2014/06/16 10:20:28 brouard
42: Summary: Merge
43: Author: Brouard
44:
45: Merge, before building revised version.
46:
47: Revision 1.145 2014/06/10 21:23:15 brouard
48: Summary: Debugging with valgrind
49: Author: Nicolas Brouard
50:
51: Lot of changes in order to output the results with some covariates
52: After the Edimburgh REVES conference 2014, it seems mandatory to
53: improve the code.
54: No more memory valgrind error but a lot has to be done in order to
55: continue the work of splitting the code into subroutines.
56: Also, decodemodel has been improved. Tricode is still not
57: optimal. nbcode should be improved. Documentation has been added in
58: the source code.
59:
60: Revision 1.143 2014/01/26 09:45:38 brouard
61: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
62:
63: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
64: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
65:
66: Revision 1.142 2014/01/26 03:57:36 brouard
67: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
68:
69: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
70:
71: Revision 1.141 2014/01/26 02:42:01 brouard
72: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
73:
74: Revision 1.140 2011/09/02 10:37:54 brouard
75: Summary: times.h is ok with mingw32 now.
76:
77: Revision 1.139 2010/06/14 07:50:17 brouard
78: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
79: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
80:
81: Revision 1.138 2010/04/30 18:19:40 brouard
82: *** empty log message ***
83:
84: Revision 1.137 2010/04/29 18:11:38 brouard
85: (Module): Checking covariates for more complex models
86: than V1+V2. A lot of change to be done. Unstable.
87:
88: Revision 1.136 2010/04/26 20:30:53 brouard
89: (Module): merging some libgsl code. Fixing computation
90: of likelione (using inter/intrapolation if mle = 0) in order to
91: get same likelihood as if mle=1.
92: Some cleaning of code and comments added.
93:
94: Revision 1.135 2009/10/29 15:33:14 brouard
95: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
96:
97: Revision 1.134 2009/10/29 13:18:53 brouard
98: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
99:
100: Revision 1.133 2009/07/06 10:21:25 brouard
101: just nforces
102:
103: Revision 1.132 2009/07/06 08:22:05 brouard
104: Many tings
105:
106: Revision 1.131 2009/06/20 16:22:47 brouard
107: Some dimensions resccaled
108:
109: Revision 1.130 2009/05/26 06:44:34 brouard
110: (Module): Max Covariate is now set to 20 instead of 8. A
111: lot of cleaning with variables initialized to 0. Trying to make
112: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
113:
114: Revision 1.129 2007/08/31 13:49:27 lievre
115: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
116:
117: Revision 1.128 2006/06/30 13:02:05 brouard
118: (Module): Clarifications on computing e.j
119:
120: Revision 1.127 2006/04/28 18:11:50 brouard
121: (Module): Yes the sum of survivors was wrong since
122: imach-114 because nhstepm was no more computed in the age
123: loop. Now we define nhstepma in the age loop.
124: (Module): In order to speed up (in case of numerous covariates) we
125: compute health expectancies (without variances) in a first step
126: and then all the health expectancies with variances or standard
127: deviation (needs data from the Hessian matrices) which slows the
128: computation.
129: In the future we should be able to stop the program is only health
130: expectancies and graph are needed without standard deviations.
131:
132: Revision 1.126 2006/04/28 17:23:28 brouard
133: (Module): Yes the sum of survivors was wrong since
134: imach-114 because nhstepm was no more computed in the age
135: loop. Now we define nhstepma in the age loop.
136: Version 0.98h
137:
138: Revision 1.125 2006/04/04 15:20:31 lievre
139: Errors in calculation of health expectancies. Age was not initialized.
140: Forecasting file added.
141:
142: Revision 1.124 2006/03/22 17:13:53 lievre
143: Parameters are printed with %lf instead of %f (more numbers after the comma).
144: The log-likelihood is printed in the log file
145:
146: Revision 1.123 2006/03/20 10:52:43 brouard
147: * imach.c (Module): <title> changed, corresponds to .htm file
148: name. <head> headers where missing.
149:
150: * imach.c (Module): Weights can have a decimal point as for
151: English (a comma might work with a correct LC_NUMERIC environment,
152: otherwise the weight is truncated).
153: Modification of warning when the covariates values are not 0 or
154: 1.
155: Version 0.98g
156:
157: Revision 1.122 2006/03/20 09:45:41 brouard
158: (Module): Weights can have a decimal point as for
159: English (a comma might work with a correct LC_NUMERIC environment,
160: otherwise the weight is truncated).
161: Modification of warning when the covariates values are not 0 or
162: 1.
163: Version 0.98g
164:
165: Revision 1.121 2006/03/16 17:45:01 lievre
166: * imach.c (Module): Comments concerning covariates added
167:
168: * imach.c (Module): refinements in the computation of lli if
169: status=-2 in order to have more reliable computation if stepm is
170: not 1 month. Version 0.98f
171:
172: Revision 1.120 2006/03/16 15:10:38 lievre
173: (Module): refinements in the computation of lli if
174: status=-2 in order to have more reliable computation if stepm is
175: not 1 month. Version 0.98f
176:
177: Revision 1.119 2006/03/15 17:42:26 brouard
178: (Module): Bug if status = -2, the loglikelihood was
179: computed as likelihood omitting the logarithm. Version O.98e
180:
181: Revision 1.118 2006/03/14 18:20:07 brouard
182: (Module): varevsij Comments added explaining the second
183: table of variances if popbased=1 .
184: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
185: (Module): Function pstamp added
186: (Module): Version 0.98d
187:
188: Revision 1.117 2006/03/14 17:16:22 brouard
189: (Module): varevsij Comments added explaining the second
190: table of variances if popbased=1 .
191: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
192: (Module): Function pstamp added
193: (Module): Version 0.98d
194:
195: Revision 1.116 2006/03/06 10:29:27 brouard
196: (Module): Variance-covariance wrong links and
197: varian-covariance of ej. is needed (Saito).
198:
199: Revision 1.115 2006/02/27 12:17:45 brouard
200: (Module): One freematrix added in mlikeli! 0.98c
201:
202: Revision 1.114 2006/02/26 12:57:58 brouard
203: (Module): Some improvements in processing parameter
204: filename with strsep.
205:
206: Revision 1.113 2006/02/24 14:20:24 brouard
207: (Module): Memory leaks checks with valgrind and:
208: datafile was not closed, some imatrix were not freed and on matrix
209: allocation too.
210:
211: Revision 1.112 2006/01/30 09:55:26 brouard
212: (Module): Back to gnuplot.exe instead of wgnuplot.exe
213:
214: Revision 1.111 2006/01/25 20:38:18 brouard
215: (Module): Lots of cleaning and bugs added (Gompertz)
216: (Module): Comments can be added in data file. Missing date values
217: can be a simple dot '.'.
218:
219: Revision 1.110 2006/01/25 00:51:50 brouard
220: (Module): Lots of cleaning and bugs added (Gompertz)
221:
222: Revision 1.109 2006/01/24 19:37:15 brouard
223: (Module): Comments (lines starting with a #) are allowed in data.
224:
225: Revision 1.108 2006/01/19 18:05:42 lievre
226: Gnuplot problem appeared...
227: To be fixed
228:
229: Revision 1.107 2006/01/19 16:20:37 brouard
230: Test existence of gnuplot in imach path
231:
232: Revision 1.106 2006/01/19 13:24:36 brouard
233: Some cleaning and links added in html output
234:
235: Revision 1.105 2006/01/05 20:23:19 lievre
236: *** empty log message ***
237:
238: Revision 1.104 2005/09/30 16:11:43 lievre
239: (Module): sump fixed, loop imx fixed, and simplifications.
240: (Module): If the status is missing at the last wave but we know
241: that the person is alive, then we can code his/her status as -2
242: (instead of missing=-1 in earlier versions) and his/her
243: contributions to the likelihood is 1 - Prob of dying from last
244: health status (= 1-p13= p11+p12 in the easiest case of somebody in
245: the healthy state at last known wave). Version is 0.98
246:
247: Revision 1.103 2005/09/30 15:54:49 lievre
248: (Module): sump fixed, loop imx fixed, and simplifications.
249:
250: Revision 1.102 2004/09/15 17:31:30 brouard
251: Add the possibility to read data file including tab characters.
252:
253: Revision 1.101 2004/09/15 10:38:38 brouard
254: Fix on curr_time
255:
256: Revision 1.100 2004/07/12 18:29:06 brouard
257: Add version for Mac OS X. Just define UNIX in Makefile
258:
259: Revision 1.99 2004/06/05 08:57:40 brouard
260: *** empty log message ***
261:
262: Revision 1.98 2004/05/16 15:05:56 brouard
263: New version 0.97 . First attempt to estimate force of mortality
264: directly from the data i.e. without the need of knowing the health
265: state at each age, but using a Gompertz model: log u =a + b*age .
266: This is the basic analysis of mortality and should be done before any
267: other analysis, in order to test if the mortality estimated from the
268: cross-longitudinal survey is different from the mortality estimated
269: from other sources like vital statistic data.
270:
271: The same imach parameter file can be used but the option for mle should be -3.
272:
273: Agnès, who wrote this part of the code, tried to keep most of the
274: former routines in order to include the new code within the former code.
275:
276: The output is very simple: only an estimate of the intercept and of
277: the slope with 95% confident intervals.
278:
279: Current limitations:
280: A) Even if you enter covariates, i.e. with the
281: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
282: B) There is no computation of Life Expectancy nor Life Table.
283:
284: Revision 1.97 2004/02/20 13:25:42 lievre
285: Version 0.96d. Population forecasting command line is (temporarily)
286: suppressed.
287:
288: Revision 1.96 2003/07/15 15:38:55 brouard
289: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
290: rewritten within the same printf. Workaround: many printfs.
291:
292: Revision 1.95 2003/07/08 07:54:34 brouard
293: * imach.c (Repository):
294: (Repository): Using imachwizard code to output a more meaningful covariance
295: matrix (cov(a12,c31) instead of numbers.
296:
297: Revision 1.94 2003/06/27 13:00:02 brouard
298: Just cleaning
299:
300: Revision 1.93 2003/06/25 16:33:55 brouard
301: (Module): On windows (cygwin) function asctime_r doesn't
302: exist so I changed back to asctime which exists.
303: (Module): Version 0.96b
304:
305: Revision 1.92 2003/06/25 16:30:45 brouard
306: (Module): On windows (cygwin) function asctime_r doesn't
307: exist so I changed back to asctime which exists.
308:
309: Revision 1.91 2003/06/25 15:30:29 brouard
310: * imach.c (Repository): Duplicated warning errors corrected.
311: (Repository): Elapsed time after each iteration is now output. It
312: helps to forecast when convergence will be reached. Elapsed time
313: is stamped in powell. We created a new html file for the graphs
314: concerning matrix of covariance. It has extension -cov.htm.
315:
316: Revision 1.90 2003/06/24 12:34:15 brouard
317: (Module): Some bugs corrected for windows. Also, when
318: mle=-1 a template is output in file "or"mypar.txt with the design
319: of the covariance matrix to be input.
320:
321: Revision 1.89 2003/06/24 12:30:52 brouard
322: (Module): Some bugs corrected for windows. Also, when
323: mle=-1 a template is output in file "or"mypar.txt with the design
324: of the covariance matrix to be input.
325:
326: Revision 1.88 2003/06/23 17:54:56 brouard
327: * 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.
328:
329: Revision 1.87 2003/06/18 12:26:01 brouard
330: Version 0.96
331:
332: Revision 1.86 2003/06/17 20:04:08 brouard
333: (Module): Change position of html and gnuplot routines and added
334: routine fileappend.
335:
336: Revision 1.85 2003/06/17 13:12:43 brouard
337: * imach.c (Repository): Check when date of death was earlier that
338: current date of interview. It may happen when the death was just
339: prior to the death. In this case, dh was negative and likelihood
340: was wrong (infinity). We still send an "Error" but patch by
341: assuming that the date of death was just one stepm after the
342: interview.
343: (Repository): Because some people have very long ID (first column)
344: we changed int to long in num[] and we added a new lvector for
345: memory allocation. But we also truncated to 8 characters (left
346: truncation)
347: (Repository): No more line truncation errors.
348:
349: Revision 1.84 2003/06/13 21:44:43 brouard
350: * imach.c (Repository): Replace "freqsummary" at a correct
351: place. It differs from routine "prevalence" which may be called
352: many times. Probs is memory consuming and must be used with
353: parcimony.
354: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
355:
356: Revision 1.83 2003/06/10 13:39:11 lievre
357: *** empty log message ***
358:
359: Revision 1.82 2003/06/05 15:57:20 brouard
360: Add log in imach.c and fullversion number is now printed.
361:
362: */
363: /*
364: Interpolated Markov Chain
365:
366: Short summary of the programme:
367:
368: This program computes Healthy Life Expectancies from
369: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
370: first survey ("cross") where individuals from different ages are
371: interviewed on their health status or degree of disability (in the
372: case of a health survey which is our main interest) -2- at least a
373: second wave of interviews ("longitudinal") which measure each change
374: (if any) in individual health status. Health expectancies are
375: computed from the time spent in each health state according to a
376: model. More health states you consider, more time is necessary to reach the
377: Maximum Likelihood of the parameters involved in the model. The
378: simplest model is the multinomial logistic model where pij is the
379: probability to be observed in state j at the second wave
380: conditional to be observed in state i at the first wave. Therefore
381: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
382: 'age' is age and 'sex' is a covariate. If you want to have a more
383: complex model than "constant and age", you should modify the program
384: where the markup *Covariates have to be included here again* invites
385: you to do it. More covariates you add, slower the
386: convergence.
387:
388: The advantage of this computer programme, compared to a simple
389: multinomial logistic model, is clear when the delay between waves is not
390: identical for each individual. Also, if a individual missed an
391: intermediate interview, the information is lost, but taken into
392: account using an interpolation or extrapolation.
393:
394: hPijx is the probability to be observed in state i at age x+h
395: conditional to the observed state i at age x. The delay 'h' can be
396: split into an exact number (nh*stepm) of unobserved intermediate
397: states. This elementary transition (by month, quarter,
398: semester or year) is modelled as a multinomial logistic. The hPx
399: matrix is simply the matrix product of nh*stepm elementary matrices
400: and the contribution of each individual to the likelihood is simply
401: hPijx.
402:
403: Also this programme outputs the covariance matrix of the parameters but also
404: of the life expectancies. It also computes the period (stable) prevalence.
405:
406: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
407: Institut national d'études démographiques, Paris.
408: This software have been partly granted by Euro-REVES, a concerted action
409: from the European Union.
410: It is copyrighted identically to a GNU software product, ie programme and
411: software can be distributed freely for non commercial use. Latest version
412: can be accessed at http://euroreves.ined.fr/imach .
413:
414: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
415: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
416:
417: **********************************************************************/
418: /*
419: main
420: read parameterfile
421: read datafile
422: concatwav
423: freqsummary
424: if (mle >= 1)
425: mlikeli
426: print results files
427: if mle==1
428: computes hessian
429: read end of parameter file: agemin, agemax, bage, fage, estepm
430: begin-prev-date,...
431: open gnuplot file
432: open html file
433: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
434: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
435: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
436: freexexit2 possible for memory heap.
437:
438: h Pij x | pij_nom ficrestpij
439: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
440: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
441: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
442:
443: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
444: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
445: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
446: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
447: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
448:
449: forecasting if prevfcast==1 prevforecast call prevalence()
450: health expectancies
451: Variance-covariance of DFLE
452: prevalence()
453: movingaverage()
454: varevsij()
455: if popbased==1 varevsij(,popbased)
456: total life expectancies
457: Variance of period (stable) prevalence
458: end
459: */
460:
461:
462:
463:
464: #include <math.h>
465: #include <stdio.h>
466: #include <stdlib.h>
467: #include <string.h>
468: #include <unistd.h>
469:
470: #include <limits.h>
471: #include <sys/types.h>
472: #include <sys/stat.h>
473: #include <errno.h>
474: extern int errno;
475:
476: #ifdef LINUX
477: #include <time.h>
478: #include "timeval.h"
479: #else
480: #include <sys/time.h>
481: #endif
482:
483: #ifdef GSL
484: #include <gsl/gsl_errno.h>
485: #include <gsl/gsl_multimin.h>
486: #endif
487:
488: /* #include <libintl.h> */
489: /* #define _(String) gettext (String) */
490:
491: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
492:
493: #define GNUPLOTPROGRAM "gnuplot"
494: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
495: #define FILENAMELENGTH 132
496:
497: #define GLOCK_ERROR_NOPATH -1 /* empty path */
498: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
499:
500: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
501: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
502:
503: #define NINTERVMAX 8
504: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
505: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
506: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
507: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
508: #define MAXN 20000
509: #define YEARM 12. /**< Number of months per year */
510: #define AGESUP 130
511: #define AGEBASE 40
512: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
513: #ifdef UNIX
514: #define DIRSEPARATOR '/'
515: #define CHARSEPARATOR "/"
516: #define ODIRSEPARATOR '\\'
517: #else
518: #define DIRSEPARATOR '\\'
519: #define CHARSEPARATOR "\\"
520: #define ODIRSEPARATOR '/'
521: #endif
522:
523: /* $Id: imach.c,v 1.156 2014/08/25 20:10:10 brouard Exp $ */
524: /* $State: Exp $ */
525:
526: char version[]="Imach version 0.98nV, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
527: char fullversion[]="$Revision: 1.156 $ $Date: 2014/08/25 20:10:10 $";
528: char strstart[80];
529: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
530: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
531: int nvar=0, nforce=0; /* Number of variables, number of forces */
532: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
533: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
534: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
535: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
536: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
537: int cptcovprodnoage=0; /**< Number of covariate products without age */
538: int cptcoveff=0; /* Total number of covariates to vary for printing results */
539: int cptcov=0; /* Working variable */
540: int npar=NPARMAX;
541: int nlstate=2; /* Number of live states */
542: int ndeath=1; /* Number of dead states */
543: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
544: int popbased=0;
545:
546: int *wav; /* Number of waves for this individuual 0 is possible */
547: int maxwav=0; /* Maxim number of waves */
548: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
549: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
550: int gipmx=0, gsw=0; /* Global variables on the number of contributions
551: to the likelihood and the sum of weights (done by funcone)*/
552: int mle=1, weightopt=0;
553: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
554: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
555: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
556: * wave mi and wave mi+1 is not an exact multiple of stepm. */
557: double jmean=1; /* Mean space between 2 waves */
558: double **matprod2(); /* test */
559: double **oldm, **newm, **savm; /* Working pointers to matrices */
560: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
561: /*FILE *fic ; */ /* Used in readdata only */
562: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
563: FILE *ficlog, *ficrespow;
564: int globpr=0; /* Global variable for printing or not */
565: double fretone; /* Only one call to likelihood */
566: long ipmx=0; /* Number of contributions */
567: double sw; /* Sum of weights */
568: char filerespow[FILENAMELENGTH];
569: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
570: FILE *ficresilk;
571: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
572: FILE *ficresprobmorprev;
573: FILE *fichtm, *fichtmcov; /* Html File */
574: FILE *ficreseij;
575: char filerese[FILENAMELENGTH];
576: FILE *ficresstdeij;
577: char fileresstde[FILENAMELENGTH];
578: FILE *ficrescveij;
579: char filerescve[FILENAMELENGTH];
580: FILE *ficresvij;
581: char fileresv[FILENAMELENGTH];
582: FILE *ficresvpl;
583: char fileresvpl[FILENAMELENGTH];
584: char title[MAXLINE];
585: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
586: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
587: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
588: char command[FILENAMELENGTH];
589: int outcmd=0;
590:
591: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
592:
593: char filelog[FILENAMELENGTH]; /* Log file */
594: char filerest[FILENAMELENGTH];
595: char fileregp[FILENAMELENGTH];
596: char popfile[FILENAMELENGTH];
597:
598: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
599:
600: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
601: struct timezone tzp;
602: extern int gettimeofday();
603: struct tm tmg, tm, tmf, *gmtime(), *localtime();
604: long time_value;
605: extern long time();
606: char strcurr[80], strfor[80];
607:
608: char *endptr;
609: long lval;
610: double dval;
611:
612: #define NR_END 1
613: #define FREE_ARG char*
614: #define FTOL 1.0e-10
615:
616: #define NRANSI
617: #define ITMAX 200
618:
619: #define TOL 2.0e-4
620:
621: #define CGOLD 0.3819660
622: #define ZEPS 1.0e-10
623: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
624:
625: #define GOLD 1.618034
626: #define GLIMIT 100.0
627: #define TINY 1.0e-20
628:
629: static double maxarg1,maxarg2;
630: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
631: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
632:
633: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
634: #define rint(a) floor(a+0.5)
635:
636: static double sqrarg;
637: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
638: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
639: int agegomp= AGEGOMP;
640:
641: int imx;
642: int stepm=1;
643: /* Stepm, step in month: minimum step interpolation*/
644:
645: int estepm;
646: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
647:
648: int m,nb;
649: long *num;
650: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
651: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
652: double **pmmij, ***probs;
653: double *ageexmed,*agecens;
654: double dateintmean=0;
655:
656: double *weight;
657: int **s; /* Status */
658: double *agedc;
659: double **covar; /**< covar[j,i], value of jth covariate for individual i,
660: * covar=matrix(0,NCOVMAX,1,n);
661: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
662: double idx;
663: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
664: int *Ndum; /** Freq of modality (tricode */
665: int **codtab; /**< codtab=imatrix(1,100,1,10); */
666: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
667: double *lsurv, *lpop, *tpop;
668:
669: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
670: double ftolhess; /**< Tolerance for computing hessian */
671:
672: /**************** split *************************/
673: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
674: {
675: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
676: the name of the file (name), its extension only (ext) and its first part of the name (finame)
677: */
678: char *ss; /* pointer */
679: int l1, l2; /* length counters */
680:
681: l1 = strlen(path ); /* length of path */
682: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
683: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
684: if ( ss == NULL ) { /* no directory, so determine current directory */
685: strcpy( name, path ); /* we got the fullname name because no directory */
686: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
687: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
688: /* get current working directory */
689: /* extern char* getcwd ( char *buf , int len);*/
690: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
691: return( GLOCK_ERROR_GETCWD );
692: }
693: /* got dirc from getcwd*/
694: printf(" DIRC = %s \n",dirc);
695: } else { /* strip direcotry from path */
696: ss++; /* after this, the filename */
697: l2 = strlen( ss ); /* length of filename */
698: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
699: strcpy( name, ss ); /* save file name */
700: strncpy( dirc, path, l1 - l2 ); /* now the directory */
701: dirc[l1-l2] = 0; /* add zero */
702: printf(" DIRC2 = %s \n",dirc);
703: }
704: /* We add a separator at the end of dirc if not exists */
705: l1 = strlen( dirc ); /* length of directory */
706: if( dirc[l1-1] != DIRSEPARATOR ){
707: dirc[l1] = DIRSEPARATOR;
708: dirc[l1+1] = 0;
709: printf(" DIRC3 = %s \n",dirc);
710: }
711: ss = strrchr( name, '.' ); /* find last / */
712: if (ss >0){
713: ss++;
714: strcpy(ext,ss); /* save extension */
715: l1= strlen( name);
716: l2= strlen(ss)+1;
717: strncpy( finame, name, l1-l2);
718: finame[l1-l2]= 0;
719: }
720:
721: return( 0 ); /* we're done */
722: }
723:
724:
725: /******************************************/
726:
727: void replace_back_to_slash(char *s, char*t)
728: {
729: int i;
730: int lg=0;
731: i=0;
732: lg=strlen(t);
733: for(i=0; i<= lg; i++) {
734: (s[i] = t[i]);
735: if (t[i]== '\\') s[i]='/';
736: }
737: }
738:
739: char *trimbb(char *out, char *in)
740: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
741: char *s;
742: s=out;
743: while (*in != '\0'){
744: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
745: in++;
746: }
747: *out++ = *in++;
748: }
749: *out='\0';
750: return s;
751: }
752:
753: char *cutl(char *blocc, char *alocc, char *in, char occ)
754: {
755: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
756: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
757: gives blocc="abcdef2ghi" and alocc="j".
758: If occ is not found blocc is null and alocc is equal to in. Returns blocc
759: */
760: char *s, *t, *bl;
761: t=in;s=in;
762: while ((*in != occ) && (*in != '\0')){
763: *alocc++ = *in++;
764: }
765: if( *in == occ){
766: *(alocc)='\0';
767: s=++in;
768: }
769:
770: if (s == t) {/* occ not found */
771: *(alocc-(in-s))='\0';
772: in=s;
773: }
774: while ( *in != '\0'){
775: *blocc++ = *in++;
776: }
777:
778: *blocc='\0';
779: return t;
780: }
781: char *cutv(char *blocc, char *alocc, char *in, char occ)
782: {
783: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
784: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
785: gives blocc="abcdef2ghi" and alocc="j".
786: If occ is not found blocc is null and alocc is equal to in. Returns alocc
787: */
788: char *s, *t;
789: t=in;s=in;
790: while (*in != '\0'){
791: while( *in == occ){
792: *blocc++ = *in++;
793: s=in;
794: }
795: *blocc++ = *in++;
796: }
797: if (s == t) /* occ not found */
798: *(blocc-(in-s))='\0';
799: else
800: *(blocc-(in-s)-1)='\0';
801: in=s;
802: while ( *in != '\0'){
803: *alocc++ = *in++;
804: }
805:
806: *alocc='\0';
807: return s;
808: }
809:
810: int nbocc(char *s, char occ)
811: {
812: int i,j=0;
813: int lg=20;
814: i=0;
815: lg=strlen(s);
816: for(i=0; i<= lg; i++) {
817: if (s[i] == occ ) j++;
818: }
819: return j;
820: }
821:
822: /* void cutv(char *u,char *v, char*t, char occ) */
823: /* { */
824: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
825: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
826: /* gives u="abcdef2ghi" and v="j" *\/ */
827: /* int i,lg,j,p=0; */
828: /* i=0; */
829: /* lg=strlen(t); */
830: /* for(j=0; j<=lg-1; j++) { */
831: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
832: /* } */
833:
834: /* for(j=0; j<p; j++) { */
835: /* (u[j] = t[j]); */
836: /* } */
837: /* u[p]='\0'; */
838:
839: /* for(j=0; j<= lg; j++) { */
840: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
841: /* } */
842: /* } */
843:
844: /********************** nrerror ********************/
845:
846: void nrerror(char error_text[])
847: {
848: fprintf(stderr,"ERREUR ...\n");
849: fprintf(stderr,"%s\n",error_text);
850: exit(EXIT_FAILURE);
851: }
852: /*********************** vector *******************/
853: double *vector(int nl, int nh)
854: {
855: double *v;
856: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
857: if (!v) nrerror("allocation failure in vector");
858: return v-nl+NR_END;
859: }
860:
861: /************************ free vector ******************/
862: void free_vector(double*v, int nl, int nh)
863: {
864: free((FREE_ARG)(v+nl-NR_END));
865: }
866:
867: /************************ivector *******************************/
868: int *ivector(long nl,long nh)
869: {
870: int *v;
871: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
872: if (!v) nrerror("allocation failure in ivector");
873: return v-nl+NR_END;
874: }
875:
876: /******************free ivector **************************/
877: void free_ivector(int *v, long nl, long nh)
878: {
879: free((FREE_ARG)(v+nl-NR_END));
880: }
881:
882: /************************lvector *******************************/
883: long *lvector(long nl,long nh)
884: {
885: long *v;
886: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
887: if (!v) nrerror("allocation failure in ivector");
888: return v-nl+NR_END;
889: }
890:
891: /******************free lvector **************************/
892: void free_lvector(long *v, long nl, long nh)
893: {
894: free((FREE_ARG)(v+nl-NR_END));
895: }
896:
897: /******************* imatrix *******************************/
898: int **imatrix(long nrl, long nrh, long ncl, long nch)
899: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
900: {
901: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
902: int **m;
903:
904: /* allocate pointers to rows */
905: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
906: if (!m) nrerror("allocation failure 1 in matrix()");
907: m += NR_END;
908: m -= nrl;
909:
910:
911: /* allocate rows and set pointers to them */
912: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
913: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
914: m[nrl] += NR_END;
915: m[nrl] -= ncl;
916:
917: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
918:
919: /* return pointer to array of pointers to rows */
920: return m;
921: }
922:
923: /****************** free_imatrix *************************/
924: void free_imatrix(m,nrl,nrh,ncl,nch)
925: int **m;
926: long nch,ncl,nrh,nrl;
927: /* free an int matrix allocated by imatrix() */
928: {
929: free((FREE_ARG) (m[nrl]+ncl-NR_END));
930: free((FREE_ARG) (m+nrl-NR_END));
931: }
932:
933: /******************* matrix *******************************/
934: double **matrix(long nrl, long nrh, long ncl, long nch)
935: {
936: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
937: double **m;
938:
939: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
940: if (!m) nrerror("allocation failure 1 in matrix()");
941: m += NR_END;
942: m -= nrl;
943:
944: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
945: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
946: m[nrl] += NR_END;
947: m[nrl] -= ncl;
948:
949: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
950: return m;
951: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
952: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
953: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
954: */
955: }
956:
957: /*************************free matrix ************************/
958: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
959: {
960: free((FREE_ARG)(m[nrl]+ncl-NR_END));
961: free((FREE_ARG)(m+nrl-NR_END));
962: }
963:
964: /******************* ma3x *******************************/
965: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
966: {
967: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
968: double ***m;
969:
970: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
971: if (!m) nrerror("allocation failure 1 in matrix()");
972: m += NR_END;
973: m -= nrl;
974:
975: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
976: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
977: m[nrl] += NR_END;
978: m[nrl] -= ncl;
979:
980: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
981:
982: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
983: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
984: m[nrl][ncl] += NR_END;
985: m[nrl][ncl] -= nll;
986: for (j=ncl+1; j<=nch; j++)
987: m[nrl][j]=m[nrl][j-1]+nlay;
988:
989: for (i=nrl+1; i<=nrh; i++) {
990: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
991: for (j=ncl+1; j<=nch; j++)
992: m[i][j]=m[i][j-1]+nlay;
993: }
994: return m;
995: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
996: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
997: */
998: }
999:
1000: /*************************free ma3x ************************/
1001: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1002: {
1003: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1004: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1005: free((FREE_ARG)(m+nrl-NR_END));
1006: }
1007:
1008: /*************** function subdirf ***********/
1009: char *subdirf(char fileres[])
1010: {
1011: /* Caution optionfilefiname is hidden */
1012: strcpy(tmpout,optionfilefiname);
1013: strcat(tmpout,"/"); /* Add to the right */
1014: strcat(tmpout,fileres);
1015: return tmpout;
1016: }
1017:
1018: /*************** function subdirf2 ***********/
1019: char *subdirf2(char fileres[], char *preop)
1020: {
1021:
1022: /* Caution optionfilefiname is hidden */
1023: strcpy(tmpout,optionfilefiname);
1024: strcat(tmpout,"/");
1025: strcat(tmpout,preop);
1026: strcat(tmpout,fileres);
1027: return tmpout;
1028: }
1029:
1030: /*************** function subdirf3 ***********/
1031: char *subdirf3(char fileres[], char *preop, char *preop2)
1032: {
1033:
1034: /* Caution optionfilefiname is hidden */
1035: strcpy(tmpout,optionfilefiname);
1036: strcat(tmpout,"/");
1037: strcat(tmpout,preop);
1038: strcat(tmpout,preop2);
1039: strcat(tmpout,fileres);
1040: return tmpout;
1041: }
1042:
1043: /***************** f1dim *************************/
1044: extern int ncom;
1045: extern double *pcom,*xicom;
1046: extern double (*nrfunc)(double []);
1047:
1048: double f1dim(double x)
1049: {
1050: int j;
1051: double f;
1052: double *xt;
1053:
1054: xt=vector(1,ncom);
1055: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1056: f=(*nrfunc)(xt);
1057: free_vector(xt,1,ncom);
1058: return f;
1059: }
1060:
1061: /*****************brent *************************/
1062: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1063: {
1064: int iter;
1065: double a,b,d,etemp;
1066: double fu,fv,fw,fx;
1067: double ftemp;
1068: double p,q,r,tol1,tol2,u,v,w,x,xm;
1069: double e=0.0;
1070:
1071: a=(ax < cx ? ax : cx);
1072: b=(ax > cx ? ax : cx);
1073: x=w=v=bx;
1074: fw=fv=fx=(*f)(x);
1075: for (iter=1;iter<=ITMAX;iter++) {
1076: xm=0.5*(a+b);
1077: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1078: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1079: printf(".");fflush(stdout);
1080: fprintf(ficlog,".");fflush(ficlog);
1081: #ifdef DEBUG
1082: 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);
1083: 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);
1084: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1085: #endif
1086: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1087: *xmin=x;
1088: return fx;
1089: }
1090: ftemp=fu;
1091: if (fabs(e) > tol1) {
1092: r=(x-w)*(fx-fv);
1093: q=(x-v)*(fx-fw);
1094: p=(x-v)*q-(x-w)*r;
1095: q=2.0*(q-r);
1096: if (q > 0.0) p = -p;
1097: q=fabs(q);
1098: etemp=e;
1099: e=d;
1100: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1101: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1102: else {
1103: d=p/q;
1104: u=x+d;
1105: if (u-a < tol2 || b-u < tol2)
1106: d=SIGN(tol1,xm-x);
1107: }
1108: } else {
1109: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1110: }
1111: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1112: fu=(*f)(u);
1113: if (fu <= fx) {
1114: if (u >= x) a=x; else b=x;
1115: SHFT(v,w,x,u)
1116: SHFT(fv,fw,fx,fu)
1117: } else {
1118: if (u < x) a=u; else b=u;
1119: if (fu <= fw || w == x) {
1120: v=w;
1121: w=u;
1122: fv=fw;
1123: fw=fu;
1124: } else if (fu <= fv || v == x || v == w) {
1125: v=u;
1126: fv=fu;
1127: }
1128: }
1129: }
1130: nrerror("Too many iterations in brent");
1131: *xmin=x;
1132: return fx;
1133: }
1134:
1135: /****************** mnbrak ***********************/
1136:
1137: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1138: double (*func)(double))
1139: {
1140: double ulim,u,r,q, dum;
1141: double fu;
1142:
1143: *fa=(*func)(*ax);
1144: *fb=(*func)(*bx);
1145: if (*fb > *fa) {
1146: SHFT(dum,*ax,*bx,dum)
1147: SHFT(dum,*fb,*fa,dum)
1148: }
1149: *cx=(*bx)+GOLD*(*bx-*ax);
1150: *fc=(*func)(*cx);
1151: while (*fb > *fc) {
1152: r=(*bx-*ax)*(*fb-*fc);
1153: q=(*bx-*cx)*(*fb-*fa);
1154: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1155: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1156: ulim=(*bx)+GLIMIT*(*cx-*bx);
1157: if ((*bx-u)*(u-*cx) > 0.0) {
1158: fu=(*func)(u);
1159: } else if ((*cx-u)*(u-ulim) > 0.0) {
1160: fu=(*func)(u);
1161: if (fu < *fc) {
1162: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1163: SHFT(*fb,*fc,fu,(*func)(u))
1164: }
1165: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1166: u=ulim;
1167: fu=(*func)(u);
1168: } else {
1169: u=(*cx)+GOLD*(*cx-*bx);
1170: fu=(*func)(u);
1171: }
1172: SHFT(*ax,*bx,*cx,u)
1173: SHFT(*fa,*fb,*fc,fu)
1174: }
1175: }
1176:
1177: /*************** linmin ************************/
1178:
1179: int ncom;
1180: double *pcom,*xicom;
1181: double (*nrfunc)(double []);
1182:
1183: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1184: {
1185: double brent(double ax, double bx, double cx,
1186: double (*f)(double), double tol, double *xmin);
1187: double f1dim(double x);
1188: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1189: double *fc, double (*func)(double));
1190: int j;
1191: double xx,xmin,bx,ax;
1192: double fx,fb,fa;
1193:
1194: ncom=n;
1195: pcom=vector(1,n);
1196: xicom=vector(1,n);
1197: nrfunc=func;
1198: for (j=1;j<=n;j++) {
1199: pcom[j]=p[j];
1200: xicom[j]=xi[j];
1201: }
1202: ax=0.0;
1203: xx=1.0;
1204: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1205: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1206: #ifdef DEBUG
1207: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1208: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1209: #endif
1210: for (j=1;j<=n;j++) {
1211: xi[j] *= xmin;
1212: p[j] += xi[j];
1213: }
1214: free_vector(xicom,1,n);
1215: free_vector(pcom,1,n);
1216: }
1217:
1218: char *asc_diff_time(long time_sec, char ascdiff[])
1219: {
1220: long sec_left, days, hours, minutes;
1221: days = (time_sec) / (60*60*24);
1222: sec_left = (time_sec) % (60*60*24);
1223: hours = (sec_left) / (60*60) ;
1224: sec_left = (sec_left) %(60*60);
1225: minutes = (sec_left) /60;
1226: sec_left = (sec_left) % (60);
1227: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1228: return ascdiff;
1229: }
1230:
1231: /*************** powell ************************/
1232: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1233: double (*func)(double []))
1234: {
1235: void linmin(double p[], double xi[], int n, double *fret,
1236: double (*func)(double []));
1237: int i,ibig,j;
1238: double del,t,*pt,*ptt,*xit;
1239: double fp,fptt;
1240: double *xits;
1241: int niterf, itmp;
1242:
1243: pt=vector(1,n);
1244: ptt=vector(1,n);
1245: xit=vector(1,n);
1246: xits=vector(1,n);
1247: *fret=(*func)(p);
1248: for (j=1;j<=n;j++) pt[j]=p[j];
1249: for (*iter=1;;++(*iter)) {
1250: fp=(*fret);
1251: ibig=0;
1252: del=0.0;
1253: last_time=curr_time;
1254: (void) gettimeofday(&curr_time,&tzp);
1255: 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);
1256: 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);
1257: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1258: for (i=1;i<=n;i++) {
1259: printf(" %d %.12f",i, p[i]);
1260: fprintf(ficlog," %d %.12lf",i, p[i]);
1261: fprintf(ficrespow," %.12lf", p[i]);
1262: }
1263: printf("\n");
1264: fprintf(ficlog,"\n");
1265: fprintf(ficrespow,"\n");fflush(ficrespow);
1266: if(*iter <=3){
1267: tm = *localtime(&curr_time.tv_sec);
1268: strcpy(strcurr,asctime(&tm));
1269: /* asctime_r(&tm,strcurr); */
1270: forecast_time=curr_time;
1271: itmp = strlen(strcurr);
1272: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1273: strcurr[itmp-1]='\0';
1274: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1275: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1276: for(niterf=10;niterf<=30;niterf+=10){
1277: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1278: tmf = *localtime(&forecast_time.tv_sec);
1279: /* asctime_r(&tmf,strfor); */
1280: strcpy(strfor,asctime(&tmf));
1281: itmp = strlen(strfor);
1282: if(strfor[itmp-1]=='\n')
1283: strfor[itmp-1]='\0';
1284: 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);
1285: 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);
1286: }
1287: }
1288: for (i=1;i<=n;i++) {
1289: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1290: fptt=(*fret);
1291: #ifdef DEBUG
1292: printf("fret=%lf \n",*fret);
1293: fprintf(ficlog,"fret=%lf \n",*fret);
1294: #endif
1295: printf("%d",i);fflush(stdout);
1296: fprintf(ficlog,"%d",i);fflush(ficlog);
1297: linmin(p,xit,n,fret,func);
1298: if (fabs(fptt-(*fret)) > del) {
1299: del=fabs(fptt-(*fret));
1300: ibig=i;
1301: }
1302: #ifdef DEBUG
1303: printf("%d %.12e",i,(*fret));
1304: fprintf(ficlog,"%d %.12e",i,(*fret));
1305: for (j=1;j<=n;j++) {
1306: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1307: printf(" x(%d)=%.12e",j,xit[j]);
1308: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1309: }
1310: for(j=1;j<=n;j++) {
1311: printf(" p=%.12e",p[j]);
1312: fprintf(ficlog," p=%.12e",p[j]);
1313: }
1314: printf("\n");
1315: fprintf(ficlog,"\n");
1316: #endif
1317: }
1318: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1319: #ifdef DEBUG
1320: int k[2],l;
1321: k[0]=1;
1322: k[1]=-1;
1323: printf("Max: %.12e",(*func)(p));
1324: fprintf(ficlog,"Max: %.12e",(*func)(p));
1325: for (j=1;j<=n;j++) {
1326: printf(" %.12e",p[j]);
1327: fprintf(ficlog," %.12e",p[j]);
1328: }
1329: printf("\n");
1330: fprintf(ficlog,"\n");
1331: for(l=0;l<=1;l++) {
1332: for (j=1;j<=n;j++) {
1333: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1334: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1335: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1336: }
1337: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1338: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1339: }
1340: #endif
1341:
1342:
1343: free_vector(xit,1,n);
1344: free_vector(xits,1,n);
1345: free_vector(ptt,1,n);
1346: free_vector(pt,1,n);
1347: return;
1348: }
1349: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1350: for (j=1;j<=n;j++) {
1351: ptt[j]=2.0*p[j]-pt[j];
1352: xit[j]=p[j]-pt[j];
1353: pt[j]=p[j];
1354: }
1355: fptt=(*func)(ptt);
1356: if (fptt < fp) {
1357: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1358: if (t < 0.0) {
1359: linmin(p,xit,n,fret,func);
1360: for (j=1;j<=n;j++) {
1361: xi[j][ibig]=xi[j][n];
1362: xi[j][n]=xit[j];
1363: }
1364: #ifdef DEBUG
1365: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1366: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1367: for(j=1;j<=n;j++){
1368: printf(" %.12e",xit[j]);
1369: fprintf(ficlog," %.12e",xit[j]);
1370: }
1371: printf("\n");
1372: fprintf(ficlog,"\n");
1373: #endif
1374: }
1375: }
1376: }
1377: }
1378:
1379: /**** Prevalence limit (stable or period prevalence) ****************/
1380:
1381: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1382: {
1383: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1384: matrix by transitions matrix until convergence is reached */
1385:
1386: int i, ii,j,k;
1387: double min, max, maxmin, maxmax,sumnew=0.;
1388: /* double **matprod2(); */ /* test */
1389: double **out, cov[NCOVMAX+1], **pmij();
1390: double **newm;
1391: double agefin, delaymax=50 ; /* Max number of years to converge */
1392:
1393: for (ii=1;ii<=nlstate+ndeath;ii++)
1394: for (j=1;j<=nlstate+ndeath;j++){
1395: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1396: }
1397:
1398: cov[1]=1.;
1399:
1400: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1401: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1402: newm=savm;
1403: /* Covariates have to be included here again */
1404: cov[2]=agefin;
1405:
1406: for (k=1; k<=cptcovn;k++) {
1407: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1408: /*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]]);*/
1409: }
1410: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1411: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1412: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1413:
1414: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1415: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1416: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1417: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1418: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1419: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1420:
1421: savm=oldm;
1422: oldm=newm;
1423: maxmax=0.;
1424: for(j=1;j<=nlstate;j++){
1425: min=1.;
1426: max=0.;
1427: for(i=1; i<=nlstate; i++) {
1428: sumnew=0;
1429: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1430: prlim[i][j]= newm[i][j]/(1-sumnew);
1431: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1432: max=FMAX(max,prlim[i][j]);
1433: min=FMIN(min,prlim[i][j]);
1434: }
1435: maxmin=max-min;
1436: maxmax=FMAX(maxmax,maxmin);
1437: }
1438: if(maxmax < ftolpl){
1439: return prlim;
1440: }
1441: }
1442: }
1443:
1444: /*************** transition probabilities ***************/
1445:
1446: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1447: {
1448: /* According to parameters values stored in x and the covariate's values stored in cov,
1449: computes the probability to be observed in state j being in state i by appying the
1450: model to the ncovmodel covariates (including constant and age).
1451: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1452: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1453: ncth covariate in the global vector x is given by the formula:
1454: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1455: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1456: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1457: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1458: Outputs ps[i][j] the probability to be observed in j being in j according to
1459: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1460: */
1461: double s1, lnpijopii;
1462: /*double t34;*/
1463: int i,j,j1, nc, ii, jj;
1464:
1465: for(i=1; i<= nlstate; i++){
1466: for(j=1; j<i;j++){
1467: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1468: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1469: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1470: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1471: }
1472: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1473: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1474: }
1475: for(j=i+1; j<=nlstate+ndeath;j++){
1476: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1477: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1478: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1479: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1480: }
1481: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1482: }
1483: }
1484:
1485: for(i=1; i<= nlstate; i++){
1486: s1=0;
1487: for(j=1; j<i; j++){
1488: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1489: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1490: }
1491: for(j=i+1; j<=nlstate+ndeath; j++){
1492: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1493: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1494: }
1495: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1496: ps[i][i]=1./(s1+1.);
1497: /* Computing other pijs */
1498: for(j=1; j<i; j++)
1499: ps[i][j]= exp(ps[i][j])*ps[i][i];
1500: for(j=i+1; j<=nlstate+ndeath; j++)
1501: ps[i][j]= exp(ps[i][j])*ps[i][i];
1502: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1503: } /* end i */
1504:
1505: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1506: for(jj=1; jj<= nlstate+ndeath; jj++){
1507: ps[ii][jj]=0;
1508: ps[ii][ii]=1;
1509: }
1510: }
1511:
1512:
1513: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1514: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1515: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1516: /* } */
1517: /* printf("\n "); */
1518: /* } */
1519: /* printf("\n ");printf("%lf ",cov[2]);*/
1520: /*
1521: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1522: goto end;*/
1523: return ps;
1524: }
1525:
1526: /**************** Product of 2 matrices ******************/
1527:
1528: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1529: {
1530: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1531: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1532: /* in, b, out are matrice of pointers which should have been initialized
1533: before: only the contents of out is modified. The function returns
1534: a pointer to pointers identical to out */
1535: int i, j, k;
1536: for(i=nrl; i<= nrh; i++)
1537: for(k=ncolol; k<=ncoloh; k++){
1538: out[i][k]=0.;
1539: for(j=ncl; j<=nch; j++)
1540: out[i][k] +=in[i][j]*b[j][k];
1541: }
1542: return out;
1543: }
1544:
1545:
1546: /************* Higher Matrix Product ***************/
1547:
1548: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1549: {
1550: /* Computes the transition matrix starting at age 'age' over
1551: 'nhstepm*hstepm*stepm' months (i.e. until
1552: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1553: nhstepm*hstepm matrices.
1554: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1555: (typically every 2 years instead of every month which is too big
1556: for the memory).
1557: Model is determined by parameters x and covariates have to be
1558: included manually here.
1559:
1560: */
1561:
1562: int i, j, d, h, k;
1563: double **out, cov[NCOVMAX+1];
1564: double **newm;
1565:
1566: /* Hstepm could be zero and should return the unit matrix */
1567: for (i=1;i<=nlstate+ndeath;i++)
1568: for (j=1;j<=nlstate+ndeath;j++){
1569: oldm[i][j]=(i==j ? 1.0 : 0.0);
1570: po[i][j][0]=(i==j ? 1.0 : 0.0);
1571: }
1572: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1573: for(h=1; h <=nhstepm; h++){
1574: for(d=1; d <=hstepm; d++){
1575: newm=savm;
1576: /* Covariates have to be included here again */
1577: cov[1]=1.;
1578: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1579: for (k=1; k<=cptcovn;k++)
1580: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1581: for (k=1; k<=cptcovage;k++)
1582: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1583: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1584: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1585:
1586:
1587: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1588: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1589: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1590: pmij(pmmij,cov,ncovmodel,x,nlstate));
1591: savm=oldm;
1592: oldm=newm;
1593: }
1594: for(i=1; i<=nlstate+ndeath; i++)
1595: for(j=1;j<=nlstate+ndeath;j++) {
1596: po[i][j][h]=newm[i][j];
1597: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1598: }
1599: /*printf("h=%d ",h);*/
1600: } /* end h */
1601: /* printf("\n H=%d \n",h); */
1602: return po;
1603: }
1604:
1605:
1606: /*************** log-likelihood *************/
1607: double func( double *x)
1608: {
1609: int i, ii, j, k, mi, d, kk;
1610: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1611: double **out;
1612: double sw; /* Sum of weights */
1613: double lli; /* Individual log likelihood */
1614: int s1, s2;
1615: double bbh, survp;
1616: long ipmx;
1617: /*extern weight */
1618: /* We are differentiating ll according to initial status */
1619: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1620: /*for(i=1;i<imx;i++)
1621: printf(" %d\n",s[4][i]);
1622: */
1623: cov[1]=1.;
1624:
1625: for(k=1; k<=nlstate; k++) ll[k]=0.;
1626:
1627: if(mle==1){
1628: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1629: /* Computes the values of the ncovmodel covariates of the model
1630: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1631: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1632: to be observed in j being in i according to the model.
1633: */
1634: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1635: cov[2+k]=covar[Tvar[k]][i];
1636: }
1637: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1638: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1639: has been calculated etc */
1640: for(mi=1; mi<= wav[i]-1; mi++){
1641: for (ii=1;ii<=nlstate+ndeath;ii++)
1642: for (j=1;j<=nlstate+ndeath;j++){
1643: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1644: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1645: }
1646: for(d=0; d<dh[mi][i]; d++){
1647: newm=savm;
1648: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1649: for (kk=1; kk<=cptcovage;kk++) {
1650: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1651: }
1652: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1653: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1654: savm=oldm;
1655: oldm=newm;
1656: } /* end mult */
1657:
1658: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1659: /* But now since version 0.9 we anticipate for bias at large stepm.
1660: * If stepm is larger than one month (smallest stepm) and if the exact delay
1661: * (in months) between two waves is not a multiple of stepm, we rounded to
1662: * the nearest (and in case of equal distance, to the lowest) interval but now
1663: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1664: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1665: * probability in order to take into account the bias as a fraction of the way
1666: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1667: * -stepm/2 to stepm/2 .
1668: * For stepm=1 the results are the same as for previous versions of Imach.
1669: * For stepm > 1 the results are less biased than in previous versions.
1670: */
1671: s1=s[mw[mi][i]][i];
1672: s2=s[mw[mi+1][i]][i];
1673: bbh=(double)bh[mi][i]/(double)stepm;
1674: /* bias bh is positive if real duration
1675: * is higher than the multiple of stepm and negative otherwise.
1676: */
1677: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1678: if( s2 > nlstate){
1679: /* i.e. if s2 is a death state and if the date of death is known
1680: then the contribution to the likelihood is the probability to
1681: die between last step unit time and current step unit time,
1682: which is also equal to probability to die before dh
1683: minus probability to die before dh-stepm .
1684: In version up to 0.92 likelihood was computed
1685: as if date of death was unknown. Death was treated as any other
1686: health state: the date of the interview describes the actual state
1687: and not the date of a change in health state. The former idea was
1688: to consider that at each interview the state was recorded
1689: (healthy, disable or death) and IMaCh was corrected; but when we
1690: introduced the exact date of death then we should have modified
1691: the contribution of an exact death to the likelihood. This new
1692: contribution is smaller and very dependent of the step unit
1693: stepm. It is no more the probability to die between last interview
1694: and month of death but the probability to survive from last
1695: interview up to one month before death multiplied by the
1696: probability to die within a month. Thanks to Chris
1697: Jackson for correcting this bug. Former versions increased
1698: mortality artificially. The bad side is that we add another loop
1699: which slows down the processing. The difference can be up to 10%
1700: lower mortality.
1701: */
1702: lli=log(out[s1][s2] - savm[s1][s2]);
1703:
1704:
1705: } else if (s2==-2) {
1706: for (j=1,survp=0. ; j<=nlstate; j++)
1707: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1708: /*survp += out[s1][j]; */
1709: lli= log(survp);
1710: }
1711:
1712: else if (s2==-4) {
1713: for (j=3,survp=0. ; j<=nlstate; j++)
1714: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1715: lli= log(survp);
1716: }
1717:
1718: else if (s2==-5) {
1719: for (j=1,survp=0. ; j<=2; j++)
1720: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1721: lli= log(survp);
1722: }
1723:
1724: else{
1725: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1726: /* 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 */
1727: }
1728: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1729: /*if(lli ==000.0)*/
1730: /*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); */
1731: ipmx +=1;
1732: sw += weight[i];
1733: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1734: } /* end of wave */
1735: } /* end of individual */
1736: } else if(mle==2){
1737: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1738: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1739: for(mi=1; mi<= wav[i]-1; mi++){
1740: for (ii=1;ii<=nlstate+ndeath;ii++)
1741: for (j=1;j<=nlstate+ndeath;j++){
1742: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1743: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1744: }
1745: for(d=0; d<=dh[mi][i]; d++){
1746: newm=savm;
1747: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1748: for (kk=1; kk<=cptcovage;kk++) {
1749: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1750: }
1751: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1752: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1753: savm=oldm;
1754: oldm=newm;
1755: } /* end mult */
1756:
1757: s1=s[mw[mi][i]][i];
1758: s2=s[mw[mi+1][i]][i];
1759: bbh=(double)bh[mi][i]/(double)stepm;
1760: 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 */
1761: ipmx +=1;
1762: sw += weight[i];
1763: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1764: } /* end of wave */
1765: } /* end of individual */
1766: } else if(mle==3){ /* exponential inter-extrapolation */
1767: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1768: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1769: for(mi=1; mi<= wav[i]-1; mi++){
1770: for (ii=1;ii<=nlstate+ndeath;ii++)
1771: for (j=1;j<=nlstate+ndeath;j++){
1772: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1773: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1774: }
1775: for(d=0; d<dh[mi][i]; d++){
1776: newm=savm;
1777: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1778: for (kk=1; kk<=cptcovage;kk++) {
1779: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1780: }
1781: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1782: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1783: savm=oldm;
1784: oldm=newm;
1785: } /* end mult */
1786:
1787: s1=s[mw[mi][i]][i];
1788: s2=s[mw[mi+1][i]][i];
1789: bbh=(double)bh[mi][i]/(double)stepm;
1790: 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 */
1791: ipmx +=1;
1792: sw += weight[i];
1793: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1794: } /* end of wave */
1795: } /* end of individual */
1796: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1797: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1798: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1799: for(mi=1; mi<= wav[i]-1; mi++){
1800: for (ii=1;ii<=nlstate+ndeath;ii++)
1801: for (j=1;j<=nlstate+ndeath;j++){
1802: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1803: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1804: }
1805: for(d=0; d<dh[mi][i]; d++){
1806: newm=savm;
1807: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1808: for (kk=1; kk<=cptcovage;kk++) {
1809: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1810: }
1811:
1812: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1813: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1814: savm=oldm;
1815: oldm=newm;
1816: } /* end mult */
1817:
1818: s1=s[mw[mi][i]][i];
1819: s2=s[mw[mi+1][i]][i];
1820: if( s2 > nlstate){
1821: lli=log(out[s1][s2] - savm[s1][s2]);
1822: }else{
1823: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1824: }
1825: ipmx +=1;
1826: sw += weight[i];
1827: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1828: /* 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]); */
1829: } /* end of wave */
1830: } /* end of individual */
1831: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1832: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1833: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1834: for(mi=1; mi<= wav[i]-1; mi++){
1835: for (ii=1;ii<=nlstate+ndeath;ii++)
1836: for (j=1;j<=nlstate+ndeath;j++){
1837: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1838: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1839: }
1840: for(d=0; d<dh[mi][i]; d++){
1841: newm=savm;
1842: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1843: for (kk=1; kk<=cptcovage;kk++) {
1844: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1845: }
1846:
1847: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1848: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1849: savm=oldm;
1850: oldm=newm;
1851: } /* end mult */
1852:
1853: s1=s[mw[mi][i]][i];
1854: s2=s[mw[mi+1][i]][i];
1855: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1856: ipmx +=1;
1857: sw += weight[i];
1858: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1859: /*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]);*/
1860: } /* end of wave */
1861: } /* end of individual */
1862: } /* End of if */
1863: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1864: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1865: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1866: return -l;
1867: }
1868:
1869: /*************** log-likelihood *************/
1870: double funcone( double *x)
1871: {
1872: /* Same as likeli but slower because of a lot of printf and if */
1873: int i, ii, j, k, mi, d, kk;
1874: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1875: double **out;
1876: double lli; /* Individual log likelihood */
1877: double llt;
1878: int s1, s2;
1879: double bbh, survp;
1880: /*extern weight */
1881: /* We are differentiating ll according to initial status */
1882: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1883: /*for(i=1;i<imx;i++)
1884: printf(" %d\n",s[4][i]);
1885: */
1886: cov[1]=1.;
1887:
1888: for(k=1; k<=nlstate; k++) ll[k]=0.;
1889:
1890: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1891: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1892: for(mi=1; mi<= wav[i]-1; mi++){
1893: for (ii=1;ii<=nlstate+ndeath;ii++)
1894: for (j=1;j<=nlstate+ndeath;j++){
1895: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1896: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1897: }
1898: for(d=0; d<dh[mi][i]; d++){
1899: newm=savm;
1900: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1901: for (kk=1; kk<=cptcovage;kk++) {
1902: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1903: }
1904: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1905: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1906: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1907: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
1908: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1909: savm=oldm;
1910: oldm=newm;
1911: } /* end mult */
1912:
1913: s1=s[mw[mi][i]][i];
1914: s2=s[mw[mi+1][i]][i];
1915: bbh=(double)bh[mi][i]/(double)stepm;
1916: /* bias is positive if real duration
1917: * is higher than the multiple of stepm and negative otherwise.
1918: */
1919: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1920: lli=log(out[s1][s2] - savm[s1][s2]);
1921: } else if (s2==-2) {
1922: for (j=1,survp=0. ; j<=nlstate; j++)
1923: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1924: lli= log(survp);
1925: }else if (mle==1){
1926: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1927: } else if(mle==2){
1928: 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 */
1929: } else if(mle==3){ /* exponential inter-extrapolation */
1930: 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 */
1931: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1932: lli=log(out[s1][s2]); /* Original formula */
1933: } else{ /* mle=0 back to 1 */
1934: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1935: /*lli=log(out[s1][s2]); */ /* Original formula */
1936: } /* End of if */
1937: ipmx +=1;
1938: sw += weight[i];
1939: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1940: /*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]); */
1941: if(globpr){
1942: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1943: %11.6f %11.6f %11.6f ", \
1944: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1945: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1946: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1947: llt +=ll[k]*gipmx/gsw;
1948: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1949: }
1950: fprintf(ficresilk," %10.6f\n", -llt);
1951: }
1952: } /* end of wave */
1953: } /* end of individual */
1954: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1955: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1956: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1957: if(globpr==0){ /* First time we count the contributions and weights */
1958: gipmx=ipmx;
1959: gsw=sw;
1960: }
1961: return -l;
1962: }
1963:
1964:
1965: /*************** function likelione ***********/
1966: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1967: {
1968: /* This routine should help understanding what is done with
1969: the selection of individuals/waves and
1970: to check the exact contribution to the likelihood.
1971: Plotting could be done.
1972: */
1973: int k;
1974:
1975: if(*globpri !=0){ /* Just counts and sums, no printings */
1976: strcpy(fileresilk,"ilk");
1977: strcat(fileresilk,fileres);
1978: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1979: printf("Problem with resultfile: %s\n", fileresilk);
1980: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1981: }
1982: 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");
1983: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1984: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1985: for(k=1; k<=nlstate; k++)
1986: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1987: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1988: }
1989:
1990: *fretone=(*funcone)(p);
1991: if(*globpri !=0){
1992: fclose(ficresilk);
1993: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1994: fflush(fichtm);
1995: }
1996: return;
1997: }
1998:
1999:
2000: /*********** Maximum Likelihood Estimation ***************/
2001:
2002: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2003: {
2004: int i,j, iter;
2005: double **xi;
2006: double fret;
2007: double fretone; /* Only one call to likelihood */
2008: /* char filerespow[FILENAMELENGTH];*/
2009: xi=matrix(1,npar,1,npar);
2010: for (i=1;i<=npar;i++)
2011: for (j=1;j<=npar;j++)
2012: xi[i][j]=(i==j ? 1.0 : 0.0);
2013: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2014: strcpy(filerespow,"pow");
2015: strcat(filerespow,fileres);
2016: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2017: printf("Problem with resultfile: %s\n", filerespow);
2018: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2019: }
2020: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2021: for (i=1;i<=nlstate;i++)
2022: for(j=1;j<=nlstate+ndeath;j++)
2023: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2024: fprintf(ficrespow,"\n");
2025:
2026: powell(p,xi,npar,ftol,&iter,&fret,func);
2027:
2028: free_matrix(xi,1,npar,1,npar);
2029: fclose(ficrespow);
2030: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
2031: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2032: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2033:
2034: }
2035:
2036: /**** Computes Hessian and covariance matrix ***/
2037: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2038: {
2039: double **a,**y,*x,pd;
2040: double **hess;
2041: int i, j,jk;
2042: int *indx;
2043:
2044: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2045: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2046: void lubksb(double **a, int npar, int *indx, double b[]) ;
2047: void ludcmp(double **a, int npar, int *indx, double *d) ;
2048: double gompertz(double p[]);
2049: hess=matrix(1,npar,1,npar);
2050:
2051: printf("\nCalculation of the hessian matrix. Wait...\n");
2052: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2053: for (i=1;i<=npar;i++){
2054: printf("%d",i);fflush(stdout);
2055: fprintf(ficlog,"%d",i);fflush(ficlog);
2056:
2057: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2058:
2059: /* printf(" %f ",p[i]);
2060: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2061: }
2062:
2063: for (i=1;i<=npar;i++) {
2064: for (j=1;j<=npar;j++) {
2065: if (j>i) {
2066: printf(".%d%d",i,j);fflush(stdout);
2067: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2068: hess[i][j]=hessij(p,delti,i,j,func,npar);
2069:
2070: hess[j][i]=hess[i][j];
2071: /*printf(" %lf ",hess[i][j]);*/
2072: }
2073: }
2074: }
2075: printf("\n");
2076: fprintf(ficlog,"\n");
2077:
2078: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2079: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2080:
2081: a=matrix(1,npar,1,npar);
2082: y=matrix(1,npar,1,npar);
2083: x=vector(1,npar);
2084: indx=ivector(1,npar);
2085: for (i=1;i<=npar;i++)
2086: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2087: ludcmp(a,npar,indx,&pd);
2088:
2089: for (j=1;j<=npar;j++) {
2090: for (i=1;i<=npar;i++) x[i]=0;
2091: x[j]=1;
2092: lubksb(a,npar,indx,x);
2093: for (i=1;i<=npar;i++){
2094: matcov[i][j]=x[i];
2095: }
2096: }
2097:
2098: printf("\n#Hessian matrix#\n");
2099: fprintf(ficlog,"\n#Hessian matrix#\n");
2100: for (i=1;i<=npar;i++) {
2101: for (j=1;j<=npar;j++) {
2102: printf("%.3e ",hess[i][j]);
2103: fprintf(ficlog,"%.3e ",hess[i][j]);
2104: }
2105: printf("\n");
2106: fprintf(ficlog,"\n");
2107: }
2108:
2109: /* Recompute Inverse */
2110: for (i=1;i<=npar;i++)
2111: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2112: ludcmp(a,npar,indx,&pd);
2113:
2114: /* printf("\n#Hessian matrix recomputed#\n");
2115:
2116: for (j=1;j<=npar;j++) {
2117: for (i=1;i<=npar;i++) x[i]=0;
2118: x[j]=1;
2119: lubksb(a,npar,indx,x);
2120: for (i=1;i<=npar;i++){
2121: y[i][j]=x[i];
2122: printf("%.3e ",y[i][j]);
2123: fprintf(ficlog,"%.3e ",y[i][j]);
2124: }
2125: printf("\n");
2126: fprintf(ficlog,"\n");
2127: }
2128: */
2129:
2130: free_matrix(a,1,npar,1,npar);
2131: free_matrix(y,1,npar,1,npar);
2132: free_vector(x,1,npar);
2133: free_ivector(indx,1,npar);
2134: free_matrix(hess,1,npar,1,npar);
2135:
2136:
2137: }
2138:
2139: /*************** hessian matrix ****************/
2140: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2141: {
2142: int i;
2143: int l=1, lmax=20;
2144: double k1,k2;
2145: double p2[MAXPARM+1]; /* identical to x */
2146: double res;
2147: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2148: double fx;
2149: int k=0,kmax=10;
2150: double l1;
2151:
2152: fx=func(x);
2153: for (i=1;i<=npar;i++) p2[i]=x[i];
2154: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2155: l1=pow(10,l);
2156: delts=delt;
2157: for(k=1 ; k <kmax; k=k+1){
2158: delt = delta*(l1*k);
2159: p2[theta]=x[theta] +delt;
2160: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2161: p2[theta]=x[theta]-delt;
2162: k2=func(p2)-fx;
2163: /*res= (k1-2.0*fx+k2)/delt/delt; */
2164: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2165:
2166: #ifdef DEBUGHESS
2167: 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);
2168: 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);
2169: #endif
2170: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2171: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2172: k=kmax;
2173: }
2174: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2175: k=kmax; l=lmax*10.;
2176: }
2177: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2178: delts=delt;
2179: }
2180: }
2181: }
2182: delti[theta]=delts;
2183: return res;
2184:
2185: }
2186:
2187: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2188: {
2189: int i;
2190: int l=1, l1, lmax=20;
2191: double k1,k2,k3,k4,res,fx;
2192: double p2[MAXPARM+1];
2193: int k;
2194:
2195: fx=func(x);
2196: for (k=1; k<=2; k++) {
2197: for (i=1;i<=npar;i++) p2[i]=x[i];
2198: p2[thetai]=x[thetai]+delti[thetai]/k;
2199: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2200: k1=func(p2)-fx;
2201:
2202: p2[thetai]=x[thetai]+delti[thetai]/k;
2203: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2204: k2=func(p2)-fx;
2205:
2206: p2[thetai]=x[thetai]-delti[thetai]/k;
2207: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2208: k3=func(p2)-fx;
2209:
2210: p2[thetai]=x[thetai]-delti[thetai]/k;
2211: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2212: k4=func(p2)-fx;
2213: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2214: #ifdef DEBUG
2215: 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);
2216: 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);
2217: #endif
2218: }
2219: return res;
2220: }
2221:
2222: /************** Inverse of matrix **************/
2223: void ludcmp(double **a, int n, int *indx, double *d)
2224: {
2225: int i,imax,j,k;
2226: double big,dum,sum,temp;
2227: double *vv;
2228:
2229: vv=vector(1,n);
2230: *d=1.0;
2231: for (i=1;i<=n;i++) {
2232: big=0.0;
2233: for (j=1;j<=n;j++)
2234: if ((temp=fabs(a[i][j])) > big) big=temp;
2235: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2236: vv[i]=1.0/big;
2237: }
2238: for (j=1;j<=n;j++) {
2239: for (i=1;i<j;i++) {
2240: sum=a[i][j];
2241: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2242: a[i][j]=sum;
2243: }
2244: big=0.0;
2245: for (i=j;i<=n;i++) {
2246: sum=a[i][j];
2247: for (k=1;k<j;k++)
2248: sum -= a[i][k]*a[k][j];
2249: a[i][j]=sum;
2250: if ( (dum=vv[i]*fabs(sum)) >= big) {
2251: big=dum;
2252: imax=i;
2253: }
2254: }
2255: if (j != imax) {
2256: for (k=1;k<=n;k++) {
2257: dum=a[imax][k];
2258: a[imax][k]=a[j][k];
2259: a[j][k]=dum;
2260: }
2261: *d = -(*d);
2262: vv[imax]=vv[j];
2263: }
2264: indx[j]=imax;
2265: if (a[j][j] == 0.0) a[j][j]=TINY;
2266: if (j != n) {
2267: dum=1.0/(a[j][j]);
2268: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2269: }
2270: }
2271: free_vector(vv,1,n); /* Doesn't work */
2272: ;
2273: }
2274:
2275: void lubksb(double **a, int n, int *indx, double b[])
2276: {
2277: int i,ii=0,ip,j;
2278: double sum;
2279:
2280: for (i=1;i<=n;i++) {
2281: ip=indx[i];
2282: sum=b[ip];
2283: b[ip]=b[i];
2284: if (ii)
2285: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2286: else if (sum) ii=i;
2287: b[i]=sum;
2288: }
2289: for (i=n;i>=1;i--) {
2290: sum=b[i];
2291: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2292: b[i]=sum/a[i][i];
2293: }
2294: }
2295:
2296: void pstamp(FILE *fichier)
2297: {
2298: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2299: }
2300:
2301: /************ Frequencies ********************/
2302: 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[])
2303: { /* Some frequencies */
2304:
2305: int i, m, jk, k1,i1, j1, bool, z1,j;
2306: int first;
2307: double ***freq; /* Frequencies */
2308: double *pp, **prop;
2309: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2310: char fileresp[FILENAMELENGTH];
2311:
2312: pp=vector(1,nlstate);
2313: prop=matrix(1,nlstate,iagemin,iagemax+3);
2314: strcpy(fileresp,"p");
2315: strcat(fileresp,fileres);
2316: if((ficresp=fopen(fileresp,"w"))==NULL) {
2317: printf("Problem with prevalence resultfile: %s\n", fileresp);
2318: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2319: exit(0);
2320: }
2321: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2322: j1=0;
2323:
2324: j=cptcoveff;
2325: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2326:
2327: first=1;
2328:
2329: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2330: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2331: /* j1++;
2332: */
2333: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2334: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2335: scanf("%d", i);*/
2336: for (i=-5; i<=nlstate+ndeath; i++)
2337: for (jk=-5; jk<=nlstate+ndeath; jk++)
2338: for(m=iagemin; m <= iagemax+3; m++)
2339: freq[i][jk][m]=0;
2340:
2341: for (i=1; i<=nlstate; i++)
2342: for(m=iagemin; m <= iagemax+3; m++)
2343: prop[i][m]=0;
2344:
2345: dateintsum=0;
2346: k2cpt=0;
2347: for (i=1; i<=imx; i++) {
2348: bool=1;
2349: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2350: for (z1=1; z1<=cptcoveff; z1++)
2351: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2352: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2353: bool=0;
2354: /* 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",
2355: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2356: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2357: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2358: }
2359: }
2360:
2361: if (bool==1){
2362: for(m=firstpass; m<=lastpass; m++){
2363: k2=anint[m][i]+(mint[m][i]/12.);
2364: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2365: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2366: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2367: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2368: if (m<lastpass) {
2369: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2370: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2371: }
2372:
2373: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2374: dateintsum=dateintsum+k2;
2375: k2cpt++;
2376: }
2377: /*}*/
2378: }
2379: }
2380: } /* end i */
2381:
2382: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2383: pstamp(ficresp);
2384: if (cptcovn>0) {
2385: fprintf(ficresp, "\n#********** Variable ");
2386: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2387: fprintf(ficresp, "**********\n#");
2388: fprintf(ficlog, "\n#********** Variable ");
2389: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2390: fprintf(ficlog, "**********\n#");
2391: }
2392: for(i=1; i<=nlstate;i++)
2393: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2394: fprintf(ficresp, "\n");
2395:
2396: for(i=iagemin; i <= iagemax+3; i++){
2397: if(i==iagemax+3){
2398: fprintf(ficlog,"Total");
2399: }else{
2400: if(first==1){
2401: first=0;
2402: printf("See log file for details...\n");
2403: }
2404: fprintf(ficlog,"Age %d", i);
2405: }
2406: for(jk=1; jk <=nlstate ; jk++){
2407: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2408: pp[jk] += freq[jk][m][i];
2409: }
2410: for(jk=1; jk <=nlstate ; jk++){
2411: for(m=-1, pos=0; m <=0 ; m++)
2412: pos += freq[jk][m][i];
2413: if(pp[jk]>=1.e-10){
2414: if(first==1){
2415: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2416: }
2417: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2418: }else{
2419: if(first==1)
2420: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2421: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2422: }
2423: }
2424:
2425: for(jk=1; jk <=nlstate ; jk++){
2426: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2427: pp[jk] += freq[jk][m][i];
2428: }
2429: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2430: pos += pp[jk];
2431: posprop += prop[jk][i];
2432: }
2433: for(jk=1; jk <=nlstate ; jk++){
2434: if(pos>=1.e-5){
2435: if(first==1)
2436: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2437: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2438: }else{
2439: if(first==1)
2440: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2441: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2442: }
2443: if( i <= iagemax){
2444: if(pos>=1.e-5){
2445: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2446: /*probs[i][jk][j1]= pp[jk]/pos;*/
2447: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2448: }
2449: else
2450: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2451: }
2452: }
2453:
2454: for(jk=-1; jk <=nlstate+ndeath; jk++)
2455: for(m=-1; m <=nlstate+ndeath; m++)
2456: if(freq[jk][m][i] !=0 ) {
2457: if(first==1)
2458: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2459: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2460: }
2461: if(i <= iagemax)
2462: fprintf(ficresp,"\n");
2463: if(first==1)
2464: printf("Others in log...\n");
2465: fprintf(ficlog,"\n");
2466: }
2467: /*}*/
2468: }
2469: dateintmean=dateintsum/k2cpt;
2470:
2471: fclose(ficresp);
2472: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2473: free_vector(pp,1,nlstate);
2474: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2475: /* End of Freq */
2476: }
2477:
2478: /************ Prevalence ********************/
2479: 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)
2480: {
2481: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2482: in each health status at the date of interview (if between dateprev1 and dateprev2).
2483: We still use firstpass and lastpass as another selection.
2484: */
2485:
2486: int i, m, jk, k1, i1, j1, bool, z1,j;
2487: double ***freq; /* Frequencies */
2488: double *pp, **prop;
2489: double pos,posprop;
2490: double y2; /* in fractional years */
2491: int iagemin, iagemax;
2492: int first; /** to stop verbosity which is redirected to log file */
2493:
2494: iagemin= (int) agemin;
2495: iagemax= (int) agemax;
2496: /*pp=vector(1,nlstate);*/
2497: prop=matrix(1,nlstate,iagemin,iagemax+3);
2498: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2499: j1=0;
2500:
2501: /*j=cptcoveff;*/
2502: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2503:
2504: first=1;
2505: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2506: /*for(i1=1; i1<=ncodemax[k1];i1++){
2507: j1++;*/
2508:
2509: for (i=1; i<=nlstate; i++)
2510: for(m=iagemin; m <= iagemax+3; m++)
2511: prop[i][m]=0.0;
2512:
2513: for (i=1; i<=imx; i++) { /* Each individual */
2514: bool=1;
2515: if (cptcovn>0) {
2516: for (z1=1; z1<=cptcoveff; z1++)
2517: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2518: bool=0;
2519: }
2520: if (bool==1) {
2521: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2522: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2523: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2524: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2525: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2526: 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);
2527: if (s[m][i]>0 && s[m][i]<=nlstate) {
2528: /*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]]);*/
2529: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2530: prop[s[m][i]][iagemax+3] += weight[i];
2531: }
2532: }
2533: } /* end selection of waves */
2534: }
2535: }
2536: for(i=iagemin; i <= iagemax+3; i++){
2537: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2538: posprop += prop[jk][i];
2539: }
2540:
2541: for(jk=1; jk <=nlstate ; jk++){
2542: if( i <= iagemax){
2543: if(posprop>=1.e-5){
2544: probs[i][jk][j1]= prop[jk][i]/posprop;
2545: } else{
2546: if(first==1){
2547: first=0;
2548: 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]);
2549: }
2550: }
2551: }
2552: }/* end jk */
2553: }/* end i */
2554: /*} *//* end i1 */
2555: } /* end j1 */
2556:
2557: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2558: /*free_vector(pp,1,nlstate);*/
2559: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2560: } /* End of prevalence */
2561:
2562: /************* Waves Concatenation ***************/
2563:
2564: 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)
2565: {
2566: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2567: Death is a valid wave (if date is known).
2568: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2569: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2570: and mw[mi+1][i]. dh depends on stepm.
2571: */
2572:
2573: int i, mi, m;
2574: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2575: double sum=0., jmean=0.;*/
2576: int first;
2577: int j, k=0,jk, ju, jl;
2578: double sum=0.;
2579: first=0;
2580: jmin=1e+5;
2581: jmax=-1;
2582: jmean=0.;
2583: for(i=1; i<=imx; i++){
2584: mi=0;
2585: m=firstpass;
2586: while(s[m][i] <= nlstate){
2587: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2588: mw[++mi][i]=m;
2589: if(m >=lastpass)
2590: break;
2591: else
2592: m++;
2593: }/* end while */
2594: if (s[m][i] > nlstate){
2595: mi++; /* Death is another wave */
2596: /* if(mi==0) never been interviewed correctly before death */
2597: /* Only death is a correct wave */
2598: mw[mi][i]=m;
2599: }
2600:
2601: wav[i]=mi;
2602: if(mi==0){
2603: nbwarn++;
2604: if(first==0){
2605: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2606: first=1;
2607: }
2608: if(first==1){
2609: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2610: }
2611: } /* end mi==0 */
2612: } /* End individuals */
2613:
2614: for(i=1; i<=imx; i++){
2615: for(mi=1; mi<wav[i];mi++){
2616: if (stepm <=0)
2617: dh[mi][i]=1;
2618: else{
2619: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2620: if (agedc[i] < 2*AGESUP) {
2621: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2622: if(j==0) j=1; /* Survives at least one month after exam */
2623: else if(j<0){
2624: nberr++;
2625: 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]);
2626: j=1; /* Temporary Dangerous patch */
2627: 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);
2628: 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]);
2629: 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);
2630: }
2631: k=k+1;
2632: if (j >= jmax){
2633: jmax=j;
2634: ijmax=i;
2635: }
2636: if (j <= jmin){
2637: jmin=j;
2638: ijmin=i;
2639: }
2640: sum=sum+j;
2641: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2642: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2643: }
2644: }
2645: else{
2646: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2647: /* 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]); */
2648:
2649: k=k+1;
2650: if (j >= jmax) {
2651: jmax=j;
2652: ijmax=i;
2653: }
2654: else if (j <= jmin){
2655: jmin=j;
2656: ijmin=i;
2657: }
2658: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2659: /*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]);*/
2660: if(j<0){
2661: nberr++;
2662: 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]);
2663: 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]);
2664: }
2665: sum=sum+j;
2666: }
2667: jk= j/stepm;
2668: jl= j -jk*stepm;
2669: ju= j -(jk+1)*stepm;
2670: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2671: if(jl==0){
2672: dh[mi][i]=jk;
2673: bh[mi][i]=0;
2674: }else{ /* We want a negative bias in order to only have interpolation ie
2675: * to avoid the price of an extra matrix product in likelihood */
2676: dh[mi][i]=jk+1;
2677: bh[mi][i]=ju;
2678: }
2679: }else{
2680: if(jl <= -ju){
2681: dh[mi][i]=jk;
2682: bh[mi][i]=jl; /* bias is positive if real duration
2683: * is higher than the multiple of stepm and negative otherwise.
2684: */
2685: }
2686: else{
2687: dh[mi][i]=jk+1;
2688: bh[mi][i]=ju;
2689: }
2690: if(dh[mi][i]==0){
2691: dh[mi][i]=1; /* At least one step */
2692: bh[mi][i]=ju; /* At least one step */
2693: /* 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);*/
2694: }
2695: } /* end if mle */
2696: }
2697: } /* end wave */
2698: }
2699: jmean=sum/k;
2700: 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);
2701: 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);
2702: }
2703:
2704: /*********** Tricode ****************************/
2705: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2706: {
2707: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2708: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2709: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2710: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2711: /* nbcode[Tvar[j]][1]=
2712: */
2713:
2714: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2715: int modmaxcovj=0; /* Modality max of covariates j */
2716: int cptcode=0; /* Modality max of covariates j */
2717: int modmincovj=0; /* Modality min of covariates j */
2718:
2719:
2720: cptcoveff=0;
2721:
2722: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2723: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2724:
2725: /* Loop on covariates without age and products */
2726: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2727: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2728: modality of this covariate Vj*/
2729: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2730: * If product of Vn*Vm, still boolean *:
2731: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2732: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2733: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2734: modality of the nth covariate of individual i. */
2735: if (ij > modmaxcovj)
2736: modmaxcovj=ij;
2737: else if (ij < modmincovj)
2738: modmincovj=ij;
2739: if ((ij < -1) && (ij > NCOVMAX)){
2740: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2741: exit(1);
2742: }else
2743: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2744: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2745: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2746: /* getting the maximum value of the modality of the covariate
2747: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2748: female is 1, then modmaxcovj=1.*/
2749: }
2750: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2751: cptcode=modmaxcovj;
2752: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2753: /*for (i=0; i<=cptcode; i++) {*/
2754: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2755: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2756: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2757: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2758: }
2759: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2760: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2761: } /* Ndum[-1] number of undefined modalities */
2762:
2763: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2764: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2765: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2766: modmincovj=3; modmaxcovj = 7;
2767: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2768: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2769: variables V1_1 and V1_2.
2770: nbcode[Tvar[j]][ij]=k;
2771: nbcode[Tvar[j]][1]=0;
2772: nbcode[Tvar[j]][2]=1;
2773: nbcode[Tvar[j]][3]=2;
2774: */
2775: ij=1; /* ij is similar to i but can jumps over null modalities */
2776: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2777: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2778: /*recode from 0 */
2779: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2780: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2781: k is a modality. If we have model=V1+V1*sex
2782: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2783: ij++;
2784: }
2785: if (ij > ncodemax[j]) break;
2786: } /* end of loop on */
2787: } /* end of loop on modality */
2788: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2789:
2790: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2791:
2792: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2793: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2794: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2795: Ndum[ij]++;
2796: }
2797:
2798: ij=1;
2799: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2800: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2801: if((Ndum[i]!=0) && (i<=ncovcol)){
2802: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2803: Tvaraff[ij]=i; /*For printing (unclear) */
2804: ij++;
2805: }else
2806: Tvaraff[ij]=0;
2807: }
2808: ij--;
2809: cptcoveff=ij; /*Number of total covariates*/
2810:
2811: }
2812:
2813:
2814: /*********** Health Expectancies ****************/
2815:
2816: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2817:
2818: {
2819: /* Health expectancies, no variances */
2820: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2821: int nhstepma, nstepma; /* Decreasing with age */
2822: double age, agelim, hf;
2823: double ***p3mat;
2824: double eip;
2825:
2826: pstamp(ficreseij);
2827: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2828: fprintf(ficreseij,"# Age");
2829: for(i=1; i<=nlstate;i++){
2830: for(j=1; j<=nlstate;j++){
2831: fprintf(ficreseij," e%1d%1d ",i,j);
2832: }
2833: fprintf(ficreseij," e%1d. ",i);
2834: }
2835: fprintf(ficreseij,"\n");
2836:
2837:
2838: if(estepm < stepm){
2839: printf ("Problem %d lower than %d\n",estepm, stepm);
2840: }
2841: else hstepm=estepm;
2842: /* We compute the life expectancy from trapezoids spaced every estepm months
2843: * This is mainly to measure the difference between two models: for example
2844: * if stepm=24 months pijx are given only every 2 years and by summing them
2845: * we are calculating an estimate of the Life Expectancy assuming a linear
2846: * progression in between and thus overestimating or underestimating according
2847: * to the curvature of the survival function. If, for the same date, we
2848: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2849: * to compare the new estimate of Life expectancy with the same linear
2850: * hypothesis. A more precise result, taking into account a more precise
2851: * curvature will be obtained if estepm is as small as stepm. */
2852:
2853: /* For example we decided to compute the life expectancy with the smallest unit */
2854: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2855: nhstepm is the number of hstepm from age to agelim
2856: nstepm is the number of stepm from age to agelin.
2857: Look at hpijx to understand the reason of that which relies in memory size
2858: and note for a fixed period like estepm months */
2859: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2860: survival function given by stepm (the optimization length). Unfortunately it
2861: means that if the survival funtion is printed only each two years of age and if
2862: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2863: results. So we changed our mind and took the option of the best precision.
2864: */
2865: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2866:
2867: agelim=AGESUP;
2868: /* If stepm=6 months */
2869: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2870: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2871:
2872: /* nhstepm age range expressed in number of stepm */
2873: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2874: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2875: /* if (stepm >= YEARM) hstepm=1;*/
2876: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2877: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2878:
2879: for (age=bage; age<=fage; age ++){
2880: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2881: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2882: /* if (stepm >= YEARM) hstepm=1;*/
2883: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2884:
2885: /* If stepm=6 months */
2886: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2887: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2888:
2889: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2890:
2891: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2892:
2893: printf("%d|",(int)age);fflush(stdout);
2894: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2895:
2896: /* Computing expectancies */
2897: for(i=1; i<=nlstate;i++)
2898: for(j=1; j<=nlstate;j++)
2899: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2900: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2901:
2902: /* 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]);*/
2903:
2904: }
2905:
2906: fprintf(ficreseij,"%3.0f",age );
2907: for(i=1; i<=nlstate;i++){
2908: eip=0;
2909: for(j=1; j<=nlstate;j++){
2910: eip +=eij[i][j][(int)age];
2911: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2912: }
2913: fprintf(ficreseij,"%9.4f", eip );
2914: }
2915: fprintf(ficreseij,"\n");
2916:
2917: }
2918: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2919: printf("\n");
2920: fprintf(ficlog,"\n");
2921:
2922: }
2923:
2924: 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[] )
2925:
2926: {
2927: /* Covariances of health expectancies eij and of total life expectancies according
2928: to initial status i, ei. .
2929: */
2930: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2931: int nhstepma, nstepma; /* Decreasing with age */
2932: double age, agelim, hf;
2933: double ***p3matp, ***p3matm, ***varhe;
2934: double **dnewm,**doldm;
2935: double *xp, *xm;
2936: double **gp, **gm;
2937: double ***gradg, ***trgradg;
2938: int theta;
2939:
2940: double eip, vip;
2941:
2942: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2943: xp=vector(1,npar);
2944: xm=vector(1,npar);
2945: dnewm=matrix(1,nlstate*nlstate,1,npar);
2946: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2947:
2948: pstamp(ficresstdeij);
2949: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2950: fprintf(ficresstdeij,"# Age");
2951: for(i=1; i<=nlstate;i++){
2952: for(j=1; j<=nlstate;j++)
2953: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2954: fprintf(ficresstdeij," e%1d. ",i);
2955: }
2956: fprintf(ficresstdeij,"\n");
2957:
2958: pstamp(ficrescveij);
2959: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2960: fprintf(ficrescveij,"# Age");
2961: for(i=1; i<=nlstate;i++)
2962: for(j=1; j<=nlstate;j++){
2963: cptj= (j-1)*nlstate+i;
2964: for(i2=1; i2<=nlstate;i2++)
2965: for(j2=1; j2<=nlstate;j2++){
2966: cptj2= (j2-1)*nlstate+i2;
2967: if(cptj2 <= cptj)
2968: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2969: }
2970: }
2971: fprintf(ficrescveij,"\n");
2972:
2973: if(estepm < stepm){
2974: printf ("Problem %d lower than %d\n",estepm, stepm);
2975: }
2976: else hstepm=estepm;
2977: /* We compute the life expectancy from trapezoids spaced every estepm months
2978: * This is mainly to measure the difference between two models: for example
2979: * if stepm=24 months pijx are given only every 2 years and by summing them
2980: * we are calculating an estimate of the Life Expectancy assuming a linear
2981: * progression in between and thus overestimating or underestimating according
2982: * to the curvature of the survival function. If, for the same date, we
2983: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2984: * to compare the new estimate of Life expectancy with the same linear
2985: * hypothesis. A more precise result, taking into account a more precise
2986: * curvature will be obtained if estepm is as small as stepm. */
2987:
2988: /* For example we decided to compute the life expectancy with the smallest unit */
2989: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2990: nhstepm is the number of hstepm from age to agelim
2991: nstepm is the number of stepm from age to agelin.
2992: Look at hpijx to understand the reason of that which relies in memory size
2993: and note for a fixed period like estepm months */
2994: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2995: survival function given by stepm (the optimization length). Unfortunately it
2996: means that if the survival funtion is printed only each two years of age and if
2997: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2998: results. So we changed our mind and took the option of the best precision.
2999: */
3000: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3001:
3002: /* If stepm=6 months */
3003: /* nhstepm age range expressed in number of stepm */
3004: agelim=AGESUP;
3005: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3006: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3007: /* if (stepm >= YEARM) hstepm=1;*/
3008: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3009:
3010: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3011: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3012: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3013: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3014: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3015: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3016:
3017: for (age=bage; age<=fage; age ++){
3018: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3019: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3020: /* if (stepm >= YEARM) hstepm=1;*/
3021: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3022:
3023: /* If stepm=6 months */
3024: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3025: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3026:
3027: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3028:
3029: /* Computing Variances of health expectancies */
3030: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3031: decrease memory allocation */
3032: for(theta=1; theta <=npar; theta++){
3033: for(i=1; i<=npar; i++){
3034: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3035: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3036: }
3037: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3038: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3039:
3040: for(j=1; j<= nlstate; j++){
3041: for(i=1; i<=nlstate; i++){
3042: for(h=0; h<=nhstepm-1; h++){
3043: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3044: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3045: }
3046: }
3047: }
3048:
3049: for(ij=1; ij<= nlstate*nlstate; ij++)
3050: for(h=0; h<=nhstepm-1; h++){
3051: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3052: }
3053: }/* End theta */
3054:
3055:
3056: for(h=0; h<=nhstepm-1; h++)
3057: for(j=1; j<=nlstate*nlstate;j++)
3058: for(theta=1; theta <=npar; theta++)
3059: trgradg[h][j][theta]=gradg[h][theta][j];
3060:
3061:
3062: for(ij=1;ij<=nlstate*nlstate;ij++)
3063: for(ji=1;ji<=nlstate*nlstate;ji++)
3064: varhe[ij][ji][(int)age] =0.;
3065:
3066: printf("%d|",(int)age);fflush(stdout);
3067: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3068: for(h=0;h<=nhstepm-1;h++){
3069: for(k=0;k<=nhstepm-1;k++){
3070: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3071: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3072: for(ij=1;ij<=nlstate*nlstate;ij++)
3073: for(ji=1;ji<=nlstate*nlstate;ji++)
3074: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3075: }
3076: }
3077:
3078: /* Computing expectancies */
3079: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3080: for(i=1; i<=nlstate;i++)
3081: for(j=1; j<=nlstate;j++)
3082: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3083: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3084:
3085: /* 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]);*/
3086:
3087: }
3088:
3089: fprintf(ficresstdeij,"%3.0f",age );
3090: for(i=1; i<=nlstate;i++){
3091: eip=0.;
3092: vip=0.;
3093: for(j=1; j<=nlstate;j++){
3094: eip += eij[i][j][(int)age];
3095: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3096: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3097: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3098: }
3099: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3100: }
3101: fprintf(ficresstdeij,"\n");
3102:
3103: fprintf(ficrescveij,"%3.0f",age );
3104: for(i=1; i<=nlstate;i++)
3105: for(j=1; j<=nlstate;j++){
3106: cptj= (j-1)*nlstate+i;
3107: for(i2=1; i2<=nlstate;i2++)
3108: for(j2=1; j2<=nlstate;j2++){
3109: cptj2= (j2-1)*nlstate+i2;
3110: if(cptj2 <= cptj)
3111: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3112: }
3113: }
3114: fprintf(ficrescveij,"\n");
3115:
3116: }
3117: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3118: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3119: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3120: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3121: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3122: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3123: printf("\n");
3124: fprintf(ficlog,"\n");
3125:
3126: free_vector(xm,1,npar);
3127: free_vector(xp,1,npar);
3128: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3129: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3130: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3131: }
3132:
3133: /************ Variance ******************/
3134: 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[])
3135: {
3136: /* Variance of health expectancies */
3137: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3138: /* double **newm;*/
3139: double **dnewm,**doldm;
3140: double **dnewmp,**doldmp;
3141: int i, j, nhstepm, hstepm, h, nstepm ;
3142: int k, cptcode;
3143: double *xp;
3144: double **gp, **gm; /* for var eij */
3145: double ***gradg, ***trgradg; /*for var eij */
3146: double **gradgp, **trgradgp; /* for var p point j */
3147: double *gpp, *gmp; /* for var p point j */
3148: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3149: double ***p3mat;
3150: double age,agelim, hf;
3151: double ***mobaverage;
3152: int theta;
3153: char digit[4];
3154: char digitp[25];
3155:
3156: char fileresprobmorprev[FILENAMELENGTH];
3157:
3158: if(popbased==1){
3159: if(mobilav!=0)
3160: strcpy(digitp,"-populbased-mobilav-");
3161: else strcpy(digitp,"-populbased-nomobil-");
3162: }
3163: else
3164: strcpy(digitp,"-stablbased-");
3165:
3166: if (mobilav!=0) {
3167: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3168: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3169: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3170: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3171: }
3172: }
3173:
3174: strcpy(fileresprobmorprev,"prmorprev");
3175: sprintf(digit,"%-d",ij);
3176: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3177: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3178: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3179: strcat(fileresprobmorprev,fileres);
3180: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3181: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3182: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3183: }
3184: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3185:
3186: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3187: pstamp(ficresprobmorprev);
3188: 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);
3189: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3190: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3191: fprintf(ficresprobmorprev," p.%-d SE",j);
3192: for(i=1; i<=nlstate;i++)
3193: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3194: }
3195: fprintf(ficresprobmorprev,"\n");
3196: fprintf(ficgp,"\n# Routine varevsij");
3197: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3198: 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");
3199: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3200: /* } */
3201: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3202: pstamp(ficresvij);
3203: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3204: if(popbased==1)
3205: 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);
3206: else
3207: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3208: fprintf(ficresvij,"# Age");
3209: for(i=1; i<=nlstate;i++)
3210: for(j=1; j<=nlstate;j++)
3211: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3212: fprintf(ficresvij,"\n");
3213:
3214: xp=vector(1,npar);
3215: dnewm=matrix(1,nlstate,1,npar);
3216: doldm=matrix(1,nlstate,1,nlstate);
3217: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3218: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3219:
3220: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3221: gpp=vector(nlstate+1,nlstate+ndeath);
3222: gmp=vector(nlstate+1,nlstate+ndeath);
3223: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3224:
3225: if(estepm < stepm){
3226: printf ("Problem %d lower than %d\n",estepm, stepm);
3227: }
3228: else hstepm=estepm;
3229: /* For example we decided to compute the life expectancy with the smallest unit */
3230: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3231: nhstepm is the number of hstepm from age to agelim
3232: nstepm is the number of stepm from age to agelin.
3233: Look at function hpijx to understand why (it is linked to memory size questions) */
3234: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3235: survival function given by stepm (the optimization length). Unfortunately it
3236: means that if the survival funtion is printed every two years of age and if
3237: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3238: results. So we changed our mind and took the option of the best precision.
3239: */
3240: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3241: agelim = AGESUP;
3242: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3243: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3244: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3245: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3246: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3247: gp=matrix(0,nhstepm,1,nlstate);
3248: gm=matrix(0,nhstepm,1,nlstate);
3249:
3250:
3251: for(theta=1; theta <=npar; theta++){
3252: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3253: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3254: }
3255: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3256: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3257:
3258: if (popbased==1) {
3259: if(mobilav ==0){
3260: for(i=1; i<=nlstate;i++)
3261: prlim[i][i]=probs[(int)age][i][ij];
3262: }else{ /* mobilav */
3263: for(i=1; i<=nlstate;i++)
3264: prlim[i][i]=mobaverage[(int)age][i][ij];
3265: }
3266: }
3267:
3268: for(j=1; j<= nlstate; j++){
3269: for(h=0; h<=nhstepm; h++){
3270: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3271: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3272: }
3273: }
3274: /* This for computing probability of death (h=1 means
3275: computed over hstepm matrices product = hstepm*stepm months)
3276: as a weighted average of prlim.
3277: */
3278: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3279: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3280: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3281: }
3282: /* end probability of death */
3283:
3284: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3285: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3286: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3287: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3288:
3289: if (popbased==1) {
3290: if(mobilav ==0){
3291: for(i=1; i<=nlstate;i++)
3292: prlim[i][i]=probs[(int)age][i][ij];
3293: }else{ /* mobilav */
3294: for(i=1; i<=nlstate;i++)
3295: prlim[i][i]=mobaverage[(int)age][i][ij];
3296: }
3297: }
3298:
3299: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3300: for(h=0; h<=nhstepm; h++){
3301: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3302: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3303: }
3304: }
3305: /* This for computing probability of death (h=1 means
3306: computed over hstepm matrices product = hstepm*stepm months)
3307: as a weighted average of prlim.
3308: */
3309: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3310: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3311: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3312: }
3313: /* end probability of death */
3314:
3315: for(j=1; j<= nlstate; j++) /* vareij */
3316: for(h=0; h<=nhstepm; h++){
3317: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3318: }
3319:
3320: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3321: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3322: }
3323:
3324: } /* End theta */
3325:
3326: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3327:
3328: for(h=0; h<=nhstepm; h++) /* veij */
3329: for(j=1; j<=nlstate;j++)
3330: for(theta=1; theta <=npar; theta++)
3331: trgradg[h][j][theta]=gradg[h][theta][j];
3332:
3333: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3334: for(theta=1; theta <=npar; theta++)
3335: trgradgp[j][theta]=gradgp[theta][j];
3336:
3337:
3338: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3339: for(i=1;i<=nlstate;i++)
3340: for(j=1;j<=nlstate;j++)
3341: vareij[i][j][(int)age] =0.;
3342:
3343: for(h=0;h<=nhstepm;h++){
3344: for(k=0;k<=nhstepm;k++){
3345: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3346: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3347: for(i=1;i<=nlstate;i++)
3348: for(j=1;j<=nlstate;j++)
3349: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3350: }
3351: }
3352:
3353: /* pptj */
3354: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3355: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3356: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3357: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3358: varppt[j][i]=doldmp[j][i];
3359: /* end ppptj */
3360: /* x centered again */
3361: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3362: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3363:
3364: if (popbased==1) {
3365: if(mobilav ==0){
3366: for(i=1; i<=nlstate;i++)
3367: prlim[i][i]=probs[(int)age][i][ij];
3368: }else{ /* mobilav */
3369: for(i=1; i<=nlstate;i++)
3370: prlim[i][i]=mobaverage[(int)age][i][ij];
3371: }
3372: }
3373:
3374: /* This for computing probability of death (h=1 means
3375: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3376: as a weighted average of prlim.
3377: */
3378: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3379: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3380: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3381: }
3382: /* end probability of death */
3383:
3384: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3385: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3386: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3387: for(i=1; i<=nlstate;i++){
3388: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3389: }
3390: }
3391: fprintf(ficresprobmorprev,"\n");
3392:
3393: fprintf(ficresvij,"%.0f ",age );
3394: for(i=1; i<=nlstate;i++)
3395: for(j=1; j<=nlstate;j++){
3396: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3397: }
3398: fprintf(ficresvij,"\n");
3399: free_matrix(gp,0,nhstepm,1,nlstate);
3400: free_matrix(gm,0,nhstepm,1,nlstate);
3401: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3402: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3403: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3404: } /* End age */
3405: free_vector(gpp,nlstate+1,nlstate+ndeath);
3406: free_vector(gmp,nlstate+1,nlstate+ndeath);
3407: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3408: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3409: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3410: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3411: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3412: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3413: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3414: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3415: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3416: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3417: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3418: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3419: 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);
3420: /* 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);
3421: */
3422: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3423: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3424:
3425: free_vector(xp,1,npar);
3426: free_matrix(doldm,1,nlstate,1,nlstate);
3427: free_matrix(dnewm,1,nlstate,1,npar);
3428: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3429: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3430: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3431: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3432: fclose(ficresprobmorprev);
3433: fflush(ficgp);
3434: fflush(fichtm);
3435: } /* end varevsij */
3436:
3437: /************ Variance of prevlim ******************/
3438: 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[])
3439: {
3440: /* Variance of prevalence limit */
3441: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3442: double **newm;
3443: double **dnewm,**doldm;
3444: int i, j, nhstepm, hstepm;
3445: int k, cptcode;
3446: double *xp;
3447: double *gp, *gm;
3448: double **gradg, **trgradg;
3449: double age,agelim;
3450: int theta;
3451:
3452: pstamp(ficresvpl);
3453: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3454: fprintf(ficresvpl,"# Age");
3455: for(i=1; i<=nlstate;i++)
3456: fprintf(ficresvpl," %1d-%1d",i,i);
3457: fprintf(ficresvpl,"\n");
3458:
3459: xp=vector(1,npar);
3460: dnewm=matrix(1,nlstate,1,npar);
3461: doldm=matrix(1,nlstate,1,nlstate);
3462:
3463: hstepm=1*YEARM; /* Every year of age */
3464: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3465: agelim = AGESUP;
3466: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3467: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3468: if (stepm >= YEARM) hstepm=1;
3469: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3470: gradg=matrix(1,npar,1,nlstate);
3471: gp=vector(1,nlstate);
3472: gm=vector(1,nlstate);
3473:
3474: for(theta=1; theta <=npar; theta++){
3475: for(i=1; i<=npar; i++){ /* Computes gradient */
3476: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3477: }
3478: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3479: for(i=1;i<=nlstate;i++)
3480: gp[i] = prlim[i][i];
3481:
3482: for(i=1; i<=npar; i++) /* Computes gradient */
3483: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3484: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3485: for(i=1;i<=nlstate;i++)
3486: gm[i] = prlim[i][i];
3487:
3488: for(i=1;i<=nlstate;i++)
3489: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3490: } /* End theta */
3491:
3492: trgradg =matrix(1,nlstate,1,npar);
3493:
3494: for(j=1; j<=nlstate;j++)
3495: for(theta=1; theta <=npar; theta++)
3496: trgradg[j][theta]=gradg[theta][j];
3497:
3498: for(i=1;i<=nlstate;i++)
3499: varpl[i][(int)age] =0.;
3500: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3501: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3502: for(i=1;i<=nlstate;i++)
3503: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3504:
3505: fprintf(ficresvpl,"%.0f ",age );
3506: for(i=1; i<=nlstate;i++)
3507: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3508: fprintf(ficresvpl,"\n");
3509: free_vector(gp,1,nlstate);
3510: free_vector(gm,1,nlstate);
3511: free_matrix(gradg,1,npar,1,nlstate);
3512: free_matrix(trgradg,1,nlstate,1,npar);
3513: } /* End age */
3514:
3515: free_vector(xp,1,npar);
3516: free_matrix(doldm,1,nlstate,1,npar);
3517: free_matrix(dnewm,1,nlstate,1,nlstate);
3518:
3519: }
3520:
3521: /************ Variance of one-step probabilities ******************/
3522: 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[])
3523: {
3524: int i, j=0, i1, k1, l1, t, tj;
3525: int k2, l2, j1, z1;
3526: int k=0,l, cptcode;
3527: int first=1, first1, first2;
3528: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3529: double **dnewm,**doldm;
3530: double *xp;
3531: double *gp, *gm;
3532: double **gradg, **trgradg;
3533: double **mu;
3534: double age,agelim, cov[NCOVMAX+1];
3535: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3536: int theta;
3537: char fileresprob[FILENAMELENGTH];
3538: char fileresprobcov[FILENAMELENGTH];
3539: char fileresprobcor[FILENAMELENGTH];
3540: double ***varpij;
3541:
3542: strcpy(fileresprob,"prob");
3543: strcat(fileresprob,fileres);
3544: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3545: printf("Problem with resultfile: %s\n", fileresprob);
3546: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3547: }
3548: strcpy(fileresprobcov,"probcov");
3549: strcat(fileresprobcov,fileres);
3550: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3551: printf("Problem with resultfile: %s\n", fileresprobcov);
3552: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3553: }
3554: strcpy(fileresprobcor,"probcor");
3555: strcat(fileresprobcor,fileres);
3556: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3557: printf("Problem with resultfile: %s\n", fileresprobcor);
3558: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3559: }
3560: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3561: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3562: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3563: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3564: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3565: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3566: pstamp(ficresprob);
3567: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3568: fprintf(ficresprob,"# Age");
3569: pstamp(ficresprobcov);
3570: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3571: fprintf(ficresprobcov,"# Age");
3572: pstamp(ficresprobcor);
3573: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3574: fprintf(ficresprobcor,"# Age");
3575:
3576:
3577: for(i=1; i<=nlstate;i++)
3578: for(j=1; j<=(nlstate+ndeath);j++){
3579: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3580: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3581: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3582: }
3583: /* fprintf(ficresprob,"\n");
3584: fprintf(ficresprobcov,"\n");
3585: fprintf(ficresprobcor,"\n");
3586: */
3587: xp=vector(1,npar);
3588: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3589: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3590: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3591: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3592: first=1;
3593: fprintf(ficgp,"\n# Routine varprob");
3594: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3595: fprintf(fichtm,"\n");
3596:
3597: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3598: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3599: file %s<br>\n",optionfilehtmcov);
3600: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3601: and drawn. It helps understanding how is the covariance between two incidences.\
3602: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3603: 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. \
3604: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3605: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3606: standard deviations wide on each axis. <br>\
3607: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3608: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3609: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3610:
3611: cov[1]=1;
3612: /* tj=cptcoveff; */
3613: tj = (int) pow(2,cptcoveff);
3614: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3615: j1=0;
3616: for(j1=1; j1<=tj;j1++){
3617: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3618: /*j1++;*/
3619: if (cptcovn>0) {
3620: fprintf(ficresprob, "\n#********** Variable ");
3621: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3622: fprintf(ficresprob, "**********\n#\n");
3623: fprintf(ficresprobcov, "\n#********** Variable ");
3624: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3625: fprintf(ficresprobcov, "**********\n#\n");
3626:
3627: fprintf(ficgp, "\n#********** Variable ");
3628: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3629: fprintf(ficgp, "**********\n#\n");
3630:
3631:
3632: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3633: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3634: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3635:
3636: fprintf(ficresprobcor, "\n#********** Variable ");
3637: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3638: fprintf(ficresprobcor, "**********\n#");
3639: }
3640:
3641: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3642: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3643: gp=vector(1,(nlstate)*(nlstate+ndeath));
3644: gm=vector(1,(nlstate)*(nlstate+ndeath));
3645: for (age=bage; age<=fage; age ++){
3646: cov[2]=age;
3647: for (k=1; k<=cptcovn;k++) {
3648: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3649: * 1 1 1 1 1
3650: * 2 2 1 1 1
3651: * 3 1 2 1 1
3652: */
3653: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3654: }
3655: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3656: for (k=1; k<=cptcovprod;k++)
3657: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3658:
3659:
3660: for(theta=1; theta <=npar; theta++){
3661: for(i=1; i<=npar; i++)
3662: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3663:
3664: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3665:
3666: k=0;
3667: for(i=1; i<= (nlstate); i++){
3668: for(j=1; j<=(nlstate+ndeath);j++){
3669: k=k+1;
3670: gp[k]=pmmij[i][j];
3671: }
3672: }
3673:
3674: for(i=1; i<=npar; i++)
3675: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3676:
3677: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3678: k=0;
3679: for(i=1; i<=(nlstate); i++){
3680: for(j=1; j<=(nlstate+ndeath);j++){
3681: k=k+1;
3682: gm[k]=pmmij[i][j];
3683: }
3684: }
3685:
3686: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3687: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3688: }
3689:
3690: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3691: for(theta=1; theta <=npar; theta++)
3692: trgradg[j][theta]=gradg[theta][j];
3693:
3694: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3695: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3696:
3697: pmij(pmmij,cov,ncovmodel,x,nlstate);
3698:
3699: k=0;
3700: for(i=1; i<=(nlstate); i++){
3701: for(j=1; j<=(nlstate+ndeath);j++){
3702: k=k+1;
3703: mu[k][(int) age]=pmmij[i][j];
3704: }
3705: }
3706: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3707: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3708: varpij[i][j][(int)age] = doldm[i][j];
3709:
3710: /*printf("\n%d ",(int)age);
3711: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3712: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3713: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3714: }*/
3715:
3716: fprintf(ficresprob,"\n%d ",(int)age);
3717: fprintf(ficresprobcov,"\n%d ",(int)age);
3718: fprintf(ficresprobcor,"\n%d ",(int)age);
3719:
3720: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3721: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3722: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3723: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3724: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3725: }
3726: i=0;
3727: for (k=1; k<=(nlstate);k++){
3728: for (l=1; l<=(nlstate+ndeath);l++){
3729: i++;
3730: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3731: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3732: for (j=1; j<=i;j++){
3733: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3734: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3735: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3736: }
3737: }
3738: }/* end of loop for state */
3739: } /* end of loop for age */
3740: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3741: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3742: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3743: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3744:
3745: /* Confidence intervalle of pij */
3746: /*
3747: fprintf(ficgp,"\nunset parametric;unset label");
3748: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3749: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3750: 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);
3751: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3752: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3753: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3754: */
3755:
3756: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3757: first1=1;first2=2;
3758: for (k2=1; k2<=(nlstate);k2++){
3759: for (l2=1; l2<=(nlstate+ndeath);l2++){
3760: if(l2==k2) continue;
3761: j=(k2-1)*(nlstate+ndeath)+l2;
3762: for (k1=1; k1<=(nlstate);k1++){
3763: for (l1=1; l1<=(nlstate+ndeath);l1++){
3764: if(l1==k1) continue;
3765: i=(k1-1)*(nlstate+ndeath)+l1;
3766: if(i<=j) continue;
3767: for (age=bage; age<=fage; age ++){
3768: if ((int)age %5==0){
3769: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3770: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3771: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3772: mu1=mu[i][(int) age]/stepm*YEARM ;
3773: mu2=mu[j][(int) age]/stepm*YEARM;
3774: c12=cv12/sqrt(v1*v2);
3775: /* Computing eigen value of matrix of covariance */
3776: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3777: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3778: if ((lc2 <0) || (lc1 <0) ){
3779: if(first2==1){
3780: first1=0;
3781: 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);
3782: }
3783: 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);
3784: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3785: /* lc2=fabs(lc2); */
3786: }
3787:
3788: /* Eigen vectors */
3789: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3790: /*v21=sqrt(1.-v11*v11); *//* error */
3791: v21=(lc1-v1)/cv12*v11;
3792: v12=-v21;
3793: v22=v11;
3794: tnalp=v21/v11;
3795: if(first1==1){
3796: first1=0;
3797: 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);
3798: }
3799: 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);
3800: /*printf(fignu*/
3801: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3802: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3803: if(first==1){
3804: first=0;
3805: fprintf(ficgp,"\nset parametric;unset label");
3806: 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);
3807: fprintf(ficgp,"\nset ter png small size 320, 240");
3808: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3809: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3810: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3811: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3812: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3813: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3814: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3815: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3816: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3817: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3818: 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",\
3819: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3820: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3821: }else{
3822: first=0;
3823: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3824: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3825: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3826: 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",\
3827: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3828: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3829: }/* if first */
3830: } /* age mod 5 */
3831: } /* end loop age */
3832: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3833: first=1;
3834: } /*l12 */
3835: } /* k12 */
3836: } /*l1 */
3837: }/* k1 */
3838: /* } /* loop covariates */
3839: }
3840: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3841: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3842: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3843: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3844: free_vector(xp,1,npar);
3845: fclose(ficresprob);
3846: fclose(ficresprobcov);
3847: fclose(ficresprobcor);
3848: fflush(ficgp);
3849: fflush(fichtmcov);
3850: }
3851:
3852:
3853: /******************* Printing html file ***********/
3854: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3855: int lastpass, int stepm, int weightopt, char model[],\
3856: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3857: int popforecast, int estepm ,\
3858: double jprev1, double mprev1,double anprev1, \
3859: double jprev2, double mprev2,double anprev2){
3860: int jj1, k1, i1, cpt;
3861:
3862: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3863: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3864: </ul>");
3865: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3866: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3867: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3868: fprintf(fichtm,"\
3869: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3870: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3871: fprintf(fichtm,"\
3872: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3873: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3874: fprintf(fichtm,"\
3875: - (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): \
3876: <a href=\"%s\">%s</a> <br>\n",
3877: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3878: fprintf(fichtm,"\
3879: - Population projections by age and states: \
3880: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3881:
3882: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3883:
3884: m=pow(2,cptcoveff);
3885: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3886:
3887: jj1=0;
3888: for(k1=1; k1<=m;k1++){
3889: for(i1=1; i1<=ncodemax[k1];i1++){
3890: jj1++;
3891: if (cptcovn > 0) {
3892: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3893: for (cpt=1; cpt<=cptcoveff;cpt++)
3894: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3895: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3896: }
3897: /* Pij */
3898: 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> \
3899: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3900: /* Quasi-incidences */
3901: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3902: 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> \
3903: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3904: /* Period (stable) prevalence in each health state */
3905: for(cpt=1; cpt<=nlstate;cpt++){
3906: fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
3907: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3908: }
3909: for(cpt=1; cpt<=nlstate;cpt++) {
3910: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3911: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3912: }
3913: } /* end i1 */
3914: }/* End k1 */
3915: fprintf(fichtm,"</ul>");
3916:
3917:
3918: fprintf(fichtm,"\
3919: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3920: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3921:
3922: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3923: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3924: fprintf(fichtm,"\
3925: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3926: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3927:
3928: fprintf(fichtm,"\
3929: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3930: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3931: fprintf(fichtm,"\
3932: - 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): \
3933: <a href=\"%s\">%s</a> <br>\n</li>",
3934: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3935: fprintf(fichtm,"\
3936: - (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): \
3937: <a href=\"%s\">%s</a> <br>\n</li>",
3938: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3939: fprintf(fichtm,"\
3940: - 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",
3941: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3942: fprintf(fichtm,"\
3943: - 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",
3944: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3945: fprintf(fichtm,"\
3946: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3947: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3948:
3949: /* if(popforecast==1) fprintf(fichtm,"\n */
3950: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3951: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3952: /* <br>",fileres,fileres,fileres,fileres); */
3953: /* else */
3954: /* 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); */
3955: fflush(fichtm);
3956: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3957:
3958: m=pow(2,cptcoveff);
3959: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3960:
3961: jj1=0;
3962: for(k1=1; k1<=m;k1++){
3963: for(i1=1; i1<=ncodemax[k1];i1++){
3964: jj1++;
3965: if (cptcovn > 0) {
3966: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3967: for (cpt=1; cpt<=cptcoveff;cpt++)
3968: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3969: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3970: }
3971: for(cpt=1; cpt<=nlstate;cpt++) {
3972: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3973: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
3974: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3975: }
3976: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3977: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3978: true period expectancies (those weighted with period prevalences are also\
3979: drawn in addition to the population based expectancies computed using\
3980: observed and cahotic prevalences: %s%d.png<br>\
3981: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3982: } /* end i1 */
3983: }/* End k1 */
3984: fprintf(fichtm,"</ul>");
3985: fflush(fichtm);
3986: }
3987:
3988: /******************* Gnuplot file **************/
3989: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3990:
3991: char dirfileres[132],optfileres[132];
3992: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3993: int ng=0;
3994: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3995: /* printf("Problem with file %s",optionfilegnuplot); */
3996: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3997: /* } */
3998:
3999: /*#ifdef windows */
4000: fprintf(ficgp,"cd \"%s\" \n",pathc);
4001: /*#endif */
4002: m=pow(2,cptcoveff);
4003:
4004: strcpy(dirfileres,optionfilefiname);
4005: strcpy(optfileres,"vpl");
4006: /* 1eme*/
4007: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4008: for (cpt=1; cpt<= nlstate ; cpt ++) {
4009: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4010: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4011: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4012: fprintf(ficgp,"set xlabel \"Age\" \n\
4013: set ylabel \"Probability\" \n\
4014: set ter png small size 320, 240\n\
4015: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4016:
4017: for (i=1; i<= nlstate ; i ++) {
4018: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4019: else fprintf(ficgp," \%%*lf (\%%*lf)");
4020: }
4021: 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);
4022: for (i=1; i<= nlstate ; i ++) {
4023: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4024: else fprintf(ficgp," \%%*lf (\%%*lf)");
4025: }
4026: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4027: for (i=1; i<= nlstate ; i ++) {
4028: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4029: else fprintf(ficgp," \%%*lf (\%%*lf)");
4030: }
4031: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4032: }
4033: }
4034: /*2 eme*/
4035: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4036: for (k1=1; k1<= m ; k1 ++) {
4037: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4038: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4039:
4040: for (i=1; i<= nlstate+1 ; i ++) {
4041: k=2*i;
4042: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4043: for (j=1; j<= nlstate+1 ; j ++) {
4044: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4045: else fprintf(ficgp," \%%*lf (\%%*lf)");
4046: }
4047: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4048: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4049: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4050: for (j=1; j<= nlstate+1 ; j ++) {
4051: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4052: else fprintf(ficgp," \%%*lf (\%%*lf)");
4053: }
4054: fprintf(ficgp,"\" t\"\" w l lt 0,");
4055: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4056: for (j=1; j<= nlstate+1 ; j ++) {
4057: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4058: else fprintf(ficgp," \%%*lf (\%%*lf)");
4059: }
4060: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4061: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4062: }
4063: }
4064:
4065: /*3eme*/
4066:
4067: for (k1=1; k1<= m ; k1 ++) {
4068: for (cpt=1; cpt<= nlstate ; cpt ++) {
4069: /* k=2+nlstate*(2*cpt-2); */
4070: k=2+(nlstate+1)*(cpt-1);
4071: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4072: fprintf(ficgp,"set ter png small size 320, 240\n\
4073: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4074: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4075: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4076: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4077: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4078: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4079: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4080:
4081: */
4082: for (i=1; i< nlstate ; i ++) {
4083: 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);
4084: /* 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);*/
4085:
4086: }
4087: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4088: }
4089: }
4090:
4091: /* CV preval stable (period) */
4092: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4093: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4094: k=3;
4095: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4096: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4097: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4098: set ter png small size 320, 240\n\
4099: unset log y\n\
4100: plot [%.f:%.f] ", ageminpar, agemaxpar);
4101: for (i=1; i<= nlstate ; i ++){
4102: if(i==1)
4103: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4104: else
4105: fprintf(ficgp,", '' ");
4106: l=(nlstate+ndeath)*(i-1)+1;
4107: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4108: for (j=1; j<= (nlstate-1) ; j ++)
4109: fprintf(ficgp,"+$%d",k+l+j);
4110: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4111: } /* nlstate */
4112: fprintf(ficgp,"\n");
4113: } /* end cpt state*/
4114: } /* end covariate */
4115:
4116: /* proba elementaires */
4117: for(i=1,jk=1; i <=nlstate; i++){
4118: for(k=1; k <=(nlstate+ndeath); k++){
4119: if (k != i) {
4120: for(j=1; j <=ncovmodel; j++){
4121: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4122: jk++;
4123: fprintf(ficgp,"\n");
4124: }
4125: }
4126: }
4127: }
4128: /*goto avoid;*/
4129: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4130: for(jk=1; jk <=m; jk++) {
4131: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4132: if (ng==2)
4133: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4134: else
4135: fprintf(ficgp,"\nset title \"Probability\"\n");
4136: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4137: i=1;
4138: for(k2=1; k2<=nlstate; k2++) {
4139: k3=i;
4140: for(k=1; k<=(nlstate+ndeath); k++) {
4141: if (k != k2){
4142: if(ng==2)
4143: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4144: else
4145: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4146: ij=1;/* To be checked else nbcode[0][0] wrong */
4147: for(j=3; j <=ncovmodel; j++) {
4148: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4149: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4150: /* ij++; */
4151: /* } */
4152: /* else */
4153: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4154: }
4155: fprintf(ficgp,")/(1");
4156:
4157: for(k1=1; k1 <=nlstate; k1++){
4158: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4159: ij=1;
4160: for(j=3; j <=ncovmodel; j++){
4161: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4162: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4163: /* ij++; */
4164: /* } */
4165: /* else */
4166: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4167: }
4168: fprintf(ficgp,")");
4169: }
4170: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4171: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4172: i=i+ncovmodel;
4173: }
4174: } /* end k */
4175: } /* end k2 */
4176: } /* end jk */
4177: } /* end ng */
4178: avoid:
4179: fflush(ficgp);
4180: } /* end gnuplot */
4181:
4182:
4183: /*************** Moving average **************/
4184: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4185:
4186: int i, cpt, cptcod;
4187: int modcovmax =1;
4188: int mobilavrange, mob;
4189: double age;
4190:
4191: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4192: a covariate has 2 modalities */
4193: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4194:
4195: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4196: if(mobilav==1) mobilavrange=5; /* default */
4197: else mobilavrange=mobilav;
4198: for (age=bage; age<=fage; age++)
4199: for (i=1; i<=nlstate;i++)
4200: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4201: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4202: /* We keep the original values on the extreme ages bage, fage and for
4203: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4204: we use a 5 terms etc. until the borders are no more concerned.
4205: */
4206: for (mob=3;mob <=mobilavrange;mob=mob+2){
4207: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4208: for (i=1; i<=nlstate;i++){
4209: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4210: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4211: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4212: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4213: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4214: }
4215: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4216: }
4217: }
4218: }/* end age */
4219: }/* end mob */
4220: }else return -1;
4221: return 0;
4222: }/* End movingaverage */
4223:
4224:
4225: /************** Forecasting ******************/
4226: 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){
4227: /* proj1, year, month, day of starting projection
4228: agemin, agemax range of age
4229: dateprev1 dateprev2 range of dates during which prevalence is computed
4230: anproj2 year of en of projection (same day and month as proj1).
4231: */
4232: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4233: int *popage;
4234: double agec; /* generic age */
4235: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4236: double *popeffectif,*popcount;
4237: double ***p3mat;
4238: double ***mobaverage;
4239: char fileresf[FILENAMELENGTH];
4240:
4241: agelim=AGESUP;
4242: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4243:
4244: strcpy(fileresf,"f");
4245: strcat(fileresf,fileres);
4246: if((ficresf=fopen(fileresf,"w"))==NULL) {
4247: printf("Problem with forecast resultfile: %s\n", fileresf);
4248: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4249: }
4250: printf("Computing forecasting: result on file '%s' \n", fileresf);
4251: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4252:
4253: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4254:
4255: if (mobilav!=0) {
4256: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4257: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4258: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4259: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4260: }
4261: }
4262:
4263: stepsize=(int) (stepm+YEARM-1)/YEARM;
4264: if (stepm<=12) stepsize=1;
4265: if(estepm < stepm){
4266: printf ("Problem %d lower than %d\n",estepm, stepm);
4267: }
4268: else hstepm=estepm;
4269:
4270: hstepm=hstepm/stepm;
4271: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4272: fractional in yp1 */
4273: anprojmean=yp;
4274: yp2=modf((yp1*12),&yp);
4275: mprojmean=yp;
4276: yp1=modf((yp2*30.5),&yp);
4277: jprojmean=yp;
4278: if(jprojmean==0) jprojmean=1;
4279: if(mprojmean==0) jprojmean=1;
4280:
4281: i1=cptcoveff;
4282: if (cptcovn < 1){i1=1;}
4283:
4284: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4285:
4286: fprintf(ficresf,"#****** Routine prevforecast **\n");
4287:
4288: /* if (h==(int)(YEARM*yearp)){ */
4289: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4290: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4291: k=k+1;
4292: fprintf(ficresf,"\n#******");
4293: for(j=1;j<=cptcoveff;j++) {
4294: 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]]);
4295: }
4296: fprintf(ficresf,"******\n");
4297: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4298: for(j=1; j<=nlstate+ndeath;j++){
4299: for(i=1; i<=nlstate;i++)
4300: fprintf(ficresf," p%d%d",i,j);
4301: fprintf(ficresf," p.%d",j);
4302: }
4303: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4304: fprintf(ficresf,"\n");
4305: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4306:
4307: for (agec=fage; agec>=(ageminpar-1); agec--){
4308: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4309: nhstepm = nhstepm/hstepm;
4310: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4311: oldm=oldms;savm=savms;
4312: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4313:
4314: for (h=0; h<=nhstepm; h++){
4315: if (h*hstepm/YEARM*stepm ==yearp) {
4316: fprintf(ficresf,"\n");
4317: for(j=1;j<=cptcoveff;j++)
4318: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4319: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4320: }
4321: for(j=1; j<=nlstate+ndeath;j++) {
4322: ppij=0.;
4323: for(i=1; i<=nlstate;i++) {
4324: if (mobilav==1)
4325: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4326: else {
4327: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4328: }
4329: if (h*hstepm/YEARM*stepm== yearp) {
4330: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4331: }
4332: } /* end i */
4333: if (h*hstepm/YEARM*stepm==yearp) {
4334: fprintf(ficresf," %.3f", ppij);
4335: }
4336: }/* end j */
4337: } /* end h */
4338: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4339: } /* end agec */
4340: } /* end yearp */
4341: } /* end cptcod */
4342: } /* end cptcov */
4343:
4344: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4345:
4346: fclose(ficresf);
4347: }
4348:
4349: /************** Forecasting *****not tested NB*************/
4350: 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){
4351:
4352: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4353: int *popage;
4354: double calagedatem, agelim, kk1, kk2;
4355: double *popeffectif,*popcount;
4356: double ***p3mat,***tabpop,***tabpopprev;
4357: double ***mobaverage;
4358: char filerespop[FILENAMELENGTH];
4359:
4360: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4361: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4362: agelim=AGESUP;
4363: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4364:
4365: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4366:
4367:
4368: strcpy(filerespop,"pop");
4369: strcat(filerespop,fileres);
4370: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4371: printf("Problem with forecast resultfile: %s\n", filerespop);
4372: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4373: }
4374: printf("Computing forecasting: result on file '%s' \n", filerespop);
4375: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4376:
4377: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4378:
4379: if (mobilav!=0) {
4380: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4381: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4382: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4383: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4384: }
4385: }
4386:
4387: stepsize=(int) (stepm+YEARM-1)/YEARM;
4388: if (stepm<=12) stepsize=1;
4389:
4390: agelim=AGESUP;
4391:
4392: hstepm=1;
4393: hstepm=hstepm/stepm;
4394:
4395: if (popforecast==1) {
4396: if((ficpop=fopen(popfile,"r"))==NULL) {
4397: printf("Problem with population file : %s\n",popfile);exit(0);
4398: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4399: }
4400: popage=ivector(0,AGESUP);
4401: popeffectif=vector(0,AGESUP);
4402: popcount=vector(0,AGESUP);
4403:
4404: i=1;
4405: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4406:
4407: imx=i;
4408: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4409: }
4410:
4411: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4412: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4413: k=k+1;
4414: fprintf(ficrespop,"\n#******");
4415: for(j=1;j<=cptcoveff;j++) {
4416: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4417: }
4418: fprintf(ficrespop,"******\n");
4419: fprintf(ficrespop,"# Age");
4420: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4421: if (popforecast==1) fprintf(ficrespop," [Population]");
4422:
4423: for (cpt=0; cpt<=0;cpt++) {
4424: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4425:
4426: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4427: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4428: nhstepm = nhstepm/hstepm;
4429:
4430: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4431: oldm=oldms;savm=savms;
4432: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4433:
4434: for (h=0; h<=nhstepm; h++){
4435: if (h==(int) (calagedatem+YEARM*cpt)) {
4436: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4437: }
4438: for(j=1; j<=nlstate+ndeath;j++) {
4439: kk1=0.;kk2=0;
4440: for(i=1; i<=nlstate;i++) {
4441: if (mobilav==1)
4442: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4443: else {
4444: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4445: }
4446: }
4447: if (h==(int)(calagedatem+12*cpt)){
4448: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4449: /*fprintf(ficrespop," %.3f", kk1);
4450: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4451: }
4452: }
4453: for(i=1; i<=nlstate;i++){
4454: kk1=0.;
4455: for(j=1; j<=nlstate;j++){
4456: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4457: }
4458: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4459: }
4460:
4461: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4462: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4463: }
4464: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4465: }
4466: }
4467:
4468: /******/
4469:
4470: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4471: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4472: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4473: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4474: nhstepm = nhstepm/hstepm;
4475:
4476: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4477: oldm=oldms;savm=savms;
4478: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4479: for (h=0; h<=nhstepm; h++){
4480: if (h==(int) (calagedatem+YEARM*cpt)) {
4481: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4482: }
4483: for(j=1; j<=nlstate+ndeath;j++) {
4484: kk1=0.;kk2=0;
4485: for(i=1; i<=nlstate;i++) {
4486: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4487: }
4488: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4489: }
4490: }
4491: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4492: }
4493: }
4494: }
4495: }
4496:
4497: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4498:
4499: if (popforecast==1) {
4500: free_ivector(popage,0,AGESUP);
4501: free_vector(popeffectif,0,AGESUP);
4502: free_vector(popcount,0,AGESUP);
4503: }
4504: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4505: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4506: fclose(ficrespop);
4507: } /* End of popforecast */
4508:
4509: int fileappend(FILE *fichier, char *optionfich)
4510: {
4511: if((fichier=fopen(optionfich,"a"))==NULL) {
4512: printf("Problem with file: %s\n", optionfich);
4513: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4514: return (0);
4515: }
4516: fflush(fichier);
4517: return (1);
4518: }
4519:
4520:
4521: /**************** function prwizard **********************/
4522: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4523: {
4524:
4525: /* Wizard to print covariance matrix template */
4526:
4527: char ca[32], cb[32], cc[32];
4528: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4529: int numlinepar;
4530:
4531: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4532: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4533: for(i=1; i <=nlstate; i++){
4534: jj=0;
4535: for(j=1; j <=nlstate+ndeath; j++){
4536: if(j==i) continue;
4537: jj++;
4538: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4539: printf("%1d%1d",i,j);
4540: fprintf(ficparo,"%1d%1d",i,j);
4541: for(k=1; k<=ncovmodel;k++){
4542: /* printf(" %lf",param[i][j][k]); */
4543: /* fprintf(ficparo," %lf",param[i][j][k]); */
4544: printf(" 0.");
4545: fprintf(ficparo," 0.");
4546: }
4547: printf("\n");
4548: fprintf(ficparo,"\n");
4549: }
4550: }
4551: printf("# Scales (for hessian or gradient estimation)\n");
4552: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4553: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4554: for(i=1; i <=nlstate; i++){
4555: jj=0;
4556: for(j=1; j <=nlstate+ndeath; j++){
4557: if(j==i) continue;
4558: jj++;
4559: fprintf(ficparo,"%1d%1d",i,j);
4560: printf("%1d%1d",i,j);
4561: fflush(stdout);
4562: for(k=1; k<=ncovmodel;k++){
4563: /* printf(" %le",delti3[i][j][k]); */
4564: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4565: printf(" 0.");
4566: fprintf(ficparo," 0.");
4567: }
4568: numlinepar++;
4569: printf("\n");
4570: fprintf(ficparo,"\n");
4571: }
4572: }
4573: printf("# Covariance matrix\n");
4574: /* # 121 Var(a12)\n\ */
4575: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4576: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4577: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4578: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4579: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4580: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4581: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4582: fflush(stdout);
4583: fprintf(ficparo,"# Covariance matrix\n");
4584: /* # 121 Var(a12)\n\ */
4585: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4586: /* # ...\n\ */
4587: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4588:
4589: for(itimes=1;itimes<=2;itimes++){
4590: jj=0;
4591: for(i=1; i <=nlstate; i++){
4592: for(j=1; j <=nlstate+ndeath; j++){
4593: if(j==i) continue;
4594: for(k=1; k<=ncovmodel;k++){
4595: jj++;
4596: ca[0]= k+'a'-1;ca[1]='\0';
4597: if(itimes==1){
4598: printf("#%1d%1d%d",i,j,k);
4599: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4600: }else{
4601: printf("%1d%1d%d",i,j,k);
4602: fprintf(ficparo,"%1d%1d%d",i,j,k);
4603: /* printf(" %.5le",matcov[i][j]); */
4604: }
4605: ll=0;
4606: for(li=1;li <=nlstate; li++){
4607: for(lj=1;lj <=nlstate+ndeath; lj++){
4608: if(lj==li) continue;
4609: for(lk=1;lk<=ncovmodel;lk++){
4610: ll++;
4611: if(ll<=jj){
4612: cb[0]= lk +'a'-1;cb[1]='\0';
4613: if(ll<jj){
4614: if(itimes==1){
4615: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4616: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4617: }else{
4618: printf(" 0.");
4619: fprintf(ficparo," 0.");
4620: }
4621: }else{
4622: if(itimes==1){
4623: printf(" Var(%s%1d%1d)",ca,i,j);
4624: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4625: }else{
4626: printf(" 0.");
4627: fprintf(ficparo," 0.");
4628: }
4629: }
4630: }
4631: } /* end lk */
4632: } /* end lj */
4633: } /* end li */
4634: printf("\n");
4635: fprintf(ficparo,"\n");
4636: numlinepar++;
4637: } /* end k*/
4638: } /*end j */
4639: } /* end i */
4640: } /* end itimes */
4641:
4642: } /* end of prwizard */
4643: /******************* Gompertz Likelihood ******************************/
4644: double gompertz(double x[])
4645: {
4646: double A,B,L=0.0,sump=0.,num=0.;
4647: int i,n=0; /* n is the size of the sample */
4648:
4649: for (i=0;i<=imx-1 ; i++) {
4650: sump=sump+weight[i];
4651: /* sump=sump+1;*/
4652: num=num+1;
4653: }
4654:
4655:
4656: /* for (i=0; i<=imx; i++)
4657: 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]);*/
4658:
4659: for (i=1;i<=imx ; i++)
4660: {
4661: if (cens[i] == 1 && wav[i]>1)
4662: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4663:
4664: if (cens[i] == 0 && wav[i]>1)
4665: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4666: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4667:
4668: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4669: if (wav[i] > 1 ) { /* ??? */
4670: L=L+A*weight[i];
4671: /* 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]);*/
4672: }
4673: }
4674:
4675: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4676:
4677: return -2*L*num/sump;
4678: }
4679:
4680: #ifdef GSL
4681: /******************* Gompertz_f Likelihood ******************************/
4682: double gompertz_f(const gsl_vector *v, void *params)
4683: {
4684: double A,B,LL=0.0,sump=0.,num=0.;
4685: double *x= (double *) v->data;
4686: int i,n=0; /* n is the size of the sample */
4687:
4688: for (i=0;i<=imx-1 ; i++) {
4689: sump=sump+weight[i];
4690: /* sump=sump+1;*/
4691: num=num+1;
4692: }
4693:
4694:
4695: /* for (i=0; i<=imx; i++)
4696: 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]);*/
4697: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4698: for (i=1;i<=imx ; i++)
4699: {
4700: if (cens[i] == 1 && wav[i]>1)
4701: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4702:
4703: if (cens[i] == 0 && wav[i]>1)
4704: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4705: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4706:
4707: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4708: if (wav[i] > 1 ) { /* ??? */
4709: LL=LL+A*weight[i];
4710: /* 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]);*/
4711: }
4712: }
4713:
4714: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4715: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4716:
4717: return -2*LL*num/sump;
4718: }
4719: #endif
4720:
4721: /******************* Printing html file ***********/
4722: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4723: int lastpass, int stepm, int weightopt, char model[],\
4724: int imx, double p[],double **matcov,double agemortsup){
4725: int i,k;
4726:
4727: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4728: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4729: for (i=1;i<=2;i++)
4730: 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]));
4731: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4732: fprintf(fichtm,"</ul>");
4733:
4734: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4735:
4736: 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>");
4737:
4738: for (k=agegomp;k<(agemortsup-2);k++)
4739: 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]);
4740:
4741:
4742: fflush(fichtm);
4743: }
4744:
4745: /******************* Gnuplot file **************/
4746: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4747:
4748: char dirfileres[132],optfileres[132];
4749: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4750: int ng;
4751:
4752:
4753: /*#ifdef windows */
4754: fprintf(ficgp,"cd \"%s\" \n",pathc);
4755: /*#endif */
4756:
4757:
4758: strcpy(dirfileres,optionfilefiname);
4759: strcpy(optfileres,"vpl");
4760: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4761: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4762: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4763: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4764: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4765:
4766: }
4767:
4768: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4769: {
4770:
4771: /*-------- data file ----------*/
4772: FILE *fic;
4773: char dummy[]=" ";
4774: int i, j, n;
4775: int linei, month, year,iout;
4776: char line[MAXLINE], linetmp[MAXLINE];
4777: char stra[80], strb[80];
4778: char *stratrunc;
4779: int lstra;
4780:
4781:
4782: if((fic=fopen(datafile,"r"))==NULL) {
4783: printf("Problem while opening datafile: %s\n", datafile);return 1;
4784: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4785: }
4786:
4787: i=1;
4788: linei=0;
4789: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4790: linei=linei+1;
4791: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4792: if(line[j] == '\t')
4793: line[j] = ' ';
4794: }
4795: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4796: ;
4797: };
4798: line[j+1]=0; /* Trims blanks at end of line */
4799: if(line[0]=='#'){
4800: fprintf(ficlog,"Comment line\n%s\n",line);
4801: printf("Comment line\n%s\n",line);
4802: continue;
4803: }
4804: trimbb(linetmp,line); /* Trims multiple blanks in line */
4805: for (j=0; line[j]!='\0';j++){
4806: line[j]=linetmp[j];
4807: }
4808:
4809:
4810: for (j=maxwav;j>=1;j--){
4811: cutv(stra, strb, line, ' ');
4812: if(strb[0]=='.') { /* Missing status */
4813: lval=-1;
4814: }else{
4815: errno=0;
4816: lval=strtol(strb,&endptr,10);
4817: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4818: if( strb[0]=='\0' || (*endptr != '\0')){
4819: 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);
4820: 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);
4821: return 1;
4822: }
4823: }
4824: s[j][i]=lval;
4825:
4826: strcpy(line,stra);
4827: cutv(stra, strb,line,' ');
4828: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4829: }
4830: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4831: month=99;
4832: year=9999;
4833: }else{
4834: 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);
4835: 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);
4836: return 1;
4837: }
4838: anint[j][i]= (double) year;
4839: mint[j][i]= (double)month;
4840: strcpy(line,stra);
4841: } /* ENd Waves */
4842:
4843: cutv(stra, strb,line,' ');
4844: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4845: }
4846: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4847: month=99;
4848: year=9999;
4849: }else{
4850: 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);
4851: 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);
4852: return 1;
4853: }
4854: andc[i]=(double) year;
4855: moisdc[i]=(double) month;
4856: strcpy(line,stra);
4857:
4858: cutv(stra, strb,line,' ');
4859: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4860: }
4861: else if(iout=sscanf(strb,"%s.", dummy) != 0){
4862: month=99;
4863: year=9999;
4864: }else{
4865: 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);
4866: 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);
4867: return 1;
4868: }
4869: if (year==9999) {
4870: 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);
4871: 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);
4872: return 1;
4873:
4874: }
4875: annais[i]=(double)(year);
4876: moisnais[i]=(double)(month);
4877: strcpy(line,stra);
4878:
4879: cutv(stra, strb,line,' ');
4880: errno=0;
4881: dval=strtod(strb,&endptr);
4882: if( strb[0]=='\0' || (*endptr != '\0')){
4883: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4884: 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);
4885: fflush(ficlog);
4886: return 1;
4887: }
4888: weight[i]=dval;
4889: strcpy(line,stra);
4890:
4891: for (j=ncovcol;j>=1;j--){
4892: cutv(stra, strb,line,' ');
4893: if(strb[0]=='.') { /* Missing status */
4894: lval=-1;
4895: }else{
4896: errno=0;
4897: lval=strtol(strb,&endptr,10);
4898: if( strb[0]=='\0' || (*endptr != '\0')){
4899: 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);
4900: 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);
4901: return 1;
4902: }
4903: }
4904: if(lval <-1 || lval >1){
4905: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4906: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4907: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4908: For example, for multinomial values like 1, 2 and 3,\n \
4909: build V1=0 V2=0 for the reference value (1),\n \
4910: V1=1 V2=0 for (2) \n \
4911: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4912: output of IMaCh is often meaningless.\n \
4913: Exiting.\n",lval,linei, i,line,j);
4914: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4915: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4916: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4917: For example, for multinomial values like 1, 2 and 3,\n \
4918: build V1=0 V2=0 for the reference value (1),\n \
4919: V1=1 V2=0 for (2) \n \
4920: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4921: output of IMaCh is often meaningless.\n \
4922: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4923: return 1;
4924: }
4925: covar[j][i]=(double)(lval);
4926: strcpy(line,stra);
4927: }
4928: lstra=strlen(stra);
4929:
4930: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4931: stratrunc = &(stra[lstra-9]);
4932: num[i]=atol(stratrunc);
4933: }
4934: else
4935: num[i]=atol(stra);
4936: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4937: 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;}*/
4938:
4939: i=i+1;
4940: } /* End loop reading data */
4941:
4942: *imax=i-1; /* Number of individuals */
4943: fclose(fic);
4944:
4945: return (0);
4946: endread:
4947: printf("Exiting readdata: ");
4948: fclose(fic);
4949: return (1);
4950:
4951:
4952:
4953: }
4954: void removespace(char *str) {
4955: char *p1 = str, *p2 = str;
4956: do
4957: while (*p2 == ' ')
4958: p2++;
4959: while (*p1++ = *p2++);
4960: }
4961:
4962: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
4963: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
4964: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
4965: * - cptcovn or number of covariates k of the models excluding age*products =6
4966: * - cptcovage number of covariates with age*products =2
4967: * - cptcovs number of simple covariates
4968: * - 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
4969: * which is a new column after the 9 (ncovcol) variables.
4970: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
4971: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
4972: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
4973: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
4974: */
4975: {
4976: int i, j, k, ks;
4977: int i1, j1, k1, k2;
4978: char modelsav[80];
4979: char stra[80], strb[80], strc[80], strd[80],stre[80];
4980:
4981: /*removespace(model);*/
4982: if (strlen(model) >1){ /* If there is at least 1 covariate */
4983: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
4984: j=nbocc(model,'+'); /**< j=Number of '+' */
4985: j1=nbocc(model,'*'); /**< j1=Number of '*' */
4986: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
4987: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
4988: /* including age products which are counted in cptcovage.
4989: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
4990: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
4991: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
4992: strcpy(modelsav,model);
4993: if (strstr(model,"AGE") !=0){
4994: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4995: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
4996: return 1;
4997: }
4998: if (strstr(model,"v") !=0){
4999: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5000: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5001: return 1;
5002: }
5003:
5004: /* Design
5005: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5006: * < ncovcol=8 >
5007: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5008: * k= 1 2 3 4 5 6 7 8
5009: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5010: * covar[k,i], value of kth covariate if not including age for individual i:
5011: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5012: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5013: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5014: * Tage[++cptcovage]=k
5015: * if products, new covar are created after ncovcol with k1
5016: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5017: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5018: * 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
5019: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5020: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5021: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5022: * < ncovcol=8 >
5023: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5024: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5025: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5026: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5027: * p Tprod[1]@2={ 6, 5}
5028: *p Tvard[1][1]@4= {7, 8, 5, 6}
5029: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5030: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5031: *How to reorganize?
5032: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5033: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5034: * {2, 1, 4, 8, 5, 6, 3, 7}
5035: * Struct []
5036: */
5037:
5038: /* This loop fills the array Tvar from the string 'model'.*/
5039: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5040: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5041: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5042: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5043: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5044: /* k=1 Tvar[1]=2 (from V2) */
5045: /* k=5 Tvar[5] */
5046: /* for (k=1; k<=cptcovn;k++) { */
5047: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5048: /* } */
5049: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5050: /*
5051: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5052: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5053: Tvar[k]=0;
5054: cptcovage=0;
5055: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5056: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5057: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5058: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5059: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5060: /*scanf("%d",i);*/
5061: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5062: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5063: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5064: /* covar is not filled and then is empty */
5065: cptcovprod--;
5066: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5067: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5068: cptcovage++; /* Sums the number of covariates which include age as a product */
5069: Tage[cptcovage]=k; /* Tage[1] = 4 */
5070: /*printf("stre=%s ", stre);*/
5071: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5072: cptcovprod--;
5073: cutl(stre,strb,strc,'V');
5074: Tvar[k]=atoi(stre);
5075: cptcovage++;
5076: Tage[cptcovage]=k;
5077: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5078: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5079: cptcovn++;
5080: cptcovprodnoage++;k1++;
5081: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5082: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5083: because this model-covariate is a construction we invent a new column
5084: ncovcol + k1
5085: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5086: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5087: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5088: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5089: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5090: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5091: k2=k2+2;
5092: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5093: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5094: for (i=1; i<=lastobs;i++){
5095: /* Computes the new covariate which is a product of
5096: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5097: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5098: }
5099: } /* End age is not in the model */
5100: } /* End if model includes a product */
5101: else { /* no more sum */
5102: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5103: /* scanf("%d",i);*/
5104: cutl(strd,strc,strb,'V');
5105: ks++; /**< Number of simple covariates */
5106: cptcovn++;
5107: Tvar[k]=atoi(strd);
5108: }
5109: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5110: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5111: scanf("%d",i);*/
5112: } /* end of loop + */
5113: } /* end model */
5114:
5115: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5116: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5117:
5118: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5119: printf("cptcovprod=%d ", cptcovprod);
5120: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5121:
5122: scanf("%d ",i);*/
5123:
5124:
5125: return (0); /* with covar[new additional covariate if product] and Tage if age */
5126: endread:
5127: printf("Exiting decodemodel: ");
5128: return (1);
5129: }
5130:
5131: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5132: {
5133: int i, m;
5134:
5135: for (i=1; i<=imx; i++) {
5136: for(m=2; (m<= maxwav); m++) {
5137: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5138: anint[m][i]=9999;
5139: s[m][i]=-1;
5140: }
5141: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5142: *nberr++;
5143: 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);
5144: 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);
5145: s[m][i]=-1;
5146: }
5147: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5148: *nberr++;
5149: 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]);
5150: 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]);
5151: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5152: }
5153: }
5154: }
5155:
5156: for (i=1; i<=imx; i++) {
5157: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5158: for(m=firstpass; (m<= lastpass); m++){
5159: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5160: if (s[m][i] >= nlstate+1) {
5161: if(agedc[i]>0)
5162: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5163: agev[m][i]=agedc[i];
5164: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5165: else {
5166: if ((int)andc[i]!=9999){
5167: nbwarn++;
5168: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5169: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5170: agev[m][i]=-1;
5171: }
5172: }
5173: }
5174: else if(s[m][i] !=9){ /* Standard case, age in fractional
5175: years but with the precision of a month */
5176: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5177: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5178: agev[m][i]=1;
5179: else if(agev[m][i] < *agemin){
5180: *agemin=agev[m][i];
5181: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5182: }
5183: else if(agev[m][i] >*agemax){
5184: *agemax=agev[m][i];
5185: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5186: }
5187: /*agev[m][i]=anint[m][i]-annais[i];*/
5188: /* agev[m][i] = age[i]+2*m;*/
5189: }
5190: else { /* =9 */
5191: agev[m][i]=1;
5192: s[m][i]=-1;
5193: }
5194: }
5195: else /*= 0 Unknown */
5196: agev[m][i]=1;
5197: }
5198:
5199: }
5200: for (i=1; i<=imx; i++) {
5201: for(m=firstpass; (m<=lastpass); m++){
5202: if (s[m][i] > (nlstate+ndeath)) {
5203: *nberr++;
5204: 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);
5205: 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);
5206: return 1;
5207: }
5208: }
5209: }
5210:
5211: /*for (i=1; i<=imx; i++){
5212: for (m=firstpass; (m<lastpass); m++){
5213: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5214: }
5215:
5216: }*/
5217:
5218:
5219: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5220: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5221:
5222: return (0);
5223: endread:
5224: printf("Exiting calandcheckages: ");
5225: return (1);
5226: }
5227:
5228:
5229: /***********************************************/
5230: /**************** Main Program *****************/
5231: /***********************************************/
5232:
5233: int main(int argc, char *argv[])
5234: {
5235: #ifdef GSL
5236: const gsl_multimin_fminimizer_type *T;
5237: size_t iteri = 0, it;
5238: int rval = GSL_CONTINUE;
5239: int status = GSL_SUCCESS;
5240: double ssval;
5241: #endif
5242: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5243: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5244: int linei, month, year,iout;
5245: int jj, ll, li, lj, lk, imk;
5246: int numlinepar=0; /* Current linenumber of parameter file */
5247: int itimes;
5248: int NDIM=2;
5249: int vpopbased=0;
5250:
5251: char ca[32], cb[32], cc[32];
5252: /* FILE *fichtm; *//* Html File */
5253: /* FILE *ficgp;*/ /*Gnuplot File */
5254: struct stat info;
5255: double agedeb, agefin,hf;
5256: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5257:
5258: double fret;
5259: double **xi,tmp,delta;
5260:
5261: double dum; /* Dummy variable */
5262: double ***p3mat;
5263: double ***mobaverage;
5264: int *indx;
5265: char line[MAXLINE], linepar[MAXLINE];
5266: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5267: char pathr[MAXLINE], pathimach[MAXLINE];
5268: char **bp, *tok, *val; /* pathtot */
5269: int firstobs=1, lastobs=10;
5270: int sdeb, sfin; /* Status at beginning and end */
5271: int c, h , cpt,l;
5272: int ju,jl, mi;
5273: int i1,j1, jk,aa,bb, stepsize, ij;
5274: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5275: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5276: int mobilav=0,popforecast=0;
5277: int hstepm, nhstepm;
5278: int agemortsup;
5279: float sumlpop=0.;
5280: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5281: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5282:
5283: double bage, fage, age, agelim, agebase;
5284: double ftolpl=FTOL;
5285: double **prlim;
5286: double ***param; /* Matrix of parameters */
5287: double *p;
5288: double **matcov; /* Matrix of covariance */
5289: double ***delti3; /* Scale */
5290: double *delti; /* Scale */
5291: double ***eij, ***vareij;
5292: double **varpl; /* Variances of prevalence limits by age */
5293: double *epj, vepp;
5294: double kk1, kk2;
5295: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5296: double **ximort;
5297: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5298: int *dcwave;
5299:
5300: char z[1]="c", occ;
5301:
5302: /*char *strt;*/
5303: char strtend[80];
5304:
5305: long total_usecs;
5306:
5307: /* setlocale (LC_ALL, ""); */
5308: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5309: /* textdomain (PACKAGE); */
5310: /* setlocale (LC_CTYPE, ""); */
5311: /* setlocale (LC_MESSAGES, ""); */
5312:
5313: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5314: (void) gettimeofday(&start_time,&tzp);
5315: curr_time=start_time;
5316: tm = *localtime(&start_time.tv_sec);
5317: tmg = *gmtime(&start_time.tv_sec);
5318: strcpy(strstart,asctime(&tm));
5319:
5320: /* printf("Localtime (at start)=%s",strstart); */
5321: /* tp.tv_sec = tp.tv_sec +86400; */
5322: /* tm = *localtime(&start_time.tv_sec); */
5323: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5324: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5325: /* tmg.tm_hour=tmg.tm_hour + 1; */
5326: /* tp.tv_sec = mktime(&tmg); */
5327: /* strt=asctime(&tmg); */
5328: /* printf("Time(after) =%s",strstart); */
5329: /* (void) time (&time_value);
5330: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5331: * tm = *localtime(&time_value);
5332: * strstart=asctime(&tm);
5333: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5334: */
5335:
5336: nberr=0; /* Number of errors and warnings */
5337: nbwarn=0;
5338: getcwd(pathcd, size);
5339:
5340: printf("\n%s\n%s",version,fullversion);
5341: if(argc <=1){
5342: printf("\nEnter the parameter file name: ");
5343: fgets(pathr,FILENAMELENGTH,stdin);
5344: i=strlen(pathr);
5345: if(pathr[i-1]=='\n')
5346: pathr[i-1]='\0';
5347: i=strlen(pathr);
5348: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5349: pathr[i-1]='\0';
5350: for (tok = pathr; tok != NULL; ){
5351: printf("Pathr |%s|\n",pathr);
5352: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5353: printf("val= |%s| pathr=%s\n",val,pathr);
5354: strcpy (pathtot, val);
5355: if(pathr[0] == '\0') break; /* Dirty */
5356: }
5357: }
5358: else{
5359: strcpy(pathtot,argv[1]);
5360: }
5361: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5362: /*cygwin_split_path(pathtot,path,optionfile);
5363: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5364: /* cutv(path,optionfile,pathtot,'\\');*/
5365:
5366: /* Split argv[0], imach program to get pathimach */
5367: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5368: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5369: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5370: /* strcpy(pathimach,argv[0]); */
5371: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5372: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5373: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5374: chdir(path); /* Can be a relative path */
5375: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5376: printf("Current directory %s!\n",pathcd);
5377: strcpy(command,"mkdir ");
5378: strcat(command,optionfilefiname);
5379: if((outcmd=system(command)) != 0){
5380: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5381: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5382: /* fclose(ficlog); */
5383: /* exit(1); */
5384: }
5385: /* if((imk=mkdir(optionfilefiname))<0){ */
5386: /* perror("mkdir"); */
5387: /* } */
5388:
5389: /*-------- arguments in the command line --------*/
5390:
5391: /* Log file */
5392: strcat(filelog, optionfilefiname);
5393: strcat(filelog,".log"); /* */
5394: if((ficlog=fopen(filelog,"w"))==NULL) {
5395: printf("Problem with logfile %s\n",filelog);
5396: goto end;
5397: }
5398: fprintf(ficlog,"Log filename:%s\n",filelog);
5399: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5400: fprintf(ficlog,"\nEnter the parameter file name: \n");
5401: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5402: path=%s \n\
5403: optionfile=%s\n\
5404: optionfilext=%s\n\
5405: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5406:
5407: printf("Local time (at start):%s",strstart);
5408: fprintf(ficlog,"Local time (at start): %s",strstart);
5409: fflush(ficlog);
5410: /* (void) gettimeofday(&curr_time,&tzp); */
5411: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5412:
5413: /* */
5414: strcpy(fileres,"r");
5415: strcat(fileres, optionfilefiname);
5416: strcat(fileres,".txt"); /* Other files have txt extension */
5417:
5418: /*---------arguments file --------*/
5419:
5420: if((ficpar=fopen(optionfile,"r"))==NULL) {
5421: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5422: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5423: fflush(ficlog);
5424: /* goto end; */
5425: exit(70);
5426: }
5427:
5428:
5429:
5430: strcpy(filereso,"o");
5431: strcat(filereso,fileres);
5432: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5433: printf("Problem with Output resultfile: %s\n", filereso);
5434: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5435: fflush(ficlog);
5436: goto end;
5437: }
5438:
5439: /* Reads comments: lines beginning with '#' */
5440: numlinepar=0;
5441: while((c=getc(ficpar))=='#' && c!= EOF){
5442: ungetc(c,ficpar);
5443: fgets(line, MAXLINE, ficpar);
5444: numlinepar++;
5445: fputs(line,stdout);
5446: fputs(line,ficparo);
5447: fputs(line,ficlog);
5448: }
5449: ungetc(c,ficpar);
5450:
5451: 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);
5452: numlinepar++;
5453: 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);
5454: 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);
5455: 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);
5456: fflush(ficlog);
5457: while((c=getc(ficpar))=='#' && c!= EOF){
5458: ungetc(c,ficpar);
5459: fgets(line, MAXLINE, ficpar);
5460: numlinepar++;
5461: fputs(line, stdout);
5462: //puts(line);
5463: fputs(line,ficparo);
5464: fputs(line,ficlog);
5465: }
5466: ungetc(c,ficpar);
5467:
5468:
5469: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5470: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5471: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5472: v1+v2*age+v2*v3 makes cptcovn = 3
5473: */
5474: if (strlen(model)>1)
5475: 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*/
5476: else
5477: ncovmodel=2;
5478: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5479: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5480: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5481: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5482: 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);
5483: 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);
5484: fflush(stdout);
5485: fclose (ficlog);
5486: goto end;
5487: }
5488: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5489: delti=delti3[1][1];
5490: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5491: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5492: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5493: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5494: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5495: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5496: fclose (ficparo);
5497: fclose (ficlog);
5498: goto end;
5499: exit(0);
5500: }
5501: else if(mle==-3) {
5502: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5503: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5504: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5505: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5506: matcov=matrix(1,npar,1,npar);
5507: }
5508: else{
5509: /* Read guessed parameters */
5510: /* Reads comments: lines beginning with '#' */
5511: while((c=getc(ficpar))=='#' && c!= EOF){
5512: ungetc(c,ficpar);
5513: fgets(line, MAXLINE, ficpar);
5514: numlinepar++;
5515: fputs(line,stdout);
5516: fputs(line,ficparo);
5517: fputs(line,ficlog);
5518: }
5519: ungetc(c,ficpar);
5520:
5521: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5522: for(i=1; i <=nlstate; i++){
5523: j=0;
5524: for(jj=1; jj <=nlstate+ndeath; jj++){
5525: if(jj==i) continue;
5526: j++;
5527: fscanf(ficpar,"%1d%1d",&i1,&j1);
5528: if ((i1 != i) && (j1 != j)){
5529: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5530: It might be a problem of design; if ncovcol and the model are correct\n \
5531: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5532: exit(1);
5533: }
5534: fprintf(ficparo,"%1d%1d",i1,j1);
5535: if(mle==1)
5536: printf("%1d%1d",i,j);
5537: fprintf(ficlog,"%1d%1d",i,j);
5538: for(k=1; k<=ncovmodel;k++){
5539: fscanf(ficpar," %lf",¶m[i][j][k]);
5540: if(mle==1){
5541: printf(" %lf",param[i][j][k]);
5542: fprintf(ficlog," %lf",param[i][j][k]);
5543: }
5544: else
5545: fprintf(ficlog," %lf",param[i][j][k]);
5546: fprintf(ficparo," %lf",param[i][j][k]);
5547: }
5548: fscanf(ficpar,"\n");
5549: numlinepar++;
5550: if(mle==1)
5551: printf("\n");
5552: fprintf(ficlog,"\n");
5553: fprintf(ficparo,"\n");
5554: }
5555: }
5556: fflush(ficlog);
5557:
5558: /* Reads scales values */
5559: p=param[1][1];
5560:
5561: /* Reads comments: lines beginning with '#' */
5562: while((c=getc(ficpar))=='#' && c!= EOF){
5563: ungetc(c,ficpar);
5564: fgets(line, MAXLINE, ficpar);
5565: numlinepar++;
5566: fputs(line,stdout);
5567: fputs(line,ficparo);
5568: fputs(line,ficlog);
5569: }
5570: ungetc(c,ficpar);
5571:
5572: for(i=1; i <=nlstate; i++){
5573: for(j=1; j <=nlstate+ndeath-1; j++){
5574: fscanf(ficpar,"%1d%1d",&i1,&j1);
5575: if ((i1-i)*(j1-j)!=0){
5576: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5577: exit(1);
5578: }
5579: printf("%1d%1d",i,j);
5580: fprintf(ficparo,"%1d%1d",i1,j1);
5581: fprintf(ficlog,"%1d%1d",i1,j1);
5582: for(k=1; k<=ncovmodel;k++){
5583: fscanf(ficpar,"%le",&delti3[i][j][k]);
5584: printf(" %le",delti3[i][j][k]);
5585: fprintf(ficparo," %le",delti3[i][j][k]);
5586: fprintf(ficlog," %le",delti3[i][j][k]);
5587: }
5588: fscanf(ficpar,"\n");
5589: numlinepar++;
5590: printf("\n");
5591: fprintf(ficparo,"\n");
5592: fprintf(ficlog,"\n");
5593: }
5594: }
5595: fflush(ficlog);
5596:
5597: /* Reads covariance matrix */
5598: delti=delti3[1][1];
5599:
5600:
5601: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5602:
5603: /* Reads comments: lines beginning with '#' */
5604: while((c=getc(ficpar))=='#' && c!= EOF){
5605: ungetc(c,ficpar);
5606: fgets(line, MAXLINE, ficpar);
5607: numlinepar++;
5608: fputs(line,stdout);
5609: fputs(line,ficparo);
5610: fputs(line,ficlog);
5611: }
5612: ungetc(c,ficpar);
5613:
5614: matcov=matrix(1,npar,1,npar);
5615: for(i=1; i <=npar; i++)
5616: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5617:
5618: for(i=1; i <=npar; i++){
5619: fscanf(ficpar,"%s",str);
5620: if(mle==1)
5621: printf("%s",str);
5622: fprintf(ficlog,"%s",str);
5623: fprintf(ficparo,"%s",str);
5624: for(j=1; j <=i; j++){
5625: fscanf(ficpar," %le",&matcov[i][j]);
5626: if(mle==1){
5627: printf(" %.5le",matcov[i][j]);
5628: }
5629: fprintf(ficlog," %.5le",matcov[i][j]);
5630: fprintf(ficparo," %.5le",matcov[i][j]);
5631: }
5632: fscanf(ficpar,"\n");
5633: numlinepar++;
5634: if(mle==1)
5635: printf("\n");
5636: fprintf(ficlog,"\n");
5637: fprintf(ficparo,"\n");
5638: }
5639: for(i=1; i <=npar; i++)
5640: for(j=i+1;j<=npar;j++)
5641: matcov[i][j]=matcov[j][i];
5642:
5643: if(mle==1)
5644: printf("\n");
5645: fprintf(ficlog,"\n");
5646:
5647: fflush(ficlog);
5648:
5649: /*-------- Rewriting parameter file ----------*/
5650: strcpy(rfileres,"r"); /* "Rparameterfile */
5651: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5652: strcat(rfileres,"."); /* */
5653: strcat(rfileres,optionfilext); /* Other files have txt extension */
5654: if((ficres =fopen(rfileres,"w"))==NULL) {
5655: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5656: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5657: }
5658: fprintf(ficres,"#%s\n",version);
5659: } /* End of mle != -3 */
5660:
5661:
5662: n= lastobs;
5663: num=lvector(1,n);
5664: moisnais=vector(1,n);
5665: annais=vector(1,n);
5666: moisdc=vector(1,n);
5667: andc=vector(1,n);
5668: agedc=vector(1,n);
5669: cod=ivector(1,n);
5670: weight=vector(1,n);
5671: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5672: mint=matrix(1,maxwav,1,n);
5673: anint=matrix(1,maxwav,1,n);
5674: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5675: tab=ivector(1,NCOVMAX);
5676: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5677:
5678: /* Reads data from file datafile */
5679: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5680: goto end;
5681:
5682: /* Calculation of the number of parameters from char model */
5683: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5684: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5685: k=3 V4 Tvar[k=3]= 4 (from V4)
5686: k=2 V1 Tvar[k=2]= 1 (from V1)
5687: k=1 Tvar[1]=2 (from V2)
5688: */
5689: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5690: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5691: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5692: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5693: */
5694: /* For model-covariate k tells which data-covariate to use but
5695: because this model-covariate is a construction we invent a new column
5696: ncovcol + k1
5697: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5698: Tvar[3=V1*V4]=4+1 etc */
5699: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5700: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5701: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5702: */
5703: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5704: 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
5705: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5706: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5707: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5708: 4 covariates (3 plus signs)
5709: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5710: */
5711:
5712: if(decodemodel(model, lastobs) == 1)
5713: goto end;
5714:
5715: if((double)(lastobs-imx)/(double)imx > 1.10){
5716: nbwarn++;
5717: 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);
5718: 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);
5719: }
5720: /* if(mle==1){*/
5721: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5722: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5723: }
5724:
5725: /*-calculation of age at interview from date of interview and age at death -*/
5726: agev=matrix(1,maxwav,1,imx);
5727:
5728: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5729: goto end;
5730:
5731:
5732: agegomp=(int)agemin;
5733: free_vector(moisnais,1,n);
5734: free_vector(annais,1,n);
5735: /* free_matrix(mint,1,maxwav,1,n);
5736: free_matrix(anint,1,maxwav,1,n);*/
5737: free_vector(moisdc,1,n);
5738: free_vector(andc,1,n);
5739: /* */
5740:
5741: wav=ivector(1,imx);
5742: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5743: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5744: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5745:
5746: /* Concatenates waves */
5747: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5748: /* */
5749:
5750: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5751:
5752: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5753: ncodemax[1]=1;
5754: Ndum =ivector(-1,NCOVMAX);
5755: if (ncovmodel > 2)
5756: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5757:
5758: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5759: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5760: h=0;
5761:
5762:
5763: /*if (cptcovn > 0) */
5764:
5765:
5766: m=pow(2,cptcoveff);
5767:
5768: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5769: 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 */
5770: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5771: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5772: h++;
5773: if (h>m)
5774: h=1;
5775: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5776: * h 1 2 3 4
5777: *______________________________
5778: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5779: * 2 2 1 1 1
5780: * 3 i=2 1 2 1 1
5781: * 4 2 2 1 1
5782: * 5 i=3 1 i=2 1 2 1
5783: * 6 2 1 2 1
5784: * 7 i=4 1 2 2 1
5785: * 8 2 2 2 1
5786: * 9 i=5 1 i=3 1 i=2 1 1
5787: * 10 2 1 1 1
5788: * 11 i=6 1 2 1 1
5789: * 12 2 2 1 1
5790: * 13 i=7 1 i=4 1 2 1
5791: * 14 2 1 2 1
5792: * 15 i=8 1 2 2 1
5793: * 16 2 2 2 1
5794: */
5795: codtab[h][k]=j;
5796: /*codtab[h][Tvar[k]]=j;*/
5797: 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]]);
5798: }
5799: }
5800: }
5801: }
5802: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5803: codtab[1][2]=1;codtab[2][2]=2; */
5804: /* for(i=1; i <=m ;i++){
5805: for(k=1; k <=cptcovn; k++){
5806: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5807: }
5808: printf("\n");
5809: }
5810: scanf("%d",i);*/
5811:
5812: free_ivector(Ndum,-1,NCOVMAX);
5813:
5814:
5815:
5816: /*------------ gnuplot -------------*/
5817: strcpy(optionfilegnuplot,optionfilefiname);
5818: if(mle==-3)
5819: strcat(optionfilegnuplot,"-mort");
5820: strcat(optionfilegnuplot,".gp");
5821:
5822: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5823: printf("Problem with file %s",optionfilegnuplot);
5824: }
5825: else{
5826: fprintf(ficgp,"\n# %s\n", version);
5827: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5828: //fprintf(ficgp,"set missing 'NaNq'\n");
5829: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5830: }
5831: /* fclose(ficgp);*/
5832: /*--------- index.htm --------*/
5833:
5834: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5835: if(mle==-3)
5836: strcat(optionfilehtm,"-mort");
5837: strcat(optionfilehtm,".htm");
5838: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5839: printf("Problem with %s \n",optionfilehtm);
5840: exit(0);
5841: }
5842:
5843: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5844: strcat(optionfilehtmcov,"-cov.htm");
5845: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5846: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5847: }
5848: else{
5849: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5850: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5851: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5852: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5853: }
5854:
5855: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5856: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5857: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5858: \n\
5859: <hr size=\"2\" color=\"#EC5E5E\">\
5860: <ul><li><h4>Parameter files</h4>\n\
5861: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5862: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5863: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5864: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5865: - Date and time at start: %s</ul>\n",\
5866: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5867: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5868: fileres,fileres,\
5869: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5870: fflush(fichtm);
5871:
5872: strcpy(pathr,path);
5873: strcat(pathr,optionfilefiname);
5874: chdir(optionfilefiname); /* Move to directory named optionfile */
5875:
5876: /* Calculates basic frequencies. Computes observed prevalence at single age
5877: and prints on file fileres'p'. */
5878: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5879:
5880: fprintf(fichtm,"\n");
5881: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5882: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5883: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5884: imx,agemin,agemax,jmin,jmax,jmean);
5885: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5886: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5887: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5888: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5889: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5890:
5891:
5892: /* For Powell, parameters are in a vector p[] starting at p[1]
5893: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5894: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5895:
5896: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5897:
5898: if (mle==-3){
5899: ximort=matrix(1,NDIM,1,NDIM);
5900: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5901: cens=ivector(1,n);
5902: ageexmed=vector(1,n);
5903: agecens=vector(1,n);
5904: dcwave=ivector(1,n);
5905:
5906: for (i=1; i<=imx; i++){
5907: dcwave[i]=-1;
5908: for (m=firstpass; m<=lastpass; m++)
5909: if (s[m][i]>nlstate) {
5910: dcwave[i]=m;
5911: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5912: break;
5913: }
5914: }
5915:
5916: for (i=1; i<=imx; i++) {
5917: if (wav[i]>0){
5918: ageexmed[i]=agev[mw[1][i]][i];
5919: j=wav[i];
5920: agecens[i]=1.;
5921:
5922: if (ageexmed[i]> 1 && wav[i] > 0){
5923: agecens[i]=agev[mw[j][i]][i];
5924: cens[i]= 1;
5925: }else if (ageexmed[i]< 1)
5926: cens[i]= -1;
5927: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5928: cens[i]=0 ;
5929: }
5930: else cens[i]=-1;
5931: }
5932:
5933: for (i=1;i<=NDIM;i++) {
5934: for (j=1;j<=NDIM;j++)
5935: ximort[i][j]=(i == j ? 1.0 : 0.0);
5936: }
5937:
5938: /*p[1]=0.0268; p[NDIM]=0.083;*/
5939: /*printf("%lf %lf", p[1], p[2]);*/
5940:
5941:
5942: #ifdef GSL
5943: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5944: #elsedef
5945: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5946: #endif
5947: strcpy(filerespow,"pow-mort");
5948: strcat(filerespow,fileres);
5949: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5950: printf("Problem with resultfile: %s\n", filerespow);
5951: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5952: }
5953: #ifdef GSL
5954: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5955: #elsedef
5956: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5957: #endif
5958: /* for (i=1;i<=nlstate;i++)
5959: for(j=1;j<=nlstate+ndeath;j++)
5960: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5961: */
5962: fprintf(ficrespow,"\n");
5963: #ifdef GSL
5964: /* gsl starts here */
5965: T = gsl_multimin_fminimizer_nmsimplex;
5966: gsl_multimin_fminimizer *sfm = NULL;
5967: gsl_vector *ss, *x;
5968: gsl_multimin_function minex_func;
5969:
5970: /* Initial vertex size vector */
5971: ss = gsl_vector_alloc (NDIM);
5972:
5973: if (ss == NULL){
5974: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5975: }
5976: /* Set all step sizes to 1 */
5977: gsl_vector_set_all (ss, 0.001);
5978:
5979: /* Starting point */
5980:
5981: x = gsl_vector_alloc (NDIM);
5982:
5983: if (x == NULL){
5984: gsl_vector_free(ss);
5985: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5986: }
5987:
5988: /* Initialize method and iterate */
5989: /* p[1]=0.0268; p[NDIM]=0.083; */
5990: /* gsl_vector_set(x, 0, 0.0268); */
5991: /* gsl_vector_set(x, 1, 0.083); */
5992: gsl_vector_set(x, 0, p[1]);
5993: gsl_vector_set(x, 1, p[2]);
5994:
5995: minex_func.f = &gompertz_f;
5996: minex_func.n = NDIM;
5997: minex_func.params = (void *)&p; /* ??? */
5998:
5999: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6000: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6001:
6002: printf("Iterations beginning .....\n\n");
6003: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6004:
6005: iteri=0;
6006: while (rval == GSL_CONTINUE){
6007: iteri++;
6008: status = gsl_multimin_fminimizer_iterate(sfm);
6009:
6010: if (status) printf("error: %s\n", gsl_strerror (status));
6011: fflush(0);
6012:
6013: if (status)
6014: break;
6015:
6016: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6017: ssval = gsl_multimin_fminimizer_size (sfm);
6018:
6019: if (rval == GSL_SUCCESS)
6020: printf ("converged to a local maximum at\n");
6021:
6022: printf("%5d ", iteri);
6023: for (it = 0; it < NDIM; it++){
6024: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6025: }
6026: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6027: }
6028:
6029: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6030:
6031: gsl_vector_free(x); /* initial values */
6032: gsl_vector_free(ss); /* inital step size */
6033: for (it=0; it<NDIM; it++){
6034: p[it+1]=gsl_vector_get(sfm->x,it);
6035: fprintf(ficrespow," %.12lf", p[it]);
6036: }
6037: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6038: #endif
6039: #ifdef POWELL
6040: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6041: #endif
6042: fclose(ficrespow);
6043:
6044: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6045:
6046: for(i=1; i <=NDIM; i++)
6047: for(j=i+1;j<=NDIM;j++)
6048: matcov[i][j]=matcov[j][i];
6049:
6050: printf("\nCovariance matrix\n ");
6051: for(i=1; i <=NDIM; i++) {
6052: for(j=1;j<=NDIM;j++){
6053: printf("%f ",matcov[i][j]);
6054: }
6055: printf("\n ");
6056: }
6057:
6058: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6059: for (i=1;i<=NDIM;i++)
6060: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6061:
6062: lsurv=vector(1,AGESUP);
6063: lpop=vector(1,AGESUP);
6064: tpop=vector(1,AGESUP);
6065: lsurv[agegomp]=100000;
6066:
6067: for (k=agegomp;k<=AGESUP;k++) {
6068: agemortsup=k;
6069: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6070: }
6071:
6072: for (k=agegomp;k<agemortsup;k++)
6073: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6074:
6075: for (k=agegomp;k<agemortsup;k++){
6076: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6077: sumlpop=sumlpop+lpop[k];
6078: }
6079:
6080: tpop[agegomp]=sumlpop;
6081: for (k=agegomp;k<(agemortsup-3);k++){
6082: /* tpop[k+1]=2;*/
6083: tpop[k+1]=tpop[k]-lpop[k];
6084: }
6085:
6086:
6087: printf("\nAge lx qx dx Lx Tx e(x)\n");
6088: for (k=agegomp;k<(agemortsup-2);k++)
6089: 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]);
6090:
6091:
6092: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6093: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6094:
6095: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6096: stepm, weightopt,\
6097: model,imx,p,matcov,agemortsup);
6098:
6099: free_vector(lsurv,1,AGESUP);
6100: free_vector(lpop,1,AGESUP);
6101: free_vector(tpop,1,AGESUP);
6102: #ifdef GSL
6103: free_ivector(cens,1,n);
6104: free_vector(agecens,1,n);
6105: free_ivector(dcwave,1,n);
6106: free_matrix(ximort,1,NDIM,1,NDIM);
6107: #endif
6108: } /* Endof if mle==-3 */
6109:
6110: else{ /* For mle >=1 */
6111: globpr=0;/* debug */
6112: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6113: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6114: for (k=1; k<=npar;k++)
6115: printf(" %d %8.5f",k,p[k]);
6116: printf("\n");
6117: globpr=1; /* to print the contributions */
6118: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6119: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6120: for (k=1; k<=npar;k++)
6121: printf(" %d %8.5f",k,p[k]);
6122: printf("\n");
6123: if(mle>=1){ /* Could be 1 or 2 */
6124: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6125: }
6126:
6127: /*--------- results files --------------*/
6128: 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);
6129:
6130:
6131: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6132: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6133: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6134: for(i=1,jk=1; i <=nlstate; i++){
6135: for(k=1; k <=(nlstate+ndeath); k++){
6136: if (k != i) {
6137: printf("%d%d ",i,k);
6138: fprintf(ficlog,"%d%d ",i,k);
6139: fprintf(ficres,"%1d%1d ",i,k);
6140: for(j=1; j <=ncovmodel; j++){
6141: printf("%lf ",p[jk]);
6142: fprintf(ficlog,"%lf ",p[jk]);
6143: fprintf(ficres,"%lf ",p[jk]);
6144: jk++;
6145: }
6146: printf("\n");
6147: fprintf(ficlog,"\n");
6148: fprintf(ficres,"\n");
6149: }
6150: }
6151: }
6152: if(mle!=0){
6153: /* Computing hessian and covariance matrix */
6154: ftolhess=ftol; /* Usually correct */
6155: hesscov(matcov, p, npar, delti, ftolhess, func);
6156: }
6157: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6158: printf("# Scales (for hessian or gradient estimation)\n");
6159: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6160: for(i=1,jk=1; i <=nlstate; i++){
6161: for(j=1; j <=nlstate+ndeath; j++){
6162: if (j!=i) {
6163: fprintf(ficres,"%1d%1d",i,j);
6164: printf("%1d%1d",i,j);
6165: fprintf(ficlog,"%1d%1d",i,j);
6166: for(k=1; k<=ncovmodel;k++){
6167: printf(" %.5e",delti[jk]);
6168: fprintf(ficlog," %.5e",delti[jk]);
6169: fprintf(ficres," %.5e",delti[jk]);
6170: jk++;
6171: }
6172: printf("\n");
6173: fprintf(ficlog,"\n");
6174: fprintf(ficres,"\n");
6175: }
6176: }
6177: }
6178:
6179: 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");
6180: if(mle>=1)
6181: 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");
6182: 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");
6183: /* # 121 Var(a12)\n\ */
6184: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6185: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6186: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6187: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6188: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6189: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6190: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6191:
6192:
6193: /* Just to have a covariance matrix which will be more understandable
6194: even is we still don't want to manage dictionary of variables
6195: */
6196: for(itimes=1;itimes<=2;itimes++){
6197: jj=0;
6198: for(i=1; i <=nlstate; i++){
6199: for(j=1; j <=nlstate+ndeath; j++){
6200: if(j==i) continue;
6201: for(k=1; k<=ncovmodel;k++){
6202: jj++;
6203: ca[0]= k+'a'-1;ca[1]='\0';
6204: if(itimes==1){
6205: if(mle>=1)
6206: printf("#%1d%1d%d",i,j,k);
6207: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6208: fprintf(ficres,"#%1d%1d%d",i,j,k);
6209: }else{
6210: if(mle>=1)
6211: printf("%1d%1d%d",i,j,k);
6212: fprintf(ficlog,"%1d%1d%d",i,j,k);
6213: fprintf(ficres,"%1d%1d%d",i,j,k);
6214: }
6215: ll=0;
6216: for(li=1;li <=nlstate; li++){
6217: for(lj=1;lj <=nlstate+ndeath; lj++){
6218: if(lj==li) continue;
6219: for(lk=1;lk<=ncovmodel;lk++){
6220: ll++;
6221: if(ll<=jj){
6222: cb[0]= lk +'a'-1;cb[1]='\0';
6223: if(ll<jj){
6224: if(itimes==1){
6225: if(mle>=1)
6226: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6227: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6228: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6229: }else{
6230: if(mle>=1)
6231: printf(" %.5e",matcov[jj][ll]);
6232: fprintf(ficlog," %.5e",matcov[jj][ll]);
6233: fprintf(ficres," %.5e",matcov[jj][ll]);
6234: }
6235: }else{
6236: if(itimes==1){
6237: if(mle>=1)
6238: printf(" Var(%s%1d%1d)",ca,i,j);
6239: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6240: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6241: }else{
6242: if(mle>=1)
6243: printf(" %.5e",matcov[jj][ll]);
6244: fprintf(ficlog," %.5e",matcov[jj][ll]);
6245: fprintf(ficres," %.5e",matcov[jj][ll]);
6246: }
6247: }
6248: }
6249: } /* end lk */
6250: } /* end lj */
6251: } /* end li */
6252: if(mle>=1)
6253: printf("\n");
6254: fprintf(ficlog,"\n");
6255: fprintf(ficres,"\n");
6256: numlinepar++;
6257: } /* end k*/
6258: } /*end j */
6259: } /* end i */
6260: } /* end itimes */
6261:
6262: fflush(ficlog);
6263: fflush(ficres);
6264:
6265: while((c=getc(ficpar))=='#' && c!= EOF){
6266: ungetc(c,ficpar);
6267: fgets(line, MAXLINE, ficpar);
6268: fputs(line,stdout);
6269: fputs(line,ficparo);
6270: }
6271: ungetc(c,ficpar);
6272:
6273: estepm=0;
6274: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6275: if (estepm==0 || estepm < stepm) estepm=stepm;
6276: if (fage <= 2) {
6277: bage = ageminpar;
6278: fage = agemaxpar;
6279: }
6280:
6281: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6282: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6283: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6284:
6285: while((c=getc(ficpar))=='#' && c!= EOF){
6286: ungetc(c,ficpar);
6287: fgets(line, MAXLINE, ficpar);
6288: fputs(line,stdout);
6289: fputs(line,ficparo);
6290: }
6291: ungetc(c,ficpar);
6292:
6293: 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);
6294: 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);
6295: 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);
6296: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6297: 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);
6298:
6299: while((c=getc(ficpar))=='#' && c!= EOF){
6300: ungetc(c,ficpar);
6301: fgets(line, MAXLINE, ficpar);
6302: fputs(line,stdout);
6303: fputs(line,ficparo);
6304: }
6305: ungetc(c,ficpar);
6306:
6307:
6308: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6309: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6310:
6311: fscanf(ficpar,"pop_based=%d\n",&popbased);
6312: fprintf(ficparo,"pop_based=%d\n",popbased);
6313: fprintf(ficres,"pop_based=%d\n",popbased);
6314:
6315: while((c=getc(ficpar))=='#' && c!= EOF){
6316: ungetc(c,ficpar);
6317: fgets(line, MAXLINE, ficpar);
6318: fputs(line,stdout);
6319: fputs(line,ficparo);
6320: }
6321: ungetc(c,ficpar);
6322:
6323: 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);
6324: 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);
6325: 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);
6326: 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);
6327: 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);
6328: /* day and month of proj2 are not used but only year anproj2.*/
6329:
6330:
6331:
6332: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6333: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6334:
6335: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6336: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6337:
6338: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6339: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6340: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6341:
6342: /*------------ free_vector -------------*/
6343: /* chdir(path); */
6344:
6345: free_ivector(wav,1,imx);
6346: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6347: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6348: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6349: free_lvector(num,1,n);
6350: free_vector(agedc,1,n);
6351: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6352: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6353: fclose(ficparo);
6354: fclose(ficres);
6355:
6356:
6357: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6358: #include "prevlim.h" /* Use ficrespl, ficlog */
6359: fclose(ficrespl);
6360:
6361: #ifdef FREEEXIT2
6362: #include "freeexit2.h"
6363: #endif
6364:
6365: /*------------- h Pij x at various ages ------------*/
6366: #include "hpijx.h"
6367: fclose(ficrespij);
6368:
6369: /*-------------- Variance of one-step probabilities---*/
6370: k=1;
6371: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6372:
6373:
6374: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6375: for(i=1;i<=AGESUP;i++)
6376: for(j=1;j<=NCOVMAX;j++)
6377: for(k=1;k<=NCOVMAX;k++)
6378: probs[i][j][k]=0.;
6379:
6380: /*---------- Forecasting ------------------*/
6381: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6382: if(prevfcast==1){
6383: /* if(stepm ==1){*/
6384: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6385: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6386: /* } */
6387: /* else{ */
6388: /* erreur=108; */
6389: /* 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); */
6390: /* 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); */
6391: /* } */
6392: }
6393:
6394:
6395: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6396:
6397: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6398: /* 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",\
6399: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6400: */
6401:
6402: if (mobilav!=0) {
6403: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6404: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6405: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6406: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6407: }
6408: }
6409:
6410:
6411: /*---------- Health expectancies, no variances ------------*/
6412:
6413: strcpy(filerese,"e");
6414: strcat(filerese,fileres);
6415: if((ficreseij=fopen(filerese,"w"))==NULL) {
6416: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6417: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6418: }
6419: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6420: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6421: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6422: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6423:
6424: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6425: fprintf(ficreseij,"\n#****** ");
6426: for(j=1;j<=cptcoveff;j++) {
6427: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6428: }
6429: fprintf(ficreseij,"******\n");
6430:
6431: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6432: oldm=oldms;savm=savms;
6433: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6434:
6435: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6436: /*}*/
6437: }
6438: fclose(ficreseij);
6439:
6440:
6441: /*---------- Health expectancies and variances ------------*/
6442:
6443:
6444: strcpy(filerest,"t");
6445: strcat(filerest,fileres);
6446: if((ficrest=fopen(filerest,"w"))==NULL) {
6447: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6448: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6449: }
6450: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6451: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6452:
6453:
6454: strcpy(fileresstde,"stde");
6455: strcat(fileresstde,fileres);
6456: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6457: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6458: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6459: }
6460: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6461: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6462:
6463: strcpy(filerescve,"cve");
6464: strcat(filerescve,fileres);
6465: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6466: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6467: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6468: }
6469: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6470: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6471:
6472: strcpy(fileresv,"v");
6473: strcat(fileresv,fileres);
6474: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6475: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6476: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6477: }
6478: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6479: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6480:
6481: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6482: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6483:
6484: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6485: fprintf(ficrest,"\n#****** ");
6486: for(j=1;j<=cptcoveff;j++)
6487: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6488: fprintf(ficrest,"******\n");
6489:
6490: fprintf(ficresstdeij,"\n#****** ");
6491: fprintf(ficrescveij,"\n#****** ");
6492: for(j=1;j<=cptcoveff;j++) {
6493: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6494: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6495: }
6496: fprintf(ficresstdeij,"******\n");
6497: fprintf(ficrescveij,"******\n");
6498:
6499: fprintf(ficresvij,"\n#****** ");
6500: for(j=1;j<=cptcoveff;j++)
6501: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6502: fprintf(ficresvij,"******\n");
6503:
6504: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6505: oldm=oldms;savm=savms;
6506: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6507: /*
6508: */
6509: /* goto endfree; */
6510:
6511: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6512: pstamp(ficrest);
6513:
6514:
6515: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6516: oldm=oldms;savm=savms; /* Segmentation fault */
6517: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
6518: 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 ");
6519: if(vpopbased==1)
6520: 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);
6521: else
6522: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6523: fprintf(ficrest,"# Age e.. (std) ");
6524: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6525: fprintf(ficrest,"\n");
6526:
6527: epj=vector(1,nlstate+1);
6528: for(age=bage; age <=fage ;age++){
6529: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6530: if (vpopbased==1) {
6531: if(mobilav ==0){
6532: for(i=1; i<=nlstate;i++)
6533: prlim[i][i]=probs[(int)age][i][k];
6534: }else{ /* mobilav */
6535: for(i=1; i<=nlstate;i++)
6536: prlim[i][i]=mobaverage[(int)age][i][k];
6537: }
6538: }
6539:
6540: fprintf(ficrest," %4.0f",age);
6541: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6542: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6543: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6544: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6545: }
6546: epj[nlstate+1] +=epj[j];
6547: }
6548:
6549: for(i=1, vepp=0.;i <=nlstate;i++)
6550: for(j=1;j <=nlstate;j++)
6551: vepp += vareij[i][j][(int)age];
6552: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6553: for(j=1;j <=nlstate;j++){
6554: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6555: }
6556: fprintf(ficrest,"\n");
6557: }
6558: }
6559: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6560: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6561: free_vector(epj,1,nlstate+1);
6562: /*}*/
6563: }
6564: free_vector(weight,1,n);
6565: free_imatrix(Tvard,1,NCOVMAX,1,2);
6566: free_imatrix(s,1,maxwav+1,1,n);
6567: free_matrix(anint,1,maxwav,1,n);
6568: free_matrix(mint,1,maxwav,1,n);
6569: free_ivector(cod,1,n);
6570: free_ivector(tab,1,NCOVMAX);
6571: fclose(ficresstdeij);
6572: fclose(ficrescveij);
6573: fclose(ficresvij);
6574: fclose(ficrest);
6575: fclose(ficpar);
6576:
6577: /*------- Variance of period (stable) prevalence------*/
6578:
6579: strcpy(fileresvpl,"vpl");
6580: strcat(fileresvpl,fileres);
6581: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6582: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6583: exit(0);
6584: }
6585: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6586:
6587: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6588: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6589:
6590: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6591: fprintf(ficresvpl,"\n#****** ");
6592: for(j=1;j<=cptcoveff;j++)
6593: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6594: fprintf(ficresvpl,"******\n");
6595:
6596: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6597: oldm=oldms;savm=savms;
6598: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6599: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6600: /*}*/
6601: }
6602:
6603: fclose(ficresvpl);
6604:
6605: /*---------- End : free ----------------*/
6606: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6607: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6608: } /* mle==-3 arrives here for freeing */
6609: endfree:
6610: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6611: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6612: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6613: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6614: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6615: free_matrix(covar,0,NCOVMAX,1,n);
6616: free_matrix(matcov,1,npar,1,npar);
6617: /*free_vector(delti,1,npar);*/
6618: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6619: free_matrix(agev,1,maxwav,1,imx);
6620: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6621:
6622: free_ivector(ncodemax,1,NCOVMAX);
6623: free_ivector(Tvar,1,NCOVMAX);
6624: free_ivector(Tprod,1,NCOVMAX);
6625: free_ivector(Tvaraff,1,NCOVMAX);
6626: free_ivector(Tage,1,NCOVMAX);
6627:
6628: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6629: free_imatrix(codtab,1,100,1,10);
6630: fflush(fichtm);
6631: fflush(ficgp);
6632:
6633:
6634: if((nberr >0) || (nbwarn>0)){
6635: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6636: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6637: }else{
6638: printf("End of Imach\n");
6639: fprintf(ficlog,"End of Imach\n");
6640: }
6641: printf("See log file on %s\n",filelog);
6642: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6643: (void) gettimeofday(&end_time,&tzp);
6644: tm = *localtime(&end_time.tv_sec);
6645: tmg = *gmtime(&end_time.tv_sec);
6646: strcpy(strtend,asctime(&tm));
6647: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6648: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6649: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6650:
6651: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6652: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6653: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6654: /* printf("Total time was %d uSec.\n", total_usecs);*/
6655: /* if(fileappend(fichtm,optionfilehtm)){ */
6656: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6657: fclose(fichtm);
6658: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6659: fclose(fichtmcov);
6660: fclose(ficgp);
6661: fclose(ficlog);
6662: /*------ End -----------*/
6663:
6664:
6665: printf("Before Current directory %s!\n",pathcd);
6666: if(chdir(pathcd) != 0)
6667: printf("Can't move to directory %s!\n",path);
6668: if(getcwd(pathcd,MAXLINE) > 0)
6669: printf("Current directory %s!\n",pathcd);
6670: /*strcat(plotcmd,CHARSEPARATOR);*/
6671: sprintf(plotcmd,"gnuplot");
6672: #ifndef UNIX
6673: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6674: #endif
6675: if(!stat(plotcmd,&info)){
6676: printf("Error or gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6677: if(!stat(getenv("GNUPLOTBIN"),&info)){
6678: printf("Error or gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6679: }else
6680: strcpy(pplotcmd,plotcmd);
6681: #ifdef UNIX
6682: strcpy(plotcmd,GNUPLOTPROGRAM);
6683: if(!stat(plotcmd,&info)){
6684: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6685: }else
6686: strcpy(pplotcmd,plotcmd);
6687: #endif
6688: }else
6689: strcpy(pplotcmd,plotcmd);
6690:
6691: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6692: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6693:
6694: if((outcmd=system(plotcmd)) != 0){
6695: printf("gnuplot command might not be in your path: %s, err=%d\n", plotcmd, outcmd);
6696: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6697: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6698: if((outcmd=system(plotcmd)) != 0)
6699: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6700: }
6701: printf(" Successul, please wait...");
6702: while (z[0] != 'q') {
6703: /* chdir(path); */
6704: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6705: scanf("%s",z);
6706: /* if (z[0] == 'c') system("./imach"); */
6707: if (z[0] == 'e') {
6708: #ifdef OSX
6709: sprintf(pplotcmd, "open %s", optionfilehtm);
6710: #else
6711: sprintf(pplotcmd, "%s", optionfilehtm);
6712: #endif
6713: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6714: system(pplotcmd);
6715: }
6716: else if (z[0] == 'g') system(plotcmd);
6717: else if (z[0] == 'q') exit(0);
6718: }
6719: end:
6720: while (z[0] != 'q') {
6721: printf("\nType q for exiting: ");
6722: scanf("%s",z);
6723: }
6724: }
6725:
6726:
6727:
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