1: /* $Id: imach.c,v 1.168 2014/12/22 15:17:42 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.168 2014/12/22 15:17:42 brouard
5: Summary: udate
6:
7: Revision 1.167 2014/12/22 13:50:56 brouard
8: Summary: Testing uname and compiler version and if compiled 32 or 64
9:
10: Testing on Linux 64
11:
12: Revision 1.166 2014/12/22 11:40:47 brouard
13: *** empty log message ***
14:
15: Revision 1.165 2014/12/16 11:20:36 brouard
16: Summary: After compiling on Visual C
17:
18: * imach.c (Module): Merging 1.61 to 1.162
19:
20: Revision 1.164 2014/12/16 10:52:11 brouard
21: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
22:
23: * imach.c (Module): Merging 1.61 to 1.162
24:
25: Revision 1.163 2014/12/16 10:30:11 brouard
26: * imach.c (Module): Merging 1.61 to 1.162
27:
28: Revision 1.162 2014/09/25 11:43:39 brouard
29: Summary: temporary backup 0.99!
30:
31: Revision 1.1 2014/09/16 11:06:58 brouard
32: Summary: With some code (wrong) for nlopt
33:
34: Author:
35:
36: Revision 1.161 2014/09/15 20:41:41 brouard
37: Summary: Problem with macro SQR on Intel compiler
38:
39: Revision 1.160 2014/09/02 09:24:05 brouard
40: *** empty log message ***
41:
42: Revision 1.159 2014/09/01 10:34:10 brouard
43: Summary: WIN32
44: Author: Brouard
45:
46: Revision 1.158 2014/08/27 17:11:51 brouard
47: *** empty log message ***
48:
49: Revision 1.157 2014/08/27 16:26:55 brouard
50: Summary: Preparing windows Visual studio version
51: Author: Brouard
52:
53: In order to compile on Visual studio, time.h is now correct and time_t
54: and tm struct should be used. difftime should be used but sometimes I
55: just make the differences in raw time format (time(&now).
56: Trying to suppress #ifdef LINUX
57: Add xdg-open for __linux in order to open default browser.
58:
59: Revision 1.156 2014/08/25 20:10:10 brouard
60: *** empty log message ***
61:
62: Revision 1.155 2014/08/25 18:32:34 brouard
63: Summary: New compile, minor changes
64: Author: Brouard
65:
66: Revision 1.154 2014/06/20 17:32:08 brouard
67: Summary: Outputs now all graphs of convergence to period prevalence
68:
69: Revision 1.153 2014/06/20 16:45:46 brouard
70: Summary: If 3 live state, convergence to period prevalence on same graph
71: Author: Brouard
72:
73: Revision 1.152 2014/06/18 17:54:09 brouard
74: Summary: open browser, use gnuplot on same dir than imach if not found in the path
75:
76: Revision 1.151 2014/06/18 16:43:30 brouard
77: *** empty log message ***
78:
79: Revision 1.150 2014/06/18 16:42:35 brouard
80: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
81: Author: brouard
82:
83: Revision 1.149 2014/06/18 15:51:14 brouard
84: Summary: Some fixes in parameter files errors
85: Author: Nicolas Brouard
86:
87: Revision 1.148 2014/06/17 17:38:48 brouard
88: Summary: Nothing new
89: Author: Brouard
90:
91: Just a new packaging for OS/X version 0.98nS
92:
93: Revision 1.147 2014/06/16 10:33:11 brouard
94: *** empty log message ***
95:
96: Revision 1.146 2014/06/16 10:20:28 brouard
97: Summary: Merge
98: Author: Brouard
99:
100: Merge, before building revised version.
101:
102: Revision 1.145 2014/06/10 21:23:15 brouard
103: Summary: Debugging with valgrind
104: Author: Nicolas Brouard
105:
106: Lot of changes in order to output the results with some covariates
107: After the Edimburgh REVES conference 2014, it seems mandatory to
108: improve the code.
109: No more memory valgrind error but a lot has to be done in order to
110: continue the work of splitting the code into subroutines.
111: Also, decodemodel has been improved. Tricode is still not
112: optimal. nbcode should be improved. Documentation has been added in
113: the source code.
114:
115: Revision 1.143 2014/01/26 09:45:38 brouard
116: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
117:
118: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
119: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
120:
121: Revision 1.142 2014/01/26 03:57:36 brouard
122: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
123:
124: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
125:
126: Revision 1.141 2014/01/26 02:42:01 brouard
127: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
128:
129: Revision 1.140 2011/09/02 10:37:54 brouard
130: Summary: times.h is ok with mingw32 now.
131:
132: Revision 1.139 2010/06/14 07:50:17 brouard
133: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
134: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
135:
136: Revision 1.138 2010/04/30 18:19:40 brouard
137: *** empty log message ***
138:
139: Revision 1.137 2010/04/29 18:11:38 brouard
140: (Module): Checking covariates for more complex models
141: than V1+V2. A lot of change to be done. Unstable.
142:
143: Revision 1.136 2010/04/26 20:30:53 brouard
144: (Module): merging some libgsl code. Fixing computation
145: of likelione (using inter/intrapolation if mle = 0) in order to
146: get same likelihood as if mle=1.
147: Some cleaning of code and comments added.
148:
149: Revision 1.135 2009/10/29 15:33:14 brouard
150: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
151:
152: Revision 1.134 2009/10/29 13:18:53 brouard
153: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
154:
155: Revision 1.133 2009/07/06 10:21:25 brouard
156: just nforces
157:
158: Revision 1.132 2009/07/06 08:22:05 brouard
159: Many tings
160:
161: Revision 1.131 2009/06/20 16:22:47 brouard
162: Some dimensions resccaled
163:
164: Revision 1.130 2009/05/26 06:44:34 brouard
165: (Module): Max Covariate is now set to 20 instead of 8. A
166: lot of cleaning with variables initialized to 0. Trying to make
167: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
168:
169: Revision 1.129 2007/08/31 13:49:27 lievre
170: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
171:
172: Revision 1.128 2006/06/30 13:02:05 brouard
173: (Module): Clarifications on computing e.j
174:
175: Revision 1.127 2006/04/28 18:11:50 brouard
176: (Module): Yes the sum of survivors was wrong since
177: imach-114 because nhstepm was no more computed in the age
178: loop. Now we define nhstepma in the age loop.
179: (Module): In order to speed up (in case of numerous covariates) we
180: compute health expectancies (without variances) in a first step
181: and then all the health expectancies with variances or standard
182: deviation (needs data from the Hessian matrices) which slows the
183: computation.
184: In the future we should be able to stop the program is only health
185: expectancies and graph are needed without standard deviations.
186:
187: Revision 1.126 2006/04/28 17:23:28 brouard
188: (Module): Yes the sum of survivors was wrong since
189: imach-114 because nhstepm was no more computed in the age
190: loop. Now we define nhstepma in the age loop.
191: Version 0.98h
192:
193: Revision 1.125 2006/04/04 15:20:31 lievre
194: Errors in calculation of health expectancies. Age was not initialized.
195: Forecasting file added.
196:
197: Revision 1.124 2006/03/22 17:13:53 lievre
198: Parameters are printed with %lf instead of %f (more numbers after the comma).
199: The log-likelihood is printed in the log file
200:
201: Revision 1.123 2006/03/20 10:52:43 brouard
202: * imach.c (Module): <title> changed, corresponds to .htm file
203: name. <head> headers where missing.
204:
205: * imach.c (Module): Weights can have a decimal point as for
206: English (a comma might work with a correct LC_NUMERIC environment,
207: otherwise the weight is truncated).
208: Modification of warning when the covariates values are not 0 or
209: 1.
210: Version 0.98g
211:
212: Revision 1.122 2006/03/20 09:45:41 brouard
213: (Module): Weights can have a decimal point as for
214: English (a comma might work with a correct LC_NUMERIC environment,
215: otherwise the weight is truncated).
216: Modification of warning when the covariates values are not 0 or
217: 1.
218: Version 0.98g
219:
220: Revision 1.121 2006/03/16 17:45:01 lievre
221: * imach.c (Module): Comments concerning covariates added
222:
223: * imach.c (Module): refinements in the computation of lli if
224: status=-2 in order to have more reliable computation if stepm is
225: not 1 month. Version 0.98f
226:
227: Revision 1.120 2006/03/16 15:10:38 lievre
228: (Module): refinements in the computation of lli if
229: status=-2 in order to have more reliable computation if stepm is
230: not 1 month. Version 0.98f
231:
232: Revision 1.119 2006/03/15 17:42:26 brouard
233: (Module): Bug if status = -2, the loglikelihood was
234: computed as likelihood omitting the logarithm. Version O.98e
235:
236: Revision 1.118 2006/03/14 18:20:07 brouard
237: (Module): varevsij Comments added explaining the second
238: table of variances if popbased=1 .
239: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
240: (Module): Function pstamp added
241: (Module): Version 0.98d
242:
243: Revision 1.117 2006/03/14 17:16:22 brouard
244: (Module): varevsij Comments added explaining the second
245: table of variances if popbased=1 .
246: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
247: (Module): Function pstamp added
248: (Module): Version 0.98d
249:
250: Revision 1.116 2006/03/06 10:29:27 brouard
251: (Module): Variance-covariance wrong links and
252: varian-covariance of ej. is needed (Saito).
253:
254: Revision 1.115 2006/02/27 12:17:45 brouard
255: (Module): One freematrix added in mlikeli! 0.98c
256:
257: Revision 1.114 2006/02/26 12:57:58 brouard
258: (Module): Some improvements in processing parameter
259: filename with strsep.
260:
261: Revision 1.113 2006/02/24 14:20:24 brouard
262: (Module): Memory leaks checks with valgrind and:
263: datafile was not closed, some imatrix were not freed and on matrix
264: allocation too.
265:
266: Revision 1.112 2006/01/30 09:55:26 brouard
267: (Module): Back to gnuplot.exe instead of wgnuplot.exe
268:
269: Revision 1.111 2006/01/25 20:38:18 brouard
270: (Module): Lots of cleaning and bugs added (Gompertz)
271: (Module): Comments can be added in data file. Missing date values
272: can be a simple dot '.'.
273:
274: Revision 1.110 2006/01/25 00:51:50 brouard
275: (Module): Lots of cleaning and bugs added (Gompertz)
276:
277: Revision 1.109 2006/01/24 19:37:15 brouard
278: (Module): Comments (lines starting with a #) are allowed in data.
279:
280: Revision 1.108 2006/01/19 18:05:42 lievre
281: Gnuplot problem appeared...
282: To be fixed
283:
284: Revision 1.107 2006/01/19 16:20:37 brouard
285: Test existence of gnuplot in imach path
286:
287: Revision 1.106 2006/01/19 13:24:36 brouard
288: Some cleaning and links added in html output
289:
290: Revision 1.105 2006/01/05 20:23:19 lievre
291: *** empty log message ***
292:
293: Revision 1.104 2005/09/30 16:11:43 lievre
294: (Module): sump fixed, loop imx fixed, and simplifications.
295: (Module): If the status is missing at the last wave but we know
296: that the person is alive, then we can code his/her status as -2
297: (instead of missing=-1 in earlier versions) and his/her
298: contributions to the likelihood is 1 - Prob of dying from last
299: health status (= 1-p13= p11+p12 in the easiest case of somebody in
300: the healthy state at last known wave). Version is 0.98
301:
302: Revision 1.103 2005/09/30 15:54:49 lievre
303: (Module): sump fixed, loop imx fixed, and simplifications.
304:
305: Revision 1.102 2004/09/15 17:31:30 brouard
306: Add the possibility to read data file including tab characters.
307:
308: Revision 1.101 2004/09/15 10:38:38 brouard
309: Fix on curr_time
310:
311: Revision 1.100 2004/07/12 18:29:06 brouard
312: Add version for Mac OS X. Just define UNIX in Makefile
313:
314: Revision 1.99 2004/06/05 08:57:40 brouard
315: *** empty log message ***
316:
317: Revision 1.98 2004/05/16 15:05:56 brouard
318: New version 0.97 . First attempt to estimate force of mortality
319: directly from the data i.e. without the need of knowing the health
320: state at each age, but using a Gompertz model: log u =a + b*age .
321: This is the basic analysis of mortality and should be done before any
322: other analysis, in order to test if the mortality estimated from the
323: cross-longitudinal survey is different from the mortality estimated
324: from other sources like vital statistic data.
325:
326: The same imach parameter file can be used but the option for mle should be -3.
327:
328: Agnès, who wrote this part of the code, tried to keep most of the
329: former routines in order to include the new code within the former code.
330:
331: The output is very simple: only an estimate of the intercept and of
332: the slope with 95% confident intervals.
333:
334: Current limitations:
335: A) Even if you enter covariates, i.e. with the
336: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
337: B) There is no computation of Life Expectancy nor Life Table.
338:
339: Revision 1.97 2004/02/20 13:25:42 lievre
340: Version 0.96d. Population forecasting command line is (temporarily)
341: suppressed.
342:
343: Revision 1.96 2003/07/15 15:38:55 brouard
344: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
345: rewritten within the same printf. Workaround: many printfs.
346:
347: Revision 1.95 2003/07/08 07:54:34 brouard
348: * imach.c (Repository):
349: (Repository): Using imachwizard code to output a more meaningful covariance
350: matrix (cov(a12,c31) instead of numbers.
351:
352: Revision 1.94 2003/06/27 13:00:02 brouard
353: Just cleaning
354:
355: Revision 1.93 2003/06/25 16:33:55 brouard
356: (Module): On windows (cygwin) function asctime_r doesn't
357: exist so I changed back to asctime which exists.
358: (Module): Version 0.96b
359:
360: Revision 1.92 2003/06/25 16:30:45 brouard
361: (Module): On windows (cygwin) function asctime_r doesn't
362: exist so I changed back to asctime which exists.
363:
364: Revision 1.91 2003/06/25 15:30:29 brouard
365: * imach.c (Repository): Duplicated warning errors corrected.
366: (Repository): Elapsed time after each iteration is now output. It
367: helps to forecast when convergence will be reached. Elapsed time
368: is stamped in powell. We created a new html file for the graphs
369: concerning matrix of covariance. It has extension -cov.htm.
370:
371: Revision 1.90 2003/06/24 12:34:15 brouard
372: (Module): Some bugs corrected for windows. Also, when
373: mle=-1 a template is output in file "or"mypar.txt with the design
374: of the covariance matrix to be input.
375:
376: Revision 1.89 2003/06/24 12:30:52 brouard
377: (Module): Some bugs corrected for windows. Also, when
378: mle=-1 a template is output in file "or"mypar.txt with the design
379: of the covariance matrix to be input.
380:
381: Revision 1.88 2003/06/23 17:54:56 brouard
382: * 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.
383:
384: Revision 1.87 2003/06/18 12:26:01 brouard
385: Version 0.96
386:
387: Revision 1.86 2003/06/17 20:04:08 brouard
388: (Module): Change position of html and gnuplot routines and added
389: routine fileappend.
390:
391: Revision 1.85 2003/06/17 13:12:43 brouard
392: * imach.c (Repository): Check when date of death was earlier that
393: current date of interview. It may happen when the death was just
394: prior to the death. In this case, dh was negative and likelihood
395: was wrong (infinity). We still send an "Error" but patch by
396: assuming that the date of death was just one stepm after the
397: interview.
398: (Repository): Because some people have very long ID (first column)
399: we changed int to long in num[] and we added a new lvector for
400: memory allocation. But we also truncated to 8 characters (left
401: truncation)
402: (Repository): No more line truncation errors.
403:
404: Revision 1.84 2003/06/13 21:44:43 brouard
405: * imach.c (Repository): Replace "freqsummary" at a correct
406: place. It differs from routine "prevalence" which may be called
407: many times. Probs is memory consuming and must be used with
408: parcimony.
409: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
410:
411: Revision 1.83 2003/06/10 13:39:11 lievre
412: *** empty log message ***
413:
414: Revision 1.82 2003/06/05 15:57:20 brouard
415: Add log in imach.c and fullversion number is now printed.
416:
417: */
418: /*
419: Interpolated Markov Chain
420:
421: Short summary of the programme:
422:
423: This program computes Healthy Life Expectancies from
424: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
425: first survey ("cross") where individuals from different ages are
426: interviewed on their health status or degree of disability (in the
427: case of a health survey which is our main interest) -2- at least a
428: second wave of interviews ("longitudinal") which measure each change
429: (if any) in individual health status. Health expectancies are
430: computed from the time spent in each health state according to a
431: model. More health states you consider, more time is necessary to reach the
432: Maximum Likelihood of the parameters involved in the model. The
433: simplest model is the multinomial logistic model where pij is the
434: probability to be observed in state j at the second wave
435: conditional to be observed in state i at the first wave. Therefore
436: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
437: 'age' is age and 'sex' is a covariate. If you want to have a more
438: complex model than "constant and age", you should modify the program
439: where the markup *Covariates have to be included here again* invites
440: you to do it. More covariates you add, slower the
441: convergence.
442:
443: The advantage of this computer programme, compared to a simple
444: multinomial logistic model, is clear when the delay between waves is not
445: identical for each individual. Also, if a individual missed an
446: intermediate interview, the information is lost, but taken into
447: account using an interpolation or extrapolation.
448:
449: hPijx is the probability to be observed in state i at age x+h
450: conditional to the observed state i at age x. The delay 'h' can be
451: split into an exact number (nh*stepm) of unobserved intermediate
452: states. This elementary transition (by month, quarter,
453: semester or year) is modelled as a multinomial logistic. The hPx
454: matrix is simply the matrix product of nh*stepm elementary matrices
455: and the contribution of each individual to the likelihood is simply
456: hPijx.
457:
458: Also this programme outputs the covariance matrix of the parameters but also
459: of the life expectancies. It also computes the period (stable) prevalence.
460:
461: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
462: Institut national d'études démographiques, Paris.
463: This software have been partly granted by Euro-REVES, a concerted action
464: from the European Union.
465: It is copyrighted identically to a GNU software product, ie programme and
466: software can be distributed freely for non commercial use. Latest version
467: can be accessed at http://euroreves.ined.fr/imach .
468:
469: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
470: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
471:
472: **********************************************************************/
473: /*
474: main
475: read parameterfile
476: read datafile
477: concatwav
478: freqsummary
479: if (mle >= 1)
480: mlikeli
481: print results files
482: if mle==1
483: computes hessian
484: read end of parameter file: agemin, agemax, bage, fage, estepm
485: begin-prev-date,...
486: open gnuplot file
487: open html file
488: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
489: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
490: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
491: freexexit2 possible for memory heap.
492:
493: h Pij x | pij_nom ficrestpij
494: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
495: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
496: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
497:
498: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
499: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
500: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
501: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
502: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
503:
504: forecasting if prevfcast==1 prevforecast call prevalence()
505: health expectancies
506: Variance-covariance of DFLE
507: prevalence()
508: movingaverage()
509: varevsij()
510: if popbased==1 varevsij(,popbased)
511: total life expectancies
512: Variance of period (stable) prevalence
513: end
514: */
515:
516: #define POWELL /* Instead of NLOPT */
517:
518: #include <math.h>
519: #include <stdio.h>
520: #include <stdlib.h>
521: #include <string.h>
522:
523: #ifdef _WIN32
524: #include <io.h>
525: #else
526: #include <unistd.h>
527: #endif
528:
529: #include <limits.h>
530: #include <sys/types.h>
531: #include <sys/utsname.h>
532: #include <sys/stat.h>
533: #include <errno.h>
534: /* extern int errno; */
535:
536: /* #ifdef LINUX */
537: /* #include <time.h> */
538: /* #include "timeval.h" */
539: /* #else */
540: /* #include <sys/time.h> */
541: /* #endif */
542:
543: #include <time.h>
544:
545: #ifdef GSL
546: #include <gsl/gsl_errno.h>
547: #include <gsl/gsl_multimin.h>
548: #endif
549:
550:
551: #ifdef NLOPT
552: #include <nlopt.h>
553: typedef struct {
554: double (* function)(double [] );
555: } myfunc_data ;
556: #endif
557:
558: /* #include <libintl.h> */
559: /* #define _(String) gettext (String) */
560:
561: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
562:
563: #define GNUPLOTPROGRAM "gnuplot"
564: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
565: #define FILENAMELENGTH 132
566:
567: #define GLOCK_ERROR_NOPATH -1 /* empty path */
568: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
569:
570: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
571: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
572:
573: #define NINTERVMAX 8
574: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
575: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
576: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
577: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
578: #define MAXN 20000
579: #define YEARM 12. /**< Number of months per year */
580: #define AGESUP 130
581: #define AGEBASE 40
582: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
583: #ifdef _WIN32
584: #define DIRSEPARATOR '\\'
585: #define CHARSEPARATOR "\\"
586: #define ODIRSEPARATOR '/'
587: #else
588: #define DIRSEPARATOR '/'
589: #define CHARSEPARATOR "/"
590: #define ODIRSEPARATOR '\\'
591: #endif
592:
593: /* $Id: imach.c,v 1.168 2014/12/22 15:17:42 brouard Exp $ */
594: /* $State: Exp $ */
595:
596: char version[]="Imach version 0.98nY, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
597: char fullversion[]="$Revision: 1.168 $ $Date: 2014/12/22 15:17:42 $";
598: char strstart[80];
599: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
600: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
601: int nvar=0, nforce=0; /* Number of variables, number of forces */
602: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
603: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
604: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
605: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
606: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
607: int cptcovprodnoage=0; /**< Number of covariate products without age */
608: int cptcoveff=0; /* Total number of covariates to vary for printing results */
609: int cptcov=0; /* Working variable */
610: int npar=NPARMAX;
611: int nlstate=2; /* Number of live states */
612: int ndeath=1; /* Number of dead states */
613: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
614: int popbased=0;
615:
616: int *wav; /* Number of waves for this individuual 0 is possible */
617: int maxwav=0; /* Maxim number of waves */
618: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
619: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
620: int gipmx=0, gsw=0; /* Global variables on the number of contributions
621: to the likelihood and the sum of weights (done by funcone)*/
622: int mle=1, weightopt=0;
623: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
624: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
625: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
626: * wave mi and wave mi+1 is not an exact multiple of stepm. */
627: int countcallfunc=0; /* Count the number of calls to func */
628: double jmean=1; /* Mean space between 2 waves */
629: double **matprod2(); /* test */
630: double **oldm, **newm, **savm; /* Working pointers to matrices */
631: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
632: /*FILE *fic ; */ /* Used in readdata only */
633: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
634: FILE *ficlog, *ficrespow;
635: int globpr=0; /* Global variable for printing or not */
636: double fretone; /* Only one call to likelihood */
637: long ipmx=0; /* Number of contributions */
638: double sw; /* Sum of weights */
639: char filerespow[FILENAMELENGTH];
640: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
641: FILE *ficresilk;
642: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
643: FILE *ficresprobmorprev;
644: FILE *fichtm, *fichtmcov; /* Html File */
645: FILE *ficreseij;
646: char filerese[FILENAMELENGTH];
647: FILE *ficresstdeij;
648: char fileresstde[FILENAMELENGTH];
649: FILE *ficrescveij;
650: char filerescve[FILENAMELENGTH];
651: FILE *ficresvij;
652: char fileresv[FILENAMELENGTH];
653: FILE *ficresvpl;
654: char fileresvpl[FILENAMELENGTH];
655: char title[MAXLINE];
656: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
657: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
658: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
659: char command[FILENAMELENGTH];
660: int outcmd=0;
661:
662: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
663:
664: char filelog[FILENAMELENGTH]; /* Log file */
665: char filerest[FILENAMELENGTH];
666: char fileregp[FILENAMELENGTH];
667: char popfile[FILENAMELENGTH];
668:
669: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
670:
671: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
672: /* struct timezone tzp; */
673: /* extern int gettimeofday(); */
674: struct tm tml, *gmtime(), *localtime();
675:
676: extern time_t time();
677:
678: struct tm start_time, end_time, curr_time, last_time, forecast_time;
679: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
680: struct tm tm;
681:
682: char strcurr[80], strfor[80];
683:
684: char *endptr;
685: long lval;
686: double dval;
687:
688: #define NR_END 1
689: #define FREE_ARG char*
690: #define FTOL 1.0e-10
691:
692: #define NRANSI
693: #define ITMAX 200
694:
695: #define TOL 2.0e-4
696:
697: #define CGOLD 0.3819660
698: #define ZEPS 1.0e-10
699: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
700:
701: #define GOLD 1.618034
702: #define GLIMIT 100.0
703: #define TINY 1.0e-20
704:
705: static double maxarg1,maxarg2;
706: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
707: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
708:
709: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
710: #define rint(a) floor(a+0.5)
711: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
712: /* #define mytinydouble 1.0e-16 */
713: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
714: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
715: /* static double dsqrarg; */
716: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
717: static double sqrarg;
718: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
719: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
720: int agegomp= AGEGOMP;
721:
722: int imx;
723: int stepm=1;
724: /* Stepm, step in month: minimum step interpolation*/
725:
726: int estepm;
727: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
728:
729: int m,nb;
730: long *num;
731: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
732: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
733: double **pmmij, ***probs;
734: double *ageexmed,*agecens;
735: double dateintmean=0;
736:
737: double *weight;
738: int **s; /* Status */
739: double *agedc;
740: double **covar; /**< covar[j,i], value of jth covariate for individual i,
741: * covar=matrix(0,NCOVMAX,1,n);
742: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
743: double idx;
744: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
745: int *Ndum; /** Freq of modality (tricode */
746: int **codtab; /**< codtab=imatrix(1,100,1,10); */
747: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
748: double *lsurv, *lpop, *tpop;
749:
750: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
751: double ftolhess; /**< Tolerance for computing hessian */
752:
753: /**************** split *************************/
754: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
755: {
756: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
757: the name of the file (name), its extension only (ext) and its first part of the name (finame)
758: */
759: char *ss; /* pointer */
760: int l1, l2; /* length counters */
761:
762: l1 = strlen(path ); /* length of path */
763: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
764: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
765: if ( ss == NULL ) { /* no directory, so determine current directory */
766: strcpy( name, path ); /* we got the fullname name because no directory */
767: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
768: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
769: /* get current working directory */
770: /* extern char* getcwd ( char *buf , int len);*/
771: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
772: return( GLOCK_ERROR_GETCWD );
773: }
774: /* got dirc from getcwd*/
775: printf(" DIRC = %s \n",dirc);
776: } else { /* strip direcotry from path */
777: ss++; /* after this, the filename */
778: l2 = strlen( ss ); /* length of filename */
779: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
780: strcpy( name, ss ); /* save file name */
781: strncpy( dirc, path, l1 - l2 ); /* now the directory */
782: dirc[l1-l2] = 0; /* add zero */
783: printf(" DIRC2 = %s \n",dirc);
784: }
785: /* We add a separator at the end of dirc if not exists */
786: l1 = strlen( dirc ); /* length of directory */
787: if( dirc[l1-1] != DIRSEPARATOR ){
788: dirc[l1] = DIRSEPARATOR;
789: dirc[l1+1] = 0;
790: printf(" DIRC3 = %s \n",dirc);
791: }
792: ss = strrchr( name, '.' ); /* find last / */
793: if (ss >0){
794: ss++;
795: strcpy(ext,ss); /* save extension */
796: l1= strlen( name);
797: l2= strlen(ss)+1;
798: strncpy( finame, name, l1-l2);
799: finame[l1-l2]= 0;
800: }
801:
802: return( 0 ); /* we're done */
803: }
804:
805:
806: /******************************************/
807:
808: void replace_back_to_slash(char *s, char*t)
809: {
810: int i;
811: int lg=0;
812: i=0;
813: lg=strlen(t);
814: for(i=0; i<= lg; i++) {
815: (s[i] = t[i]);
816: if (t[i]== '\\') s[i]='/';
817: }
818: }
819:
820: char *trimbb(char *out, char *in)
821: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
822: char *s;
823: s=out;
824: while (*in != '\0'){
825: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
826: in++;
827: }
828: *out++ = *in++;
829: }
830: *out='\0';
831: return s;
832: }
833:
834: char *cutl(char *blocc, char *alocc, char *in, char occ)
835: {
836: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
837: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
838: gives blocc="abcdef2ghi" and alocc="j".
839: If occ is not found blocc is null and alocc is equal to in. Returns blocc
840: */
841: char *s, *t;
842: t=in;s=in;
843: while ((*in != occ) && (*in != '\0')){
844: *alocc++ = *in++;
845: }
846: if( *in == occ){
847: *(alocc)='\0';
848: s=++in;
849: }
850:
851: if (s == t) {/* occ not found */
852: *(alocc-(in-s))='\0';
853: in=s;
854: }
855: while ( *in != '\0'){
856: *blocc++ = *in++;
857: }
858:
859: *blocc='\0';
860: return t;
861: }
862: char *cutv(char *blocc, char *alocc, char *in, char occ)
863: {
864: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
865: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
866: gives blocc="abcdef2ghi" and alocc="j".
867: If occ is not found blocc is null and alocc is equal to in. Returns alocc
868: */
869: char *s, *t;
870: t=in;s=in;
871: while (*in != '\0'){
872: while( *in == occ){
873: *blocc++ = *in++;
874: s=in;
875: }
876: *blocc++ = *in++;
877: }
878: if (s == t) /* occ not found */
879: *(blocc-(in-s))='\0';
880: else
881: *(blocc-(in-s)-1)='\0';
882: in=s;
883: while ( *in != '\0'){
884: *alocc++ = *in++;
885: }
886:
887: *alocc='\0';
888: return s;
889: }
890:
891: int nbocc(char *s, char occ)
892: {
893: int i,j=0;
894: int lg=20;
895: i=0;
896: lg=strlen(s);
897: for(i=0; i<= lg; i++) {
898: if (s[i] == occ ) j++;
899: }
900: return j;
901: }
902:
903: /* void cutv(char *u,char *v, char*t, char occ) */
904: /* { */
905: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
906: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
907: /* gives u="abcdef2ghi" and v="j" *\/ */
908: /* int i,lg,j,p=0; */
909: /* i=0; */
910: /* lg=strlen(t); */
911: /* for(j=0; j<=lg-1; j++) { */
912: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
913: /* } */
914:
915: /* for(j=0; j<p; j++) { */
916: /* (u[j] = t[j]); */
917: /* } */
918: /* u[p]='\0'; */
919:
920: /* for(j=0; j<= lg; j++) { */
921: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
922: /* } */
923: /* } */
924:
925: #ifdef _WIN32
926: char * strsep(char **pp, const char *delim)
927: {
928: char *p, *q;
929:
930: if ((p = *pp) == NULL)
931: return 0;
932: if ((q = strpbrk (p, delim)) != NULL)
933: {
934: *pp = q + 1;
935: *q = '\0';
936: }
937: else
938: *pp = 0;
939: return p;
940: }
941: #endif
942:
943: /********************** nrerror ********************/
944:
945: void nrerror(char error_text[])
946: {
947: fprintf(stderr,"ERREUR ...\n");
948: fprintf(stderr,"%s\n",error_text);
949: exit(EXIT_FAILURE);
950: }
951: /*********************** vector *******************/
952: double *vector(int nl, int nh)
953: {
954: double *v;
955: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
956: if (!v) nrerror("allocation failure in vector");
957: return v-nl+NR_END;
958: }
959:
960: /************************ free vector ******************/
961: void free_vector(double*v, int nl, int nh)
962: {
963: free((FREE_ARG)(v+nl-NR_END));
964: }
965:
966: /************************ivector *******************************/
967: int *ivector(long nl,long nh)
968: {
969: int *v;
970: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
971: if (!v) nrerror("allocation failure in ivector");
972: return v-nl+NR_END;
973: }
974:
975: /******************free ivector **************************/
976: void free_ivector(int *v, long nl, long nh)
977: {
978: free((FREE_ARG)(v+nl-NR_END));
979: }
980:
981: /************************lvector *******************************/
982: long *lvector(long nl,long nh)
983: {
984: long *v;
985: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
986: if (!v) nrerror("allocation failure in ivector");
987: return v-nl+NR_END;
988: }
989:
990: /******************free lvector **************************/
991: void free_lvector(long *v, long nl, long nh)
992: {
993: free((FREE_ARG)(v+nl-NR_END));
994: }
995:
996: /******************* imatrix *******************************/
997: int **imatrix(long nrl, long nrh, long ncl, long nch)
998: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
999: {
1000: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1001: int **m;
1002:
1003: /* allocate pointers to rows */
1004: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1005: if (!m) nrerror("allocation failure 1 in matrix()");
1006: m += NR_END;
1007: m -= nrl;
1008:
1009:
1010: /* allocate rows and set pointers to them */
1011: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1012: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1013: m[nrl] += NR_END;
1014: m[nrl] -= ncl;
1015:
1016: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1017:
1018: /* return pointer to array of pointers to rows */
1019: return m;
1020: }
1021:
1022: /****************** free_imatrix *************************/
1023: void free_imatrix(m,nrl,nrh,ncl,nch)
1024: int **m;
1025: long nch,ncl,nrh,nrl;
1026: /* free an int matrix allocated by imatrix() */
1027: {
1028: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1029: free((FREE_ARG) (m+nrl-NR_END));
1030: }
1031:
1032: /******************* matrix *******************************/
1033: double **matrix(long nrl, long nrh, long ncl, long nch)
1034: {
1035: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1036: double **m;
1037:
1038: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1039: if (!m) nrerror("allocation failure 1 in matrix()");
1040: m += NR_END;
1041: m -= nrl;
1042:
1043: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1044: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1045: m[nrl] += NR_END;
1046: m[nrl] -= ncl;
1047:
1048: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1049: return m;
1050: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1051: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1052: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1053: */
1054: }
1055:
1056: /*************************free matrix ************************/
1057: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1058: {
1059: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1060: free((FREE_ARG)(m+nrl-NR_END));
1061: }
1062:
1063: /******************* ma3x *******************************/
1064: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1065: {
1066: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1067: double ***m;
1068:
1069: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1070: if (!m) nrerror("allocation failure 1 in matrix()");
1071: m += NR_END;
1072: m -= nrl;
1073:
1074: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1075: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1076: m[nrl] += NR_END;
1077: m[nrl] -= ncl;
1078:
1079: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1080:
1081: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1082: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1083: m[nrl][ncl] += NR_END;
1084: m[nrl][ncl] -= nll;
1085: for (j=ncl+1; j<=nch; j++)
1086: m[nrl][j]=m[nrl][j-1]+nlay;
1087:
1088: for (i=nrl+1; i<=nrh; i++) {
1089: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1090: for (j=ncl+1; j<=nch; j++)
1091: m[i][j]=m[i][j-1]+nlay;
1092: }
1093: return m;
1094: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1095: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1096: */
1097: }
1098:
1099: /*************************free ma3x ************************/
1100: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1101: {
1102: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1103: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1104: free((FREE_ARG)(m+nrl-NR_END));
1105: }
1106:
1107: /*************** function subdirf ***********/
1108: char *subdirf(char fileres[])
1109: {
1110: /* Caution optionfilefiname is hidden */
1111: strcpy(tmpout,optionfilefiname);
1112: strcat(tmpout,"/"); /* Add to the right */
1113: strcat(tmpout,fileres);
1114: return tmpout;
1115: }
1116:
1117: /*************** function subdirf2 ***********/
1118: char *subdirf2(char fileres[], char *preop)
1119: {
1120:
1121: /* Caution optionfilefiname is hidden */
1122: strcpy(tmpout,optionfilefiname);
1123: strcat(tmpout,"/");
1124: strcat(tmpout,preop);
1125: strcat(tmpout,fileres);
1126: return tmpout;
1127: }
1128:
1129: /*************** function subdirf3 ***********/
1130: char *subdirf3(char fileres[], char *preop, char *preop2)
1131: {
1132:
1133: /* Caution optionfilefiname is hidden */
1134: strcpy(tmpout,optionfilefiname);
1135: strcat(tmpout,"/");
1136: strcat(tmpout,preop);
1137: strcat(tmpout,preop2);
1138: strcat(tmpout,fileres);
1139: return tmpout;
1140: }
1141:
1142: char *asc_diff_time(long time_sec, char ascdiff[])
1143: {
1144: long sec_left, days, hours, minutes;
1145: days = (time_sec) / (60*60*24);
1146: sec_left = (time_sec) % (60*60*24);
1147: hours = (sec_left) / (60*60) ;
1148: sec_left = (sec_left) %(60*60);
1149: minutes = (sec_left) /60;
1150: sec_left = (sec_left) % (60);
1151: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1152: return ascdiff;
1153: }
1154:
1155: /***************** f1dim *************************/
1156: extern int ncom;
1157: extern double *pcom,*xicom;
1158: extern double (*nrfunc)(double []);
1159:
1160: double f1dim(double x)
1161: {
1162: int j;
1163: double f;
1164: double *xt;
1165:
1166: xt=vector(1,ncom);
1167: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1168: f=(*nrfunc)(xt);
1169: free_vector(xt,1,ncom);
1170: return f;
1171: }
1172:
1173: /*****************brent *************************/
1174: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1175: {
1176: int iter;
1177: double a,b,d,etemp;
1178: double fu=0,fv,fw,fx;
1179: double ftemp=0.;
1180: double p,q,r,tol1,tol2,u,v,w,x,xm;
1181: double e=0.0;
1182:
1183: a=(ax < cx ? ax : cx);
1184: b=(ax > cx ? ax : cx);
1185: x=w=v=bx;
1186: fw=fv=fx=(*f)(x);
1187: for (iter=1;iter<=ITMAX;iter++) {
1188: xm=0.5*(a+b);
1189: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1190: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1191: printf(".");fflush(stdout);
1192: fprintf(ficlog,".");fflush(ficlog);
1193: #ifdef DEBUGBRENT
1194: 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);
1195: 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);
1196: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1197: #endif
1198: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1199: *xmin=x;
1200: return fx;
1201: }
1202: ftemp=fu;
1203: if (fabs(e) > tol1) {
1204: r=(x-w)*(fx-fv);
1205: q=(x-v)*(fx-fw);
1206: p=(x-v)*q-(x-w)*r;
1207: q=2.0*(q-r);
1208: if (q > 0.0) p = -p;
1209: q=fabs(q);
1210: etemp=e;
1211: e=d;
1212: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1213: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1214: else {
1215: d=p/q;
1216: u=x+d;
1217: if (u-a < tol2 || b-u < tol2)
1218: d=SIGN(tol1,xm-x);
1219: }
1220: } else {
1221: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1222: }
1223: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1224: fu=(*f)(u);
1225: if (fu <= fx) {
1226: if (u >= x) a=x; else b=x;
1227: SHFT(v,w,x,u)
1228: SHFT(fv,fw,fx,fu)
1229: } else {
1230: if (u < x) a=u; else b=u;
1231: if (fu <= fw || w == x) {
1232: v=w;
1233: w=u;
1234: fv=fw;
1235: fw=fu;
1236: } else if (fu <= fv || v == x || v == w) {
1237: v=u;
1238: fv=fu;
1239: }
1240: }
1241: }
1242: nrerror("Too many iterations in brent");
1243: *xmin=x;
1244: return fx;
1245: }
1246:
1247: /****************** mnbrak ***********************/
1248:
1249: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1250: double (*func)(double))
1251: {
1252: double ulim,u,r,q, dum;
1253: double fu;
1254:
1255: *fa=(*func)(*ax);
1256: *fb=(*func)(*bx);
1257: if (*fb > *fa) {
1258: SHFT(dum,*ax,*bx,dum)
1259: SHFT(dum,*fb,*fa,dum)
1260: }
1261: *cx=(*bx)+GOLD*(*bx-*ax);
1262: *fc=(*func)(*cx);
1263: while (*fb > *fc) { /* Declining fa, fb, fc */
1264: r=(*bx-*ax)*(*fb-*fc);
1265: q=(*bx-*cx)*(*fb-*fa);
1266: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1267: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1268: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1269: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1270: fu=(*func)(u);
1271: #ifdef DEBUG
1272: /* f(x)=A(x-u)**2+f(u) */
1273: double A, fparabu;
1274: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1275: fparabu= *fa - A*(*ax-u)*(*ax-u);
1276: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1277: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1278: #endif
1279: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1280: fu=(*func)(u);
1281: if (fu < *fc) {
1282: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1283: SHFT(*fb,*fc,fu,(*func)(u))
1284: }
1285: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1286: u=ulim;
1287: fu=(*func)(u);
1288: } else {
1289: u=(*cx)+GOLD*(*cx-*bx);
1290: fu=(*func)(u);
1291: }
1292: SHFT(*ax,*bx,*cx,u)
1293: SHFT(*fa,*fb,*fc,fu)
1294: }
1295: }
1296:
1297: /*************** linmin ************************/
1298: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1299: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1300: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1301: the value of func at the returned location p . This is actually all accomplished by calling the
1302: routines mnbrak and brent .*/
1303: int ncom;
1304: double *pcom,*xicom;
1305: double (*nrfunc)(double []);
1306:
1307: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1308: {
1309: double brent(double ax, double bx, double cx,
1310: double (*f)(double), double tol, double *xmin);
1311: double f1dim(double x);
1312: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1313: double *fc, double (*func)(double));
1314: int j;
1315: double xx,xmin,bx,ax;
1316: double fx,fb,fa;
1317:
1318: ncom=n;
1319: pcom=vector(1,n);
1320: xicom=vector(1,n);
1321: nrfunc=func;
1322: for (j=1;j<=n;j++) {
1323: pcom[j]=p[j];
1324: xicom[j]=xi[j];
1325: }
1326: ax=0.0;
1327: xx=1.0;
1328: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1329: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1330: #ifdef DEBUG
1331: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1332: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1333: #endif
1334: for (j=1;j<=n;j++) {
1335: xi[j] *= xmin;
1336: p[j] += xi[j];
1337: }
1338: free_vector(xicom,1,n);
1339: free_vector(pcom,1,n);
1340: }
1341:
1342:
1343: /*************** powell ************************/
1344: /*
1345: Minimization of a function func of n variables. Input consists of an initial starting point
1346: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1347: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1348: such that failure to decrease by more than this amount on one iteration signals doneness. On
1349: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1350: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1351: */
1352: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1353: double (*func)(double []))
1354: {
1355: void linmin(double p[], double xi[], int n, double *fret,
1356: double (*func)(double []));
1357: int i,ibig,j;
1358: double del,t,*pt,*ptt,*xit;
1359: double fp,fptt;
1360: double *xits;
1361: int niterf, itmp;
1362:
1363: pt=vector(1,n);
1364: ptt=vector(1,n);
1365: xit=vector(1,n);
1366: xits=vector(1,n);
1367: *fret=(*func)(p);
1368: for (j=1;j<=n;j++) pt[j]=p[j];
1369: rcurr_time = time(NULL);
1370: for (*iter=1;;++(*iter)) {
1371: fp=(*fret);
1372: ibig=0;
1373: del=0.0;
1374: rlast_time=rcurr_time;
1375: /* (void) gettimeofday(&curr_time,&tzp); */
1376: rcurr_time = time(NULL);
1377: curr_time = *localtime(&rcurr_time);
1378: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1379: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1380: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1381: for (i=1;i<=n;i++) {
1382: printf(" %d %.12f",i, p[i]);
1383: fprintf(ficlog," %d %.12lf",i, p[i]);
1384: fprintf(ficrespow," %.12lf", p[i]);
1385: }
1386: printf("\n");
1387: fprintf(ficlog,"\n");
1388: fprintf(ficrespow,"\n");fflush(ficrespow);
1389: if(*iter <=3){
1390: tml = *localtime(&rcurr_time);
1391: strcpy(strcurr,asctime(&tml));
1392: rforecast_time=rcurr_time;
1393: itmp = strlen(strcurr);
1394: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1395: strcurr[itmp-1]='\0';
1396: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1397: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1398: for(niterf=10;niterf<=30;niterf+=10){
1399: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1400: forecast_time = *localtime(&rforecast_time);
1401: strcpy(strfor,asctime(&forecast_time));
1402: itmp = strlen(strfor);
1403: if(strfor[itmp-1]=='\n')
1404: strfor[itmp-1]='\0';
1405: 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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1406: 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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1407: }
1408: }
1409: for (i=1;i<=n;i++) {
1410: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1411: fptt=(*fret);
1412: #ifdef DEBUG
1413: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1414: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1415: #endif
1416: printf("%d",i);fflush(stdout);
1417: fprintf(ficlog,"%d",i);fflush(ficlog);
1418: linmin(p,xit,n,fret,func);
1419: if (fabs(fptt-(*fret)) > del) {
1420: del=fabs(fptt-(*fret));
1421: ibig=i;
1422: }
1423: #ifdef DEBUG
1424: printf("%d %.12e",i,(*fret));
1425: fprintf(ficlog,"%d %.12e",i,(*fret));
1426: for (j=1;j<=n;j++) {
1427: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1428: printf(" x(%d)=%.12e",j,xit[j]);
1429: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1430: }
1431: for(j=1;j<=n;j++) {
1432: printf(" p(%d)=%.12e",j,p[j]);
1433: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1434: }
1435: printf("\n");
1436: fprintf(ficlog,"\n");
1437: #endif
1438: } /* end i */
1439: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1440: #ifdef DEBUG
1441: int k[2],l;
1442: k[0]=1;
1443: k[1]=-1;
1444: printf("Max: %.12e",(*func)(p));
1445: fprintf(ficlog,"Max: %.12e",(*func)(p));
1446: for (j=1;j<=n;j++) {
1447: printf(" %.12e",p[j]);
1448: fprintf(ficlog," %.12e",p[j]);
1449: }
1450: printf("\n");
1451: fprintf(ficlog,"\n");
1452: for(l=0;l<=1;l++) {
1453: for (j=1;j<=n;j++) {
1454: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1455: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1456: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1457: }
1458: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1459: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1460: }
1461: #endif
1462:
1463:
1464: free_vector(xit,1,n);
1465: free_vector(xits,1,n);
1466: free_vector(ptt,1,n);
1467: free_vector(pt,1,n);
1468: return;
1469: }
1470: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1471: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1472: ptt[j]=2.0*p[j]-pt[j];
1473: xit[j]=p[j]-pt[j];
1474: pt[j]=p[j];
1475: }
1476: fptt=(*func)(ptt);
1477: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1478: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1479: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1480: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1481: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1482: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1483: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1484: /* Thus we compare delta(2h) with observed f1-f3 */
1485: /* or best gain on one ancient line 'del' with total */
1486: /* gain f1-f2 = f1 - f2 - 'del' with del */
1487: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1488:
1489: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1490: t= t- del*SQR(fp-fptt);
1491: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1492: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1493: #ifdef DEBUG
1494: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1495: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1496: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1497: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1498: printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
1499: fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
1500: #endif
1501: if (t < 0.0) { /* Then we use it for last direction */
1502: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1503: for (j=1;j<=n;j++) {
1504: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1505: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1506: }
1507: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1508: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
1509:
1510: #ifdef DEBUG
1511: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1512: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1513: for(j=1;j<=n;j++){
1514: printf(" %.12e",xit[j]);
1515: fprintf(ficlog," %.12e",xit[j]);
1516: }
1517: printf("\n");
1518: fprintf(ficlog,"\n");
1519: #endif
1520: } /* end of t negative */
1521: } /* end if (fptt < fp) */
1522: }
1523: }
1524:
1525: /**** Prevalence limit (stable or period prevalence) ****************/
1526:
1527: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1528: {
1529: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1530: matrix by transitions matrix until convergence is reached */
1531:
1532: int i, ii,j,k;
1533: double min, max, maxmin, maxmax,sumnew=0.;
1534: /* double **matprod2(); */ /* test */
1535: double **out, cov[NCOVMAX+1], **pmij();
1536: double **newm;
1537: double agefin, delaymax=50 ; /* Max number of years to converge */
1538:
1539: for (ii=1;ii<=nlstate+ndeath;ii++)
1540: for (j=1;j<=nlstate+ndeath;j++){
1541: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1542: }
1543:
1544: cov[1]=1.;
1545:
1546: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1547: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1548: newm=savm;
1549: /* Covariates have to be included here again */
1550: cov[2]=agefin;
1551:
1552: for (k=1; k<=cptcovn;k++) {
1553: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1554: /*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]]);*/
1555: }
1556: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1557: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1558: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1559:
1560: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1561: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1562: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1563: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1564: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1565: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1566:
1567: savm=oldm;
1568: oldm=newm;
1569: maxmax=0.;
1570: for(j=1;j<=nlstate;j++){
1571: min=1.;
1572: max=0.;
1573: for(i=1; i<=nlstate; i++) {
1574: sumnew=0;
1575: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1576: prlim[i][j]= newm[i][j]/(1-sumnew);
1577: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1578: max=FMAX(max,prlim[i][j]);
1579: min=FMIN(min,prlim[i][j]);
1580: }
1581: maxmin=max-min;
1582: maxmax=FMAX(maxmax,maxmin);
1583: }
1584: if(maxmax < ftolpl){
1585: return prlim;
1586: }
1587: }
1588: }
1589:
1590: /*************** transition probabilities ***************/
1591:
1592: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1593: {
1594: /* According to parameters values stored in x and the covariate's values stored in cov,
1595: computes the probability to be observed in state j being in state i by appying the
1596: model to the ncovmodel covariates (including constant and age).
1597: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1598: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1599: ncth covariate in the global vector x is given by the formula:
1600: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1601: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1602: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1603: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1604: Outputs ps[i][j] the probability to be observed in j being in j according to
1605: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1606: */
1607: double s1, lnpijopii;
1608: /*double t34;*/
1609: int i,j, nc, ii, jj;
1610:
1611: for(i=1; i<= nlstate; i++){
1612: for(j=1; j<i;j++){
1613: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1614: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1615: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1616: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1617: }
1618: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1619: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1620: }
1621: for(j=i+1; j<=nlstate+ndeath;j++){
1622: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1623: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1624: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1625: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1626: }
1627: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1628: }
1629: }
1630:
1631: for(i=1; i<= nlstate; i++){
1632: s1=0;
1633: for(j=1; j<i; j++){
1634: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1635: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1636: }
1637: for(j=i+1; j<=nlstate+ndeath; j++){
1638: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1639: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1640: }
1641: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1642: ps[i][i]=1./(s1+1.);
1643: /* Computing other pijs */
1644: for(j=1; j<i; j++)
1645: ps[i][j]= exp(ps[i][j])*ps[i][i];
1646: for(j=i+1; j<=nlstate+ndeath; j++)
1647: ps[i][j]= exp(ps[i][j])*ps[i][i];
1648: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1649: } /* end i */
1650:
1651: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1652: for(jj=1; jj<= nlstate+ndeath; jj++){
1653: ps[ii][jj]=0;
1654: ps[ii][ii]=1;
1655: }
1656: }
1657:
1658:
1659: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1660: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1661: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1662: /* } */
1663: /* printf("\n "); */
1664: /* } */
1665: /* printf("\n ");printf("%lf ",cov[2]);*/
1666: /*
1667: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1668: goto end;*/
1669: return ps;
1670: }
1671:
1672: /**************** Product of 2 matrices ******************/
1673:
1674: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1675: {
1676: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1677: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1678: /* in, b, out are matrice of pointers which should have been initialized
1679: before: only the contents of out is modified. The function returns
1680: a pointer to pointers identical to out */
1681: int i, j, k;
1682: for(i=nrl; i<= nrh; i++)
1683: for(k=ncolol; k<=ncoloh; k++){
1684: out[i][k]=0.;
1685: for(j=ncl; j<=nch; j++)
1686: out[i][k] +=in[i][j]*b[j][k];
1687: }
1688: return out;
1689: }
1690:
1691:
1692: /************* Higher Matrix Product ***************/
1693:
1694: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1695: {
1696: /* Computes the transition matrix starting at age 'age' over
1697: 'nhstepm*hstepm*stepm' months (i.e. until
1698: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1699: nhstepm*hstepm matrices.
1700: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1701: (typically every 2 years instead of every month which is too big
1702: for the memory).
1703: Model is determined by parameters x and covariates have to be
1704: included manually here.
1705:
1706: */
1707:
1708: int i, j, d, h, k;
1709: double **out, cov[NCOVMAX+1];
1710: double **newm;
1711:
1712: /* Hstepm could be zero and should return the unit matrix */
1713: for (i=1;i<=nlstate+ndeath;i++)
1714: for (j=1;j<=nlstate+ndeath;j++){
1715: oldm[i][j]=(i==j ? 1.0 : 0.0);
1716: po[i][j][0]=(i==j ? 1.0 : 0.0);
1717: }
1718: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1719: for(h=1; h <=nhstepm; h++){
1720: for(d=1; d <=hstepm; d++){
1721: newm=savm;
1722: /* Covariates have to be included here again */
1723: cov[1]=1.;
1724: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1725: for (k=1; k<=cptcovn;k++)
1726: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1727: for (k=1; k<=cptcovage;k++)
1728: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1729: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1730: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1731:
1732:
1733: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1734: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1735: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1736: pmij(pmmij,cov,ncovmodel,x,nlstate));
1737: savm=oldm;
1738: oldm=newm;
1739: }
1740: for(i=1; i<=nlstate+ndeath; i++)
1741: for(j=1;j<=nlstate+ndeath;j++) {
1742: po[i][j][h]=newm[i][j];
1743: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1744: }
1745: /*printf("h=%d ",h);*/
1746: } /* end h */
1747: /* printf("\n H=%d \n",h); */
1748: return po;
1749: }
1750:
1751: #ifdef NLOPT
1752: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1753: double fret;
1754: double *xt;
1755: int j;
1756: myfunc_data *d2 = (myfunc_data *) pd;
1757: /* xt = (p1-1); */
1758: xt=vector(1,n);
1759: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1760:
1761: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1762: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1763: printf("Function = %.12lf ",fret);
1764: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1765: printf("\n");
1766: free_vector(xt,1,n);
1767: return fret;
1768: }
1769: #endif
1770:
1771: /*************** log-likelihood *************/
1772: double func( double *x)
1773: {
1774: int i, ii, j, k, mi, d, kk;
1775: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1776: double **out;
1777: double sw; /* Sum of weights */
1778: double lli; /* Individual log likelihood */
1779: int s1, s2;
1780: double bbh, survp;
1781: long ipmx;
1782: /*extern weight */
1783: /* We are differentiating ll according to initial status */
1784: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1785: /*for(i=1;i<imx;i++)
1786: printf(" %d\n",s[4][i]);
1787: */
1788:
1789: ++countcallfunc;
1790:
1791: cov[1]=1.;
1792:
1793: for(k=1; k<=nlstate; k++) ll[k]=0.;
1794:
1795: if(mle==1){
1796: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1797: /* Computes the values of the ncovmodel covariates of the model
1798: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1799: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1800: to be observed in j being in i according to the model.
1801: */
1802: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1803: cov[2+k]=covar[Tvar[k]][i];
1804: }
1805: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1806: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1807: has been calculated etc */
1808: for(mi=1; mi<= wav[i]-1; mi++){
1809: for (ii=1;ii<=nlstate+ndeath;ii++)
1810: for (j=1;j<=nlstate+ndeath;j++){
1811: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1812: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1813: }
1814: for(d=0; d<dh[mi][i]; d++){
1815: newm=savm;
1816: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1817: for (kk=1; kk<=cptcovage;kk++) {
1818: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1819: }
1820: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1821: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1822: savm=oldm;
1823: oldm=newm;
1824: } /* end mult */
1825:
1826: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1827: /* But now since version 0.9 we anticipate for bias at large stepm.
1828: * If stepm is larger than one month (smallest stepm) and if the exact delay
1829: * (in months) between two waves is not a multiple of stepm, we rounded to
1830: * the nearest (and in case of equal distance, to the lowest) interval but now
1831: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1832: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1833: * probability in order to take into account the bias as a fraction of the way
1834: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1835: * -stepm/2 to stepm/2 .
1836: * For stepm=1 the results are the same as for previous versions of Imach.
1837: * For stepm > 1 the results are less biased than in previous versions.
1838: */
1839: s1=s[mw[mi][i]][i];
1840: s2=s[mw[mi+1][i]][i];
1841: bbh=(double)bh[mi][i]/(double)stepm;
1842: /* bias bh is positive if real duration
1843: * is higher than the multiple of stepm and negative otherwise.
1844: */
1845: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1846: if( s2 > nlstate){
1847: /* i.e. if s2 is a death state and if the date of death is known
1848: then the contribution to the likelihood is the probability to
1849: die between last step unit time and current step unit time,
1850: which is also equal to probability to die before dh
1851: minus probability to die before dh-stepm .
1852: In version up to 0.92 likelihood was computed
1853: as if date of death was unknown. Death was treated as any other
1854: health state: the date of the interview describes the actual state
1855: and not the date of a change in health state. The former idea was
1856: to consider that at each interview the state was recorded
1857: (healthy, disable or death) and IMaCh was corrected; but when we
1858: introduced the exact date of death then we should have modified
1859: the contribution of an exact death to the likelihood. This new
1860: contribution is smaller and very dependent of the step unit
1861: stepm. It is no more the probability to die between last interview
1862: and month of death but the probability to survive from last
1863: interview up to one month before death multiplied by the
1864: probability to die within a month. Thanks to Chris
1865: Jackson for correcting this bug. Former versions increased
1866: mortality artificially. The bad side is that we add another loop
1867: which slows down the processing. The difference can be up to 10%
1868: lower mortality.
1869: */
1870: lli=log(out[s1][s2] - savm[s1][s2]);
1871:
1872:
1873: } else if (s2==-2) {
1874: for (j=1,survp=0. ; j<=nlstate; j++)
1875: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1876: /*survp += out[s1][j]; */
1877: lli= log(survp);
1878: }
1879:
1880: else if (s2==-4) {
1881: for (j=3,survp=0. ; j<=nlstate; j++)
1882: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1883: lli= log(survp);
1884: }
1885:
1886: else if (s2==-5) {
1887: for (j=1,survp=0. ; j<=2; j++)
1888: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1889: lli= log(survp);
1890: }
1891:
1892: else{
1893: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1894: /* 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 */
1895: }
1896: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1897: /*if(lli ==000.0)*/
1898: /*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); */
1899: ipmx +=1;
1900: sw += weight[i];
1901: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1902: } /* end of wave */
1903: } /* end of individual */
1904: } else if(mle==2){
1905: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1906: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1907: for(mi=1; mi<= wav[i]-1; mi++){
1908: for (ii=1;ii<=nlstate+ndeath;ii++)
1909: for (j=1;j<=nlstate+ndeath;j++){
1910: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1911: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1912: }
1913: for(d=0; d<=dh[mi][i]; d++){
1914: newm=savm;
1915: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1916: for (kk=1; kk<=cptcovage;kk++) {
1917: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1918: }
1919: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1920: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1921: savm=oldm;
1922: oldm=newm;
1923: } /* end mult */
1924:
1925: s1=s[mw[mi][i]][i];
1926: s2=s[mw[mi+1][i]][i];
1927: bbh=(double)bh[mi][i]/(double)stepm;
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: ipmx +=1;
1930: sw += weight[i];
1931: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1932: } /* end of wave */
1933: } /* end of individual */
1934: } else if(mle==3){ /* exponential inter-extrapolation */
1935: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1936: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1937: for(mi=1; mi<= wav[i]-1; mi++){
1938: for (ii=1;ii<=nlstate+ndeath;ii++)
1939: for (j=1;j<=nlstate+ndeath;j++){
1940: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1941: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1942: }
1943: for(d=0; d<dh[mi][i]; d++){
1944: newm=savm;
1945: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1946: for (kk=1; kk<=cptcovage;kk++) {
1947: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1948: }
1949: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1950: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1951: savm=oldm;
1952: oldm=newm;
1953: } /* end mult */
1954:
1955: s1=s[mw[mi][i]][i];
1956: s2=s[mw[mi+1][i]][i];
1957: bbh=(double)bh[mi][i]/(double)stepm;
1958: 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 */
1959: ipmx +=1;
1960: sw += weight[i];
1961: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1962: } /* end of wave */
1963: } /* end of individual */
1964: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1965: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1966: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1967: for(mi=1; mi<= wav[i]-1; mi++){
1968: for (ii=1;ii<=nlstate+ndeath;ii++)
1969: for (j=1;j<=nlstate+ndeath;j++){
1970: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1971: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1972: }
1973: for(d=0; d<dh[mi][i]; d++){
1974: newm=savm;
1975: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1976: for (kk=1; kk<=cptcovage;kk++) {
1977: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1978: }
1979:
1980: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1981: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1982: savm=oldm;
1983: oldm=newm;
1984: } /* end mult */
1985:
1986: s1=s[mw[mi][i]][i];
1987: s2=s[mw[mi+1][i]][i];
1988: if( s2 > nlstate){
1989: lli=log(out[s1][s2] - savm[s1][s2]);
1990: }else{
1991: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1992: }
1993: ipmx +=1;
1994: sw += weight[i];
1995: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1996: /* 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]); */
1997: } /* end of wave */
1998: } /* end of individual */
1999: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2000: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2001: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2002: for(mi=1; mi<= wav[i]-1; mi++){
2003: for (ii=1;ii<=nlstate+ndeath;ii++)
2004: for (j=1;j<=nlstate+ndeath;j++){
2005: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2006: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2007: }
2008: for(d=0; d<dh[mi][i]; d++){
2009: newm=savm;
2010: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2011: for (kk=1; kk<=cptcovage;kk++) {
2012: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2013: }
2014:
2015: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2016: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2017: savm=oldm;
2018: oldm=newm;
2019: } /* end mult */
2020:
2021: s1=s[mw[mi][i]][i];
2022: s2=s[mw[mi+1][i]][i];
2023: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2024: ipmx +=1;
2025: sw += weight[i];
2026: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2027: /*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]);*/
2028: } /* end of wave */
2029: } /* end of individual */
2030: } /* End of if */
2031: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2032: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2033: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2034: return -l;
2035: }
2036:
2037: /*************** log-likelihood *************/
2038: double funcone( double *x)
2039: {
2040: /* Same as likeli but slower because of a lot of printf and if */
2041: int i, ii, j, k, mi, d, kk;
2042: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2043: double **out;
2044: double lli; /* Individual log likelihood */
2045: double llt;
2046: int s1, s2;
2047: double bbh, survp;
2048: /*extern weight */
2049: /* We are differentiating ll according to initial status */
2050: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2051: /*for(i=1;i<imx;i++)
2052: printf(" %d\n",s[4][i]);
2053: */
2054: cov[1]=1.;
2055:
2056: for(k=1; k<=nlstate; k++) ll[k]=0.;
2057:
2058: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2059: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2060: for(mi=1; mi<= wav[i]-1; mi++){
2061: for (ii=1;ii<=nlstate+ndeath;ii++)
2062: for (j=1;j<=nlstate+ndeath;j++){
2063: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2064: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2065: }
2066: for(d=0; d<dh[mi][i]; d++){
2067: newm=savm;
2068: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2069: for (kk=1; kk<=cptcovage;kk++) {
2070: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2071: }
2072: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2073: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2074: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2075: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2076: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2077: savm=oldm;
2078: oldm=newm;
2079: } /* end mult */
2080:
2081: s1=s[mw[mi][i]][i];
2082: s2=s[mw[mi+1][i]][i];
2083: bbh=(double)bh[mi][i]/(double)stepm;
2084: /* bias is positive if real duration
2085: * is higher than the multiple of stepm and negative otherwise.
2086: */
2087: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2088: lli=log(out[s1][s2] - savm[s1][s2]);
2089: } else if (s2==-2) {
2090: for (j=1,survp=0. ; j<=nlstate; j++)
2091: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2092: lli= log(survp);
2093: }else if (mle==1){
2094: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2095: } else if(mle==2){
2096: 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 */
2097: } else if(mle==3){ /* exponential inter-extrapolation */
2098: 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 */
2099: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2100: lli=log(out[s1][s2]); /* Original formula */
2101: } else{ /* mle=0 back to 1 */
2102: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2103: /*lli=log(out[s1][s2]); */ /* Original formula */
2104: } /* End of if */
2105: ipmx +=1;
2106: sw += weight[i];
2107: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2108: /*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]); */
2109: if(globpr){
2110: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2111: %11.6f %11.6f %11.6f ", \
2112: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2113: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2114: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2115: llt +=ll[k]*gipmx/gsw;
2116: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2117: }
2118: fprintf(ficresilk," %10.6f\n", -llt);
2119: }
2120: } /* end of wave */
2121: } /* end of individual */
2122: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2123: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2124: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2125: if(globpr==0){ /* First time we count the contributions and weights */
2126: gipmx=ipmx;
2127: gsw=sw;
2128: }
2129: return -l;
2130: }
2131:
2132:
2133: /*************** function likelione ***********/
2134: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2135: {
2136: /* This routine should help understanding what is done with
2137: the selection of individuals/waves and
2138: to check the exact contribution to the likelihood.
2139: Plotting could be done.
2140: */
2141: int k;
2142:
2143: if(*globpri !=0){ /* Just counts and sums, no printings */
2144: strcpy(fileresilk,"ilk");
2145: strcat(fileresilk,fileres);
2146: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2147: printf("Problem with resultfile: %s\n", fileresilk);
2148: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2149: }
2150: 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");
2151: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2152: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2153: for(k=1; k<=nlstate; k++)
2154: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2155: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2156: }
2157:
2158: *fretone=(*funcone)(p);
2159: if(*globpri !=0){
2160: fclose(ficresilk);
2161: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2162: fflush(fichtm);
2163: }
2164: return;
2165: }
2166:
2167:
2168: /*********** Maximum Likelihood Estimation ***************/
2169:
2170: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2171: {
2172: int i,j, iter=0;
2173: double **xi;
2174: double fret;
2175: double fretone; /* Only one call to likelihood */
2176: /* char filerespow[FILENAMELENGTH];*/
2177:
2178: #ifdef NLOPT
2179: int creturn;
2180: nlopt_opt opt;
2181: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2182: double *lb;
2183: double minf; /* the minimum objective value, upon return */
2184: double * p1; /* Shifted parameters from 0 instead of 1 */
2185: myfunc_data dinst, *d = &dinst;
2186: #endif
2187:
2188:
2189: xi=matrix(1,npar,1,npar);
2190: for (i=1;i<=npar;i++)
2191: for (j=1;j<=npar;j++)
2192: xi[i][j]=(i==j ? 1.0 : 0.0);
2193: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2194: strcpy(filerespow,"pow");
2195: strcat(filerespow,fileres);
2196: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2197: printf("Problem with resultfile: %s\n", filerespow);
2198: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2199: }
2200: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2201: for (i=1;i<=nlstate;i++)
2202: for(j=1;j<=nlstate+ndeath;j++)
2203: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2204: fprintf(ficrespow,"\n");
2205: #ifdef POWELL
2206: powell(p,xi,npar,ftol,&iter,&fret,func);
2207: #endif
2208:
2209: #ifdef NLOPT
2210: #ifdef NEWUOA
2211: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2212: #else
2213: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2214: #endif
2215: lb=vector(0,npar-1);
2216: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2217: nlopt_set_lower_bounds(opt, lb);
2218: nlopt_set_initial_step1(opt, 0.1);
2219:
2220: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2221: d->function = func;
2222: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2223: nlopt_set_min_objective(opt, myfunc, d);
2224: nlopt_set_xtol_rel(opt, ftol);
2225: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2226: printf("nlopt failed! %d\n",creturn);
2227: }
2228: else {
2229: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2230: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2231: iter=1; /* not equal */
2232: }
2233: nlopt_destroy(opt);
2234: #endif
2235: free_matrix(xi,1,npar,1,npar);
2236: fclose(ficrespow);
2237: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2238: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2239: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2240:
2241: }
2242:
2243: /**** Computes Hessian and covariance matrix ***/
2244: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2245: {
2246: double **a,**y,*x,pd;
2247: double **hess;
2248: int i, j;
2249: int *indx;
2250:
2251: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2252: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2253: void lubksb(double **a, int npar, int *indx, double b[]) ;
2254: void ludcmp(double **a, int npar, int *indx, double *d) ;
2255: double gompertz(double p[]);
2256: hess=matrix(1,npar,1,npar);
2257:
2258: printf("\nCalculation of the hessian matrix. Wait...\n");
2259: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2260: for (i=1;i<=npar;i++){
2261: printf("%d",i);fflush(stdout);
2262: fprintf(ficlog,"%d",i);fflush(ficlog);
2263:
2264: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2265:
2266: /* printf(" %f ",p[i]);
2267: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2268: }
2269:
2270: for (i=1;i<=npar;i++) {
2271: for (j=1;j<=npar;j++) {
2272: if (j>i) {
2273: printf(".%d%d",i,j);fflush(stdout);
2274: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2275: hess[i][j]=hessij(p,delti,i,j,func,npar);
2276:
2277: hess[j][i]=hess[i][j];
2278: /*printf(" %lf ",hess[i][j]);*/
2279: }
2280: }
2281: }
2282: printf("\n");
2283: fprintf(ficlog,"\n");
2284:
2285: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2286: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2287:
2288: a=matrix(1,npar,1,npar);
2289: y=matrix(1,npar,1,npar);
2290: x=vector(1,npar);
2291: indx=ivector(1,npar);
2292: for (i=1;i<=npar;i++)
2293: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2294: ludcmp(a,npar,indx,&pd);
2295:
2296: for (j=1;j<=npar;j++) {
2297: for (i=1;i<=npar;i++) x[i]=0;
2298: x[j]=1;
2299: lubksb(a,npar,indx,x);
2300: for (i=1;i<=npar;i++){
2301: matcov[i][j]=x[i];
2302: }
2303: }
2304:
2305: printf("\n#Hessian matrix#\n");
2306: fprintf(ficlog,"\n#Hessian matrix#\n");
2307: for (i=1;i<=npar;i++) {
2308: for (j=1;j<=npar;j++) {
2309: printf("%.3e ",hess[i][j]);
2310: fprintf(ficlog,"%.3e ",hess[i][j]);
2311: }
2312: printf("\n");
2313: fprintf(ficlog,"\n");
2314: }
2315:
2316: /* Recompute Inverse */
2317: for (i=1;i<=npar;i++)
2318: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2319: ludcmp(a,npar,indx,&pd);
2320:
2321: /* printf("\n#Hessian matrix recomputed#\n");
2322:
2323: for (j=1;j<=npar;j++) {
2324: for (i=1;i<=npar;i++) x[i]=0;
2325: x[j]=1;
2326: lubksb(a,npar,indx,x);
2327: for (i=1;i<=npar;i++){
2328: y[i][j]=x[i];
2329: printf("%.3e ",y[i][j]);
2330: fprintf(ficlog,"%.3e ",y[i][j]);
2331: }
2332: printf("\n");
2333: fprintf(ficlog,"\n");
2334: }
2335: */
2336:
2337: free_matrix(a,1,npar,1,npar);
2338: free_matrix(y,1,npar,1,npar);
2339: free_vector(x,1,npar);
2340: free_ivector(indx,1,npar);
2341: free_matrix(hess,1,npar,1,npar);
2342:
2343:
2344: }
2345:
2346: /*************** hessian matrix ****************/
2347: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2348: {
2349: int i;
2350: int l=1, lmax=20;
2351: double k1,k2;
2352: double p2[MAXPARM+1]; /* identical to x */
2353: double res;
2354: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2355: double fx;
2356: int k=0,kmax=10;
2357: double l1;
2358:
2359: fx=func(x);
2360: for (i=1;i<=npar;i++) p2[i]=x[i];
2361: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2362: l1=pow(10,l);
2363: delts=delt;
2364: for(k=1 ; k <kmax; k=k+1){
2365: delt = delta*(l1*k);
2366: p2[theta]=x[theta] +delt;
2367: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2368: p2[theta]=x[theta]-delt;
2369: k2=func(p2)-fx;
2370: /*res= (k1-2.0*fx+k2)/delt/delt; */
2371: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2372:
2373: #ifdef DEBUGHESS
2374: 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);
2375: 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);
2376: #endif
2377: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2378: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2379: k=kmax;
2380: }
2381: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2382: k=kmax; l=lmax*10;
2383: }
2384: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2385: delts=delt;
2386: }
2387: }
2388: }
2389: delti[theta]=delts;
2390: return res;
2391:
2392: }
2393:
2394: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2395: {
2396: int i;
2397: int l=1, lmax=20;
2398: double k1,k2,k3,k4,res,fx;
2399: double p2[MAXPARM+1];
2400: int k;
2401:
2402: fx=func(x);
2403: for (k=1; k<=2; k++) {
2404: for (i=1;i<=npar;i++) p2[i]=x[i];
2405: p2[thetai]=x[thetai]+delti[thetai]/k;
2406: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2407: k1=func(p2)-fx;
2408:
2409: p2[thetai]=x[thetai]+delti[thetai]/k;
2410: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2411: k2=func(p2)-fx;
2412:
2413: p2[thetai]=x[thetai]-delti[thetai]/k;
2414: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2415: k3=func(p2)-fx;
2416:
2417: p2[thetai]=x[thetai]-delti[thetai]/k;
2418: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2419: k4=func(p2)-fx;
2420: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2421: #ifdef DEBUG
2422: 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);
2423: 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);
2424: #endif
2425: }
2426: return res;
2427: }
2428:
2429: /************** Inverse of matrix **************/
2430: void ludcmp(double **a, int n, int *indx, double *d)
2431: {
2432: int i,imax,j,k;
2433: double big,dum,sum,temp;
2434: double *vv;
2435:
2436: vv=vector(1,n);
2437: *d=1.0;
2438: for (i=1;i<=n;i++) {
2439: big=0.0;
2440: for (j=1;j<=n;j++)
2441: if ((temp=fabs(a[i][j])) > big) big=temp;
2442: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2443: vv[i]=1.0/big;
2444: }
2445: for (j=1;j<=n;j++) {
2446: for (i=1;i<j;i++) {
2447: sum=a[i][j];
2448: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2449: a[i][j]=sum;
2450: }
2451: big=0.0;
2452: for (i=j;i<=n;i++) {
2453: sum=a[i][j];
2454: for (k=1;k<j;k++)
2455: sum -= a[i][k]*a[k][j];
2456: a[i][j]=sum;
2457: if ( (dum=vv[i]*fabs(sum)) >= big) {
2458: big=dum;
2459: imax=i;
2460: }
2461: }
2462: if (j != imax) {
2463: for (k=1;k<=n;k++) {
2464: dum=a[imax][k];
2465: a[imax][k]=a[j][k];
2466: a[j][k]=dum;
2467: }
2468: *d = -(*d);
2469: vv[imax]=vv[j];
2470: }
2471: indx[j]=imax;
2472: if (a[j][j] == 0.0) a[j][j]=TINY;
2473: if (j != n) {
2474: dum=1.0/(a[j][j]);
2475: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2476: }
2477: }
2478: free_vector(vv,1,n); /* Doesn't work */
2479: ;
2480: }
2481:
2482: void lubksb(double **a, int n, int *indx, double b[])
2483: {
2484: int i,ii=0,ip,j;
2485: double sum;
2486:
2487: for (i=1;i<=n;i++) {
2488: ip=indx[i];
2489: sum=b[ip];
2490: b[ip]=b[i];
2491: if (ii)
2492: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2493: else if (sum) ii=i;
2494: b[i]=sum;
2495: }
2496: for (i=n;i>=1;i--) {
2497: sum=b[i];
2498: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2499: b[i]=sum/a[i][i];
2500: }
2501: }
2502:
2503: void pstamp(FILE *fichier)
2504: {
2505: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2506: }
2507:
2508: /************ Frequencies ********************/
2509: 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[])
2510: { /* Some frequencies */
2511:
2512: int i, m, jk, j1, bool, z1,j;
2513: int first;
2514: double ***freq; /* Frequencies */
2515: double *pp, **prop;
2516: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2517: char fileresp[FILENAMELENGTH];
2518:
2519: pp=vector(1,nlstate);
2520: prop=matrix(1,nlstate,iagemin,iagemax+3);
2521: strcpy(fileresp,"p");
2522: strcat(fileresp,fileres);
2523: if((ficresp=fopen(fileresp,"w"))==NULL) {
2524: printf("Problem with prevalence resultfile: %s\n", fileresp);
2525: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2526: exit(0);
2527: }
2528: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2529: j1=0;
2530:
2531: j=cptcoveff;
2532: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2533:
2534: first=1;
2535:
2536: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2537: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2538: /* j1++;
2539: */
2540: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2541: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2542: scanf("%d", i);*/
2543: for (i=-5; i<=nlstate+ndeath; i++)
2544: for (jk=-5; jk<=nlstate+ndeath; jk++)
2545: for(m=iagemin; m <= iagemax+3; m++)
2546: freq[i][jk][m]=0;
2547:
2548: for (i=1; i<=nlstate; i++)
2549: for(m=iagemin; m <= iagemax+3; m++)
2550: prop[i][m]=0;
2551:
2552: dateintsum=0;
2553: k2cpt=0;
2554: for (i=1; i<=imx; i++) {
2555: bool=1;
2556: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2557: for (z1=1; z1<=cptcoveff; z1++)
2558: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2559: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2560: bool=0;
2561: /* 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",
2562: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2563: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2564: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2565: }
2566: }
2567:
2568: if (bool==1){
2569: for(m=firstpass; m<=lastpass; m++){
2570: k2=anint[m][i]+(mint[m][i]/12.);
2571: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2572: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2573: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2574: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2575: if (m<lastpass) {
2576: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2577: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2578: }
2579:
2580: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2581: dateintsum=dateintsum+k2;
2582: k2cpt++;
2583: }
2584: /*}*/
2585: }
2586: }
2587: } /* end i */
2588:
2589: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2590: pstamp(ficresp);
2591: if (cptcovn>0) {
2592: fprintf(ficresp, "\n#********** Variable ");
2593: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2594: fprintf(ficresp, "**********\n#");
2595: fprintf(ficlog, "\n#********** Variable ");
2596: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2597: fprintf(ficlog, "**********\n#");
2598: }
2599: for(i=1; i<=nlstate;i++)
2600: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2601: fprintf(ficresp, "\n");
2602:
2603: for(i=iagemin; i <= iagemax+3; i++){
2604: if(i==iagemax+3){
2605: fprintf(ficlog,"Total");
2606: }else{
2607: if(first==1){
2608: first=0;
2609: printf("See log file for details...\n");
2610: }
2611: fprintf(ficlog,"Age %d", i);
2612: }
2613: for(jk=1; jk <=nlstate ; jk++){
2614: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2615: pp[jk] += freq[jk][m][i];
2616: }
2617: for(jk=1; jk <=nlstate ; jk++){
2618: for(m=-1, pos=0; m <=0 ; m++)
2619: pos += freq[jk][m][i];
2620: if(pp[jk]>=1.e-10){
2621: if(first==1){
2622: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2623: }
2624: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2625: }else{
2626: if(first==1)
2627: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2628: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2629: }
2630: }
2631:
2632: for(jk=1; jk <=nlstate ; jk++){
2633: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2634: pp[jk] += freq[jk][m][i];
2635: }
2636: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2637: pos += pp[jk];
2638: posprop += prop[jk][i];
2639: }
2640: for(jk=1; jk <=nlstate ; jk++){
2641: if(pos>=1.e-5){
2642: if(first==1)
2643: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2644: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2645: }else{
2646: if(first==1)
2647: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2648: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2649: }
2650: if( i <= iagemax){
2651: if(pos>=1.e-5){
2652: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2653: /*probs[i][jk][j1]= pp[jk]/pos;*/
2654: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2655: }
2656: else
2657: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2658: }
2659: }
2660:
2661: for(jk=-1; jk <=nlstate+ndeath; jk++)
2662: for(m=-1; m <=nlstate+ndeath; m++)
2663: if(freq[jk][m][i] !=0 ) {
2664: if(first==1)
2665: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2666: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2667: }
2668: if(i <= iagemax)
2669: fprintf(ficresp,"\n");
2670: if(first==1)
2671: printf("Others in log...\n");
2672: fprintf(ficlog,"\n");
2673: }
2674: /*}*/
2675: }
2676: dateintmean=dateintsum/k2cpt;
2677:
2678: fclose(ficresp);
2679: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2680: free_vector(pp,1,nlstate);
2681: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2682: /* End of Freq */
2683: }
2684:
2685: /************ Prevalence ********************/
2686: 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)
2687: {
2688: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2689: in each health status at the date of interview (if between dateprev1 and dateprev2).
2690: We still use firstpass and lastpass as another selection.
2691: */
2692:
2693: int i, m, jk, j1, bool, z1,j;
2694:
2695: double **prop;
2696: double posprop;
2697: double y2; /* in fractional years */
2698: int iagemin, iagemax;
2699: int first; /** to stop verbosity which is redirected to log file */
2700:
2701: iagemin= (int) agemin;
2702: iagemax= (int) agemax;
2703: /*pp=vector(1,nlstate);*/
2704: prop=matrix(1,nlstate,iagemin,iagemax+3);
2705: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2706: j1=0;
2707:
2708: /*j=cptcoveff;*/
2709: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2710:
2711: first=1;
2712: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2713: /*for(i1=1; i1<=ncodemax[k1];i1++){
2714: j1++;*/
2715:
2716: for (i=1; i<=nlstate; i++)
2717: for(m=iagemin; m <= iagemax+3; m++)
2718: prop[i][m]=0.0;
2719:
2720: for (i=1; i<=imx; i++) { /* Each individual */
2721: bool=1;
2722: if (cptcovn>0) {
2723: for (z1=1; z1<=cptcoveff; z1++)
2724: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2725: bool=0;
2726: }
2727: if (bool==1) {
2728: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2729: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2730: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2731: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2732: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2733: 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);
2734: if (s[m][i]>0 && s[m][i]<=nlstate) {
2735: /*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]]);*/
2736: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2737: prop[s[m][i]][iagemax+3] += weight[i];
2738: }
2739: }
2740: } /* end selection of waves */
2741: }
2742: }
2743: for(i=iagemin; i <= iagemax+3; i++){
2744: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2745: posprop += prop[jk][i];
2746: }
2747:
2748: for(jk=1; jk <=nlstate ; jk++){
2749: if( i <= iagemax){
2750: if(posprop>=1.e-5){
2751: probs[i][jk][j1]= prop[jk][i]/posprop;
2752: } else{
2753: if(first==1){
2754: first=0;
2755: 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]);
2756: }
2757: }
2758: }
2759: }/* end jk */
2760: }/* end i */
2761: /*} *//* end i1 */
2762: } /* end j1 */
2763:
2764: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2765: /*free_vector(pp,1,nlstate);*/
2766: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2767: } /* End of prevalence */
2768:
2769: /************* Waves Concatenation ***************/
2770:
2771: 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)
2772: {
2773: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2774: Death is a valid wave (if date is known).
2775: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2776: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2777: and mw[mi+1][i]. dh depends on stepm.
2778: */
2779:
2780: int i, mi, m;
2781: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2782: double sum=0., jmean=0.;*/
2783: int first;
2784: int j, k=0,jk, ju, jl;
2785: double sum=0.;
2786: first=0;
2787: jmin=100000;
2788: jmax=-1;
2789: jmean=0.;
2790: for(i=1; i<=imx; i++){
2791: mi=0;
2792: m=firstpass;
2793: while(s[m][i] <= nlstate){
2794: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2795: mw[++mi][i]=m;
2796: if(m >=lastpass)
2797: break;
2798: else
2799: m++;
2800: }/* end while */
2801: if (s[m][i] > nlstate){
2802: mi++; /* Death is another wave */
2803: /* if(mi==0) never been interviewed correctly before death */
2804: /* Only death is a correct wave */
2805: mw[mi][i]=m;
2806: }
2807:
2808: wav[i]=mi;
2809: if(mi==0){
2810: nbwarn++;
2811: if(first==0){
2812: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2813: first=1;
2814: }
2815: if(first==1){
2816: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2817: }
2818: } /* end mi==0 */
2819: } /* End individuals */
2820:
2821: for(i=1; i<=imx; i++){
2822: for(mi=1; mi<wav[i];mi++){
2823: if (stepm <=0)
2824: dh[mi][i]=1;
2825: else{
2826: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2827: if (agedc[i] < 2*AGESUP) {
2828: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2829: if(j==0) j=1; /* Survives at least one month after exam */
2830: else if(j<0){
2831: nberr++;
2832: 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]);
2833: j=1; /* Temporary Dangerous patch */
2834: 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);
2835: 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]);
2836: 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);
2837: }
2838: k=k+1;
2839: if (j >= jmax){
2840: jmax=j;
2841: ijmax=i;
2842: }
2843: if (j <= jmin){
2844: jmin=j;
2845: ijmin=i;
2846: }
2847: sum=sum+j;
2848: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2849: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2850: }
2851: }
2852: else{
2853: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2854: /* 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]); */
2855:
2856: k=k+1;
2857: if (j >= jmax) {
2858: jmax=j;
2859: ijmax=i;
2860: }
2861: else if (j <= jmin){
2862: jmin=j;
2863: ijmin=i;
2864: }
2865: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2866: /*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]);*/
2867: if(j<0){
2868: nberr++;
2869: 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]);
2870: 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]);
2871: }
2872: sum=sum+j;
2873: }
2874: jk= j/stepm;
2875: jl= j -jk*stepm;
2876: ju= j -(jk+1)*stepm;
2877: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2878: if(jl==0){
2879: dh[mi][i]=jk;
2880: bh[mi][i]=0;
2881: }else{ /* We want a negative bias in order to only have interpolation ie
2882: * to avoid the price of an extra matrix product in likelihood */
2883: dh[mi][i]=jk+1;
2884: bh[mi][i]=ju;
2885: }
2886: }else{
2887: if(jl <= -ju){
2888: dh[mi][i]=jk;
2889: bh[mi][i]=jl; /* bias is positive if real duration
2890: * is higher than the multiple of stepm and negative otherwise.
2891: */
2892: }
2893: else{
2894: dh[mi][i]=jk+1;
2895: bh[mi][i]=ju;
2896: }
2897: if(dh[mi][i]==0){
2898: dh[mi][i]=1; /* At least one step */
2899: bh[mi][i]=ju; /* At least one step */
2900: /* 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);*/
2901: }
2902: } /* end if mle */
2903: }
2904: } /* end wave */
2905: }
2906: jmean=sum/k;
2907: 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);
2908: 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);
2909: }
2910:
2911: /*********** Tricode ****************************/
2912: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2913: {
2914: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2915: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2916: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2917: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2918: /* nbcode[Tvar[j]][1]=
2919: */
2920:
2921: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2922: int modmaxcovj=0; /* Modality max of covariates j */
2923: int cptcode=0; /* Modality max of covariates j */
2924: int modmincovj=0; /* Modality min of covariates j */
2925:
2926:
2927: cptcoveff=0;
2928:
2929: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2930: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2931:
2932: /* Loop on covariates without age and products */
2933: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2934: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2935: modality of this covariate Vj*/
2936: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2937: * If product of Vn*Vm, still boolean *:
2938: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2939: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2940: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2941: modality of the nth covariate of individual i. */
2942: if (ij > modmaxcovj)
2943: modmaxcovj=ij;
2944: else if (ij < modmincovj)
2945: modmincovj=ij;
2946: if ((ij < -1) && (ij > NCOVMAX)){
2947: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2948: exit(1);
2949: }else
2950: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2951: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2952: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2953: /* getting the maximum value of the modality of the covariate
2954: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2955: female is 1, then modmaxcovj=1.*/
2956: }
2957: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2958: cptcode=modmaxcovj;
2959: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2960: /*for (i=0; i<=cptcode; i++) {*/
2961: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2962: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2963: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2964: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2965: }
2966: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2967: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2968: } /* Ndum[-1] number of undefined modalities */
2969:
2970: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2971: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2972: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2973: modmincovj=3; modmaxcovj = 7;
2974: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2975: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2976: variables V1_1 and V1_2.
2977: nbcode[Tvar[j]][ij]=k;
2978: nbcode[Tvar[j]][1]=0;
2979: nbcode[Tvar[j]][2]=1;
2980: nbcode[Tvar[j]][3]=2;
2981: */
2982: ij=1; /* ij is similar to i but can jumps over null modalities */
2983: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2984: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2985: /*recode from 0 */
2986: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2987: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2988: k is a modality. If we have model=V1+V1*sex
2989: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2990: ij++;
2991: }
2992: if (ij > ncodemax[j]) break;
2993: } /* end of loop on */
2994: } /* end of loop on modality */
2995: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2996:
2997: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2998:
2999: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3000: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3001: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3002: Ndum[ij]++;
3003: }
3004:
3005: ij=1;
3006: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3007: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3008: if((Ndum[i]!=0) && (i<=ncovcol)){
3009: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3010: Tvaraff[ij]=i; /*For printing (unclear) */
3011: ij++;
3012: }else
3013: Tvaraff[ij]=0;
3014: }
3015: ij--;
3016: cptcoveff=ij; /*Number of total covariates*/
3017:
3018: }
3019:
3020:
3021: /*********** Health Expectancies ****************/
3022:
3023: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3024:
3025: {
3026: /* Health expectancies, no variances */
3027: int i, j, nhstepm, hstepm, h, nstepm;
3028: int nhstepma, nstepma; /* Decreasing with age */
3029: double age, agelim, hf;
3030: double ***p3mat;
3031: double eip;
3032:
3033: pstamp(ficreseij);
3034: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3035: fprintf(ficreseij,"# Age");
3036: for(i=1; i<=nlstate;i++){
3037: for(j=1; j<=nlstate;j++){
3038: fprintf(ficreseij," e%1d%1d ",i,j);
3039: }
3040: fprintf(ficreseij," e%1d. ",i);
3041: }
3042: fprintf(ficreseij,"\n");
3043:
3044:
3045: if(estepm < stepm){
3046: printf ("Problem %d lower than %d\n",estepm, stepm);
3047: }
3048: else hstepm=estepm;
3049: /* We compute the life expectancy from trapezoids spaced every estepm months
3050: * This is mainly to measure the difference between two models: for example
3051: * if stepm=24 months pijx are given only every 2 years and by summing them
3052: * we are calculating an estimate of the Life Expectancy assuming a linear
3053: * progression in between and thus overestimating or underestimating according
3054: * to the curvature of the survival function. If, for the same date, we
3055: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3056: * to compare the new estimate of Life expectancy with the same linear
3057: * hypothesis. A more precise result, taking into account a more precise
3058: * curvature will be obtained if estepm is as small as stepm. */
3059:
3060: /* For example we decided to compute the life expectancy with the smallest unit */
3061: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3062: nhstepm is the number of hstepm from age to agelim
3063: nstepm is the number of stepm from age to agelin.
3064: Look at hpijx to understand the reason of that which relies in memory size
3065: and note for a fixed period like estepm months */
3066: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3067: survival function given by stepm (the optimization length). Unfortunately it
3068: means that if the survival funtion is printed only each two years of age and if
3069: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3070: results. So we changed our mind and took the option of the best precision.
3071: */
3072: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3073:
3074: agelim=AGESUP;
3075: /* If stepm=6 months */
3076: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3077: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3078:
3079: /* nhstepm age range expressed in number of stepm */
3080: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3081: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3082: /* if (stepm >= YEARM) hstepm=1;*/
3083: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3084: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3085:
3086: for (age=bage; age<=fage; age ++){
3087: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3088: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3089: /* if (stepm >= YEARM) hstepm=1;*/
3090: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3091:
3092: /* If stepm=6 months */
3093: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3094: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3095:
3096: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3097:
3098: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3099:
3100: printf("%d|",(int)age);fflush(stdout);
3101: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3102:
3103: /* Computing expectancies */
3104: for(i=1; i<=nlstate;i++)
3105: for(j=1; j<=nlstate;j++)
3106: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3107: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3108:
3109: /* 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]);*/
3110:
3111: }
3112:
3113: fprintf(ficreseij,"%3.0f",age );
3114: for(i=1; i<=nlstate;i++){
3115: eip=0;
3116: for(j=1; j<=nlstate;j++){
3117: eip +=eij[i][j][(int)age];
3118: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3119: }
3120: fprintf(ficreseij,"%9.4f", eip );
3121: }
3122: fprintf(ficreseij,"\n");
3123:
3124: }
3125: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3126: printf("\n");
3127: fprintf(ficlog,"\n");
3128:
3129: }
3130:
3131: 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[] )
3132:
3133: {
3134: /* Covariances of health expectancies eij and of total life expectancies according
3135: to initial status i, ei. .
3136: */
3137: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3138: int nhstepma, nstepma; /* Decreasing with age */
3139: double age, agelim, hf;
3140: double ***p3matp, ***p3matm, ***varhe;
3141: double **dnewm,**doldm;
3142: double *xp, *xm;
3143: double **gp, **gm;
3144: double ***gradg, ***trgradg;
3145: int theta;
3146:
3147: double eip, vip;
3148:
3149: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3150: xp=vector(1,npar);
3151: xm=vector(1,npar);
3152: dnewm=matrix(1,nlstate*nlstate,1,npar);
3153: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3154:
3155: pstamp(ficresstdeij);
3156: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3157: fprintf(ficresstdeij,"# Age");
3158: for(i=1; i<=nlstate;i++){
3159: for(j=1; j<=nlstate;j++)
3160: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3161: fprintf(ficresstdeij," e%1d. ",i);
3162: }
3163: fprintf(ficresstdeij,"\n");
3164:
3165: pstamp(ficrescveij);
3166: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3167: fprintf(ficrescveij,"# Age");
3168: for(i=1; i<=nlstate;i++)
3169: for(j=1; j<=nlstate;j++){
3170: cptj= (j-1)*nlstate+i;
3171: for(i2=1; i2<=nlstate;i2++)
3172: for(j2=1; j2<=nlstate;j2++){
3173: cptj2= (j2-1)*nlstate+i2;
3174: if(cptj2 <= cptj)
3175: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3176: }
3177: }
3178: fprintf(ficrescveij,"\n");
3179:
3180: if(estepm < stepm){
3181: printf ("Problem %d lower than %d\n",estepm, stepm);
3182: }
3183: else hstepm=estepm;
3184: /* We compute the life expectancy from trapezoids spaced every estepm months
3185: * This is mainly to measure the difference between two models: for example
3186: * if stepm=24 months pijx are given only every 2 years and by summing them
3187: * we are calculating an estimate of the Life Expectancy assuming a linear
3188: * progression in between and thus overestimating or underestimating according
3189: * to the curvature of the survival function. If, for the same date, we
3190: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3191: * to compare the new estimate of Life expectancy with the same linear
3192: * hypothesis. A more precise result, taking into account a more precise
3193: * curvature will be obtained if estepm is as small as stepm. */
3194:
3195: /* For example we decided to compute the life expectancy with the smallest unit */
3196: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3197: nhstepm is the number of hstepm from age to agelim
3198: nstepm is the number of stepm from age to agelin.
3199: Look at hpijx to understand the reason of that which relies in memory size
3200: and note for a fixed period like estepm months */
3201: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3202: survival function given by stepm (the optimization length). Unfortunately it
3203: means that if the survival funtion is printed only each two years of age and if
3204: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3205: results. So we changed our mind and took the option of the best precision.
3206: */
3207: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3208:
3209: /* If stepm=6 months */
3210: /* nhstepm age range expressed in number of stepm */
3211: agelim=AGESUP;
3212: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3213: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3214: /* if (stepm >= YEARM) hstepm=1;*/
3215: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3216:
3217: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3218: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3219: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3220: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3221: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3222: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3223:
3224: for (age=bage; age<=fage; age ++){
3225: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3226: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3227: /* if (stepm >= YEARM) hstepm=1;*/
3228: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3229:
3230: /* If stepm=6 months */
3231: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3232: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3233:
3234: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3235:
3236: /* Computing Variances of health expectancies */
3237: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3238: decrease memory allocation */
3239: for(theta=1; theta <=npar; theta++){
3240: for(i=1; i<=npar; i++){
3241: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3242: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3243: }
3244: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3245: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3246:
3247: for(j=1; j<= nlstate; j++){
3248: for(i=1; i<=nlstate; i++){
3249: for(h=0; h<=nhstepm-1; h++){
3250: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3251: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3252: }
3253: }
3254: }
3255:
3256: for(ij=1; ij<= nlstate*nlstate; ij++)
3257: for(h=0; h<=nhstepm-1; h++){
3258: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3259: }
3260: }/* End theta */
3261:
3262:
3263: for(h=0; h<=nhstepm-1; h++)
3264: for(j=1; j<=nlstate*nlstate;j++)
3265: for(theta=1; theta <=npar; theta++)
3266: trgradg[h][j][theta]=gradg[h][theta][j];
3267:
3268:
3269: for(ij=1;ij<=nlstate*nlstate;ij++)
3270: for(ji=1;ji<=nlstate*nlstate;ji++)
3271: varhe[ij][ji][(int)age] =0.;
3272:
3273: printf("%d|",(int)age);fflush(stdout);
3274: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3275: for(h=0;h<=nhstepm-1;h++){
3276: for(k=0;k<=nhstepm-1;k++){
3277: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3278: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3279: for(ij=1;ij<=nlstate*nlstate;ij++)
3280: for(ji=1;ji<=nlstate*nlstate;ji++)
3281: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3282: }
3283: }
3284:
3285: /* Computing expectancies */
3286: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3287: for(i=1; i<=nlstate;i++)
3288: for(j=1; j<=nlstate;j++)
3289: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3290: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3291:
3292: /* 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]);*/
3293:
3294: }
3295:
3296: fprintf(ficresstdeij,"%3.0f",age );
3297: for(i=1; i<=nlstate;i++){
3298: eip=0.;
3299: vip=0.;
3300: for(j=1; j<=nlstate;j++){
3301: eip += eij[i][j][(int)age];
3302: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3303: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3304: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3305: }
3306: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3307: }
3308: fprintf(ficresstdeij,"\n");
3309:
3310: fprintf(ficrescveij,"%3.0f",age );
3311: for(i=1; i<=nlstate;i++)
3312: for(j=1; j<=nlstate;j++){
3313: cptj= (j-1)*nlstate+i;
3314: for(i2=1; i2<=nlstate;i2++)
3315: for(j2=1; j2<=nlstate;j2++){
3316: cptj2= (j2-1)*nlstate+i2;
3317: if(cptj2 <= cptj)
3318: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3319: }
3320: }
3321: fprintf(ficrescveij,"\n");
3322:
3323: }
3324: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3325: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3326: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3327: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3328: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3329: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3330: printf("\n");
3331: fprintf(ficlog,"\n");
3332:
3333: free_vector(xm,1,npar);
3334: free_vector(xp,1,npar);
3335: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3336: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3337: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3338: }
3339:
3340: /************ Variance ******************/
3341: 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[])
3342: {
3343: /* Variance of health expectancies */
3344: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3345: /* double **newm;*/
3346: double **dnewm,**doldm;
3347: double **dnewmp,**doldmp;
3348: int i, j, nhstepm, hstepm, h, nstepm ;
3349: int k;
3350: double *xp;
3351: double **gp, **gm; /* for var eij */
3352: double ***gradg, ***trgradg; /*for var eij */
3353: double **gradgp, **trgradgp; /* for var p point j */
3354: double *gpp, *gmp; /* for var p point j */
3355: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3356: double ***p3mat;
3357: double age,agelim, hf;
3358: double ***mobaverage;
3359: int theta;
3360: char digit[4];
3361: char digitp[25];
3362:
3363: char fileresprobmorprev[FILENAMELENGTH];
3364:
3365: if(popbased==1){
3366: if(mobilav!=0)
3367: strcpy(digitp,"-populbased-mobilav-");
3368: else strcpy(digitp,"-populbased-nomobil-");
3369: }
3370: else
3371: strcpy(digitp,"-stablbased-");
3372:
3373: if (mobilav!=0) {
3374: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3375: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3376: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3377: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3378: }
3379: }
3380:
3381: strcpy(fileresprobmorprev,"prmorprev");
3382: sprintf(digit,"%-d",ij);
3383: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3384: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3385: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3386: strcat(fileresprobmorprev,fileres);
3387: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3388: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3389: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3390: }
3391: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3392:
3393: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3394: pstamp(ficresprobmorprev);
3395: 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);
3396: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3397: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3398: fprintf(ficresprobmorprev," p.%-d SE",j);
3399: for(i=1; i<=nlstate;i++)
3400: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3401: }
3402: fprintf(ficresprobmorprev,"\n");
3403: fprintf(ficgp,"\n# Routine varevsij");
3404: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3405: 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");
3406: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3407: /* } */
3408: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3409: pstamp(ficresvij);
3410: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3411: if(popbased==1)
3412: 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);
3413: else
3414: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3415: fprintf(ficresvij,"# Age");
3416: for(i=1; i<=nlstate;i++)
3417: for(j=1; j<=nlstate;j++)
3418: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3419: fprintf(ficresvij,"\n");
3420:
3421: xp=vector(1,npar);
3422: dnewm=matrix(1,nlstate,1,npar);
3423: doldm=matrix(1,nlstate,1,nlstate);
3424: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3425: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3426:
3427: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3428: gpp=vector(nlstate+1,nlstate+ndeath);
3429: gmp=vector(nlstate+1,nlstate+ndeath);
3430: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3431:
3432: if(estepm < stepm){
3433: printf ("Problem %d lower than %d\n",estepm, stepm);
3434: }
3435: else hstepm=estepm;
3436: /* For example we decided to compute the life expectancy with the smallest unit */
3437: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3438: nhstepm is the number of hstepm from age to agelim
3439: nstepm is the number of stepm from age to agelin.
3440: Look at function hpijx to understand why (it is linked to memory size questions) */
3441: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3442: survival function given by stepm (the optimization length). Unfortunately it
3443: means that if the survival funtion is printed every two years of age and if
3444: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3445: results. So we changed our mind and took the option of the best precision.
3446: */
3447: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3448: agelim = AGESUP;
3449: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3450: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3451: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3452: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3453: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3454: gp=matrix(0,nhstepm,1,nlstate);
3455: gm=matrix(0,nhstepm,1,nlstate);
3456:
3457:
3458: for(theta=1; theta <=npar; theta++){
3459: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3460: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3461: }
3462: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3463: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3464:
3465: if (popbased==1) {
3466: if(mobilav ==0){
3467: for(i=1; i<=nlstate;i++)
3468: prlim[i][i]=probs[(int)age][i][ij];
3469: }else{ /* mobilav */
3470: for(i=1; i<=nlstate;i++)
3471: prlim[i][i]=mobaverage[(int)age][i][ij];
3472: }
3473: }
3474:
3475: for(j=1; j<= nlstate; j++){
3476: for(h=0; h<=nhstepm; h++){
3477: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3478: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3479: }
3480: }
3481: /* This for computing probability of death (h=1 means
3482: computed over hstepm matrices product = hstepm*stepm months)
3483: as a weighted average of prlim.
3484: */
3485: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3486: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3487: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3488: }
3489: /* end probability of death */
3490:
3491: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3492: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3493: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3494: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3495:
3496: if (popbased==1) {
3497: if(mobilav ==0){
3498: for(i=1; i<=nlstate;i++)
3499: prlim[i][i]=probs[(int)age][i][ij];
3500: }else{ /* mobilav */
3501: for(i=1; i<=nlstate;i++)
3502: prlim[i][i]=mobaverage[(int)age][i][ij];
3503: }
3504: }
3505:
3506: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3507: for(h=0; h<=nhstepm; h++){
3508: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3509: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3510: }
3511: }
3512: /* This for computing probability of death (h=1 means
3513: computed over hstepm matrices product = hstepm*stepm months)
3514: as a weighted average of prlim.
3515: */
3516: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3517: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3518: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3519: }
3520: /* end probability of death */
3521:
3522: for(j=1; j<= nlstate; j++) /* vareij */
3523: for(h=0; h<=nhstepm; h++){
3524: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3525: }
3526:
3527: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3528: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3529: }
3530:
3531: } /* End theta */
3532:
3533: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3534:
3535: for(h=0; h<=nhstepm; h++) /* veij */
3536: for(j=1; j<=nlstate;j++)
3537: for(theta=1; theta <=npar; theta++)
3538: trgradg[h][j][theta]=gradg[h][theta][j];
3539:
3540: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3541: for(theta=1; theta <=npar; theta++)
3542: trgradgp[j][theta]=gradgp[theta][j];
3543:
3544:
3545: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3546: for(i=1;i<=nlstate;i++)
3547: for(j=1;j<=nlstate;j++)
3548: vareij[i][j][(int)age] =0.;
3549:
3550: for(h=0;h<=nhstepm;h++){
3551: for(k=0;k<=nhstepm;k++){
3552: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3553: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3554: for(i=1;i<=nlstate;i++)
3555: for(j=1;j<=nlstate;j++)
3556: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3557: }
3558: }
3559:
3560: /* pptj */
3561: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3562: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3563: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3564: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3565: varppt[j][i]=doldmp[j][i];
3566: /* end ppptj */
3567: /* x centered again */
3568: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3569: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3570:
3571: if (popbased==1) {
3572: if(mobilav ==0){
3573: for(i=1; i<=nlstate;i++)
3574: prlim[i][i]=probs[(int)age][i][ij];
3575: }else{ /* mobilav */
3576: for(i=1; i<=nlstate;i++)
3577: prlim[i][i]=mobaverage[(int)age][i][ij];
3578: }
3579: }
3580:
3581: /* This for computing probability of death (h=1 means
3582: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3583: as a weighted average of prlim.
3584: */
3585: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3586: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3587: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3588: }
3589: /* end probability of death */
3590:
3591: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3592: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3593: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3594: for(i=1; i<=nlstate;i++){
3595: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3596: }
3597: }
3598: fprintf(ficresprobmorprev,"\n");
3599:
3600: fprintf(ficresvij,"%.0f ",age );
3601: for(i=1; i<=nlstate;i++)
3602: for(j=1; j<=nlstate;j++){
3603: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3604: }
3605: fprintf(ficresvij,"\n");
3606: free_matrix(gp,0,nhstepm,1,nlstate);
3607: free_matrix(gm,0,nhstepm,1,nlstate);
3608: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3609: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3610: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3611: } /* End age */
3612: free_vector(gpp,nlstate+1,nlstate+ndeath);
3613: free_vector(gmp,nlstate+1,nlstate+ndeath);
3614: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3615: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3616: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3617: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3618: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3619: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3620: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3621: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3622: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3623: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3624: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3625: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3626: 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);
3627: /* 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);
3628: */
3629: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3630: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3631:
3632: free_vector(xp,1,npar);
3633: free_matrix(doldm,1,nlstate,1,nlstate);
3634: free_matrix(dnewm,1,nlstate,1,npar);
3635: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3636: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3637: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3638: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3639: fclose(ficresprobmorprev);
3640: fflush(ficgp);
3641: fflush(fichtm);
3642: } /* end varevsij */
3643:
3644: /************ Variance of prevlim ******************/
3645: 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[])
3646: {
3647: /* Variance of prevalence limit */
3648: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3649:
3650: double **dnewm,**doldm;
3651: int i, j, nhstepm, hstepm;
3652: double *xp;
3653: double *gp, *gm;
3654: double **gradg, **trgradg;
3655: double age,agelim;
3656: int theta;
3657:
3658: pstamp(ficresvpl);
3659: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3660: fprintf(ficresvpl,"# Age");
3661: for(i=1; i<=nlstate;i++)
3662: fprintf(ficresvpl," %1d-%1d",i,i);
3663: fprintf(ficresvpl,"\n");
3664:
3665: xp=vector(1,npar);
3666: dnewm=matrix(1,nlstate,1,npar);
3667: doldm=matrix(1,nlstate,1,nlstate);
3668:
3669: hstepm=1*YEARM; /* Every year of age */
3670: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3671: agelim = AGESUP;
3672: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3673: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3674: if (stepm >= YEARM) hstepm=1;
3675: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3676: gradg=matrix(1,npar,1,nlstate);
3677: gp=vector(1,nlstate);
3678: gm=vector(1,nlstate);
3679:
3680: for(theta=1; theta <=npar; theta++){
3681: for(i=1; i<=npar; i++){ /* Computes gradient */
3682: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3683: }
3684: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3685: for(i=1;i<=nlstate;i++)
3686: gp[i] = prlim[i][i];
3687:
3688: for(i=1; i<=npar; i++) /* Computes gradient */
3689: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3690: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3691: for(i=1;i<=nlstate;i++)
3692: gm[i] = prlim[i][i];
3693:
3694: for(i=1;i<=nlstate;i++)
3695: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3696: } /* End theta */
3697:
3698: trgradg =matrix(1,nlstate,1,npar);
3699:
3700: for(j=1; j<=nlstate;j++)
3701: for(theta=1; theta <=npar; theta++)
3702: trgradg[j][theta]=gradg[theta][j];
3703:
3704: for(i=1;i<=nlstate;i++)
3705: varpl[i][(int)age] =0.;
3706: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3707: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3708: for(i=1;i<=nlstate;i++)
3709: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3710:
3711: fprintf(ficresvpl,"%.0f ",age );
3712: for(i=1; i<=nlstate;i++)
3713: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3714: fprintf(ficresvpl,"\n");
3715: free_vector(gp,1,nlstate);
3716: free_vector(gm,1,nlstate);
3717: free_matrix(gradg,1,npar,1,nlstate);
3718: free_matrix(trgradg,1,nlstate,1,npar);
3719: } /* End age */
3720:
3721: free_vector(xp,1,npar);
3722: free_matrix(doldm,1,nlstate,1,npar);
3723: free_matrix(dnewm,1,nlstate,1,nlstate);
3724:
3725: }
3726:
3727: /************ Variance of one-step probabilities ******************/
3728: 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[])
3729: {
3730: int i, j=0, k1, l1, tj;
3731: int k2, l2, j1, z1;
3732: int k=0, l;
3733: int first=1, first1, first2;
3734: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3735: double **dnewm,**doldm;
3736: double *xp;
3737: double *gp, *gm;
3738: double **gradg, **trgradg;
3739: double **mu;
3740: double age, cov[NCOVMAX+1];
3741: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3742: int theta;
3743: char fileresprob[FILENAMELENGTH];
3744: char fileresprobcov[FILENAMELENGTH];
3745: char fileresprobcor[FILENAMELENGTH];
3746: double ***varpij;
3747:
3748: strcpy(fileresprob,"prob");
3749: strcat(fileresprob,fileres);
3750: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3751: printf("Problem with resultfile: %s\n", fileresprob);
3752: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3753: }
3754: strcpy(fileresprobcov,"probcov");
3755: strcat(fileresprobcov,fileres);
3756: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3757: printf("Problem with resultfile: %s\n", fileresprobcov);
3758: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3759: }
3760: strcpy(fileresprobcor,"probcor");
3761: strcat(fileresprobcor,fileres);
3762: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3763: printf("Problem with resultfile: %s\n", fileresprobcor);
3764: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3765: }
3766: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3767: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3768: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3769: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3770: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3771: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3772: pstamp(ficresprob);
3773: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3774: fprintf(ficresprob,"# Age");
3775: pstamp(ficresprobcov);
3776: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3777: fprintf(ficresprobcov,"# Age");
3778: pstamp(ficresprobcor);
3779: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3780: fprintf(ficresprobcor,"# Age");
3781:
3782:
3783: for(i=1; i<=nlstate;i++)
3784: for(j=1; j<=(nlstate+ndeath);j++){
3785: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3786: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3787: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3788: }
3789: /* fprintf(ficresprob,"\n");
3790: fprintf(ficresprobcov,"\n");
3791: fprintf(ficresprobcor,"\n");
3792: */
3793: xp=vector(1,npar);
3794: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3795: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3796: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3797: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3798: first=1;
3799: fprintf(ficgp,"\n# Routine varprob");
3800: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3801: fprintf(fichtm,"\n");
3802:
3803: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3804: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3805: file %s<br>\n",optionfilehtmcov);
3806: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3807: and drawn. It helps understanding how is the covariance between two incidences.\
3808: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3809: 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. \
3810: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3811: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3812: standard deviations wide on each axis. <br>\
3813: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3814: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3815: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3816:
3817: cov[1]=1;
3818: /* tj=cptcoveff; */
3819: tj = (int) pow(2,cptcoveff);
3820: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3821: j1=0;
3822: for(j1=1; j1<=tj;j1++){
3823: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3824: /*j1++;*/
3825: if (cptcovn>0) {
3826: fprintf(ficresprob, "\n#********** Variable ");
3827: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3828: fprintf(ficresprob, "**********\n#\n");
3829: fprintf(ficresprobcov, "\n#********** Variable ");
3830: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3831: fprintf(ficresprobcov, "**********\n#\n");
3832:
3833: fprintf(ficgp, "\n#********** Variable ");
3834: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3835: fprintf(ficgp, "**********\n#\n");
3836:
3837:
3838: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3839: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3840: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3841:
3842: fprintf(ficresprobcor, "\n#********** Variable ");
3843: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3844: fprintf(ficresprobcor, "**********\n#");
3845: }
3846:
3847: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3848: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3849: gp=vector(1,(nlstate)*(nlstate+ndeath));
3850: gm=vector(1,(nlstate)*(nlstate+ndeath));
3851: for (age=bage; age<=fage; age ++){
3852: cov[2]=age;
3853: for (k=1; k<=cptcovn;k++) {
3854: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3855: * 1 1 1 1 1
3856: * 2 2 1 1 1
3857: * 3 1 2 1 1
3858: */
3859: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3860: }
3861: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3862: for (k=1; k<=cptcovprod;k++)
3863: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3864:
3865:
3866: for(theta=1; theta <=npar; theta++){
3867: for(i=1; i<=npar; i++)
3868: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3869:
3870: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3871:
3872: k=0;
3873: for(i=1; i<= (nlstate); i++){
3874: for(j=1; j<=(nlstate+ndeath);j++){
3875: k=k+1;
3876: gp[k]=pmmij[i][j];
3877: }
3878: }
3879:
3880: for(i=1; i<=npar; i++)
3881: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3882:
3883: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3884: k=0;
3885: for(i=1; i<=(nlstate); i++){
3886: for(j=1; j<=(nlstate+ndeath);j++){
3887: k=k+1;
3888: gm[k]=pmmij[i][j];
3889: }
3890: }
3891:
3892: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3893: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3894: }
3895:
3896: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3897: for(theta=1; theta <=npar; theta++)
3898: trgradg[j][theta]=gradg[theta][j];
3899:
3900: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3901: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3902:
3903: pmij(pmmij,cov,ncovmodel,x,nlstate);
3904:
3905: k=0;
3906: for(i=1; i<=(nlstate); i++){
3907: for(j=1; j<=(nlstate+ndeath);j++){
3908: k=k+1;
3909: mu[k][(int) age]=pmmij[i][j];
3910: }
3911: }
3912: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3913: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3914: varpij[i][j][(int)age] = doldm[i][j];
3915:
3916: /*printf("\n%d ",(int)age);
3917: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3918: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3919: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3920: }*/
3921:
3922: fprintf(ficresprob,"\n%d ",(int)age);
3923: fprintf(ficresprobcov,"\n%d ",(int)age);
3924: fprintf(ficresprobcor,"\n%d ",(int)age);
3925:
3926: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3927: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3928: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3929: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3930: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3931: }
3932: i=0;
3933: for (k=1; k<=(nlstate);k++){
3934: for (l=1; l<=(nlstate+ndeath);l++){
3935: i++;
3936: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3937: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3938: for (j=1; j<=i;j++){
3939: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3940: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3941: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3942: }
3943: }
3944: }/* end of loop for state */
3945: } /* end of loop for age */
3946: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3947: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3948: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3949: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3950:
3951: /* Confidence intervalle of pij */
3952: /*
3953: fprintf(ficgp,"\nunset parametric;unset label");
3954: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3955: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3956: 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);
3957: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3958: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3959: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3960: */
3961:
3962: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3963: first1=1;first2=2;
3964: for (k2=1; k2<=(nlstate);k2++){
3965: for (l2=1; l2<=(nlstate+ndeath);l2++){
3966: if(l2==k2) continue;
3967: j=(k2-1)*(nlstate+ndeath)+l2;
3968: for (k1=1; k1<=(nlstate);k1++){
3969: for (l1=1; l1<=(nlstate+ndeath);l1++){
3970: if(l1==k1) continue;
3971: i=(k1-1)*(nlstate+ndeath)+l1;
3972: if(i<=j) continue;
3973: for (age=bage; age<=fage; age ++){
3974: if ((int)age %5==0){
3975: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3976: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3977: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3978: mu1=mu[i][(int) age]/stepm*YEARM ;
3979: mu2=mu[j][(int) age]/stepm*YEARM;
3980: c12=cv12/sqrt(v1*v2);
3981: /* Computing eigen value of matrix of covariance */
3982: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3983: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3984: if ((lc2 <0) || (lc1 <0) ){
3985: if(first2==1){
3986: first1=0;
3987: 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);
3988: }
3989: 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);
3990: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3991: /* lc2=fabs(lc2); */
3992: }
3993:
3994: /* Eigen vectors */
3995: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3996: /*v21=sqrt(1.-v11*v11); *//* error */
3997: v21=(lc1-v1)/cv12*v11;
3998: v12=-v21;
3999: v22=v11;
4000: tnalp=v21/v11;
4001: if(first1==1){
4002: first1=0;
4003: 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);
4004: }
4005: 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);
4006: /*printf(fignu*/
4007: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4008: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4009: if(first==1){
4010: first=0;
4011: fprintf(ficgp,"\nset parametric;unset label");
4012: 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);
4013: fprintf(ficgp,"\nset ter png small size 320, 240");
4014: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4015: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4016: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4017: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4018: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4019: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4020: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4021: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4022: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4023: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4024: 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",\
4025: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4026: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4027: }else{
4028: first=0;
4029: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4030: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4031: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4032: 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",\
4033: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4034: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4035: }/* if first */
4036: } /* age mod 5 */
4037: } /* end loop age */
4038: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4039: first=1;
4040: } /*l12 */
4041: } /* k12 */
4042: } /*l1 */
4043: }/* k1 */
4044: /* } /* loop covariates */
4045: }
4046: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4047: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4048: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4049: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4050: free_vector(xp,1,npar);
4051: fclose(ficresprob);
4052: fclose(ficresprobcov);
4053: fclose(ficresprobcor);
4054: fflush(ficgp);
4055: fflush(fichtmcov);
4056: }
4057:
4058:
4059: /******************* Printing html file ***********/
4060: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4061: int lastpass, int stepm, int weightopt, char model[],\
4062: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4063: int popforecast, int estepm ,\
4064: double jprev1, double mprev1,double anprev1, \
4065: double jprev2, double mprev2,double anprev2){
4066: int jj1, k1, i1, cpt;
4067:
4068: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4069: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4070: </ul>");
4071: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4072: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4073: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4074: fprintf(fichtm,"\
4075: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4076: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4077: fprintf(fichtm,"\
4078: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4079: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4080: fprintf(fichtm,"\
4081: - (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): \
4082: <a href=\"%s\">%s</a> <br>\n",
4083: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4084: fprintf(fichtm,"\
4085: - Population projections by age and states: \
4086: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4087:
4088: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4089:
4090: m=pow(2,cptcoveff);
4091: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4092:
4093: jj1=0;
4094: for(k1=1; k1<=m;k1++){
4095: for(i1=1; i1<=ncodemax[k1];i1++){
4096: jj1++;
4097: if (cptcovn > 0) {
4098: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4099: for (cpt=1; cpt<=cptcoveff;cpt++)
4100: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4101: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4102: }
4103: /* Pij */
4104: 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> \
4105: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4106: /* Quasi-incidences */
4107: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4108: 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> \
4109: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4110: /* Period (stable) prevalence in each health state */
4111: for(cpt=1; cpt<=nlstate;cpt++){
4112: fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
4113: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4114: }
4115: for(cpt=1; cpt<=nlstate;cpt++) {
4116: 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> \
4117: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4118: }
4119: } /* end i1 */
4120: }/* End k1 */
4121: fprintf(fichtm,"</ul>");
4122:
4123:
4124: fprintf(fichtm,"\
4125: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4126: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4127:
4128: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4129: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4130: fprintf(fichtm,"\
4131: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4132: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4133:
4134: fprintf(fichtm,"\
4135: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4136: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4137: fprintf(fichtm,"\
4138: - 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): \
4139: <a href=\"%s\">%s</a> <br>\n</li>",
4140: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4141: fprintf(fichtm,"\
4142: - (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): \
4143: <a href=\"%s\">%s</a> <br>\n</li>",
4144: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4145: fprintf(fichtm,"\
4146: - 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",
4147: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4148: fprintf(fichtm,"\
4149: - 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",
4150: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4151: fprintf(fichtm,"\
4152: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4153: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4154:
4155: /* if(popforecast==1) fprintf(fichtm,"\n */
4156: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4157: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4158: /* <br>",fileres,fileres,fileres,fileres); */
4159: /* else */
4160: /* 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); */
4161: fflush(fichtm);
4162: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4163:
4164: m=pow(2,cptcoveff);
4165: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4166:
4167: jj1=0;
4168: for(k1=1; k1<=m;k1++){
4169: for(i1=1; i1<=ncodemax[k1];i1++){
4170: jj1++;
4171: if (cptcovn > 0) {
4172: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4173: for (cpt=1; cpt<=cptcoveff;cpt++)
4174: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4175: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4176: }
4177: for(cpt=1; cpt<=nlstate;cpt++) {
4178: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4179: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4180: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4181: }
4182: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4183: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4184: true period expectancies (those weighted with period prevalences are also\
4185: drawn in addition to the population based expectancies computed using\
4186: observed and cahotic prevalences: %s%d.png<br>\
4187: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4188: } /* end i1 */
4189: }/* End k1 */
4190: fprintf(fichtm,"</ul>");
4191: fflush(fichtm);
4192: }
4193:
4194: /******************* Gnuplot file **************/
4195: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4196:
4197: char dirfileres[132],optfileres[132];
4198: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4199: int ng=0;
4200: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4201: /* printf("Problem with file %s",optionfilegnuplot); */
4202: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4203: /* } */
4204:
4205: /*#ifdef windows */
4206: fprintf(ficgp,"cd \"%s\" \n",pathc);
4207: /*#endif */
4208: m=pow(2,cptcoveff);
4209:
4210: strcpy(dirfileres,optionfilefiname);
4211: strcpy(optfileres,"vpl");
4212: /* 1eme*/
4213: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4214: for (cpt=1; cpt<= nlstate ; cpt ++) {
4215: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4216: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4217: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4218: fprintf(ficgp,"set xlabel \"Age\" \n\
4219: set ylabel \"Probability\" \n\
4220: set ter png small size 320, 240\n\
4221: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4222:
4223: for (i=1; i<= nlstate ; i ++) {
4224: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4225: else fprintf(ficgp," \%%*lf (\%%*lf)");
4226: }
4227: 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);
4228: for (i=1; i<= nlstate ; i ++) {
4229: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4230: else fprintf(ficgp," \%%*lf (\%%*lf)");
4231: }
4232: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4233: for (i=1; i<= nlstate ; i ++) {
4234: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4235: else fprintf(ficgp," \%%*lf (\%%*lf)");
4236: }
4237: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4238: }
4239: }
4240: /*2 eme*/
4241: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4242: for (k1=1; k1<= m ; k1 ++) {
4243: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4244: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4245:
4246: for (i=1; i<= nlstate+1 ; i ++) {
4247: k=2*i;
4248: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4249: for (j=1; j<= nlstate+1 ; j ++) {
4250: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4251: else fprintf(ficgp," \%%*lf (\%%*lf)");
4252: }
4253: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4254: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4255: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4256: for (j=1; j<= nlstate+1 ; j ++) {
4257: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4258: else fprintf(ficgp," \%%*lf (\%%*lf)");
4259: }
4260: fprintf(ficgp,"\" t\"\" w l lt 0,");
4261: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4262: for (j=1; j<= nlstate+1 ; j ++) {
4263: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4264: else fprintf(ficgp," \%%*lf (\%%*lf)");
4265: }
4266: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4267: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4268: }
4269: }
4270:
4271: /*3eme*/
4272:
4273: for (k1=1; k1<= m ; k1 ++) {
4274: for (cpt=1; cpt<= nlstate ; cpt ++) {
4275: /* k=2+nlstate*(2*cpt-2); */
4276: k=2+(nlstate+1)*(cpt-1);
4277: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4278: fprintf(ficgp,"set ter png small size 320, 240\n\
4279: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4280: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4281: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4282: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4283: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4284: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4285: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4286:
4287: */
4288: for (i=1; i< nlstate ; i ++) {
4289: 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);
4290: /* 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);*/
4291:
4292: }
4293: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4294: }
4295: }
4296:
4297: /* CV preval stable (period) */
4298: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4299: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4300: k=3;
4301: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4302: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4303: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4304: set ter png small size 320, 240\n\
4305: unset log y\n\
4306: plot [%.f:%.f] ", ageminpar, agemaxpar);
4307: for (i=1; i<= nlstate ; i ++){
4308: if(i==1)
4309: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4310: else
4311: fprintf(ficgp,", '' ");
4312: l=(nlstate+ndeath)*(i-1)+1;
4313: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4314: for (j=1; j<= (nlstate-1) ; j ++)
4315: fprintf(ficgp,"+$%d",k+l+j);
4316: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4317: } /* nlstate */
4318: fprintf(ficgp,"\n");
4319: } /* end cpt state*/
4320: } /* end covariate */
4321:
4322: /* proba elementaires */
4323: for(i=1,jk=1; i <=nlstate; i++){
4324: for(k=1; k <=(nlstate+ndeath); k++){
4325: if (k != i) {
4326: for(j=1; j <=ncovmodel; j++){
4327: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4328: jk++;
4329: fprintf(ficgp,"\n");
4330: }
4331: }
4332: }
4333: }
4334: /*goto avoid;*/
4335: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4336: for(jk=1; jk <=m; jk++) {
4337: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4338: if (ng==2)
4339: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4340: else
4341: fprintf(ficgp,"\nset title \"Probability\"\n");
4342: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4343: i=1;
4344: for(k2=1; k2<=nlstate; k2++) {
4345: k3=i;
4346: for(k=1; k<=(nlstate+ndeath); k++) {
4347: if (k != k2){
4348: if(ng==2)
4349: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4350: else
4351: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4352: ij=1;/* To be checked else nbcode[0][0] wrong */
4353: for(j=3; j <=ncovmodel; j++) {
4354: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4355: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4356: /* ij++; */
4357: /* } */
4358: /* else */
4359: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4360: }
4361: fprintf(ficgp,")/(1");
4362:
4363: for(k1=1; k1 <=nlstate; k1++){
4364: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4365: ij=1;
4366: for(j=3; j <=ncovmodel; j++){
4367: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4368: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4369: /* ij++; */
4370: /* } */
4371: /* else */
4372: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4373: }
4374: fprintf(ficgp,")");
4375: }
4376: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4377: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4378: i=i+ncovmodel;
4379: }
4380: } /* end k */
4381: } /* end k2 */
4382: } /* end jk */
4383: } /* end ng */
4384: /* avoid: */
4385: fflush(ficgp);
4386: } /* end gnuplot */
4387:
4388:
4389: /*************** Moving average **************/
4390: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4391:
4392: int i, cpt, cptcod;
4393: int modcovmax =1;
4394: int mobilavrange, mob;
4395: double age;
4396:
4397: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4398: a covariate has 2 modalities */
4399: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4400:
4401: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4402: if(mobilav==1) mobilavrange=5; /* default */
4403: else mobilavrange=mobilav;
4404: for (age=bage; age<=fage; age++)
4405: for (i=1; i<=nlstate;i++)
4406: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4407: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4408: /* We keep the original values on the extreme ages bage, fage and for
4409: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4410: we use a 5 terms etc. until the borders are no more concerned.
4411: */
4412: for (mob=3;mob <=mobilavrange;mob=mob+2){
4413: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4414: for (i=1; i<=nlstate;i++){
4415: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4416: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4417: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4418: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4419: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4420: }
4421: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4422: }
4423: }
4424: }/* end age */
4425: }/* end mob */
4426: }else return -1;
4427: return 0;
4428: }/* End movingaverage */
4429:
4430:
4431: /************** Forecasting ******************/
4432: 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){
4433: /* proj1, year, month, day of starting projection
4434: agemin, agemax range of age
4435: dateprev1 dateprev2 range of dates during which prevalence is computed
4436: anproj2 year of en of projection (same day and month as proj1).
4437: */
4438: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4439: double agec; /* generic age */
4440: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4441: double *popeffectif,*popcount;
4442: double ***p3mat;
4443: double ***mobaverage;
4444: char fileresf[FILENAMELENGTH];
4445:
4446: agelim=AGESUP;
4447: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4448:
4449: strcpy(fileresf,"f");
4450: strcat(fileresf,fileres);
4451: if((ficresf=fopen(fileresf,"w"))==NULL) {
4452: printf("Problem with forecast resultfile: %s\n", fileresf);
4453: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4454: }
4455: printf("Computing forecasting: result on file '%s' \n", fileresf);
4456: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4457:
4458: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4459:
4460: if (mobilav!=0) {
4461: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4462: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4463: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4464: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4465: }
4466: }
4467:
4468: stepsize=(int) (stepm+YEARM-1)/YEARM;
4469: if (stepm<=12) stepsize=1;
4470: if(estepm < stepm){
4471: printf ("Problem %d lower than %d\n",estepm, stepm);
4472: }
4473: else hstepm=estepm;
4474:
4475: hstepm=hstepm/stepm;
4476: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4477: fractional in yp1 */
4478: anprojmean=yp;
4479: yp2=modf((yp1*12),&yp);
4480: mprojmean=yp;
4481: yp1=modf((yp2*30.5),&yp);
4482: jprojmean=yp;
4483: if(jprojmean==0) jprojmean=1;
4484: if(mprojmean==0) jprojmean=1;
4485:
4486: i1=cptcoveff;
4487: if (cptcovn < 1){i1=1;}
4488:
4489: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4490:
4491: fprintf(ficresf,"#****** Routine prevforecast **\n");
4492:
4493: /* if (h==(int)(YEARM*yearp)){ */
4494: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4495: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4496: k=k+1;
4497: fprintf(ficresf,"\n#******");
4498: for(j=1;j<=cptcoveff;j++) {
4499: 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]]);
4500: }
4501: fprintf(ficresf,"******\n");
4502: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4503: for(j=1; j<=nlstate+ndeath;j++){
4504: for(i=1; i<=nlstate;i++)
4505: fprintf(ficresf," p%d%d",i,j);
4506: fprintf(ficresf," p.%d",j);
4507: }
4508: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4509: fprintf(ficresf,"\n");
4510: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4511:
4512: for (agec=fage; agec>=(ageminpar-1); agec--){
4513: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4514: nhstepm = nhstepm/hstepm;
4515: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4516: oldm=oldms;savm=savms;
4517: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4518:
4519: for (h=0; h<=nhstepm; h++){
4520: if (h*hstepm/YEARM*stepm ==yearp) {
4521: fprintf(ficresf,"\n");
4522: for(j=1;j<=cptcoveff;j++)
4523: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4524: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4525: }
4526: for(j=1; j<=nlstate+ndeath;j++) {
4527: ppij=0.;
4528: for(i=1; i<=nlstate;i++) {
4529: if (mobilav==1)
4530: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4531: else {
4532: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4533: }
4534: if (h*hstepm/YEARM*stepm== yearp) {
4535: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4536: }
4537: } /* end i */
4538: if (h*hstepm/YEARM*stepm==yearp) {
4539: fprintf(ficresf," %.3f", ppij);
4540: }
4541: }/* end j */
4542: } /* end h */
4543: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4544: } /* end agec */
4545: } /* end yearp */
4546: } /* end cptcod */
4547: } /* end cptcov */
4548:
4549: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4550:
4551: fclose(ficresf);
4552: }
4553:
4554: /************** Forecasting *****not tested NB*************/
4555: 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){
4556:
4557: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4558: int *popage;
4559: double calagedatem, agelim, kk1, kk2;
4560: double *popeffectif,*popcount;
4561: double ***p3mat,***tabpop,***tabpopprev;
4562: double ***mobaverage;
4563: char filerespop[FILENAMELENGTH];
4564:
4565: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4566: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4567: agelim=AGESUP;
4568: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4569:
4570: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4571:
4572:
4573: strcpy(filerespop,"pop");
4574: strcat(filerespop,fileres);
4575: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4576: printf("Problem with forecast resultfile: %s\n", filerespop);
4577: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4578: }
4579: printf("Computing forecasting: result on file '%s' \n", filerespop);
4580: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4581:
4582: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4583:
4584: if (mobilav!=0) {
4585: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4586: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4587: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4588: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4589: }
4590: }
4591:
4592: stepsize=(int) (stepm+YEARM-1)/YEARM;
4593: if (stepm<=12) stepsize=1;
4594:
4595: agelim=AGESUP;
4596:
4597: hstepm=1;
4598: hstepm=hstepm/stepm;
4599:
4600: if (popforecast==1) {
4601: if((ficpop=fopen(popfile,"r"))==NULL) {
4602: printf("Problem with population file : %s\n",popfile);exit(0);
4603: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4604: }
4605: popage=ivector(0,AGESUP);
4606: popeffectif=vector(0,AGESUP);
4607: popcount=vector(0,AGESUP);
4608:
4609: i=1;
4610: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4611:
4612: imx=i;
4613: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4614: }
4615:
4616: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4617: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4618: k=k+1;
4619: fprintf(ficrespop,"\n#******");
4620: for(j=1;j<=cptcoveff;j++) {
4621: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4622: }
4623: fprintf(ficrespop,"******\n");
4624: fprintf(ficrespop,"# Age");
4625: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4626: if (popforecast==1) fprintf(ficrespop," [Population]");
4627:
4628: for (cpt=0; cpt<=0;cpt++) {
4629: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4630:
4631: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4632: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4633: nhstepm = nhstepm/hstepm;
4634:
4635: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4636: oldm=oldms;savm=savms;
4637: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4638:
4639: for (h=0; h<=nhstepm; h++){
4640: if (h==(int) (calagedatem+YEARM*cpt)) {
4641: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4642: }
4643: for(j=1; j<=nlstate+ndeath;j++) {
4644: kk1=0.;kk2=0;
4645: for(i=1; i<=nlstate;i++) {
4646: if (mobilav==1)
4647: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4648: else {
4649: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4650: }
4651: }
4652: if (h==(int)(calagedatem+12*cpt)){
4653: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4654: /*fprintf(ficrespop," %.3f", kk1);
4655: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4656: }
4657: }
4658: for(i=1; i<=nlstate;i++){
4659: kk1=0.;
4660: for(j=1; j<=nlstate;j++){
4661: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4662: }
4663: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4664: }
4665:
4666: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4667: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4668: }
4669: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4670: }
4671: }
4672:
4673: /******/
4674:
4675: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4676: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4677: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4678: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4679: nhstepm = nhstepm/hstepm;
4680:
4681: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4682: oldm=oldms;savm=savms;
4683: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4684: for (h=0; h<=nhstepm; h++){
4685: if (h==(int) (calagedatem+YEARM*cpt)) {
4686: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4687: }
4688: for(j=1; j<=nlstate+ndeath;j++) {
4689: kk1=0.;kk2=0;
4690: for(i=1; i<=nlstate;i++) {
4691: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4692: }
4693: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4694: }
4695: }
4696: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4697: }
4698: }
4699: }
4700: }
4701:
4702: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4703:
4704: if (popforecast==1) {
4705: free_ivector(popage,0,AGESUP);
4706: free_vector(popeffectif,0,AGESUP);
4707: free_vector(popcount,0,AGESUP);
4708: }
4709: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4710: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4711: fclose(ficrespop);
4712: } /* End of popforecast */
4713:
4714: int fileappend(FILE *fichier, char *optionfich)
4715: {
4716: if((fichier=fopen(optionfich,"a"))==NULL) {
4717: printf("Problem with file: %s\n", optionfich);
4718: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4719: return (0);
4720: }
4721: fflush(fichier);
4722: return (1);
4723: }
4724:
4725:
4726: /**************** function prwizard **********************/
4727: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4728: {
4729:
4730: /* Wizard to print covariance matrix template */
4731:
4732: char ca[32], cb[32];
4733: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4734: int numlinepar;
4735:
4736: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4737: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4738: for(i=1; i <=nlstate; i++){
4739: jj=0;
4740: for(j=1; j <=nlstate+ndeath; j++){
4741: if(j==i) continue;
4742: jj++;
4743: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4744: printf("%1d%1d",i,j);
4745: fprintf(ficparo,"%1d%1d",i,j);
4746: for(k=1; k<=ncovmodel;k++){
4747: /* printf(" %lf",param[i][j][k]); */
4748: /* fprintf(ficparo," %lf",param[i][j][k]); */
4749: printf(" 0.");
4750: fprintf(ficparo," 0.");
4751: }
4752: printf("\n");
4753: fprintf(ficparo,"\n");
4754: }
4755: }
4756: printf("# Scales (for hessian or gradient estimation)\n");
4757: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4758: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4759: for(i=1; i <=nlstate; i++){
4760: jj=0;
4761: for(j=1; j <=nlstate+ndeath; j++){
4762: if(j==i) continue;
4763: jj++;
4764: fprintf(ficparo,"%1d%1d",i,j);
4765: printf("%1d%1d",i,j);
4766: fflush(stdout);
4767: for(k=1; k<=ncovmodel;k++){
4768: /* printf(" %le",delti3[i][j][k]); */
4769: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4770: printf(" 0.");
4771: fprintf(ficparo," 0.");
4772: }
4773: numlinepar++;
4774: printf("\n");
4775: fprintf(ficparo,"\n");
4776: }
4777: }
4778: printf("# Covariance matrix\n");
4779: /* # 121 Var(a12)\n\ */
4780: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4781: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4782: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4783: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4784: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4785: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4786: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4787: fflush(stdout);
4788: fprintf(ficparo,"# Covariance matrix\n");
4789: /* # 121 Var(a12)\n\ */
4790: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4791: /* # ...\n\ */
4792: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4793:
4794: for(itimes=1;itimes<=2;itimes++){
4795: jj=0;
4796: for(i=1; i <=nlstate; i++){
4797: for(j=1; j <=nlstate+ndeath; j++){
4798: if(j==i) continue;
4799: for(k=1; k<=ncovmodel;k++){
4800: jj++;
4801: ca[0]= k+'a'-1;ca[1]='\0';
4802: if(itimes==1){
4803: printf("#%1d%1d%d",i,j,k);
4804: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4805: }else{
4806: printf("%1d%1d%d",i,j,k);
4807: fprintf(ficparo,"%1d%1d%d",i,j,k);
4808: /* printf(" %.5le",matcov[i][j]); */
4809: }
4810: ll=0;
4811: for(li=1;li <=nlstate; li++){
4812: for(lj=1;lj <=nlstate+ndeath; lj++){
4813: if(lj==li) continue;
4814: for(lk=1;lk<=ncovmodel;lk++){
4815: ll++;
4816: if(ll<=jj){
4817: cb[0]= lk +'a'-1;cb[1]='\0';
4818: if(ll<jj){
4819: if(itimes==1){
4820: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4821: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4822: }else{
4823: printf(" 0.");
4824: fprintf(ficparo," 0.");
4825: }
4826: }else{
4827: if(itimes==1){
4828: printf(" Var(%s%1d%1d)",ca,i,j);
4829: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4830: }else{
4831: printf(" 0.");
4832: fprintf(ficparo," 0.");
4833: }
4834: }
4835: }
4836: } /* end lk */
4837: } /* end lj */
4838: } /* end li */
4839: printf("\n");
4840: fprintf(ficparo,"\n");
4841: numlinepar++;
4842: } /* end k*/
4843: } /*end j */
4844: } /* end i */
4845: } /* end itimes */
4846:
4847: } /* end of prwizard */
4848: /******************* Gompertz Likelihood ******************************/
4849: double gompertz(double x[])
4850: {
4851: double A,B,L=0.0,sump=0.,num=0.;
4852: int i,n=0; /* n is the size of the sample */
4853:
4854: for (i=0;i<=imx-1 ; i++) {
4855: sump=sump+weight[i];
4856: /* sump=sump+1;*/
4857: num=num+1;
4858: }
4859:
4860:
4861: /* for (i=0; i<=imx; i++)
4862: 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]);*/
4863:
4864: for (i=1;i<=imx ; i++)
4865: {
4866: if (cens[i] == 1 && wav[i]>1)
4867: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4868:
4869: if (cens[i] == 0 && wav[i]>1)
4870: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4871: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4872:
4873: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4874: if (wav[i] > 1 ) { /* ??? */
4875: L=L+A*weight[i];
4876: /* 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]);*/
4877: }
4878: }
4879:
4880: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4881:
4882: return -2*L*num/sump;
4883: }
4884:
4885: #ifdef GSL
4886: /******************* Gompertz_f Likelihood ******************************/
4887: double gompertz_f(const gsl_vector *v, void *params)
4888: {
4889: double A,B,LL=0.0,sump=0.,num=0.;
4890: double *x= (double *) v->data;
4891: int i,n=0; /* n is the size of the sample */
4892:
4893: for (i=0;i<=imx-1 ; i++) {
4894: sump=sump+weight[i];
4895: /* sump=sump+1;*/
4896: num=num+1;
4897: }
4898:
4899:
4900: /* for (i=0; i<=imx; i++)
4901: 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]);*/
4902: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4903: for (i=1;i<=imx ; i++)
4904: {
4905: if (cens[i] == 1 && wav[i]>1)
4906: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4907:
4908: if (cens[i] == 0 && wav[i]>1)
4909: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4910: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4911:
4912: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4913: if (wav[i] > 1 ) { /* ??? */
4914: LL=LL+A*weight[i];
4915: /* 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]);*/
4916: }
4917: }
4918:
4919: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4920: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4921:
4922: return -2*LL*num/sump;
4923: }
4924: #endif
4925:
4926: /******************* Printing html file ***********/
4927: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4928: int lastpass, int stepm, int weightopt, char model[],\
4929: int imx, double p[],double **matcov,double agemortsup){
4930: int i,k;
4931:
4932: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4933: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4934: for (i=1;i<=2;i++)
4935: 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]));
4936: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4937: fprintf(fichtm,"</ul>");
4938:
4939: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4940:
4941: 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>");
4942:
4943: for (k=agegomp;k<(agemortsup-2);k++)
4944: 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]);
4945:
4946:
4947: fflush(fichtm);
4948: }
4949:
4950: /******************* Gnuplot file **************/
4951: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4952:
4953: char dirfileres[132],optfileres[132];
4954:
4955: int ng;
4956:
4957:
4958: /*#ifdef windows */
4959: fprintf(ficgp,"cd \"%s\" \n",pathc);
4960: /*#endif */
4961:
4962:
4963: strcpy(dirfileres,optionfilefiname);
4964: strcpy(optfileres,"vpl");
4965: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4966: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4967: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4968: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4969: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4970:
4971: }
4972:
4973: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4974: {
4975:
4976: /*-------- data file ----------*/
4977: FILE *fic;
4978: char dummy[]=" ";
4979: int i=0, j=0, n=0;
4980: int linei, month, year,iout;
4981: char line[MAXLINE], linetmp[MAXLINE];
4982: char stra[MAXLINE], strb[MAXLINE];
4983: char *stratrunc;
4984: int lstra;
4985:
4986:
4987: if((fic=fopen(datafile,"r"))==NULL) {
4988: printf("Problem while opening datafile: %s\n", datafile);return 1;
4989: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4990: }
4991:
4992: i=1;
4993: linei=0;
4994: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4995: linei=linei+1;
4996: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4997: if(line[j] == '\t')
4998: line[j] = ' ';
4999: }
5000: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5001: ;
5002: };
5003: line[j+1]=0; /* Trims blanks at end of line */
5004: if(line[0]=='#'){
5005: fprintf(ficlog,"Comment line\n%s\n",line);
5006: printf("Comment line\n%s\n",line);
5007: continue;
5008: }
5009: trimbb(linetmp,line); /* Trims multiple blanks in line */
5010: strcpy(line, linetmp);
5011:
5012:
5013: for (j=maxwav;j>=1;j--){
5014: cutv(stra, strb, line, ' ');
5015: if(strb[0]=='.') { /* Missing status */
5016: lval=-1;
5017: }else{
5018: errno=0;
5019: lval=strtol(strb,&endptr,10);
5020: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5021: if( strb[0]=='\0' || (*endptr != '\0')){
5022: 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);
5023: 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);
5024: return 1;
5025: }
5026: }
5027: s[j][i]=lval;
5028:
5029: strcpy(line,stra);
5030: cutv(stra, strb,line,' ');
5031: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5032: }
5033: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5034: month=99;
5035: year=9999;
5036: }else{
5037: 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);
5038: 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);
5039: return 1;
5040: }
5041: anint[j][i]= (double) year;
5042: mint[j][i]= (double)month;
5043: strcpy(line,stra);
5044: } /* ENd Waves */
5045:
5046: cutv(stra, strb,line,' ');
5047: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5048: }
5049: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5050: month=99;
5051: year=9999;
5052: }else{
5053: 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);
5054: 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);
5055: return 1;
5056: }
5057: andc[i]=(double) year;
5058: moisdc[i]=(double) month;
5059: strcpy(line,stra);
5060:
5061: cutv(stra, strb,line,' ');
5062: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5063: }
5064: else if(iout=sscanf(strb,"%s.", dummy) != 0){
5065: month=99;
5066: year=9999;
5067: }else{
5068: 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);
5069: 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);
5070: return 1;
5071: }
5072: if (year==9999) {
5073: 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);
5074: 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);
5075: return 1;
5076:
5077: }
5078: annais[i]=(double)(year);
5079: moisnais[i]=(double)(month);
5080: strcpy(line,stra);
5081:
5082: cutv(stra, strb,line,' ');
5083: errno=0;
5084: dval=strtod(strb,&endptr);
5085: if( strb[0]=='\0' || (*endptr != '\0')){
5086: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5087: 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);
5088: fflush(ficlog);
5089: return 1;
5090: }
5091: weight[i]=dval;
5092: strcpy(line,stra);
5093:
5094: for (j=ncovcol;j>=1;j--){
5095: cutv(stra, strb,line,' ');
5096: if(strb[0]=='.') { /* Missing status */
5097: lval=-1;
5098: }else{
5099: errno=0;
5100: lval=strtol(strb,&endptr,10);
5101: if( strb[0]=='\0' || (*endptr != '\0')){
5102: 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);
5103: 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);
5104: return 1;
5105: }
5106: }
5107: if(lval <-1 || lval >1){
5108: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5109: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5110: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5111: For example, for multinomial values like 1, 2 and 3,\n \
5112: build V1=0 V2=0 for the reference value (1),\n \
5113: V1=1 V2=0 for (2) \n \
5114: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5115: output of IMaCh is often meaningless.\n \
5116: Exiting.\n",lval,linei, i,line,j);
5117: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5118: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5119: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5120: For example, for multinomial values like 1, 2 and 3,\n \
5121: build V1=0 V2=0 for the reference value (1),\n \
5122: V1=1 V2=0 for (2) \n \
5123: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5124: output of IMaCh is often meaningless.\n \
5125: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5126: return 1;
5127: }
5128: covar[j][i]=(double)(lval);
5129: strcpy(line,stra);
5130: }
5131: lstra=strlen(stra);
5132:
5133: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5134: stratrunc = &(stra[lstra-9]);
5135: num[i]=atol(stratrunc);
5136: }
5137: else
5138: num[i]=atol(stra);
5139: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5140: 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;}*/
5141:
5142: i=i+1;
5143: } /* End loop reading data */
5144:
5145: *imax=i-1; /* Number of individuals */
5146: fclose(fic);
5147:
5148: return (0);
5149: /* endread: */
5150: printf("Exiting readdata: ");
5151: fclose(fic);
5152: return (1);
5153:
5154:
5155:
5156: }
5157: void removespace(char *str) {
5158: char *p1 = str, *p2 = str;
5159: do
5160: while (*p2 == ' ')
5161: p2++;
5162: while (*p1++ = *p2++);
5163: }
5164:
5165: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5166: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5167: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5168: * - cptcovn or number of covariates k of the models excluding age*products =6
5169: * - cptcovage number of covariates with age*products =2
5170: * - cptcovs number of simple covariates
5171: * - 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
5172: * which is a new column after the 9 (ncovcol) variables.
5173: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5174: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5175: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5176: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5177: */
5178: {
5179: int i, j, k, ks;
5180: int j1, k1, k2;
5181: char modelsav[80];
5182: char stra[80], strb[80], strc[80], strd[80],stre[80];
5183:
5184: /*removespace(model);*/
5185: if (strlen(model) >1){ /* If there is at least 1 covariate */
5186: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5187: j=nbocc(model,'+'); /**< j=Number of '+' */
5188: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5189: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5190: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5191: /* including age products which are counted in cptcovage.
5192: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5193: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5194: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5195: strcpy(modelsav,model);
5196: if (strstr(model,"AGE") !=0){
5197: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5198: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5199: return 1;
5200: }
5201: if (strstr(model,"v") !=0){
5202: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5203: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5204: return 1;
5205: }
5206:
5207: /* Design
5208: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5209: * < ncovcol=8 >
5210: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5211: * k= 1 2 3 4 5 6 7 8
5212: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5213: * covar[k,i], value of kth covariate if not including age for individual i:
5214: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5215: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5216: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5217: * Tage[++cptcovage]=k
5218: * if products, new covar are created after ncovcol with k1
5219: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5220: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5221: * 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
5222: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5223: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5224: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5225: * < ncovcol=8 >
5226: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5227: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5228: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5229: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5230: * p Tprod[1]@2={ 6, 5}
5231: *p Tvard[1][1]@4= {7, 8, 5, 6}
5232: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5233: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5234: *How to reorganize?
5235: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5236: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5237: * {2, 1, 4, 8, 5, 6, 3, 7}
5238: * Struct []
5239: */
5240:
5241: /* This loop fills the array Tvar from the string 'model'.*/
5242: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5243: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5244: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5245: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5246: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5247: /* k=1 Tvar[1]=2 (from V2) */
5248: /* k=5 Tvar[5] */
5249: /* for (k=1; k<=cptcovn;k++) { */
5250: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5251: /* } */
5252: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5253: /*
5254: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5255: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5256: Tvar[k]=0;
5257: cptcovage=0;
5258: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5259: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5260: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5261: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5262: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5263: /*scanf("%d",i);*/
5264: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5265: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5266: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5267: /* covar is not filled and then is empty */
5268: cptcovprod--;
5269: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5270: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5271: cptcovage++; /* Sums the number of covariates which include age as a product */
5272: Tage[cptcovage]=k; /* Tage[1] = 4 */
5273: /*printf("stre=%s ", stre);*/
5274: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5275: cptcovprod--;
5276: cutl(stre,strb,strc,'V');
5277: Tvar[k]=atoi(stre);
5278: cptcovage++;
5279: Tage[cptcovage]=k;
5280: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5281: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5282: cptcovn++;
5283: cptcovprodnoage++;k1++;
5284: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5285: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5286: because this model-covariate is a construction we invent a new column
5287: ncovcol + k1
5288: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5289: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5290: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5291: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5292: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5293: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5294: k2=k2+2;
5295: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5296: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5297: for (i=1; i<=lastobs;i++){
5298: /* Computes the new covariate which is a product of
5299: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5300: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5301: }
5302: } /* End age is not in the model */
5303: } /* End if model includes a product */
5304: else { /* no more sum */
5305: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5306: /* scanf("%d",i);*/
5307: cutl(strd,strc,strb,'V');
5308: ks++; /**< Number of simple covariates */
5309: cptcovn++;
5310: Tvar[k]=atoi(strd);
5311: }
5312: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5313: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5314: scanf("%d",i);*/
5315: } /* end of loop + */
5316: } /* end model */
5317:
5318: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5319: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5320:
5321: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5322: printf("cptcovprod=%d ", cptcovprod);
5323: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5324:
5325: scanf("%d ",i);*/
5326:
5327:
5328: return (0); /* with covar[new additional covariate if product] and Tage if age */
5329: /*endread:*/
5330: printf("Exiting decodemodel: ");
5331: return (1);
5332: }
5333:
5334: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5335: {
5336: int i, m;
5337:
5338: for (i=1; i<=imx; i++) {
5339: for(m=2; (m<= maxwav); m++) {
5340: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5341: anint[m][i]=9999;
5342: s[m][i]=-1;
5343: }
5344: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5345: *nberr++;
5346: 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);
5347: 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);
5348: s[m][i]=-1;
5349: }
5350: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5351: *nberr++;
5352: 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]);
5353: 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]);
5354: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5355: }
5356: }
5357: }
5358:
5359: for (i=1; i<=imx; i++) {
5360: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5361: for(m=firstpass; (m<= lastpass); m++){
5362: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5363: if (s[m][i] >= nlstate+1) {
5364: if(agedc[i]>0)
5365: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5366: agev[m][i]=agedc[i];
5367: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5368: else {
5369: if ((int)andc[i]!=9999){
5370: nbwarn++;
5371: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5372: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5373: agev[m][i]=-1;
5374: }
5375: }
5376: }
5377: else if(s[m][i] !=9){ /* Standard case, age in fractional
5378: years but with the precision of a month */
5379: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5380: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5381: agev[m][i]=1;
5382: else if(agev[m][i] < *agemin){
5383: *agemin=agev[m][i];
5384: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5385: }
5386: else if(agev[m][i] >*agemax){
5387: *agemax=agev[m][i];
5388: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5389: }
5390: /*agev[m][i]=anint[m][i]-annais[i];*/
5391: /* agev[m][i] = age[i]+2*m;*/
5392: }
5393: else { /* =9 */
5394: agev[m][i]=1;
5395: s[m][i]=-1;
5396: }
5397: }
5398: else /*= 0 Unknown */
5399: agev[m][i]=1;
5400: }
5401:
5402: }
5403: for (i=1; i<=imx; i++) {
5404: for(m=firstpass; (m<=lastpass); m++){
5405: if (s[m][i] > (nlstate+ndeath)) {
5406: *nberr++;
5407: 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);
5408: 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);
5409: return 1;
5410: }
5411: }
5412: }
5413:
5414: /*for (i=1; i<=imx; i++){
5415: for (m=firstpass; (m<lastpass); m++){
5416: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5417: }
5418:
5419: }*/
5420:
5421:
5422: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5423: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5424:
5425: return (0);
5426: /* endread:*/
5427: printf("Exiting calandcheckages: ");
5428: return (1);
5429: }
5430:
5431: syscompilerinfo()
5432: {
5433: /* #include "syscompilerinfo.h"*/
5434: #include <gnu/libc-version.h>
5435: #if defined(__GNUC__)
5436: # if defined(__GNUC_PATCHLEVEL__)
5437: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5438: + __GNUC_MINOR__ * 100 \
5439: + __GNUC_PATCHLEVEL__)
5440: # else
5441: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5442: + __GNUC_MINOR__ * 100)
5443: # endif
5444: #endif
5445:
5446: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5447: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5448: // Windows (x64 and x86)
5449: #elif __unix__ // all unices, not all compilers
5450: // Unix
5451: #elif __linux__
5452: // linux
5453: #elif __APPLE__
5454: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5455: #endif
5456:
5457: /* __MINGW32__ */
5458: /* __CYGWIN__ */
5459: /* __MINGW64__ */
5460: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5461: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5462: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5463: /* _WIN64 // Defined for applications for Win64. */
5464: /* _M_X64 // Defined for compilations that target x64 processors. */
5465: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5466: #include <stdint.h>
5467: #if UINTPTR_MAX == 0xffffffff
5468: printf("32-bit \n"); /* 32-bit */
5469: #elif UINTPTR_MAX == 0xffffffffffffffff
5470: printf("64-bit \n");/* 64-bit */
5471: #else
5472: printf("wtf-bit \n"); /* wtf */
5473: #endif
5474:
5475: struct utsname sysInfo;
5476:
5477: if (uname(&sysInfo) != -1) {
5478: puts(sysInfo.sysname);
5479: puts(sysInfo.nodename);
5480: puts(sysInfo.release);
5481: puts(sysInfo.version);
5482: puts(sysInfo.machine);
5483: }
5484: else
5485: perror("uname() error");
5486: printf("GNU C version %d\n", __GNUC_VERSION__);
5487: printf("GNU libc version: %s\n", gnu_get_libc_version());
5488:
5489: }
5490:
5491: /***********************************************/
5492: /**************** Main Program *****************/
5493: /***********************************************/
5494:
5495: int main(int argc, char *argv[])
5496: {
5497: #ifdef GSL
5498: const gsl_multimin_fminimizer_type *T;
5499: size_t iteri = 0, it;
5500: int rval = GSL_CONTINUE;
5501: int status = GSL_SUCCESS;
5502: double ssval;
5503: #endif
5504: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5505: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5506:
5507: int jj, ll, li, lj, lk;
5508: int numlinepar=0; /* Current linenumber of parameter file */
5509: int itimes;
5510: int NDIM=2;
5511: int vpopbased=0;
5512:
5513: char ca[32], cb[32];
5514: /* FILE *fichtm; *//* Html File */
5515: /* FILE *ficgp;*/ /*Gnuplot File */
5516: struct stat info;
5517: double agedeb;
5518: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5519:
5520: double fret;
5521: double dum; /* Dummy variable */
5522: double ***p3mat;
5523: double ***mobaverage;
5524:
5525: char line[MAXLINE];
5526: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5527: char pathr[MAXLINE], pathimach[MAXLINE];
5528: char *tok, *val; /* pathtot */
5529: int firstobs=1, lastobs=10;
5530: int c, h , cpt;
5531: int jl;
5532: int i1, j1, jk, stepsize;
5533: int *tab;
5534: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5535: int mobilav=0,popforecast=0;
5536: int hstepm, nhstepm;
5537: int agemortsup;
5538: float sumlpop=0.;
5539: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5540: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5541:
5542: double bage=0, fage=110, age, agelim, agebase;
5543: double ftolpl=FTOL;
5544: double **prlim;
5545: double ***param; /* Matrix of parameters */
5546: double *p;
5547: double **matcov; /* Matrix of covariance */
5548: double ***delti3; /* Scale */
5549: double *delti; /* Scale */
5550: double ***eij, ***vareij;
5551: double **varpl; /* Variances of prevalence limits by age */
5552: double *epj, vepp;
5553:
5554: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5555: double **ximort;
5556: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5557: int *dcwave;
5558:
5559: char z[1]="c";
5560:
5561: /*char *strt;*/
5562: char strtend[80];
5563:
5564:
5565: /* setlocale (LC_ALL, ""); */
5566: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5567: /* textdomain (PACKAGE); */
5568: /* setlocale (LC_CTYPE, ""); */
5569: /* setlocale (LC_MESSAGES, ""); */
5570:
5571: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5572: rstart_time = time(NULL);
5573: /* (void) gettimeofday(&start_time,&tzp);*/
5574: start_time = *localtime(&rstart_time);
5575: curr_time=start_time;
5576: /*tml = *localtime(&start_time.tm_sec);*/
5577: /* strcpy(strstart,asctime(&tml)); */
5578: strcpy(strstart,asctime(&start_time));
5579:
5580: /* printf("Localtime (at start)=%s",strstart); */
5581: /* tp.tm_sec = tp.tm_sec +86400; */
5582: /* tm = *localtime(&start_time.tm_sec); */
5583: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5584: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5585: /* tmg.tm_hour=tmg.tm_hour + 1; */
5586: /* tp.tm_sec = mktime(&tmg); */
5587: /* strt=asctime(&tmg); */
5588: /* printf("Time(after) =%s",strstart); */
5589: /* (void) time (&time_value);
5590: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5591: * tm = *localtime(&time_value);
5592: * strstart=asctime(&tm);
5593: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5594: */
5595:
5596: nberr=0; /* Number of errors and warnings */
5597: nbwarn=0;
5598: getcwd(pathcd, size);
5599:
5600: printf("\n%s\n%s",version,fullversion);
5601: if(argc <=1){
5602: printf("\nEnter the parameter file name: ");
5603: fgets(pathr,FILENAMELENGTH,stdin);
5604: i=strlen(pathr);
5605: if(pathr[i-1]=='\n')
5606: pathr[i-1]='\0';
5607: i=strlen(pathr);
5608: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5609: pathr[i-1]='\0';
5610: for (tok = pathr; tok != NULL; ){
5611: printf("Pathr |%s|\n",pathr);
5612: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5613: printf("val= |%s| pathr=%s\n",val,pathr);
5614: strcpy (pathtot, val);
5615: if(pathr[0] == '\0') break; /* Dirty */
5616: }
5617: }
5618: else{
5619: strcpy(pathtot,argv[1]);
5620: }
5621: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5622: /*cygwin_split_path(pathtot,path,optionfile);
5623: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5624: /* cutv(path,optionfile,pathtot,'\\');*/
5625:
5626: /* Split argv[0], imach program to get pathimach */
5627: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5628: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5629: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5630: /* strcpy(pathimach,argv[0]); */
5631: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5632: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5633: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5634: chdir(path); /* Can be a relative path */
5635: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5636: printf("Current directory %s!\n",pathcd);
5637: strcpy(command,"mkdir ");
5638: strcat(command,optionfilefiname);
5639: if((outcmd=system(command)) != 0){
5640: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5641: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5642: /* fclose(ficlog); */
5643: /* exit(1); */
5644: }
5645: /* if((imk=mkdir(optionfilefiname))<0){ */
5646: /* perror("mkdir"); */
5647: /* } */
5648:
5649: /*-------- arguments in the command line --------*/
5650:
5651: /* Log file */
5652: strcat(filelog, optionfilefiname);
5653: strcat(filelog,".log"); /* */
5654: if((ficlog=fopen(filelog,"w"))==NULL) {
5655: printf("Problem with logfile %s\n",filelog);
5656: goto end;
5657: }
5658: fprintf(ficlog,"Log filename:%s\n",filelog);
5659: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5660: fprintf(ficlog,"\nEnter the parameter file name: \n");
5661: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5662: path=%s \n\
5663: optionfile=%s\n\
5664: optionfilext=%s\n\
5665: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5666:
5667: syscompilerinfo();
5668:
5669: printf("Local time (at start):%s",strstart);
5670: fprintf(ficlog,"Local time (at start): %s",strstart);
5671: fflush(ficlog);
5672: /* (void) gettimeofday(&curr_time,&tzp); */
5673: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5674:
5675: /* */
5676: strcpy(fileres,"r");
5677: strcat(fileres, optionfilefiname);
5678: strcat(fileres,".txt"); /* Other files have txt extension */
5679:
5680: /*---------arguments file --------*/
5681:
5682: if((ficpar=fopen(optionfile,"r"))==NULL) {
5683: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5684: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5685: fflush(ficlog);
5686: /* goto end; */
5687: exit(70);
5688: }
5689:
5690:
5691:
5692: strcpy(filereso,"o");
5693: strcat(filereso,fileres);
5694: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5695: printf("Problem with Output resultfile: %s\n", filereso);
5696: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5697: fflush(ficlog);
5698: goto end;
5699: }
5700:
5701: /* Reads comments: lines beginning with '#' */
5702: numlinepar=0;
5703: while((c=getc(ficpar))=='#' && c!= EOF){
5704: ungetc(c,ficpar);
5705: fgets(line, MAXLINE, ficpar);
5706: numlinepar++;
5707: fputs(line,stdout);
5708: fputs(line,ficparo);
5709: fputs(line,ficlog);
5710: }
5711: ungetc(c,ficpar);
5712:
5713: 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);
5714: numlinepar++;
5715: 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);
5716: 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);
5717: 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);
5718: fflush(ficlog);
5719: while((c=getc(ficpar))=='#' && c!= EOF){
5720: ungetc(c,ficpar);
5721: fgets(line, MAXLINE, ficpar);
5722: numlinepar++;
5723: fputs(line, stdout);
5724: //puts(line);
5725: fputs(line,ficparo);
5726: fputs(line,ficlog);
5727: }
5728: ungetc(c,ficpar);
5729:
5730:
5731: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5732: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5733: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5734: v1+v2*age+v2*v3 makes cptcovn = 3
5735: */
5736: if (strlen(model)>1)
5737: 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*/
5738: else
5739: ncovmodel=2;
5740: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5741: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5742: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5743: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5744: 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);
5745: 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);
5746: fflush(stdout);
5747: fclose (ficlog);
5748: goto end;
5749: }
5750: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5751: delti=delti3[1][1];
5752: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5753: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5754: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5755: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5756: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5757: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5758: fclose (ficparo);
5759: fclose (ficlog);
5760: goto end;
5761: exit(0);
5762: }
5763: else if(mle==-3) {
5764: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5765: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5766: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5767: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5768: matcov=matrix(1,npar,1,npar);
5769: }
5770: else{
5771: /* Read guessed parameters */
5772: /* Reads comments: lines beginning with '#' */
5773: while((c=getc(ficpar))=='#' && c!= EOF){
5774: ungetc(c,ficpar);
5775: fgets(line, MAXLINE, ficpar);
5776: numlinepar++;
5777: fputs(line,stdout);
5778: fputs(line,ficparo);
5779: fputs(line,ficlog);
5780: }
5781: ungetc(c,ficpar);
5782:
5783: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5784: for(i=1; i <=nlstate; i++){
5785: j=0;
5786: for(jj=1; jj <=nlstate+ndeath; jj++){
5787: if(jj==i) continue;
5788: j++;
5789: fscanf(ficpar,"%1d%1d",&i1,&j1);
5790: if ((i1 != i) && (j1 != j)){
5791: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5792: It might be a problem of design; if ncovcol and the model are correct\n \
5793: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5794: exit(1);
5795: }
5796: fprintf(ficparo,"%1d%1d",i1,j1);
5797: if(mle==1)
5798: printf("%1d%1d",i,j);
5799: fprintf(ficlog,"%1d%1d",i,j);
5800: for(k=1; k<=ncovmodel;k++){
5801: fscanf(ficpar," %lf",¶m[i][j][k]);
5802: if(mle==1){
5803: printf(" %lf",param[i][j][k]);
5804: fprintf(ficlog," %lf",param[i][j][k]);
5805: }
5806: else
5807: fprintf(ficlog," %lf",param[i][j][k]);
5808: fprintf(ficparo," %lf",param[i][j][k]);
5809: }
5810: fscanf(ficpar,"\n");
5811: numlinepar++;
5812: if(mle==1)
5813: printf("\n");
5814: fprintf(ficlog,"\n");
5815: fprintf(ficparo,"\n");
5816: }
5817: }
5818: fflush(ficlog);
5819:
5820: /* Reads scales values */
5821: p=param[1][1];
5822:
5823: /* Reads comments: lines beginning with '#' */
5824: while((c=getc(ficpar))=='#' && c!= EOF){
5825: ungetc(c,ficpar);
5826: fgets(line, MAXLINE, ficpar);
5827: numlinepar++;
5828: fputs(line,stdout);
5829: fputs(line,ficparo);
5830: fputs(line,ficlog);
5831: }
5832: ungetc(c,ficpar);
5833:
5834: for(i=1; i <=nlstate; i++){
5835: for(j=1; j <=nlstate+ndeath-1; j++){
5836: fscanf(ficpar,"%1d%1d",&i1,&j1);
5837: if ( (i1-i) * (j1-j) != 0){
5838: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5839: exit(1);
5840: }
5841: printf("%1d%1d",i,j);
5842: fprintf(ficparo,"%1d%1d",i1,j1);
5843: fprintf(ficlog,"%1d%1d",i1,j1);
5844: for(k=1; k<=ncovmodel;k++){
5845: fscanf(ficpar,"%le",&delti3[i][j][k]);
5846: printf(" %le",delti3[i][j][k]);
5847: fprintf(ficparo," %le",delti3[i][j][k]);
5848: fprintf(ficlog," %le",delti3[i][j][k]);
5849: }
5850: fscanf(ficpar,"\n");
5851: numlinepar++;
5852: printf("\n");
5853: fprintf(ficparo,"\n");
5854: fprintf(ficlog,"\n");
5855: }
5856: }
5857: fflush(ficlog);
5858:
5859: /* Reads covariance matrix */
5860: delti=delti3[1][1];
5861:
5862:
5863: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5864:
5865: /* Reads comments: lines beginning with '#' */
5866: while((c=getc(ficpar))=='#' && c!= EOF){
5867: ungetc(c,ficpar);
5868: fgets(line, MAXLINE, ficpar);
5869: numlinepar++;
5870: fputs(line,stdout);
5871: fputs(line,ficparo);
5872: fputs(line,ficlog);
5873: }
5874: ungetc(c,ficpar);
5875:
5876: matcov=matrix(1,npar,1,npar);
5877: for(i=1; i <=npar; i++)
5878: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5879:
5880: for(i=1; i <=npar; i++){
5881: fscanf(ficpar,"%s",str);
5882: if(mle==1)
5883: printf("%s",str);
5884: fprintf(ficlog,"%s",str);
5885: fprintf(ficparo,"%s",str);
5886: for(j=1; j <=i; j++){
5887: fscanf(ficpar," %le",&matcov[i][j]);
5888: if(mle==1){
5889: printf(" %.5le",matcov[i][j]);
5890: }
5891: fprintf(ficlog," %.5le",matcov[i][j]);
5892: fprintf(ficparo," %.5le",matcov[i][j]);
5893: }
5894: fscanf(ficpar,"\n");
5895: numlinepar++;
5896: if(mle==1)
5897: printf("\n");
5898: fprintf(ficlog,"\n");
5899: fprintf(ficparo,"\n");
5900: }
5901: for(i=1; i <=npar; i++)
5902: for(j=i+1;j<=npar;j++)
5903: matcov[i][j]=matcov[j][i];
5904:
5905: if(mle==1)
5906: printf("\n");
5907: fprintf(ficlog,"\n");
5908:
5909: fflush(ficlog);
5910:
5911: /*-------- Rewriting parameter file ----------*/
5912: strcpy(rfileres,"r"); /* "Rparameterfile */
5913: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5914: strcat(rfileres,"."); /* */
5915: strcat(rfileres,optionfilext); /* Other files have txt extension */
5916: if((ficres =fopen(rfileres,"w"))==NULL) {
5917: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5918: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5919: }
5920: fprintf(ficres,"#%s\n",version);
5921: } /* End of mle != -3 */
5922:
5923:
5924: n= lastobs;
5925: num=lvector(1,n);
5926: moisnais=vector(1,n);
5927: annais=vector(1,n);
5928: moisdc=vector(1,n);
5929: andc=vector(1,n);
5930: agedc=vector(1,n);
5931: cod=ivector(1,n);
5932: weight=vector(1,n);
5933: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5934: mint=matrix(1,maxwav,1,n);
5935: anint=matrix(1,maxwav,1,n);
5936: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5937: tab=ivector(1,NCOVMAX);
5938: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5939:
5940: /* Reads data from file datafile */
5941: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5942: goto end;
5943:
5944: /* Calculation of the number of parameters from char model */
5945: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5946: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5947: k=3 V4 Tvar[k=3]= 4 (from V4)
5948: k=2 V1 Tvar[k=2]= 1 (from V1)
5949: k=1 Tvar[1]=2 (from V2)
5950: */
5951: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5952: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5953: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5954: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5955: */
5956: /* For model-covariate k tells which data-covariate to use but
5957: because this model-covariate is a construction we invent a new column
5958: ncovcol + k1
5959: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5960: Tvar[3=V1*V4]=4+1 etc */
5961: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5962: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5963: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5964: */
5965: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5966: 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
5967: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5968: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5969: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5970: 4 covariates (3 plus signs)
5971: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5972: */
5973:
5974: if(decodemodel(model, lastobs) == 1)
5975: goto end;
5976:
5977: if((double)(lastobs-imx)/(double)imx > 1.10){
5978: nbwarn++;
5979: 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);
5980: 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);
5981: }
5982: /* if(mle==1){*/
5983: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5984: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5985: }
5986:
5987: /*-calculation of age at interview from date of interview and age at death -*/
5988: agev=matrix(1,maxwav,1,imx);
5989:
5990: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5991: goto end;
5992:
5993:
5994: agegomp=(int)agemin;
5995: free_vector(moisnais,1,n);
5996: free_vector(annais,1,n);
5997: /* free_matrix(mint,1,maxwav,1,n);
5998: free_matrix(anint,1,maxwav,1,n);*/
5999: free_vector(moisdc,1,n);
6000: free_vector(andc,1,n);
6001: /* */
6002:
6003: wav=ivector(1,imx);
6004: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6005: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6006: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6007:
6008: /* Concatenates waves */
6009: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6010: /* */
6011:
6012: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6013:
6014: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6015: ncodemax[1]=1;
6016: Ndum =ivector(-1,NCOVMAX);
6017: if (ncovmodel > 2)
6018: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6019:
6020: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6021: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6022: h=0;
6023:
6024:
6025: /*if (cptcovn > 0) */
6026:
6027:
6028: m=pow(2,cptcoveff);
6029:
6030: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6031: 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 */
6032: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6033: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6034: h++;
6035: if (h>m)
6036: h=1;
6037: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6038: * h 1 2 3 4
6039: *______________________________
6040: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6041: * 2 2 1 1 1
6042: * 3 i=2 1 2 1 1
6043: * 4 2 2 1 1
6044: * 5 i=3 1 i=2 1 2 1
6045: * 6 2 1 2 1
6046: * 7 i=4 1 2 2 1
6047: * 8 2 2 2 1
6048: * 9 i=5 1 i=3 1 i=2 1 1
6049: * 10 2 1 1 1
6050: * 11 i=6 1 2 1 1
6051: * 12 2 2 1 1
6052: * 13 i=7 1 i=4 1 2 1
6053: * 14 2 1 2 1
6054: * 15 i=8 1 2 2 1
6055: * 16 2 2 2 1
6056: */
6057: codtab[h][k]=j;
6058: /*codtab[h][Tvar[k]]=j;*/
6059: 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]]);
6060: }
6061: }
6062: }
6063: }
6064: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6065: codtab[1][2]=1;codtab[2][2]=2; */
6066: /* for(i=1; i <=m ;i++){
6067: for(k=1; k <=cptcovn; k++){
6068: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6069: }
6070: printf("\n");
6071: }
6072: scanf("%d",i);*/
6073:
6074: free_ivector(Ndum,-1,NCOVMAX);
6075:
6076:
6077:
6078: /*------------ gnuplot -------------*/
6079: strcpy(optionfilegnuplot,optionfilefiname);
6080: if(mle==-3)
6081: strcat(optionfilegnuplot,"-mort");
6082: strcat(optionfilegnuplot,".gp");
6083:
6084: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6085: printf("Problem with file %s",optionfilegnuplot);
6086: }
6087: else{
6088: fprintf(ficgp,"\n# %s\n", version);
6089: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6090: //fprintf(ficgp,"set missing 'NaNq'\n");
6091: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6092: }
6093: /* fclose(ficgp);*/
6094: /*--------- index.htm --------*/
6095:
6096: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6097: if(mle==-3)
6098: strcat(optionfilehtm,"-mort");
6099: strcat(optionfilehtm,".htm");
6100: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6101: printf("Problem with %s \n",optionfilehtm);
6102: exit(0);
6103: }
6104:
6105: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6106: strcat(optionfilehtmcov,"-cov.htm");
6107: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6108: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6109: }
6110: else{
6111: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6112: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6113: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6114: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6115: }
6116:
6117: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6118: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6119: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6120: \n\
6121: <hr size=\"2\" color=\"#EC5E5E\">\
6122: <ul><li><h4>Parameter files</h4>\n\
6123: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6124: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6125: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6126: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6127: - Date and time at start: %s</ul>\n",\
6128: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6129: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6130: fileres,fileres,\
6131: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6132: fflush(fichtm);
6133:
6134: strcpy(pathr,path);
6135: strcat(pathr,optionfilefiname);
6136: chdir(optionfilefiname); /* Move to directory named optionfile */
6137:
6138: /* Calculates basic frequencies. Computes observed prevalence at single age
6139: and prints on file fileres'p'. */
6140: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6141:
6142: fprintf(fichtm,"\n");
6143: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6144: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6145: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6146: imx,agemin,agemax,jmin,jmax,jmean);
6147: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6148: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6149: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6150: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6151: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6152:
6153:
6154: /* For Powell, parameters are in a vector p[] starting at p[1]
6155: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6156: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6157:
6158: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6159:
6160: if (mle==-3){
6161: ximort=matrix(1,NDIM,1,NDIM);
6162: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6163: cens=ivector(1,n);
6164: ageexmed=vector(1,n);
6165: agecens=vector(1,n);
6166: dcwave=ivector(1,n);
6167:
6168: for (i=1; i<=imx; i++){
6169: dcwave[i]=-1;
6170: for (m=firstpass; m<=lastpass; m++)
6171: if (s[m][i]>nlstate) {
6172: dcwave[i]=m;
6173: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6174: break;
6175: }
6176: }
6177:
6178: for (i=1; i<=imx; i++) {
6179: if (wav[i]>0){
6180: ageexmed[i]=agev[mw[1][i]][i];
6181: j=wav[i];
6182: agecens[i]=1.;
6183:
6184: if (ageexmed[i]> 1 && wav[i] > 0){
6185: agecens[i]=agev[mw[j][i]][i];
6186: cens[i]= 1;
6187: }else if (ageexmed[i]< 1)
6188: cens[i]= -1;
6189: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6190: cens[i]=0 ;
6191: }
6192: else cens[i]=-1;
6193: }
6194:
6195: for (i=1;i<=NDIM;i++) {
6196: for (j=1;j<=NDIM;j++)
6197: ximort[i][j]=(i == j ? 1.0 : 0.0);
6198: }
6199:
6200: /*p[1]=0.0268; p[NDIM]=0.083;*/
6201: /*printf("%lf %lf", p[1], p[2]);*/
6202:
6203:
6204: #ifdef GSL
6205: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6206: #else
6207: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6208: #endif
6209: strcpy(filerespow,"pow-mort");
6210: strcat(filerespow,fileres);
6211: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6212: printf("Problem with resultfile: %s\n", filerespow);
6213: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6214: }
6215: #ifdef GSL
6216: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6217: #else
6218: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6219: #endif
6220: /* for (i=1;i<=nlstate;i++)
6221: for(j=1;j<=nlstate+ndeath;j++)
6222: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6223: */
6224: fprintf(ficrespow,"\n");
6225: #ifdef GSL
6226: /* gsl starts here */
6227: T = gsl_multimin_fminimizer_nmsimplex;
6228: gsl_multimin_fminimizer *sfm = NULL;
6229: gsl_vector *ss, *x;
6230: gsl_multimin_function minex_func;
6231:
6232: /* Initial vertex size vector */
6233: ss = gsl_vector_alloc (NDIM);
6234:
6235: if (ss == NULL){
6236: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6237: }
6238: /* Set all step sizes to 1 */
6239: gsl_vector_set_all (ss, 0.001);
6240:
6241: /* Starting point */
6242:
6243: x = gsl_vector_alloc (NDIM);
6244:
6245: if (x == NULL){
6246: gsl_vector_free(ss);
6247: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6248: }
6249:
6250: /* Initialize method and iterate */
6251: /* p[1]=0.0268; p[NDIM]=0.083; */
6252: /* gsl_vector_set(x, 0, 0.0268); */
6253: /* gsl_vector_set(x, 1, 0.083); */
6254: gsl_vector_set(x, 0, p[1]);
6255: gsl_vector_set(x, 1, p[2]);
6256:
6257: minex_func.f = &gompertz_f;
6258: minex_func.n = NDIM;
6259: minex_func.params = (void *)&p; /* ??? */
6260:
6261: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6262: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6263:
6264: printf("Iterations beginning .....\n\n");
6265: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6266:
6267: iteri=0;
6268: while (rval == GSL_CONTINUE){
6269: iteri++;
6270: status = gsl_multimin_fminimizer_iterate(sfm);
6271:
6272: if (status) printf("error: %s\n", gsl_strerror (status));
6273: fflush(0);
6274:
6275: if (status)
6276: break;
6277:
6278: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6279: ssval = gsl_multimin_fminimizer_size (sfm);
6280:
6281: if (rval == GSL_SUCCESS)
6282: printf ("converged to a local maximum at\n");
6283:
6284: printf("%5d ", iteri);
6285: for (it = 0; it < NDIM; it++){
6286: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6287: }
6288: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6289: }
6290:
6291: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6292:
6293: gsl_vector_free(x); /* initial values */
6294: gsl_vector_free(ss); /* inital step size */
6295: for (it=0; it<NDIM; it++){
6296: p[it+1]=gsl_vector_get(sfm->x,it);
6297: fprintf(ficrespow," %.12lf", p[it]);
6298: }
6299: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6300: #endif
6301: #ifdef POWELL
6302: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6303: #endif
6304: fclose(ficrespow);
6305:
6306: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6307:
6308: for(i=1; i <=NDIM; i++)
6309: for(j=i+1;j<=NDIM;j++)
6310: matcov[i][j]=matcov[j][i];
6311:
6312: printf("\nCovariance matrix\n ");
6313: for(i=1; i <=NDIM; i++) {
6314: for(j=1;j<=NDIM;j++){
6315: printf("%f ",matcov[i][j]);
6316: }
6317: printf("\n ");
6318: }
6319:
6320: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6321: for (i=1;i<=NDIM;i++)
6322: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6323:
6324: lsurv=vector(1,AGESUP);
6325: lpop=vector(1,AGESUP);
6326: tpop=vector(1,AGESUP);
6327: lsurv[agegomp]=100000;
6328:
6329: for (k=agegomp;k<=AGESUP;k++) {
6330: agemortsup=k;
6331: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6332: }
6333:
6334: for (k=agegomp;k<agemortsup;k++)
6335: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6336:
6337: for (k=agegomp;k<agemortsup;k++){
6338: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6339: sumlpop=sumlpop+lpop[k];
6340: }
6341:
6342: tpop[agegomp]=sumlpop;
6343: for (k=agegomp;k<(agemortsup-3);k++){
6344: /* tpop[k+1]=2;*/
6345: tpop[k+1]=tpop[k]-lpop[k];
6346: }
6347:
6348:
6349: printf("\nAge lx qx dx Lx Tx e(x)\n");
6350: for (k=agegomp;k<(agemortsup-2);k++)
6351: 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]);
6352:
6353:
6354: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6355: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6356:
6357: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6358: stepm, weightopt,\
6359: model,imx,p,matcov,agemortsup);
6360:
6361: free_vector(lsurv,1,AGESUP);
6362: free_vector(lpop,1,AGESUP);
6363: free_vector(tpop,1,AGESUP);
6364: #ifdef GSL
6365: free_ivector(cens,1,n);
6366: free_vector(agecens,1,n);
6367: free_ivector(dcwave,1,n);
6368: free_matrix(ximort,1,NDIM,1,NDIM);
6369: #endif
6370: } /* Endof if mle==-3 */
6371:
6372: else{ /* For mle >=1 */
6373: globpr=0;/* debug */
6374: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6375: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6376: for (k=1; k<=npar;k++)
6377: printf(" %d %8.5f",k,p[k]);
6378: printf("\n");
6379: globpr=1; /* to print the contributions */
6380: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6381: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6382: for (k=1; k<=npar;k++)
6383: printf(" %d %8.5f",k,p[k]);
6384: printf("\n");
6385: if(mle>=1){ /* Could be 1 or 2 */
6386: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6387: }
6388:
6389: /*--------- results files --------------*/
6390: 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);
6391:
6392:
6393: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6394: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6395: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6396: for(i=1,jk=1; i <=nlstate; i++){
6397: for(k=1; k <=(nlstate+ndeath); k++){
6398: if (k != i) {
6399: printf("%d%d ",i,k);
6400: fprintf(ficlog,"%d%d ",i,k);
6401: fprintf(ficres,"%1d%1d ",i,k);
6402: for(j=1; j <=ncovmodel; j++){
6403: printf("%lf ",p[jk]);
6404: fprintf(ficlog,"%lf ",p[jk]);
6405: fprintf(ficres,"%lf ",p[jk]);
6406: jk++;
6407: }
6408: printf("\n");
6409: fprintf(ficlog,"\n");
6410: fprintf(ficres,"\n");
6411: }
6412: }
6413: }
6414: if(mle!=0){
6415: /* Computing hessian and covariance matrix */
6416: ftolhess=ftol; /* Usually correct */
6417: hesscov(matcov, p, npar, delti, ftolhess, func);
6418: }
6419: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6420: printf("# Scales (for hessian or gradient estimation)\n");
6421: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6422: for(i=1,jk=1; i <=nlstate; i++){
6423: for(j=1; j <=nlstate+ndeath; j++){
6424: if (j!=i) {
6425: fprintf(ficres,"%1d%1d",i,j);
6426: printf("%1d%1d",i,j);
6427: fprintf(ficlog,"%1d%1d",i,j);
6428: for(k=1; k<=ncovmodel;k++){
6429: printf(" %.5e",delti[jk]);
6430: fprintf(ficlog," %.5e",delti[jk]);
6431: fprintf(ficres," %.5e",delti[jk]);
6432: jk++;
6433: }
6434: printf("\n");
6435: fprintf(ficlog,"\n");
6436: fprintf(ficres,"\n");
6437: }
6438: }
6439: }
6440:
6441: 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");
6442: if(mle>=1)
6443: 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");
6444: 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");
6445: /* # 121 Var(a12)\n\ */
6446: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6447: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6448: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6449: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6450: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6451: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6452: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6453:
6454:
6455: /* Just to have a covariance matrix which will be more understandable
6456: even is we still don't want to manage dictionary of variables
6457: */
6458: for(itimes=1;itimes<=2;itimes++){
6459: jj=0;
6460: for(i=1; i <=nlstate; i++){
6461: for(j=1; j <=nlstate+ndeath; j++){
6462: if(j==i) continue;
6463: for(k=1; k<=ncovmodel;k++){
6464: jj++;
6465: ca[0]= k+'a'-1;ca[1]='\0';
6466: if(itimes==1){
6467: if(mle>=1)
6468: printf("#%1d%1d%d",i,j,k);
6469: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6470: fprintf(ficres,"#%1d%1d%d",i,j,k);
6471: }else{
6472: if(mle>=1)
6473: printf("%1d%1d%d",i,j,k);
6474: fprintf(ficlog,"%1d%1d%d",i,j,k);
6475: fprintf(ficres,"%1d%1d%d",i,j,k);
6476: }
6477: ll=0;
6478: for(li=1;li <=nlstate; li++){
6479: for(lj=1;lj <=nlstate+ndeath; lj++){
6480: if(lj==li) continue;
6481: for(lk=1;lk<=ncovmodel;lk++){
6482: ll++;
6483: if(ll<=jj){
6484: cb[0]= lk +'a'-1;cb[1]='\0';
6485: if(ll<jj){
6486: if(itimes==1){
6487: if(mle>=1)
6488: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6489: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6490: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6491: }else{
6492: if(mle>=1)
6493: printf(" %.5e",matcov[jj][ll]);
6494: fprintf(ficlog," %.5e",matcov[jj][ll]);
6495: fprintf(ficres," %.5e",matcov[jj][ll]);
6496: }
6497: }else{
6498: if(itimes==1){
6499: if(mle>=1)
6500: printf(" Var(%s%1d%1d)",ca,i,j);
6501: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6502: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6503: }else{
6504: if(mle>=1)
6505: printf(" %.5e",matcov[jj][ll]);
6506: fprintf(ficlog," %.5e",matcov[jj][ll]);
6507: fprintf(ficres," %.5e",matcov[jj][ll]);
6508: }
6509: }
6510: }
6511: } /* end lk */
6512: } /* end lj */
6513: } /* end li */
6514: if(mle>=1)
6515: printf("\n");
6516: fprintf(ficlog,"\n");
6517: fprintf(ficres,"\n");
6518: numlinepar++;
6519: } /* end k*/
6520: } /*end j */
6521: } /* end i */
6522: } /* end itimes */
6523:
6524: fflush(ficlog);
6525: fflush(ficres);
6526:
6527: while((c=getc(ficpar))=='#' && c!= EOF){
6528: ungetc(c,ficpar);
6529: fgets(line, MAXLINE, ficpar);
6530: fputs(line,stdout);
6531: fputs(line,ficparo);
6532: }
6533: ungetc(c,ficpar);
6534:
6535: estepm=0;
6536: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6537: if (estepm==0 || estepm < stepm) estepm=stepm;
6538: if (fage <= 2) {
6539: bage = ageminpar;
6540: fage = agemaxpar;
6541: }
6542:
6543: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6544: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6545: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6546:
6547: while((c=getc(ficpar))=='#' && c!= EOF){
6548: ungetc(c,ficpar);
6549: fgets(line, MAXLINE, ficpar);
6550: fputs(line,stdout);
6551: fputs(line,ficparo);
6552: }
6553: ungetc(c,ficpar);
6554:
6555: 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);
6556: 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);
6557: 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);
6558: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6559: 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);
6560:
6561: while((c=getc(ficpar))=='#' && c!= EOF){
6562: ungetc(c,ficpar);
6563: fgets(line, MAXLINE, ficpar);
6564: fputs(line,stdout);
6565: fputs(line,ficparo);
6566: }
6567: ungetc(c,ficpar);
6568:
6569:
6570: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6571: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6572:
6573: fscanf(ficpar,"pop_based=%d\n",&popbased);
6574: fprintf(ficparo,"pop_based=%d\n",popbased);
6575: fprintf(ficres,"pop_based=%d\n",popbased);
6576:
6577: while((c=getc(ficpar))=='#' && c!= EOF){
6578: ungetc(c,ficpar);
6579: fgets(line, MAXLINE, ficpar);
6580: fputs(line,stdout);
6581: fputs(line,ficparo);
6582: }
6583: ungetc(c,ficpar);
6584:
6585: 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);
6586: 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);
6587: 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);
6588: 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);
6589: 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);
6590: /* day and month of proj2 are not used but only year anproj2.*/
6591:
6592:
6593:
6594: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6595: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6596:
6597: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6598: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6599:
6600: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6601: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6602: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6603:
6604: /*------------ free_vector -------------*/
6605: /* chdir(path); */
6606:
6607: free_ivector(wav,1,imx);
6608: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6609: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6610: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6611: free_lvector(num,1,n);
6612: free_vector(agedc,1,n);
6613: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6614: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6615: fclose(ficparo);
6616: fclose(ficres);
6617:
6618:
6619: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6620: #include "prevlim.h" /* Use ficrespl, ficlog */
6621: fclose(ficrespl);
6622:
6623: #ifdef FREEEXIT2
6624: #include "freeexit2.h"
6625: #endif
6626:
6627: /*------------- h Pij x at various ages ------------*/
6628: #include "hpijx.h"
6629: fclose(ficrespij);
6630:
6631: /*-------------- Variance of one-step probabilities---*/
6632: k=1;
6633: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6634:
6635:
6636: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6637: for(i=1;i<=AGESUP;i++)
6638: for(j=1;j<=NCOVMAX;j++)
6639: for(k=1;k<=NCOVMAX;k++)
6640: probs[i][j][k]=0.;
6641:
6642: /*---------- Forecasting ------------------*/
6643: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6644: if(prevfcast==1){
6645: /* if(stepm ==1){*/
6646: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6647: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6648: /* } */
6649: /* else{ */
6650: /* erreur=108; */
6651: /* 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); */
6652: /* 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); */
6653: /* } */
6654: }
6655:
6656:
6657: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6658:
6659: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6660: /* 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",\
6661: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6662: */
6663:
6664: if (mobilav!=0) {
6665: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6666: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6667: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6668: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6669: }
6670: }
6671:
6672:
6673: /*---------- Health expectancies, no variances ------------*/
6674:
6675: strcpy(filerese,"e");
6676: strcat(filerese,fileres);
6677: if((ficreseij=fopen(filerese,"w"))==NULL) {
6678: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6679: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6680: }
6681: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6682: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6683: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6684: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6685:
6686: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6687: fprintf(ficreseij,"\n#****** ");
6688: for(j=1;j<=cptcoveff;j++) {
6689: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6690: }
6691: fprintf(ficreseij,"******\n");
6692:
6693: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6694: oldm=oldms;savm=savms;
6695: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6696:
6697: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6698: /*}*/
6699: }
6700: fclose(ficreseij);
6701:
6702:
6703: /*---------- Health expectancies and variances ------------*/
6704:
6705:
6706: strcpy(filerest,"t");
6707: strcat(filerest,fileres);
6708: if((ficrest=fopen(filerest,"w"))==NULL) {
6709: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6710: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6711: }
6712: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6713: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6714:
6715:
6716: strcpy(fileresstde,"stde");
6717: strcat(fileresstde,fileres);
6718: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6719: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6720: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6721: }
6722: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6723: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6724:
6725: strcpy(filerescve,"cve");
6726: strcat(filerescve,fileres);
6727: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6728: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6729: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6730: }
6731: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6732: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6733:
6734: strcpy(fileresv,"v");
6735: strcat(fileresv,fileres);
6736: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6737: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6738: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6739: }
6740: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6741: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6742:
6743: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6744: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6745:
6746: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6747: fprintf(ficrest,"\n#****** ");
6748: for(j=1;j<=cptcoveff;j++)
6749: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6750: fprintf(ficrest,"******\n");
6751:
6752: fprintf(ficresstdeij,"\n#****** ");
6753: fprintf(ficrescveij,"\n#****** ");
6754: for(j=1;j<=cptcoveff;j++) {
6755: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6756: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6757: }
6758: fprintf(ficresstdeij,"******\n");
6759: fprintf(ficrescveij,"******\n");
6760:
6761: fprintf(ficresvij,"\n#****** ");
6762: for(j=1;j<=cptcoveff;j++)
6763: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6764: fprintf(ficresvij,"******\n");
6765:
6766: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6767: oldm=oldms;savm=savms;
6768: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6769: /*
6770: */
6771: /* goto endfree; */
6772:
6773: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6774: pstamp(ficrest);
6775:
6776:
6777: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6778: oldm=oldms;savm=savms; /* Segmentation fault */
6779: cptcod= 0; /* To be deleted */
6780: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
6781: 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 ");
6782: if(vpopbased==1)
6783: 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);
6784: else
6785: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6786: fprintf(ficrest,"# Age e.. (std) ");
6787: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6788: fprintf(ficrest,"\n");
6789:
6790: epj=vector(1,nlstate+1);
6791: for(age=bage; age <=fage ;age++){
6792: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6793: if (vpopbased==1) {
6794: if(mobilav ==0){
6795: for(i=1; i<=nlstate;i++)
6796: prlim[i][i]=probs[(int)age][i][k];
6797: }else{ /* mobilav */
6798: for(i=1; i<=nlstate;i++)
6799: prlim[i][i]=mobaverage[(int)age][i][k];
6800: }
6801: }
6802:
6803: fprintf(ficrest," %4.0f",age);
6804: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6805: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6806: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6807: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6808: }
6809: epj[nlstate+1] +=epj[j];
6810: }
6811:
6812: for(i=1, vepp=0.;i <=nlstate;i++)
6813: for(j=1;j <=nlstate;j++)
6814: vepp += vareij[i][j][(int)age];
6815: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6816: for(j=1;j <=nlstate;j++){
6817: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6818: }
6819: fprintf(ficrest,"\n");
6820: }
6821: }
6822: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6823: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6824: free_vector(epj,1,nlstate+1);
6825: /*}*/
6826: }
6827: free_vector(weight,1,n);
6828: free_imatrix(Tvard,1,NCOVMAX,1,2);
6829: free_imatrix(s,1,maxwav+1,1,n);
6830: free_matrix(anint,1,maxwav,1,n);
6831: free_matrix(mint,1,maxwav,1,n);
6832: free_ivector(cod,1,n);
6833: free_ivector(tab,1,NCOVMAX);
6834: fclose(ficresstdeij);
6835: fclose(ficrescveij);
6836: fclose(ficresvij);
6837: fclose(ficrest);
6838: fclose(ficpar);
6839:
6840: /*------- Variance of period (stable) prevalence------*/
6841:
6842: strcpy(fileresvpl,"vpl");
6843: strcat(fileresvpl,fileres);
6844: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6845: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6846: exit(0);
6847: }
6848: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6849:
6850: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6851: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6852:
6853: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6854: fprintf(ficresvpl,"\n#****** ");
6855: for(j=1;j<=cptcoveff;j++)
6856: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6857: fprintf(ficresvpl,"******\n");
6858:
6859: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6860: oldm=oldms;savm=savms;
6861: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6862: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6863: /*}*/
6864: }
6865:
6866: fclose(ficresvpl);
6867:
6868: /*---------- End : free ----------------*/
6869: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6870: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6871: } /* mle==-3 arrives here for freeing */
6872: /* endfree:*/
6873: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6874: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6875: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6876: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6877: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6878: free_matrix(covar,0,NCOVMAX,1,n);
6879: free_matrix(matcov,1,npar,1,npar);
6880: /*free_vector(delti,1,npar);*/
6881: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6882: free_matrix(agev,1,maxwav,1,imx);
6883: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6884:
6885: free_ivector(ncodemax,1,NCOVMAX);
6886: free_ivector(Tvar,1,NCOVMAX);
6887: free_ivector(Tprod,1,NCOVMAX);
6888: free_ivector(Tvaraff,1,NCOVMAX);
6889: free_ivector(Tage,1,NCOVMAX);
6890:
6891: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6892: free_imatrix(codtab,1,100,1,10);
6893: fflush(fichtm);
6894: fflush(ficgp);
6895:
6896:
6897: if((nberr >0) || (nbwarn>0)){
6898: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6899: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6900: }else{
6901: printf("End of Imach\n");
6902: fprintf(ficlog,"End of Imach\n");
6903: }
6904: printf("See log file on %s\n",filelog);
6905: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6906: /*(void) gettimeofday(&end_time,&tzp);*/
6907: rend_time = time(NULL);
6908: end_time = *localtime(&rend_time);
6909: /* tml = *localtime(&end_time.tm_sec); */
6910: strcpy(strtend,asctime(&end_time));
6911: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6912: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6913: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6914:
6915: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6916: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6917: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6918: /* printf("Total time was %d uSec.\n", total_usecs);*/
6919: /* if(fileappend(fichtm,optionfilehtm)){ */
6920: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6921: fclose(fichtm);
6922: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6923: fclose(fichtmcov);
6924: fclose(ficgp);
6925: fclose(ficlog);
6926: /*------ End -----------*/
6927:
6928:
6929: printf("Before Current directory %s!\n",pathcd);
6930: if(chdir(pathcd) != 0)
6931: printf("Can't move to directory %s!\n",path);
6932: if(getcwd(pathcd,MAXLINE) > 0)
6933: printf("Current directory %s!\n",pathcd);
6934: /*strcat(plotcmd,CHARSEPARATOR);*/
6935: sprintf(plotcmd,"gnuplot");
6936: #ifdef _WIN32
6937: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6938: #endif
6939: if(!stat(plotcmd,&info)){
6940: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6941: if(!stat(getenv("GNUPLOTBIN"),&info)){
6942: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6943: }else
6944: strcpy(pplotcmd,plotcmd);
6945: #ifdef __unix
6946: strcpy(plotcmd,GNUPLOTPROGRAM);
6947: if(!stat(plotcmd,&info)){
6948: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6949: }else
6950: strcpy(pplotcmd,plotcmd);
6951: #endif
6952: }else
6953: strcpy(pplotcmd,plotcmd);
6954:
6955: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6956: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6957:
6958: if((outcmd=system(plotcmd)) != 0){
6959: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6960: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6961: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6962: if((outcmd=system(plotcmd)) != 0)
6963: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6964: }
6965: printf(" Successful, please wait...");
6966: while (z[0] != 'q') {
6967: /* chdir(path); */
6968: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6969: scanf("%s",z);
6970: /* if (z[0] == 'c') system("./imach"); */
6971: if (z[0] == 'e') {
6972: #ifdef __APPLE__
6973: sprintf(pplotcmd, "open %s", optionfilehtm);
6974: #elif __linux
6975: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
6976: #else
6977: sprintf(pplotcmd, "%s", optionfilehtm);
6978: #endif
6979: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6980: system(pplotcmd);
6981: }
6982: else if (z[0] == 'g') system(plotcmd);
6983: else if (z[0] == 'q') exit(0);
6984: }
6985: end:
6986: while (z[0] != 'q') {
6987: printf("\nType q for exiting: ");
6988: scanf("%s",z);
6989: }
6990: }
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