1: /* $Id: imach.c,v 1.173 2015/01/03 12:06:26 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.173 2015/01/03 12:06:26 brouard
5: Summary: trying to detect cross-compilation
6:
7: Revision 1.172 2014/12/27 12:07:47 brouard
8: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
9:
10: Revision 1.171 2014/12/23 13:26:59 brouard
11: Summary: Back from Visual C
12:
13: Still problem with utsname.h on Windows
14:
15: Revision 1.170 2014/12/23 11:17:12 brouard
16: Summary: Cleaning some \%% back to %%
17:
18: The escape was mandatory for a specific compiler (which one?), but too many warnings.
19:
20: Revision 1.169 2014/12/22 23:08:31 brouard
21: Summary: 0.98p
22:
23: Outputs some informations on compiler used, OS etc. Testing on different platforms.
24:
25: Revision 1.168 2014/12/22 15:17:42 brouard
26: Summary: update
27:
28: Revision 1.167 2014/12/22 13:50:56 brouard
29: Summary: Testing uname and compiler version and if compiled 32 or 64
30:
31: Testing on Linux 64
32:
33: Revision 1.166 2014/12/22 11:40:47 brouard
34: *** empty log message ***
35:
36: Revision 1.165 2014/12/16 11:20:36 brouard
37: Summary: After compiling on Visual C
38:
39: * imach.c (Module): Merging 1.61 to 1.162
40:
41: Revision 1.164 2014/12/16 10:52:11 brouard
42: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
43:
44: * imach.c (Module): Merging 1.61 to 1.162
45:
46: Revision 1.163 2014/12/16 10:30:11 brouard
47: * imach.c (Module): Merging 1.61 to 1.162
48:
49: Revision 1.162 2014/09/25 11:43:39 brouard
50: Summary: temporary backup 0.99!
51:
52: Revision 1.1 2014/09/16 11:06:58 brouard
53: Summary: With some code (wrong) for nlopt
54:
55: Author:
56:
57: Revision 1.161 2014/09/15 20:41:41 brouard
58: Summary: Problem with macro SQR on Intel compiler
59:
60: Revision 1.160 2014/09/02 09:24:05 brouard
61: *** empty log message ***
62:
63: Revision 1.159 2014/09/01 10:34:10 brouard
64: Summary: WIN32
65: Author: Brouard
66:
67: Revision 1.158 2014/08/27 17:11:51 brouard
68: *** empty log message ***
69:
70: Revision 1.157 2014/08/27 16:26:55 brouard
71: Summary: Preparing windows Visual studio version
72: Author: Brouard
73:
74: In order to compile on Visual studio, time.h is now correct and time_t
75: and tm struct should be used. difftime should be used but sometimes I
76: just make the differences in raw time format (time(&now).
77: Trying to suppress #ifdef LINUX
78: Add xdg-open for __linux in order to open default browser.
79:
80: Revision 1.156 2014/08/25 20:10:10 brouard
81: *** empty log message ***
82:
83: Revision 1.155 2014/08/25 18:32:34 brouard
84: Summary: New compile, minor changes
85: Author: Brouard
86:
87: Revision 1.154 2014/06/20 17:32:08 brouard
88: Summary: Outputs now all graphs of convergence to period prevalence
89:
90: Revision 1.153 2014/06/20 16:45:46 brouard
91: Summary: If 3 live state, convergence to period prevalence on same graph
92: Author: Brouard
93:
94: Revision 1.152 2014/06/18 17:54:09 brouard
95: Summary: open browser, use gnuplot on same dir than imach if not found in the path
96:
97: Revision 1.151 2014/06/18 16:43:30 brouard
98: *** empty log message ***
99:
100: Revision 1.150 2014/06/18 16:42:35 brouard
101: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
102: Author: brouard
103:
104: Revision 1.149 2014/06/18 15:51:14 brouard
105: Summary: Some fixes in parameter files errors
106: Author: Nicolas Brouard
107:
108: Revision 1.148 2014/06/17 17:38:48 brouard
109: Summary: Nothing new
110: Author: Brouard
111:
112: Just a new packaging for OS/X version 0.98nS
113:
114: Revision 1.147 2014/06/16 10:33:11 brouard
115: *** empty log message ***
116:
117: Revision 1.146 2014/06/16 10:20:28 brouard
118: Summary: Merge
119: Author: Brouard
120:
121: Merge, before building revised version.
122:
123: Revision 1.145 2014/06/10 21:23:15 brouard
124: Summary: Debugging with valgrind
125: Author: Nicolas Brouard
126:
127: Lot of changes in order to output the results with some covariates
128: After the Edimburgh REVES conference 2014, it seems mandatory to
129: improve the code.
130: No more memory valgrind error but a lot has to be done in order to
131: continue the work of splitting the code into subroutines.
132: Also, decodemodel has been improved. Tricode is still not
133: optimal. nbcode should be improved. Documentation has been added in
134: the source code.
135:
136: Revision 1.143 2014/01/26 09:45:38 brouard
137: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
138:
139: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
140: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
141:
142: Revision 1.142 2014/01/26 03:57:36 brouard
143: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
144:
145: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
146:
147: Revision 1.141 2014/01/26 02:42:01 brouard
148: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
149:
150: Revision 1.140 2011/09/02 10:37:54 brouard
151: Summary: times.h is ok with mingw32 now.
152:
153: Revision 1.139 2010/06/14 07:50:17 brouard
154: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
155: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
156:
157: Revision 1.138 2010/04/30 18:19:40 brouard
158: *** empty log message ***
159:
160: Revision 1.137 2010/04/29 18:11:38 brouard
161: (Module): Checking covariates for more complex models
162: than V1+V2. A lot of change to be done. Unstable.
163:
164: Revision 1.136 2010/04/26 20:30:53 brouard
165: (Module): merging some libgsl code. Fixing computation
166: of likelione (using inter/intrapolation if mle = 0) in order to
167: get same likelihood as if mle=1.
168: Some cleaning of code and comments added.
169:
170: Revision 1.135 2009/10/29 15:33:14 brouard
171: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
172:
173: Revision 1.134 2009/10/29 13:18:53 brouard
174: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
175:
176: Revision 1.133 2009/07/06 10:21:25 brouard
177: just nforces
178:
179: Revision 1.132 2009/07/06 08:22:05 brouard
180: Many tings
181:
182: Revision 1.131 2009/06/20 16:22:47 brouard
183: Some dimensions resccaled
184:
185: Revision 1.130 2009/05/26 06:44:34 brouard
186: (Module): Max Covariate is now set to 20 instead of 8. A
187: lot of cleaning with variables initialized to 0. Trying to make
188: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
189:
190: Revision 1.129 2007/08/31 13:49:27 lievre
191: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
192:
193: Revision 1.128 2006/06/30 13:02:05 brouard
194: (Module): Clarifications on computing e.j
195:
196: Revision 1.127 2006/04/28 18:11:50 brouard
197: (Module): Yes the sum of survivors was wrong since
198: imach-114 because nhstepm was no more computed in the age
199: loop. Now we define nhstepma in the age loop.
200: (Module): In order to speed up (in case of numerous covariates) we
201: compute health expectancies (without variances) in a first step
202: and then all the health expectancies with variances or standard
203: deviation (needs data from the Hessian matrices) which slows the
204: computation.
205: In the future we should be able to stop the program is only health
206: expectancies and graph are needed without standard deviations.
207:
208: Revision 1.126 2006/04/28 17:23:28 brouard
209: (Module): Yes the sum of survivors was wrong since
210: imach-114 because nhstepm was no more computed in the age
211: loop. Now we define nhstepma in the age loop.
212: Version 0.98h
213:
214: Revision 1.125 2006/04/04 15:20:31 lievre
215: Errors in calculation of health expectancies. Age was not initialized.
216: Forecasting file added.
217:
218: Revision 1.124 2006/03/22 17:13:53 lievre
219: Parameters are printed with %lf instead of %f (more numbers after the comma).
220: The log-likelihood is printed in the log file
221:
222: Revision 1.123 2006/03/20 10:52:43 brouard
223: * imach.c (Module): <title> changed, corresponds to .htm file
224: name. <head> headers where missing.
225:
226: * imach.c (Module): Weights can have a decimal point as for
227: English (a comma might work with a correct LC_NUMERIC environment,
228: otherwise the weight is truncated).
229: Modification of warning when the covariates values are not 0 or
230: 1.
231: Version 0.98g
232:
233: Revision 1.122 2006/03/20 09:45:41 brouard
234: (Module): Weights can have a decimal point as for
235: English (a comma might work with a correct LC_NUMERIC environment,
236: otherwise the weight is truncated).
237: Modification of warning when the covariates values are not 0 or
238: 1.
239: Version 0.98g
240:
241: Revision 1.121 2006/03/16 17:45:01 lievre
242: * imach.c (Module): Comments concerning covariates added
243:
244: * imach.c (Module): refinements in the computation of lli if
245: status=-2 in order to have more reliable computation if stepm is
246: not 1 month. Version 0.98f
247:
248: Revision 1.120 2006/03/16 15:10:38 lievre
249: (Module): refinements in the computation of lli if
250: status=-2 in order to have more reliable computation if stepm is
251: not 1 month. Version 0.98f
252:
253: Revision 1.119 2006/03/15 17:42:26 brouard
254: (Module): Bug if status = -2, the loglikelihood was
255: computed as likelihood omitting the logarithm. Version O.98e
256:
257: Revision 1.118 2006/03/14 18:20:07 brouard
258: (Module): varevsij Comments added explaining the second
259: table of variances if popbased=1 .
260: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
261: (Module): Function pstamp added
262: (Module): Version 0.98d
263:
264: Revision 1.117 2006/03/14 17:16:22 brouard
265: (Module): varevsij Comments added explaining the second
266: table of variances if popbased=1 .
267: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
268: (Module): Function pstamp added
269: (Module): Version 0.98d
270:
271: Revision 1.116 2006/03/06 10:29:27 brouard
272: (Module): Variance-covariance wrong links and
273: varian-covariance of ej. is needed (Saito).
274:
275: Revision 1.115 2006/02/27 12:17:45 brouard
276: (Module): One freematrix added in mlikeli! 0.98c
277:
278: Revision 1.114 2006/02/26 12:57:58 brouard
279: (Module): Some improvements in processing parameter
280: filename with strsep.
281:
282: Revision 1.113 2006/02/24 14:20:24 brouard
283: (Module): Memory leaks checks with valgrind and:
284: datafile was not closed, some imatrix were not freed and on matrix
285: allocation too.
286:
287: Revision 1.112 2006/01/30 09:55:26 brouard
288: (Module): Back to gnuplot.exe instead of wgnuplot.exe
289:
290: Revision 1.111 2006/01/25 20:38:18 brouard
291: (Module): Lots of cleaning and bugs added (Gompertz)
292: (Module): Comments can be added in data file. Missing date values
293: can be a simple dot '.'.
294:
295: Revision 1.110 2006/01/25 00:51:50 brouard
296: (Module): Lots of cleaning and bugs added (Gompertz)
297:
298: Revision 1.109 2006/01/24 19:37:15 brouard
299: (Module): Comments (lines starting with a #) are allowed in data.
300:
301: Revision 1.108 2006/01/19 18:05:42 lievre
302: Gnuplot problem appeared...
303: To be fixed
304:
305: Revision 1.107 2006/01/19 16:20:37 brouard
306: Test existence of gnuplot in imach path
307:
308: Revision 1.106 2006/01/19 13:24:36 brouard
309: Some cleaning and links added in html output
310:
311: Revision 1.105 2006/01/05 20:23:19 lievre
312: *** empty log message ***
313:
314: Revision 1.104 2005/09/30 16:11:43 lievre
315: (Module): sump fixed, loop imx fixed, and simplifications.
316: (Module): If the status is missing at the last wave but we know
317: that the person is alive, then we can code his/her status as -2
318: (instead of missing=-1 in earlier versions) and his/her
319: contributions to the likelihood is 1 - Prob of dying from last
320: health status (= 1-p13= p11+p12 in the easiest case of somebody in
321: the healthy state at last known wave). Version is 0.98
322:
323: Revision 1.103 2005/09/30 15:54:49 lievre
324: (Module): sump fixed, loop imx fixed, and simplifications.
325:
326: Revision 1.102 2004/09/15 17:31:30 brouard
327: Add the possibility to read data file including tab characters.
328:
329: Revision 1.101 2004/09/15 10:38:38 brouard
330: Fix on curr_time
331:
332: Revision 1.100 2004/07/12 18:29:06 brouard
333: Add version for Mac OS X. Just define UNIX in Makefile
334:
335: Revision 1.99 2004/06/05 08:57:40 brouard
336: *** empty log message ***
337:
338: Revision 1.98 2004/05/16 15:05:56 brouard
339: New version 0.97 . First attempt to estimate force of mortality
340: directly from the data i.e. without the need of knowing the health
341: state at each age, but using a Gompertz model: log u =a + b*age .
342: This is the basic analysis of mortality and should be done before any
343: other analysis, in order to test if the mortality estimated from the
344: cross-longitudinal survey is different from the mortality estimated
345: from other sources like vital statistic data.
346:
347: The same imach parameter file can be used but the option for mle should be -3.
348:
349: Agnès, who wrote this part of the code, tried to keep most of the
350: former routines in order to include the new code within the former code.
351:
352: The output is very simple: only an estimate of the intercept and of
353: the slope with 95% confident intervals.
354:
355: Current limitations:
356: A) Even if you enter covariates, i.e. with the
357: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
358: B) There is no computation of Life Expectancy nor Life Table.
359:
360: Revision 1.97 2004/02/20 13:25:42 lievre
361: Version 0.96d. Population forecasting command line is (temporarily)
362: suppressed.
363:
364: Revision 1.96 2003/07/15 15:38:55 brouard
365: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
366: rewritten within the same printf. Workaround: many printfs.
367:
368: Revision 1.95 2003/07/08 07:54:34 brouard
369: * imach.c (Repository):
370: (Repository): Using imachwizard code to output a more meaningful covariance
371: matrix (cov(a12,c31) instead of numbers.
372:
373: Revision 1.94 2003/06/27 13:00:02 brouard
374: Just cleaning
375:
376: Revision 1.93 2003/06/25 16:33:55 brouard
377: (Module): On windows (cygwin) function asctime_r doesn't
378: exist so I changed back to asctime which exists.
379: (Module): Version 0.96b
380:
381: Revision 1.92 2003/06/25 16:30:45 brouard
382: (Module): On windows (cygwin) function asctime_r doesn't
383: exist so I changed back to asctime which exists.
384:
385: Revision 1.91 2003/06/25 15:30:29 brouard
386: * imach.c (Repository): Duplicated warning errors corrected.
387: (Repository): Elapsed time after each iteration is now output. It
388: helps to forecast when convergence will be reached. Elapsed time
389: is stamped in powell. We created a new html file for the graphs
390: concerning matrix of covariance. It has extension -cov.htm.
391:
392: Revision 1.90 2003/06/24 12:34:15 brouard
393: (Module): Some bugs corrected for windows. Also, when
394: mle=-1 a template is output in file "or"mypar.txt with the design
395: of the covariance matrix to be input.
396:
397: Revision 1.89 2003/06/24 12:30:52 brouard
398: (Module): Some bugs corrected for windows. Also, when
399: mle=-1 a template is output in file "or"mypar.txt with the design
400: of the covariance matrix to be input.
401:
402: Revision 1.88 2003/06/23 17:54:56 brouard
403: * 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.
404:
405: Revision 1.87 2003/06/18 12:26:01 brouard
406: Version 0.96
407:
408: Revision 1.86 2003/06/17 20:04:08 brouard
409: (Module): Change position of html and gnuplot routines and added
410: routine fileappend.
411:
412: Revision 1.85 2003/06/17 13:12:43 brouard
413: * imach.c (Repository): Check when date of death was earlier that
414: current date of interview. It may happen when the death was just
415: prior to the death. In this case, dh was negative and likelihood
416: was wrong (infinity). We still send an "Error" but patch by
417: assuming that the date of death was just one stepm after the
418: interview.
419: (Repository): Because some people have very long ID (first column)
420: we changed int to long in num[] and we added a new lvector for
421: memory allocation. But we also truncated to 8 characters (left
422: truncation)
423: (Repository): No more line truncation errors.
424:
425: Revision 1.84 2003/06/13 21:44:43 brouard
426: * imach.c (Repository): Replace "freqsummary" at a correct
427: place. It differs from routine "prevalence" which may be called
428: many times. Probs is memory consuming and must be used with
429: parcimony.
430: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
431:
432: Revision 1.83 2003/06/10 13:39:11 lievre
433: *** empty log message ***
434:
435: Revision 1.82 2003/06/05 15:57:20 brouard
436: Add log in imach.c and fullversion number is now printed.
437:
438: */
439: /*
440: Interpolated Markov Chain
441:
442: Short summary of the programme:
443:
444: This program computes Healthy Life Expectancies from
445: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
446: first survey ("cross") where individuals from different ages are
447: interviewed on their health status or degree of disability (in the
448: case of a health survey which is our main interest) -2- at least a
449: second wave of interviews ("longitudinal") which measure each change
450: (if any) in individual health status. Health expectancies are
451: computed from the time spent in each health state according to a
452: model. More health states you consider, more time is necessary to reach the
453: Maximum Likelihood of the parameters involved in the model. The
454: simplest model is the multinomial logistic model where pij is the
455: probability to be observed in state j at the second wave
456: conditional to be observed in state i at the first wave. Therefore
457: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
458: 'age' is age and 'sex' is a covariate. If you want to have a more
459: complex model than "constant and age", you should modify the program
460: where the markup *Covariates have to be included here again* invites
461: you to do it. More covariates you add, slower the
462: convergence.
463:
464: The advantage of this computer programme, compared to a simple
465: multinomial logistic model, is clear when the delay between waves is not
466: identical for each individual. Also, if a individual missed an
467: intermediate interview, the information is lost, but taken into
468: account using an interpolation or extrapolation.
469:
470: hPijx is the probability to be observed in state i at age x+h
471: conditional to the observed state i at age x. The delay 'h' can be
472: split into an exact number (nh*stepm) of unobserved intermediate
473: states. This elementary transition (by month, quarter,
474: semester or year) is modelled as a multinomial logistic. The hPx
475: matrix is simply the matrix product of nh*stepm elementary matrices
476: and the contribution of each individual to the likelihood is simply
477: hPijx.
478:
479: Also this programme outputs the covariance matrix of the parameters but also
480: of the life expectancies. It also computes the period (stable) prevalence.
481:
482: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
483: Institut national d'études démographiques, Paris.
484: This software have been partly granted by Euro-REVES, a concerted action
485: from the European Union.
486: It is copyrighted identically to a GNU software product, ie programme and
487: software can be distributed freely for non commercial use. Latest version
488: can be accessed at http://euroreves.ined.fr/imach .
489:
490: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
491: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
492:
493: **********************************************************************/
494: /*
495: main
496: read parameterfile
497: read datafile
498: concatwav
499: freqsummary
500: if (mle >= 1)
501: mlikeli
502: print results files
503: if mle==1
504: computes hessian
505: read end of parameter file: agemin, agemax, bage, fage, estepm
506: begin-prev-date,...
507: open gnuplot file
508: open html file
509: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
510: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
511: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
512: freexexit2 possible for memory heap.
513:
514: h Pij x | pij_nom ficrestpij
515: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
516: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
517: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
518:
519: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
520: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
521: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
522: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
523: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
524:
525: forecasting if prevfcast==1 prevforecast call prevalence()
526: health expectancies
527: Variance-covariance of DFLE
528: prevalence()
529: movingaverage()
530: varevsij()
531: if popbased==1 varevsij(,popbased)
532: total life expectancies
533: Variance of period (stable) prevalence
534: end
535: */
536:
537: #define POWELL /* Instead of NLOPT */
538:
539: #include <math.h>
540: #include <stdio.h>
541: #include <stdlib.h>
542: #include <string.h>
543:
544: #ifdef _WIN32
545: #include <io.h>
546: #include <windows.h>
547: #include <tchar.h>
548: #else
549: #include <unistd.h>
550: #endif
551:
552: #include <limits.h>
553: #include <sys/types.h>
554:
555: #if defined(__GNUC__)
556: #include <sys/utsname.h> /* Doesn't work on Windows */
557: #endif
558:
559: #include <sys/stat.h>
560: #include <errno.h>
561: /* extern int errno; */
562:
563: /* #ifdef LINUX */
564: /* #include <time.h> */
565: /* #include "timeval.h" */
566: /* #else */
567: /* #include <sys/time.h> */
568: /* #endif */
569:
570: #include <time.h>
571:
572: #ifdef GSL
573: #include <gsl/gsl_errno.h>
574: #include <gsl/gsl_multimin.h>
575: #endif
576:
577:
578: #ifdef NLOPT
579: #include <nlopt.h>
580: typedef struct {
581: double (* function)(double [] );
582: } myfunc_data ;
583: #endif
584:
585: /* #include <libintl.h> */
586: /* #define _(String) gettext (String) */
587:
588: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
589:
590: #define GNUPLOTPROGRAM "gnuplot"
591: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
592: #define FILENAMELENGTH 132
593:
594: #define GLOCK_ERROR_NOPATH -1 /* empty path */
595: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
596:
597: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
598: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
599:
600: #define NINTERVMAX 8
601: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
602: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
603: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
604: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
605: #define MAXN 20000
606: #define YEARM 12. /**< Number of months per year */
607: #define AGESUP 130
608: #define AGEBASE 40
609: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
610: #ifdef _WIN32
611: #define DIRSEPARATOR '\\'
612: #define CHARSEPARATOR "\\"
613: #define ODIRSEPARATOR '/'
614: #else
615: #define DIRSEPARATOR '/'
616: #define CHARSEPARATOR "/"
617: #define ODIRSEPARATOR '\\'
618: #endif
619:
620: /* $Id: imach.c,v 1.173 2015/01/03 12:06:26 brouard Exp $ */
621: /* $State: Exp $ */
622:
623: char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
624: char fullversion[]="$Revision: 1.173 $ $Date: 2015/01/03 12:06:26 $";
625: char strstart[80];
626: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
627: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
628: int nvar=0, nforce=0; /* Number of variables, number of forces */
629: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
630: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
631: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
632: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
633: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
634: int cptcovprodnoage=0; /**< Number of covariate products without age */
635: int cptcoveff=0; /* Total number of covariates to vary for printing results */
636: int cptcov=0; /* Working variable */
637: int npar=NPARMAX;
638: int nlstate=2; /* Number of live states */
639: int ndeath=1; /* Number of dead states */
640: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
641: int popbased=0;
642:
643: int *wav; /* Number of waves for this individuual 0 is possible */
644: int maxwav=0; /* Maxim number of waves */
645: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
646: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
647: int gipmx=0, gsw=0; /* Global variables on the number of contributions
648: to the likelihood and the sum of weights (done by funcone)*/
649: int mle=1, weightopt=0;
650: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
651: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
652: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
653: * wave mi and wave mi+1 is not an exact multiple of stepm. */
654: int countcallfunc=0; /* Count the number of calls to func */
655: double jmean=1; /* Mean space between 2 waves */
656: double **matprod2(); /* test */
657: double **oldm, **newm, **savm; /* Working pointers to matrices */
658: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
659: /*FILE *fic ; */ /* Used in readdata only */
660: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
661: FILE *ficlog, *ficrespow;
662: int globpr=0; /* Global variable for printing or not */
663: double fretone; /* Only one call to likelihood */
664: long ipmx=0; /* Number of contributions */
665: double sw; /* Sum of weights */
666: char filerespow[FILENAMELENGTH];
667: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
668: FILE *ficresilk;
669: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
670: FILE *ficresprobmorprev;
671: FILE *fichtm, *fichtmcov; /* Html File */
672: FILE *ficreseij;
673: char filerese[FILENAMELENGTH];
674: FILE *ficresstdeij;
675: char fileresstde[FILENAMELENGTH];
676: FILE *ficrescveij;
677: char filerescve[FILENAMELENGTH];
678: FILE *ficresvij;
679: char fileresv[FILENAMELENGTH];
680: FILE *ficresvpl;
681: char fileresvpl[FILENAMELENGTH];
682: char title[MAXLINE];
683: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
684: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
685: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
686: char command[FILENAMELENGTH];
687: int outcmd=0;
688:
689: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
690:
691: char filelog[FILENAMELENGTH]; /* Log file */
692: char filerest[FILENAMELENGTH];
693: char fileregp[FILENAMELENGTH];
694: char popfile[FILENAMELENGTH];
695:
696: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
697:
698: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
699: /* struct timezone tzp; */
700: /* extern int gettimeofday(); */
701: struct tm tml, *gmtime(), *localtime();
702:
703: extern time_t time();
704:
705: struct tm start_time, end_time, curr_time, last_time, forecast_time;
706: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
707: struct tm tm;
708:
709: char strcurr[80], strfor[80];
710:
711: char *endptr;
712: long lval;
713: double dval;
714:
715: #define NR_END 1
716: #define FREE_ARG char*
717: #define FTOL 1.0e-10
718:
719: #define NRANSI
720: #define ITMAX 200
721:
722: #define TOL 2.0e-4
723:
724: #define CGOLD 0.3819660
725: #define ZEPS 1.0e-10
726: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
727:
728: #define GOLD 1.618034
729: #define GLIMIT 100.0
730: #define TINY 1.0e-20
731:
732: static double maxarg1,maxarg2;
733: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
734: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
735:
736: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
737: #define rint(a) floor(a+0.5)
738: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
739: /* #define mytinydouble 1.0e-16 */
740: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
741: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
742: /* static double dsqrarg; */
743: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
744: static double sqrarg;
745: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
746: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
747: int agegomp= AGEGOMP;
748:
749: int imx;
750: int stepm=1;
751: /* Stepm, step in month: minimum step interpolation*/
752:
753: int estepm;
754: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
755:
756: int m,nb;
757: long *num;
758: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
759: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
760: double **pmmij, ***probs;
761: double *ageexmed,*agecens;
762: double dateintmean=0;
763:
764: double *weight;
765: int **s; /* Status */
766: double *agedc;
767: double **covar; /**< covar[j,i], value of jth covariate for individual i,
768: * covar=matrix(0,NCOVMAX,1,n);
769: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
770: double idx;
771: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
772: int *Ndum; /** Freq of modality (tricode */
773: int **codtab; /**< codtab=imatrix(1,100,1,10); */
774: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
775: double *lsurv, *lpop, *tpop;
776:
777: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
778: double ftolhess; /**< Tolerance for computing hessian */
779:
780: /**************** split *************************/
781: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
782: {
783: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
784: the name of the file (name), its extension only (ext) and its first part of the name (finame)
785: */
786: char *ss; /* pointer */
787: int l1, l2; /* length counters */
788:
789: l1 = strlen(path ); /* length of path */
790: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
791: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
792: if ( ss == NULL ) { /* no directory, so determine current directory */
793: strcpy( name, path ); /* we got the fullname name because no directory */
794: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
795: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
796: /* get current working directory */
797: /* extern char* getcwd ( char *buf , int len);*/
798: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
799: return( GLOCK_ERROR_GETCWD );
800: }
801: /* got dirc from getcwd*/
802: printf(" DIRC = %s \n",dirc);
803: } else { /* strip direcotry from path */
804: ss++; /* after this, the filename */
805: l2 = strlen( ss ); /* length of filename */
806: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
807: strcpy( name, ss ); /* save file name */
808: strncpy( dirc, path, l1 - l2 ); /* now the directory */
809: dirc[l1-l2] = 0; /* add zero */
810: printf(" DIRC2 = %s \n",dirc);
811: }
812: /* We add a separator at the end of dirc if not exists */
813: l1 = strlen( dirc ); /* length of directory */
814: if( dirc[l1-1] != DIRSEPARATOR ){
815: dirc[l1] = DIRSEPARATOR;
816: dirc[l1+1] = 0;
817: printf(" DIRC3 = %s \n",dirc);
818: }
819: ss = strrchr( name, '.' ); /* find last / */
820: if (ss >0){
821: ss++;
822: strcpy(ext,ss); /* save extension */
823: l1= strlen( name);
824: l2= strlen(ss)+1;
825: strncpy( finame, name, l1-l2);
826: finame[l1-l2]= 0;
827: }
828:
829: return( 0 ); /* we're done */
830: }
831:
832:
833: /******************************************/
834:
835: void replace_back_to_slash(char *s, char*t)
836: {
837: int i;
838: int lg=0;
839: i=0;
840: lg=strlen(t);
841: for(i=0; i<= lg; i++) {
842: (s[i] = t[i]);
843: if (t[i]== '\\') s[i]='/';
844: }
845: }
846:
847: char *trimbb(char *out, char *in)
848: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
849: char *s;
850: s=out;
851: while (*in != '\0'){
852: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
853: in++;
854: }
855: *out++ = *in++;
856: }
857: *out='\0';
858: return s;
859: }
860:
861: char *cutl(char *blocc, char *alocc, char *in, char occ)
862: {
863: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
864: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
865: gives blocc="abcdef2ghi" and alocc="j".
866: If occ is not found blocc is null and alocc is equal to in. Returns blocc
867: */
868: char *s, *t;
869: t=in;s=in;
870: while ((*in != occ) && (*in != '\0')){
871: *alocc++ = *in++;
872: }
873: if( *in == occ){
874: *(alocc)='\0';
875: s=++in;
876: }
877:
878: if (s == t) {/* occ not found */
879: *(alocc-(in-s))='\0';
880: in=s;
881: }
882: while ( *in != '\0'){
883: *blocc++ = *in++;
884: }
885:
886: *blocc='\0';
887: return t;
888: }
889: char *cutv(char *blocc, char *alocc, char *in, char occ)
890: {
891: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
892: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
893: gives blocc="abcdef2ghi" and alocc="j".
894: If occ is not found blocc is null and alocc is equal to in. Returns alocc
895: */
896: char *s, *t;
897: t=in;s=in;
898: while (*in != '\0'){
899: while( *in == occ){
900: *blocc++ = *in++;
901: s=in;
902: }
903: *blocc++ = *in++;
904: }
905: if (s == t) /* occ not found */
906: *(blocc-(in-s))='\0';
907: else
908: *(blocc-(in-s)-1)='\0';
909: in=s;
910: while ( *in != '\0'){
911: *alocc++ = *in++;
912: }
913:
914: *alocc='\0';
915: return s;
916: }
917:
918: int nbocc(char *s, char occ)
919: {
920: int i,j=0;
921: int lg=20;
922: i=0;
923: lg=strlen(s);
924: for(i=0; i<= lg; i++) {
925: if (s[i] == occ ) j++;
926: }
927: return j;
928: }
929:
930: /* void cutv(char *u,char *v, char*t, char occ) */
931: /* { */
932: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
933: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
934: /* gives u="abcdef2ghi" and v="j" *\/ */
935: /* int i,lg,j,p=0; */
936: /* i=0; */
937: /* lg=strlen(t); */
938: /* for(j=0; j<=lg-1; j++) { */
939: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
940: /* } */
941:
942: /* for(j=0; j<p; j++) { */
943: /* (u[j] = t[j]); */
944: /* } */
945: /* u[p]='\0'; */
946:
947: /* for(j=0; j<= lg; j++) { */
948: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
949: /* } */
950: /* } */
951:
952: #ifdef _WIN32
953: char * strsep(char **pp, const char *delim)
954: {
955: char *p, *q;
956:
957: if ((p = *pp) == NULL)
958: return 0;
959: if ((q = strpbrk (p, delim)) != NULL)
960: {
961: *pp = q + 1;
962: *q = '\0';
963: }
964: else
965: *pp = 0;
966: return p;
967: }
968: #endif
969:
970: /********************** nrerror ********************/
971:
972: void nrerror(char error_text[])
973: {
974: fprintf(stderr,"ERREUR ...\n");
975: fprintf(stderr,"%s\n",error_text);
976: exit(EXIT_FAILURE);
977: }
978: /*********************** vector *******************/
979: double *vector(int nl, int nh)
980: {
981: double *v;
982: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
983: if (!v) nrerror("allocation failure in vector");
984: return v-nl+NR_END;
985: }
986:
987: /************************ free vector ******************/
988: void free_vector(double*v, int nl, int nh)
989: {
990: free((FREE_ARG)(v+nl-NR_END));
991: }
992:
993: /************************ivector *******************************/
994: int *ivector(long nl,long nh)
995: {
996: int *v;
997: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
998: if (!v) nrerror("allocation failure in ivector");
999: return v-nl+NR_END;
1000: }
1001:
1002: /******************free ivector **************************/
1003: void free_ivector(int *v, long nl, long nh)
1004: {
1005: free((FREE_ARG)(v+nl-NR_END));
1006: }
1007:
1008: /************************lvector *******************************/
1009: long *lvector(long nl,long nh)
1010: {
1011: long *v;
1012: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1013: if (!v) nrerror("allocation failure in ivector");
1014: return v-nl+NR_END;
1015: }
1016:
1017: /******************free lvector **************************/
1018: void free_lvector(long *v, long nl, long nh)
1019: {
1020: free((FREE_ARG)(v+nl-NR_END));
1021: }
1022:
1023: /******************* imatrix *******************************/
1024: int **imatrix(long nrl, long nrh, long ncl, long nch)
1025: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1026: {
1027: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1028: int **m;
1029:
1030: /* allocate pointers to rows */
1031: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1032: if (!m) nrerror("allocation failure 1 in matrix()");
1033: m += NR_END;
1034: m -= nrl;
1035:
1036:
1037: /* allocate rows and set pointers to them */
1038: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1039: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1040: m[nrl] += NR_END;
1041: m[nrl] -= ncl;
1042:
1043: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1044:
1045: /* return pointer to array of pointers to rows */
1046: return m;
1047: }
1048:
1049: /****************** free_imatrix *************************/
1050: void free_imatrix(m,nrl,nrh,ncl,nch)
1051: int **m;
1052: long nch,ncl,nrh,nrl;
1053: /* free an int matrix allocated by imatrix() */
1054: {
1055: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1056: free((FREE_ARG) (m+nrl-NR_END));
1057: }
1058:
1059: /******************* matrix *******************************/
1060: double **matrix(long nrl, long nrh, long ncl, long nch)
1061: {
1062: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1063: double **m;
1064:
1065: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1066: if (!m) nrerror("allocation failure 1 in matrix()");
1067: m += NR_END;
1068: m -= nrl;
1069:
1070: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1071: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1072: m[nrl] += NR_END;
1073: m[nrl] -= ncl;
1074:
1075: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1076: return m;
1077: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1078: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1079: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1080: */
1081: }
1082:
1083: /*************************free matrix ************************/
1084: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1085: {
1086: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1087: free((FREE_ARG)(m+nrl-NR_END));
1088: }
1089:
1090: /******************* ma3x *******************************/
1091: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1092: {
1093: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1094: double ***m;
1095:
1096: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1097: if (!m) nrerror("allocation failure 1 in matrix()");
1098: m += NR_END;
1099: m -= nrl;
1100:
1101: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1102: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1103: m[nrl] += NR_END;
1104: m[nrl] -= ncl;
1105:
1106: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1107:
1108: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1109: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1110: m[nrl][ncl] += NR_END;
1111: m[nrl][ncl] -= nll;
1112: for (j=ncl+1; j<=nch; j++)
1113: m[nrl][j]=m[nrl][j-1]+nlay;
1114:
1115: for (i=nrl+1; i<=nrh; i++) {
1116: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1117: for (j=ncl+1; j<=nch; j++)
1118: m[i][j]=m[i][j-1]+nlay;
1119: }
1120: return m;
1121: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1122: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1123: */
1124: }
1125:
1126: /*************************free ma3x ************************/
1127: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1128: {
1129: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1130: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1131: free((FREE_ARG)(m+nrl-NR_END));
1132: }
1133:
1134: /*************** function subdirf ***********/
1135: char *subdirf(char fileres[])
1136: {
1137: /* Caution optionfilefiname is hidden */
1138: strcpy(tmpout,optionfilefiname);
1139: strcat(tmpout,"/"); /* Add to the right */
1140: strcat(tmpout,fileres);
1141: return tmpout;
1142: }
1143:
1144: /*************** function subdirf2 ***********/
1145: char *subdirf2(char fileres[], char *preop)
1146: {
1147:
1148: /* Caution optionfilefiname is hidden */
1149: strcpy(tmpout,optionfilefiname);
1150: strcat(tmpout,"/");
1151: strcat(tmpout,preop);
1152: strcat(tmpout,fileres);
1153: return tmpout;
1154: }
1155:
1156: /*************** function subdirf3 ***********/
1157: char *subdirf3(char fileres[], char *preop, char *preop2)
1158: {
1159:
1160: /* Caution optionfilefiname is hidden */
1161: strcpy(tmpout,optionfilefiname);
1162: strcat(tmpout,"/");
1163: strcat(tmpout,preop);
1164: strcat(tmpout,preop2);
1165: strcat(tmpout,fileres);
1166: return tmpout;
1167: }
1168:
1169: char *asc_diff_time(long time_sec, char ascdiff[])
1170: {
1171: long sec_left, days, hours, minutes;
1172: days = (time_sec) / (60*60*24);
1173: sec_left = (time_sec) % (60*60*24);
1174: hours = (sec_left) / (60*60) ;
1175: sec_left = (sec_left) %(60*60);
1176: minutes = (sec_left) /60;
1177: sec_left = (sec_left) % (60);
1178: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1179: return ascdiff;
1180: }
1181:
1182: /***************** f1dim *************************/
1183: extern int ncom;
1184: extern double *pcom,*xicom;
1185: extern double (*nrfunc)(double []);
1186:
1187: double f1dim(double x)
1188: {
1189: int j;
1190: double f;
1191: double *xt;
1192:
1193: xt=vector(1,ncom);
1194: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1195: f=(*nrfunc)(xt);
1196: free_vector(xt,1,ncom);
1197: return f;
1198: }
1199:
1200: /*****************brent *************************/
1201: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1202: {
1203: int iter;
1204: double a,b,d,etemp;
1205: double fu=0,fv,fw,fx;
1206: double ftemp=0.;
1207: double p,q,r,tol1,tol2,u,v,w,x,xm;
1208: double e=0.0;
1209:
1210: a=(ax < cx ? ax : cx);
1211: b=(ax > cx ? ax : cx);
1212: x=w=v=bx;
1213: fw=fv=fx=(*f)(x);
1214: for (iter=1;iter<=ITMAX;iter++) {
1215: xm=0.5*(a+b);
1216: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1217: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1218: printf(".");fflush(stdout);
1219: fprintf(ficlog,".");fflush(ficlog);
1220: #ifdef DEBUGBRENT
1221: 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);
1222: 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);
1223: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1224: #endif
1225: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1226: *xmin=x;
1227: return fx;
1228: }
1229: ftemp=fu;
1230: if (fabs(e) > tol1) {
1231: r=(x-w)*(fx-fv);
1232: q=(x-v)*(fx-fw);
1233: p=(x-v)*q-(x-w)*r;
1234: q=2.0*(q-r);
1235: if (q > 0.0) p = -p;
1236: q=fabs(q);
1237: etemp=e;
1238: e=d;
1239: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1240: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1241: else {
1242: d=p/q;
1243: u=x+d;
1244: if (u-a < tol2 || b-u < tol2)
1245: d=SIGN(tol1,xm-x);
1246: }
1247: } else {
1248: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1249: }
1250: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1251: fu=(*f)(u);
1252: if (fu <= fx) {
1253: if (u >= x) a=x; else b=x;
1254: SHFT(v,w,x,u)
1255: SHFT(fv,fw,fx,fu)
1256: } else {
1257: if (u < x) a=u; else b=u;
1258: if (fu <= fw || w == x) {
1259: v=w;
1260: w=u;
1261: fv=fw;
1262: fw=fu;
1263: } else if (fu <= fv || v == x || v == w) {
1264: v=u;
1265: fv=fu;
1266: }
1267: }
1268: }
1269: nrerror("Too many iterations in brent");
1270: *xmin=x;
1271: return fx;
1272: }
1273:
1274: /****************** mnbrak ***********************/
1275:
1276: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1277: double (*func)(double))
1278: {
1279: double ulim,u,r,q, dum;
1280: double fu;
1281:
1282: *fa=(*func)(*ax);
1283: *fb=(*func)(*bx);
1284: if (*fb > *fa) {
1285: SHFT(dum,*ax,*bx,dum)
1286: SHFT(dum,*fb,*fa,dum)
1287: }
1288: *cx=(*bx)+GOLD*(*bx-*ax);
1289: *fc=(*func)(*cx);
1290: while (*fb > *fc) { /* Declining fa, fb, fc */
1291: r=(*bx-*ax)*(*fb-*fc);
1292: q=(*bx-*cx)*(*fb-*fa);
1293: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1294: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1295: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1296: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1297: fu=(*func)(u);
1298: #ifdef DEBUG
1299: /* f(x)=A(x-u)**2+f(u) */
1300: double A, fparabu;
1301: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1302: fparabu= *fa - A*(*ax-u)*(*ax-u);
1303: 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);
1304: 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);
1305: #endif
1306: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1307: fu=(*func)(u);
1308: if (fu < *fc) {
1309: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1310: SHFT(*fb,*fc,fu,(*func)(u))
1311: }
1312: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1313: u=ulim;
1314: fu=(*func)(u);
1315: } else {
1316: u=(*cx)+GOLD*(*cx-*bx);
1317: fu=(*func)(u);
1318: }
1319: SHFT(*ax,*bx,*cx,u)
1320: SHFT(*fa,*fb,*fc,fu)
1321: }
1322: }
1323:
1324: /*************** linmin ************************/
1325: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1326: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1327: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1328: the value of func at the returned location p . This is actually all accomplished by calling the
1329: routines mnbrak and brent .*/
1330: int ncom;
1331: double *pcom,*xicom;
1332: double (*nrfunc)(double []);
1333:
1334: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1335: {
1336: double brent(double ax, double bx, double cx,
1337: double (*f)(double), double tol, double *xmin);
1338: double f1dim(double x);
1339: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1340: double *fc, double (*func)(double));
1341: int j;
1342: double xx,xmin,bx,ax;
1343: double fx,fb,fa;
1344:
1345: ncom=n;
1346: pcom=vector(1,n);
1347: xicom=vector(1,n);
1348: nrfunc=func;
1349: for (j=1;j<=n;j++) {
1350: pcom[j]=p[j];
1351: xicom[j]=xi[j];
1352: }
1353: ax=0.0;
1354: xx=1.0;
1355: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1356: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1357: #ifdef DEBUG
1358: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1359: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1360: #endif
1361: for (j=1;j<=n;j++) {
1362: xi[j] *= xmin;
1363: p[j] += xi[j];
1364: }
1365: free_vector(xicom,1,n);
1366: free_vector(pcom,1,n);
1367: }
1368:
1369:
1370: /*************** powell ************************/
1371: /*
1372: Minimization of a function func of n variables. Input consists of an initial starting point
1373: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1374: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1375: such that failure to decrease by more than this amount on one iteration signals doneness. On
1376: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1377: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1378: */
1379: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1380: double (*func)(double []))
1381: {
1382: void linmin(double p[], double xi[], int n, double *fret,
1383: double (*func)(double []));
1384: int i,ibig,j;
1385: double del,t,*pt,*ptt,*xit;
1386: double fp,fptt;
1387: double *xits;
1388: int niterf, itmp;
1389:
1390: pt=vector(1,n);
1391: ptt=vector(1,n);
1392: xit=vector(1,n);
1393: xits=vector(1,n);
1394: *fret=(*func)(p);
1395: for (j=1;j<=n;j++) pt[j]=p[j];
1396: rcurr_time = time(NULL);
1397: for (*iter=1;;++(*iter)) {
1398: fp=(*fret);
1399: ibig=0;
1400: del=0.0;
1401: rlast_time=rcurr_time;
1402: /* (void) gettimeofday(&curr_time,&tzp); */
1403: rcurr_time = time(NULL);
1404: curr_time = *localtime(&rcurr_time);
1405: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1406: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1407: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1408: for (i=1;i<=n;i++) {
1409: printf(" %d %.12f",i, p[i]);
1410: fprintf(ficlog," %d %.12lf",i, p[i]);
1411: fprintf(ficrespow," %.12lf", p[i]);
1412: }
1413: printf("\n");
1414: fprintf(ficlog,"\n");
1415: fprintf(ficrespow,"\n");fflush(ficrespow);
1416: if(*iter <=3){
1417: tml = *localtime(&rcurr_time);
1418: strcpy(strcurr,asctime(&tml));
1419: rforecast_time=rcurr_time;
1420: itmp = strlen(strcurr);
1421: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1422: strcurr[itmp-1]='\0';
1423: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1424: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1425: for(niterf=10;niterf<=30;niterf+=10){
1426: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1427: forecast_time = *localtime(&rforecast_time);
1428: strcpy(strfor,asctime(&forecast_time));
1429: itmp = strlen(strfor);
1430: if(strfor[itmp-1]=='\n')
1431: strfor[itmp-1]='\0';
1432: 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);
1433: 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);
1434: }
1435: }
1436: for (i=1;i<=n;i++) {
1437: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1438: fptt=(*fret);
1439: #ifdef DEBUG
1440: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1441: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1442: #endif
1443: printf("%d",i);fflush(stdout);
1444: fprintf(ficlog,"%d",i);fflush(ficlog);
1445: linmin(p,xit,n,fret,func);
1446: if (fabs(fptt-(*fret)) > del) {
1447: del=fabs(fptt-(*fret));
1448: ibig=i;
1449: }
1450: #ifdef DEBUG
1451: printf("%d %.12e",i,(*fret));
1452: fprintf(ficlog,"%d %.12e",i,(*fret));
1453: for (j=1;j<=n;j++) {
1454: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1455: printf(" x(%d)=%.12e",j,xit[j]);
1456: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1457: }
1458: for(j=1;j<=n;j++) {
1459: printf(" p(%d)=%.12e",j,p[j]);
1460: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1461: }
1462: printf("\n");
1463: fprintf(ficlog,"\n");
1464: #endif
1465: } /* end i */
1466: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1467: #ifdef DEBUG
1468: int k[2],l;
1469: k[0]=1;
1470: k[1]=-1;
1471: printf("Max: %.12e",(*func)(p));
1472: fprintf(ficlog,"Max: %.12e",(*func)(p));
1473: for (j=1;j<=n;j++) {
1474: printf(" %.12e",p[j]);
1475: fprintf(ficlog," %.12e",p[j]);
1476: }
1477: printf("\n");
1478: fprintf(ficlog,"\n");
1479: for(l=0;l<=1;l++) {
1480: for (j=1;j<=n;j++) {
1481: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1482: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1483: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1484: }
1485: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1486: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1487: }
1488: #endif
1489:
1490:
1491: free_vector(xit,1,n);
1492: free_vector(xits,1,n);
1493: free_vector(ptt,1,n);
1494: free_vector(pt,1,n);
1495: return;
1496: }
1497: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1498: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1499: ptt[j]=2.0*p[j]-pt[j];
1500: xit[j]=p[j]-pt[j];
1501: pt[j]=p[j];
1502: }
1503: fptt=(*func)(ptt);
1504: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1505: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1506: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1507: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1508: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1509: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1510: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1511: /* Thus we compare delta(2h) with observed f1-f3 */
1512: /* or best gain on one ancient line 'del' with total */
1513: /* gain f1-f2 = f1 - f2 - 'del' with del */
1514: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1515:
1516: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1517: t= t- del*SQR(fp-fptt);
1518: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1519: 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);
1520: #ifdef DEBUG
1521: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1522: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1523: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1524: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1525: 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);
1526: 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);
1527: #endif
1528: if (t < 0.0) { /* Then we use it for last direction */
1529: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1530: for (j=1;j<=n;j++) {
1531: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1532: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1533: }
1534: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1535: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1536:
1537: #ifdef DEBUG
1538: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1539: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1540: for(j=1;j<=n;j++){
1541: printf(" %.12e",xit[j]);
1542: fprintf(ficlog," %.12e",xit[j]);
1543: }
1544: printf("\n");
1545: fprintf(ficlog,"\n");
1546: #endif
1547: } /* end of t negative */
1548: } /* end if (fptt < fp) */
1549: }
1550: }
1551:
1552: /**** Prevalence limit (stable or period prevalence) ****************/
1553:
1554: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1555: {
1556: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1557: matrix by transitions matrix until convergence is reached */
1558:
1559: int i, ii,j,k;
1560: double min, max, maxmin, maxmax,sumnew=0.;
1561: /* double **matprod2(); */ /* test */
1562: double **out, cov[NCOVMAX+1], **pmij();
1563: double **newm;
1564: double agefin, delaymax=50 ; /* Max number of years to converge */
1565:
1566: for (ii=1;ii<=nlstate+ndeath;ii++)
1567: for (j=1;j<=nlstate+ndeath;j++){
1568: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1569: }
1570:
1571: cov[1]=1.;
1572:
1573: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1574: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1575: newm=savm;
1576: /* Covariates have to be included here again */
1577: cov[2]=agefin;
1578:
1579: for (k=1; k<=cptcovn;k++) {
1580: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1581: /*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]]);*/
1582: }
1583: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1584: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1585: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1586:
1587: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1588: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1589: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1590: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1591: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1592: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1593:
1594: savm=oldm;
1595: oldm=newm;
1596: maxmax=0.;
1597: for(j=1;j<=nlstate;j++){
1598: min=1.;
1599: max=0.;
1600: for(i=1; i<=nlstate; i++) {
1601: sumnew=0;
1602: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1603: prlim[i][j]= newm[i][j]/(1-sumnew);
1604: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1605: max=FMAX(max,prlim[i][j]);
1606: min=FMIN(min,prlim[i][j]);
1607: }
1608: maxmin=max-min;
1609: maxmax=FMAX(maxmax,maxmin);
1610: } /* j loop */
1611: if(maxmax < ftolpl){
1612: return prlim;
1613: }
1614: } /* age loop */
1615: return prlim; /* should not reach here */
1616: }
1617:
1618: /*************** transition probabilities ***************/
1619:
1620: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1621: {
1622: /* According to parameters values stored in x and the covariate's values stored in cov,
1623: computes the probability to be observed in state j being in state i by appying the
1624: model to the ncovmodel covariates (including constant and age).
1625: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1626: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1627: ncth covariate in the global vector x is given by the formula:
1628: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1629: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1630: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1631: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1632: Outputs ps[i][j] the probability to be observed in j being in j according to
1633: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1634: */
1635: double s1, lnpijopii;
1636: /*double t34;*/
1637: int i,j, nc, ii, jj;
1638:
1639: for(i=1; i<= nlstate; i++){
1640: for(j=1; j<i;j++){
1641: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1642: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1643: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1644: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1645: }
1646: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1647: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1648: }
1649: for(j=i+1; j<=nlstate+ndeath;j++){
1650: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1651: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1652: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1653: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1654: }
1655: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1656: }
1657: }
1658:
1659: for(i=1; i<= nlstate; i++){
1660: s1=0;
1661: for(j=1; j<i; j++){
1662: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1663: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1664: }
1665: for(j=i+1; j<=nlstate+ndeath; j++){
1666: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1667: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1668: }
1669: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1670: ps[i][i]=1./(s1+1.);
1671: /* Computing other pijs */
1672: for(j=1; j<i; j++)
1673: ps[i][j]= exp(ps[i][j])*ps[i][i];
1674: for(j=i+1; j<=nlstate+ndeath; j++)
1675: ps[i][j]= exp(ps[i][j])*ps[i][i];
1676: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1677: } /* end i */
1678:
1679: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1680: for(jj=1; jj<= nlstate+ndeath; jj++){
1681: ps[ii][jj]=0;
1682: ps[ii][ii]=1;
1683: }
1684: }
1685:
1686:
1687: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1688: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1689: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1690: /* } */
1691: /* printf("\n "); */
1692: /* } */
1693: /* printf("\n ");printf("%lf ",cov[2]);*/
1694: /*
1695: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1696: goto end;*/
1697: return ps;
1698: }
1699:
1700: /**************** Product of 2 matrices ******************/
1701:
1702: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1703: {
1704: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1705: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1706: /* in, b, out are matrice of pointers which should have been initialized
1707: before: only the contents of out is modified. The function returns
1708: a pointer to pointers identical to out */
1709: int i, j, k;
1710: for(i=nrl; i<= nrh; i++)
1711: for(k=ncolol; k<=ncoloh; k++){
1712: out[i][k]=0.;
1713: for(j=ncl; j<=nch; j++)
1714: out[i][k] +=in[i][j]*b[j][k];
1715: }
1716: return out;
1717: }
1718:
1719:
1720: /************* Higher Matrix Product ***************/
1721:
1722: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1723: {
1724: /* Computes the transition matrix starting at age 'age' over
1725: 'nhstepm*hstepm*stepm' months (i.e. until
1726: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1727: nhstepm*hstepm matrices.
1728: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1729: (typically every 2 years instead of every month which is too big
1730: for the memory).
1731: Model is determined by parameters x and covariates have to be
1732: included manually here.
1733:
1734: */
1735:
1736: int i, j, d, h, k;
1737: double **out, cov[NCOVMAX+1];
1738: double **newm;
1739:
1740: /* Hstepm could be zero and should return the unit matrix */
1741: for (i=1;i<=nlstate+ndeath;i++)
1742: for (j=1;j<=nlstate+ndeath;j++){
1743: oldm[i][j]=(i==j ? 1.0 : 0.0);
1744: po[i][j][0]=(i==j ? 1.0 : 0.0);
1745: }
1746: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1747: for(h=1; h <=nhstepm; h++){
1748: for(d=1; d <=hstepm; d++){
1749: newm=savm;
1750: /* Covariates have to be included here again */
1751: cov[1]=1.;
1752: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1753: for (k=1; k<=cptcovn;k++)
1754: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1755: for (k=1; k<=cptcovage;k++)
1756: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1757: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1758: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1759:
1760:
1761: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1762: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1763: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1764: pmij(pmmij,cov,ncovmodel,x,nlstate));
1765: savm=oldm;
1766: oldm=newm;
1767: }
1768: for(i=1; i<=nlstate+ndeath; i++)
1769: for(j=1;j<=nlstate+ndeath;j++) {
1770: po[i][j][h]=newm[i][j];
1771: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1772: }
1773: /*printf("h=%d ",h);*/
1774: } /* end h */
1775: /* printf("\n H=%d \n",h); */
1776: return po;
1777: }
1778:
1779: #ifdef NLOPT
1780: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1781: double fret;
1782: double *xt;
1783: int j;
1784: myfunc_data *d2 = (myfunc_data *) pd;
1785: /* xt = (p1-1); */
1786: xt=vector(1,n);
1787: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1788:
1789: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1790: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1791: printf("Function = %.12lf ",fret);
1792: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1793: printf("\n");
1794: free_vector(xt,1,n);
1795: return fret;
1796: }
1797: #endif
1798:
1799: /*************** log-likelihood *************/
1800: double func( double *x)
1801: {
1802: int i, ii, j, k, mi, d, kk;
1803: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1804: double **out;
1805: double sw; /* Sum of weights */
1806: double lli; /* Individual log likelihood */
1807: int s1, s2;
1808: double bbh, survp;
1809: long ipmx;
1810: /*extern weight */
1811: /* We are differentiating ll according to initial status */
1812: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1813: /*for(i=1;i<imx;i++)
1814: printf(" %d\n",s[4][i]);
1815: */
1816:
1817: ++countcallfunc;
1818:
1819: cov[1]=1.;
1820:
1821: for(k=1; k<=nlstate; k++) ll[k]=0.;
1822:
1823: if(mle==1){
1824: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1825: /* Computes the values of the ncovmodel covariates of the model
1826: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1827: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1828: to be observed in j being in i according to the model.
1829: */
1830: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1831: cov[2+k]=covar[Tvar[k]][i];
1832: }
1833: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1834: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1835: has been calculated etc */
1836: for(mi=1; mi<= wav[i]-1; mi++){
1837: for (ii=1;ii<=nlstate+ndeath;ii++)
1838: for (j=1;j<=nlstate+ndeath;j++){
1839: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1840: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1841: }
1842: for(d=0; d<dh[mi][i]; d++){
1843: newm=savm;
1844: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1845: for (kk=1; kk<=cptcovage;kk++) {
1846: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1847: }
1848: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1849: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1850: savm=oldm;
1851: oldm=newm;
1852: } /* end mult */
1853:
1854: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1855: /* But now since version 0.9 we anticipate for bias at large stepm.
1856: * If stepm is larger than one month (smallest stepm) and if the exact delay
1857: * (in months) between two waves is not a multiple of stepm, we rounded to
1858: * the nearest (and in case of equal distance, to the lowest) interval but now
1859: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1860: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1861: * probability in order to take into account the bias as a fraction of the way
1862: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1863: * -stepm/2 to stepm/2 .
1864: * For stepm=1 the results are the same as for previous versions of Imach.
1865: * For stepm > 1 the results are less biased than in previous versions.
1866: */
1867: s1=s[mw[mi][i]][i];
1868: s2=s[mw[mi+1][i]][i];
1869: bbh=(double)bh[mi][i]/(double)stepm;
1870: /* bias bh is positive if real duration
1871: * is higher than the multiple of stepm and negative otherwise.
1872: */
1873: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1874: if( s2 > nlstate){
1875: /* i.e. if s2 is a death state and if the date of death is known
1876: then the contribution to the likelihood is the probability to
1877: die between last step unit time and current step unit time,
1878: which is also equal to probability to die before dh
1879: minus probability to die before dh-stepm .
1880: In version up to 0.92 likelihood was computed
1881: as if date of death was unknown. Death was treated as any other
1882: health state: the date of the interview describes the actual state
1883: and not the date of a change in health state. The former idea was
1884: to consider that at each interview the state was recorded
1885: (healthy, disable or death) and IMaCh was corrected; but when we
1886: introduced the exact date of death then we should have modified
1887: the contribution of an exact death to the likelihood. This new
1888: contribution is smaller and very dependent of the step unit
1889: stepm. It is no more the probability to die between last interview
1890: and month of death but the probability to survive from last
1891: interview up to one month before death multiplied by the
1892: probability to die within a month. Thanks to Chris
1893: Jackson for correcting this bug. Former versions increased
1894: mortality artificially. The bad side is that we add another loop
1895: which slows down the processing. The difference can be up to 10%
1896: lower mortality.
1897: */
1898: lli=log(out[s1][s2] - savm[s1][s2]);
1899:
1900:
1901: } else if (s2==-2) {
1902: for (j=1,survp=0. ; j<=nlstate; j++)
1903: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1904: /*survp += out[s1][j]; */
1905: lli= log(survp);
1906: }
1907:
1908: else if (s2==-4) {
1909: for (j=3,survp=0. ; j<=nlstate; j++)
1910: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1911: lli= log(survp);
1912: }
1913:
1914: else if (s2==-5) {
1915: for (j=1,survp=0. ; j<=2; j++)
1916: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1917: lli= log(survp);
1918: }
1919:
1920: else{
1921: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1922: /* 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 */
1923: }
1924: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1925: /*if(lli ==000.0)*/
1926: /*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); */
1927: ipmx +=1;
1928: sw += weight[i];
1929: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1930: } /* end of wave */
1931: } /* end of individual */
1932: } else if(mle==2){
1933: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1934: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1935: for(mi=1; mi<= wav[i]-1; mi++){
1936: for (ii=1;ii<=nlstate+ndeath;ii++)
1937: for (j=1;j<=nlstate+ndeath;j++){
1938: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1939: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1940: }
1941: for(d=0; d<=dh[mi][i]; d++){
1942: newm=savm;
1943: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1944: for (kk=1; kk<=cptcovage;kk++) {
1945: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1946: }
1947: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1948: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1949: savm=oldm;
1950: oldm=newm;
1951: } /* end mult */
1952:
1953: s1=s[mw[mi][i]][i];
1954: s2=s[mw[mi+1][i]][i];
1955: bbh=(double)bh[mi][i]/(double)stepm;
1956: 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 */
1957: ipmx +=1;
1958: sw += weight[i];
1959: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1960: } /* end of wave */
1961: } /* end of individual */
1962: } else if(mle==3){ /* exponential inter-extrapolation */
1963: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1964: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1965: for(mi=1; mi<= wav[i]-1; mi++){
1966: for (ii=1;ii<=nlstate+ndeath;ii++)
1967: for (j=1;j<=nlstate+ndeath;j++){
1968: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1969: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1970: }
1971: for(d=0; d<dh[mi][i]; d++){
1972: newm=savm;
1973: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1974: for (kk=1; kk<=cptcovage;kk++) {
1975: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1976: }
1977: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1978: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1979: savm=oldm;
1980: oldm=newm;
1981: } /* end mult */
1982:
1983: s1=s[mw[mi][i]][i];
1984: s2=s[mw[mi+1][i]][i];
1985: bbh=(double)bh[mi][i]/(double)stepm;
1986: 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 */
1987: ipmx +=1;
1988: sw += weight[i];
1989: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1990: } /* end of wave */
1991: } /* end of individual */
1992: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1993: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1994: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1995: for(mi=1; mi<= wav[i]-1; mi++){
1996: for (ii=1;ii<=nlstate+ndeath;ii++)
1997: for (j=1;j<=nlstate+ndeath;j++){
1998: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1999: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2000: }
2001: for(d=0; d<dh[mi][i]; d++){
2002: newm=savm;
2003: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2004: for (kk=1; kk<=cptcovage;kk++) {
2005: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2006: }
2007:
2008: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2009: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2010: savm=oldm;
2011: oldm=newm;
2012: } /* end mult */
2013:
2014: s1=s[mw[mi][i]][i];
2015: s2=s[mw[mi+1][i]][i];
2016: if( s2 > nlstate){
2017: lli=log(out[s1][s2] - savm[s1][s2]);
2018: }else{
2019: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2020: }
2021: ipmx +=1;
2022: sw += weight[i];
2023: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2024: /* 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]); */
2025: } /* end of wave */
2026: } /* end of individual */
2027: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2028: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2029: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2030: for(mi=1; mi<= wav[i]-1; mi++){
2031: for (ii=1;ii<=nlstate+ndeath;ii++)
2032: for (j=1;j<=nlstate+ndeath;j++){
2033: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2034: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2035: }
2036: for(d=0; d<dh[mi][i]; d++){
2037: newm=savm;
2038: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2039: for (kk=1; kk<=cptcovage;kk++) {
2040: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2041: }
2042:
2043: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2044: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2045: savm=oldm;
2046: oldm=newm;
2047: } /* end mult */
2048:
2049: s1=s[mw[mi][i]][i];
2050: s2=s[mw[mi+1][i]][i];
2051: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2052: ipmx +=1;
2053: sw += weight[i];
2054: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2055: /*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]);*/
2056: } /* end of wave */
2057: } /* end of individual */
2058: } /* End of if */
2059: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2060: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2061: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2062: return -l;
2063: }
2064:
2065: /*************** log-likelihood *************/
2066: double funcone( double *x)
2067: {
2068: /* Same as likeli but slower because of a lot of printf and if */
2069: int i, ii, j, k, mi, d, kk;
2070: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2071: double **out;
2072: double lli; /* Individual log likelihood */
2073: double llt;
2074: int s1, s2;
2075: double bbh, survp;
2076: /*extern weight */
2077: /* We are differentiating ll according to initial status */
2078: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2079: /*for(i=1;i<imx;i++)
2080: printf(" %d\n",s[4][i]);
2081: */
2082: cov[1]=1.;
2083:
2084: for(k=1; k<=nlstate; k++) ll[k]=0.;
2085:
2086: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2087: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2088: for(mi=1; mi<= wav[i]-1; mi++){
2089: for (ii=1;ii<=nlstate+ndeath;ii++)
2090: for (j=1;j<=nlstate+ndeath;j++){
2091: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2092: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2093: }
2094: for(d=0; d<dh[mi][i]; d++){
2095: newm=savm;
2096: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2097: for (kk=1; kk<=cptcovage;kk++) {
2098: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2099: }
2100: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2101: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2102: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2103: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2104: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2105: savm=oldm;
2106: oldm=newm;
2107: } /* end mult */
2108:
2109: s1=s[mw[mi][i]][i];
2110: s2=s[mw[mi+1][i]][i];
2111: bbh=(double)bh[mi][i]/(double)stepm;
2112: /* bias is positive if real duration
2113: * is higher than the multiple of stepm and negative otherwise.
2114: */
2115: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2116: lli=log(out[s1][s2] - savm[s1][s2]);
2117: } else if (s2==-2) {
2118: for (j=1,survp=0. ; j<=nlstate; j++)
2119: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2120: lli= log(survp);
2121: }else if (mle==1){
2122: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2123: } else if(mle==2){
2124: 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 */
2125: } else if(mle==3){ /* exponential inter-extrapolation */
2126: 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 */
2127: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2128: lli=log(out[s1][s2]); /* Original formula */
2129: } else{ /* mle=0 back to 1 */
2130: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2131: /*lli=log(out[s1][s2]); */ /* Original formula */
2132: } /* End of if */
2133: ipmx +=1;
2134: sw += weight[i];
2135: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2136: /*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]); */
2137: if(globpr){
2138: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2139: %11.6f %11.6f %11.6f ", \
2140: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2141: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2142: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2143: llt +=ll[k]*gipmx/gsw;
2144: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2145: }
2146: fprintf(ficresilk," %10.6f\n", -llt);
2147: }
2148: } /* end of wave */
2149: } /* end of individual */
2150: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2151: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2152: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2153: if(globpr==0){ /* First time we count the contributions and weights */
2154: gipmx=ipmx;
2155: gsw=sw;
2156: }
2157: return -l;
2158: }
2159:
2160:
2161: /*************** function likelione ***********/
2162: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2163: {
2164: /* This routine should help understanding what is done with
2165: the selection of individuals/waves and
2166: to check the exact contribution to the likelihood.
2167: Plotting could be done.
2168: */
2169: int k;
2170:
2171: if(*globpri !=0){ /* Just counts and sums, no printings */
2172: strcpy(fileresilk,"ilk");
2173: strcat(fileresilk,fileres);
2174: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2175: printf("Problem with resultfile: %s\n", fileresilk);
2176: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2177: }
2178: 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");
2179: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2180: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2181: for(k=1; k<=nlstate; k++)
2182: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2183: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2184: }
2185:
2186: *fretone=(*funcone)(p);
2187: if(*globpri !=0){
2188: fclose(ficresilk);
2189: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2190: fflush(fichtm);
2191: }
2192: return;
2193: }
2194:
2195:
2196: /*********** Maximum Likelihood Estimation ***************/
2197:
2198: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2199: {
2200: int i,j, iter=0;
2201: double **xi;
2202: double fret;
2203: double fretone; /* Only one call to likelihood */
2204: /* char filerespow[FILENAMELENGTH];*/
2205:
2206: #ifdef NLOPT
2207: int creturn;
2208: nlopt_opt opt;
2209: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2210: double *lb;
2211: double minf; /* the minimum objective value, upon return */
2212: double * p1; /* Shifted parameters from 0 instead of 1 */
2213: myfunc_data dinst, *d = &dinst;
2214: #endif
2215:
2216:
2217: xi=matrix(1,npar,1,npar);
2218: for (i=1;i<=npar;i++)
2219: for (j=1;j<=npar;j++)
2220: xi[i][j]=(i==j ? 1.0 : 0.0);
2221: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2222: strcpy(filerespow,"pow");
2223: strcat(filerespow,fileres);
2224: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2225: printf("Problem with resultfile: %s\n", filerespow);
2226: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2227: }
2228: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2229: for (i=1;i<=nlstate;i++)
2230: for(j=1;j<=nlstate+ndeath;j++)
2231: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2232: fprintf(ficrespow,"\n");
2233: #ifdef POWELL
2234: powell(p,xi,npar,ftol,&iter,&fret,func);
2235: #endif
2236:
2237: #ifdef NLOPT
2238: #ifdef NEWUOA
2239: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2240: #else
2241: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2242: #endif
2243: lb=vector(0,npar-1);
2244: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2245: nlopt_set_lower_bounds(opt, lb);
2246: nlopt_set_initial_step1(opt, 0.1);
2247:
2248: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2249: d->function = func;
2250: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2251: nlopt_set_min_objective(opt, myfunc, d);
2252: nlopt_set_xtol_rel(opt, ftol);
2253: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2254: printf("nlopt failed! %d\n",creturn);
2255: }
2256: else {
2257: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2258: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2259: iter=1; /* not equal */
2260: }
2261: nlopt_destroy(opt);
2262: #endif
2263: free_matrix(xi,1,npar,1,npar);
2264: fclose(ficrespow);
2265: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2266: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2267: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2268:
2269: }
2270:
2271: /**** Computes Hessian and covariance matrix ***/
2272: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2273: {
2274: double **a,**y,*x,pd;
2275: double **hess;
2276: int i, j;
2277: int *indx;
2278:
2279: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2280: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2281: void lubksb(double **a, int npar, int *indx, double b[]) ;
2282: void ludcmp(double **a, int npar, int *indx, double *d) ;
2283: double gompertz(double p[]);
2284: hess=matrix(1,npar,1,npar);
2285:
2286: printf("\nCalculation of the hessian matrix. Wait...\n");
2287: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2288: for (i=1;i<=npar;i++){
2289: printf("%d",i);fflush(stdout);
2290: fprintf(ficlog,"%d",i);fflush(ficlog);
2291:
2292: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2293:
2294: /* printf(" %f ",p[i]);
2295: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2296: }
2297:
2298: for (i=1;i<=npar;i++) {
2299: for (j=1;j<=npar;j++) {
2300: if (j>i) {
2301: printf(".%d%d",i,j);fflush(stdout);
2302: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2303: hess[i][j]=hessij(p,delti,i,j,func,npar);
2304:
2305: hess[j][i]=hess[i][j];
2306: /*printf(" %lf ",hess[i][j]);*/
2307: }
2308: }
2309: }
2310: printf("\n");
2311: fprintf(ficlog,"\n");
2312:
2313: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2314: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2315:
2316: a=matrix(1,npar,1,npar);
2317: y=matrix(1,npar,1,npar);
2318: x=vector(1,npar);
2319: indx=ivector(1,npar);
2320: for (i=1;i<=npar;i++)
2321: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2322: ludcmp(a,npar,indx,&pd);
2323:
2324: for (j=1;j<=npar;j++) {
2325: for (i=1;i<=npar;i++) x[i]=0;
2326: x[j]=1;
2327: lubksb(a,npar,indx,x);
2328: for (i=1;i<=npar;i++){
2329: matcov[i][j]=x[i];
2330: }
2331: }
2332:
2333: printf("\n#Hessian matrix#\n");
2334: fprintf(ficlog,"\n#Hessian matrix#\n");
2335: for (i=1;i<=npar;i++) {
2336: for (j=1;j<=npar;j++) {
2337: printf("%.3e ",hess[i][j]);
2338: fprintf(ficlog,"%.3e ",hess[i][j]);
2339: }
2340: printf("\n");
2341: fprintf(ficlog,"\n");
2342: }
2343:
2344: /* Recompute Inverse */
2345: for (i=1;i<=npar;i++)
2346: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2347: ludcmp(a,npar,indx,&pd);
2348:
2349: /* printf("\n#Hessian matrix recomputed#\n");
2350:
2351: for (j=1;j<=npar;j++) {
2352: for (i=1;i<=npar;i++) x[i]=0;
2353: x[j]=1;
2354: lubksb(a,npar,indx,x);
2355: for (i=1;i<=npar;i++){
2356: y[i][j]=x[i];
2357: printf("%.3e ",y[i][j]);
2358: fprintf(ficlog,"%.3e ",y[i][j]);
2359: }
2360: printf("\n");
2361: fprintf(ficlog,"\n");
2362: }
2363: */
2364:
2365: free_matrix(a,1,npar,1,npar);
2366: free_matrix(y,1,npar,1,npar);
2367: free_vector(x,1,npar);
2368: free_ivector(indx,1,npar);
2369: free_matrix(hess,1,npar,1,npar);
2370:
2371:
2372: }
2373:
2374: /*************** hessian matrix ****************/
2375: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2376: {
2377: int i;
2378: int l=1, lmax=20;
2379: double k1,k2;
2380: double p2[MAXPARM+1]; /* identical to x */
2381: double res;
2382: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2383: double fx;
2384: int k=0,kmax=10;
2385: double l1;
2386:
2387: fx=func(x);
2388: for (i=1;i<=npar;i++) p2[i]=x[i];
2389: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2390: l1=pow(10,l);
2391: delts=delt;
2392: for(k=1 ; k <kmax; k=k+1){
2393: delt = delta*(l1*k);
2394: p2[theta]=x[theta] +delt;
2395: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2396: p2[theta]=x[theta]-delt;
2397: k2=func(p2)-fx;
2398: /*res= (k1-2.0*fx+k2)/delt/delt; */
2399: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2400:
2401: #ifdef DEBUGHESS
2402: 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);
2403: 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);
2404: #endif
2405: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2406: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2407: k=kmax;
2408: }
2409: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2410: k=kmax; l=lmax*10;
2411: }
2412: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2413: delts=delt;
2414: }
2415: }
2416: }
2417: delti[theta]=delts;
2418: return res;
2419:
2420: }
2421:
2422: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2423: {
2424: int i;
2425: int l=1, lmax=20;
2426: double k1,k2,k3,k4,res,fx;
2427: double p2[MAXPARM+1];
2428: int k;
2429:
2430: fx=func(x);
2431: for (k=1; k<=2; k++) {
2432: for (i=1;i<=npar;i++) p2[i]=x[i];
2433: p2[thetai]=x[thetai]+delti[thetai]/k;
2434: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2435: k1=func(p2)-fx;
2436:
2437: p2[thetai]=x[thetai]+delti[thetai]/k;
2438: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2439: k2=func(p2)-fx;
2440:
2441: p2[thetai]=x[thetai]-delti[thetai]/k;
2442: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2443: k3=func(p2)-fx;
2444:
2445: p2[thetai]=x[thetai]-delti[thetai]/k;
2446: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2447: k4=func(p2)-fx;
2448: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2449: #ifdef DEBUG
2450: 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);
2451: 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);
2452: #endif
2453: }
2454: return res;
2455: }
2456:
2457: /************** Inverse of matrix **************/
2458: void ludcmp(double **a, int n, int *indx, double *d)
2459: {
2460: int i,imax,j,k;
2461: double big,dum,sum,temp;
2462: double *vv;
2463:
2464: vv=vector(1,n);
2465: *d=1.0;
2466: for (i=1;i<=n;i++) {
2467: big=0.0;
2468: for (j=1;j<=n;j++)
2469: if ((temp=fabs(a[i][j])) > big) big=temp;
2470: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2471: vv[i]=1.0/big;
2472: }
2473: for (j=1;j<=n;j++) {
2474: for (i=1;i<j;i++) {
2475: sum=a[i][j];
2476: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2477: a[i][j]=sum;
2478: }
2479: big=0.0;
2480: for (i=j;i<=n;i++) {
2481: sum=a[i][j];
2482: for (k=1;k<j;k++)
2483: sum -= a[i][k]*a[k][j];
2484: a[i][j]=sum;
2485: if ( (dum=vv[i]*fabs(sum)) >= big) {
2486: big=dum;
2487: imax=i;
2488: }
2489: }
2490: if (j != imax) {
2491: for (k=1;k<=n;k++) {
2492: dum=a[imax][k];
2493: a[imax][k]=a[j][k];
2494: a[j][k]=dum;
2495: }
2496: *d = -(*d);
2497: vv[imax]=vv[j];
2498: }
2499: indx[j]=imax;
2500: if (a[j][j] == 0.0) a[j][j]=TINY;
2501: if (j != n) {
2502: dum=1.0/(a[j][j]);
2503: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2504: }
2505: }
2506: free_vector(vv,1,n); /* Doesn't work */
2507: ;
2508: }
2509:
2510: void lubksb(double **a, int n, int *indx, double b[])
2511: {
2512: int i,ii=0,ip,j;
2513: double sum;
2514:
2515: for (i=1;i<=n;i++) {
2516: ip=indx[i];
2517: sum=b[ip];
2518: b[ip]=b[i];
2519: if (ii)
2520: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2521: else if (sum) ii=i;
2522: b[i]=sum;
2523: }
2524: for (i=n;i>=1;i--) {
2525: sum=b[i];
2526: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2527: b[i]=sum/a[i][i];
2528: }
2529: }
2530:
2531: void pstamp(FILE *fichier)
2532: {
2533: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2534: }
2535:
2536: /************ Frequencies ********************/
2537: 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[])
2538: { /* Some frequencies */
2539:
2540: int i, m, jk, j1, bool, z1,j;
2541: int first;
2542: double ***freq; /* Frequencies */
2543: double *pp, **prop;
2544: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2545: char fileresp[FILENAMELENGTH];
2546:
2547: pp=vector(1,nlstate);
2548: prop=matrix(1,nlstate,iagemin,iagemax+3);
2549: strcpy(fileresp,"p");
2550: strcat(fileresp,fileres);
2551: if((ficresp=fopen(fileresp,"w"))==NULL) {
2552: printf("Problem with prevalence resultfile: %s\n", fileresp);
2553: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2554: exit(0);
2555: }
2556: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2557: j1=0;
2558:
2559: j=cptcoveff;
2560: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2561:
2562: first=1;
2563:
2564: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2565: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2566: /* j1++; */
2567: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2568: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2569: scanf("%d", i);*/
2570: for (i=-5; i<=nlstate+ndeath; i++)
2571: for (jk=-5; jk<=nlstate+ndeath; jk++)
2572: for(m=iagemin; m <= iagemax+3; m++)
2573: freq[i][jk][m]=0;
2574:
2575: for (i=1; i<=nlstate; i++)
2576: for(m=iagemin; m <= iagemax+3; m++)
2577: prop[i][m]=0;
2578:
2579: dateintsum=0;
2580: k2cpt=0;
2581: for (i=1; i<=imx; i++) {
2582: bool=1;
2583: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2584: for (z1=1; z1<=cptcoveff; z1++)
2585: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2586: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2587: bool=0;
2588: /* 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",
2589: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2590: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2591: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2592: }
2593: }
2594:
2595: if (bool==1){
2596: for(m=firstpass; m<=lastpass; m++){
2597: k2=anint[m][i]+(mint[m][i]/12.);
2598: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2599: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2600: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2601: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2602: if (m<lastpass) {
2603: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2604: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2605: }
2606:
2607: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2608: dateintsum=dateintsum+k2;
2609: k2cpt++;
2610: }
2611: /*}*/
2612: }
2613: }
2614: } /* end i */
2615:
2616: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2617: pstamp(ficresp);
2618: if (cptcovn>0) {
2619: fprintf(ficresp, "\n#********** Variable ");
2620: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2621: fprintf(ficresp, "**********\n#");
2622: fprintf(ficlog, "\n#********** Variable ");
2623: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2624: fprintf(ficlog, "**********\n#");
2625: }
2626: for(i=1; i<=nlstate;i++)
2627: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2628: fprintf(ficresp, "\n");
2629:
2630: for(i=iagemin; i <= iagemax+3; i++){
2631: if(i==iagemax+3){
2632: fprintf(ficlog,"Total");
2633: }else{
2634: if(first==1){
2635: first=0;
2636: printf("See log file for details...\n");
2637: }
2638: fprintf(ficlog,"Age %d", i);
2639: }
2640: for(jk=1; jk <=nlstate ; jk++){
2641: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2642: pp[jk] += freq[jk][m][i];
2643: }
2644: for(jk=1; jk <=nlstate ; jk++){
2645: for(m=-1, pos=0; m <=0 ; m++)
2646: pos += freq[jk][m][i];
2647: if(pp[jk]>=1.e-10){
2648: if(first==1){
2649: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2650: }
2651: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2652: }else{
2653: if(first==1)
2654: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2655: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2656: }
2657: }
2658:
2659: for(jk=1; jk <=nlstate ; jk++){
2660: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2661: pp[jk] += freq[jk][m][i];
2662: }
2663: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2664: pos += pp[jk];
2665: posprop += prop[jk][i];
2666: }
2667: for(jk=1; jk <=nlstate ; jk++){
2668: if(pos>=1.e-5){
2669: if(first==1)
2670: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2671: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2672: }else{
2673: if(first==1)
2674: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2675: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2676: }
2677: if( i <= iagemax){
2678: if(pos>=1.e-5){
2679: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2680: /*probs[i][jk][j1]= pp[jk]/pos;*/
2681: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2682: }
2683: else
2684: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2685: }
2686: }
2687:
2688: for(jk=-1; jk <=nlstate+ndeath; jk++)
2689: for(m=-1; m <=nlstate+ndeath; m++)
2690: if(freq[jk][m][i] !=0 ) {
2691: if(first==1)
2692: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2693: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2694: }
2695: if(i <= iagemax)
2696: fprintf(ficresp,"\n");
2697: if(first==1)
2698: printf("Others in log...\n");
2699: fprintf(ficlog,"\n");
2700: }
2701: /*}*/
2702: }
2703: dateintmean=dateintsum/k2cpt;
2704:
2705: fclose(ficresp);
2706: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2707: free_vector(pp,1,nlstate);
2708: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2709: /* End of Freq */
2710: }
2711:
2712: /************ Prevalence ********************/
2713: 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)
2714: {
2715: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2716: in each health status at the date of interview (if between dateprev1 and dateprev2).
2717: We still use firstpass and lastpass as another selection.
2718: */
2719:
2720: int i, m, jk, j1, bool, z1,j;
2721:
2722: double **prop;
2723: double posprop;
2724: double y2; /* in fractional years */
2725: int iagemin, iagemax;
2726: int first; /** to stop verbosity which is redirected to log file */
2727:
2728: iagemin= (int) agemin;
2729: iagemax= (int) agemax;
2730: /*pp=vector(1,nlstate);*/
2731: prop=matrix(1,nlstate,iagemin,iagemax+3);
2732: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2733: j1=0;
2734:
2735: /*j=cptcoveff;*/
2736: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2737:
2738: first=1;
2739: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2740: /*for(i1=1; i1<=ncodemax[k1];i1++){
2741: j1++;*/
2742:
2743: for (i=1; i<=nlstate; i++)
2744: for(m=iagemin; m <= iagemax+3; m++)
2745: prop[i][m]=0.0;
2746:
2747: for (i=1; i<=imx; i++) { /* Each individual */
2748: bool=1;
2749: if (cptcovn>0) {
2750: for (z1=1; z1<=cptcoveff; z1++)
2751: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2752: bool=0;
2753: }
2754: if (bool==1) {
2755: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2756: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2757: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2758: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2759: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2760: 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);
2761: if (s[m][i]>0 && s[m][i]<=nlstate) {
2762: /*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]]);*/
2763: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2764: prop[s[m][i]][iagemax+3] += weight[i];
2765: }
2766: }
2767: } /* end selection of waves */
2768: }
2769: }
2770: for(i=iagemin; i <= iagemax+3; i++){
2771: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2772: posprop += prop[jk][i];
2773: }
2774:
2775: for(jk=1; jk <=nlstate ; jk++){
2776: if( i <= iagemax){
2777: if(posprop>=1.e-5){
2778: probs[i][jk][j1]= prop[jk][i]/posprop;
2779: } else{
2780: if(first==1){
2781: first=0;
2782: 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]);
2783: }
2784: }
2785: }
2786: }/* end jk */
2787: }/* end i */
2788: /*} *//* end i1 */
2789: } /* end j1 */
2790:
2791: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2792: /*free_vector(pp,1,nlstate);*/
2793: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2794: } /* End of prevalence */
2795:
2796: /************* Waves Concatenation ***************/
2797:
2798: 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)
2799: {
2800: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2801: Death is a valid wave (if date is known).
2802: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2803: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2804: and mw[mi+1][i]. dh depends on stepm.
2805: */
2806:
2807: int i, mi, m;
2808: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2809: double sum=0., jmean=0.;*/
2810: int first;
2811: int j, k=0,jk, ju, jl;
2812: double sum=0.;
2813: first=0;
2814: jmin=100000;
2815: jmax=-1;
2816: jmean=0.;
2817: for(i=1; i<=imx; i++){
2818: mi=0;
2819: m=firstpass;
2820: while(s[m][i] <= nlstate){
2821: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2822: mw[++mi][i]=m;
2823: if(m >=lastpass)
2824: break;
2825: else
2826: m++;
2827: }/* end while */
2828: if (s[m][i] > nlstate){
2829: mi++; /* Death is another wave */
2830: /* if(mi==0) never been interviewed correctly before death */
2831: /* Only death is a correct wave */
2832: mw[mi][i]=m;
2833: }
2834:
2835: wav[i]=mi;
2836: if(mi==0){
2837: nbwarn++;
2838: if(first==0){
2839: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2840: first=1;
2841: }
2842: if(first==1){
2843: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2844: }
2845: } /* end mi==0 */
2846: } /* End individuals */
2847:
2848: for(i=1; i<=imx; i++){
2849: for(mi=1; mi<wav[i];mi++){
2850: if (stepm <=0)
2851: dh[mi][i]=1;
2852: else{
2853: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2854: if (agedc[i] < 2*AGESUP) {
2855: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2856: if(j==0) j=1; /* Survives at least one month after exam */
2857: else if(j<0){
2858: nberr++;
2859: 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]);
2860: j=1; /* Temporary Dangerous patch */
2861: 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);
2862: 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]);
2863: 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);
2864: }
2865: k=k+1;
2866: if (j >= jmax){
2867: jmax=j;
2868: ijmax=i;
2869: }
2870: if (j <= jmin){
2871: jmin=j;
2872: ijmin=i;
2873: }
2874: sum=sum+j;
2875: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2876: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2877: }
2878: }
2879: else{
2880: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2881: /* 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]); */
2882:
2883: k=k+1;
2884: if (j >= jmax) {
2885: jmax=j;
2886: ijmax=i;
2887: }
2888: else if (j <= jmin){
2889: jmin=j;
2890: ijmin=i;
2891: }
2892: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2893: /*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]);*/
2894: if(j<0){
2895: nberr++;
2896: 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]);
2897: 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]);
2898: }
2899: sum=sum+j;
2900: }
2901: jk= j/stepm;
2902: jl= j -jk*stepm;
2903: ju= j -(jk+1)*stepm;
2904: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2905: if(jl==0){
2906: dh[mi][i]=jk;
2907: bh[mi][i]=0;
2908: }else{ /* We want a negative bias in order to only have interpolation ie
2909: * to avoid the price of an extra matrix product in likelihood */
2910: dh[mi][i]=jk+1;
2911: bh[mi][i]=ju;
2912: }
2913: }else{
2914: if(jl <= -ju){
2915: dh[mi][i]=jk;
2916: bh[mi][i]=jl; /* bias is positive if real duration
2917: * is higher than the multiple of stepm and negative otherwise.
2918: */
2919: }
2920: else{
2921: dh[mi][i]=jk+1;
2922: bh[mi][i]=ju;
2923: }
2924: if(dh[mi][i]==0){
2925: dh[mi][i]=1; /* At least one step */
2926: bh[mi][i]=ju; /* At least one step */
2927: /* 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);*/
2928: }
2929: } /* end if mle */
2930: }
2931: } /* end wave */
2932: }
2933: jmean=sum/k;
2934: 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);
2935: 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);
2936: }
2937:
2938: /*********** Tricode ****************************/
2939: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2940: {
2941: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2942: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2943: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2944: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2945: * nbcode[Tvar[j]][1]=
2946: */
2947:
2948: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2949: int modmaxcovj=0; /* Modality max of covariates j */
2950: int cptcode=0; /* Modality max of covariates j */
2951: int modmincovj=0; /* Modality min of covariates j */
2952:
2953:
2954: cptcoveff=0;
2955:
2956: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2957: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2958:
2959: /* Loop on covariates without age and products */
2960: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2961: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2962: modality of this covariate Vj*/
2963: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2964: * If product of Vn*Vm, still boolean *:
2965: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2966: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2967: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2968: modality of the nth covariate of individual i. */
2969: if (ij > modmaxcovj)
2970: modmaxcovj=ij;
2971: else if (ij < modmincovj)
2972: modmincovj=ij;
2973: if ((ij < -1) && (ij > NCOVMAX)){
2974: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2975: exit(1);
2976: }else
2977: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2978: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2979: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2980: /* getting the maximum value of the modality of the covariate
2981: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2982: female is 1, then modmaxcovj=1.*/
2983: }
2984: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2985: cptcode=modmaxcovj;
2986: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2987: /*for (i=0; i<=cptcode; i++) {*/
2988: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2989: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2990: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2991: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2992: }
2993: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2994: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2995: } /* Ndum[-1] number of undefined modalities */
2996:
2997: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2998: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2999: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3000: modmincovj=3; modmaxcovj = 7;
3001: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3002: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3003: variables V1_1 and V1_2.
3004: nbcode[Tvar[j]][ij]=k;
3005: nbcode[Tvar[j]][1]=0;
3006: nbcode[Tvar[j]][2]=1;
3007: nbcode[Tvar[j]][3]=2;
3008: */
3009: ij=1; /* ij is similar to i but can jumps over null modalities */
3010: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3011: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3012: /*recode from 0 */
3013: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3014: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3015: k is a modality. If we have model=V1+V1*sex
3016: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3017: ij++;
3018: }
3019: if (ij > ncodemax[j]) break;
3020: } /* end of loop on */
3021: } /* end of loop on modality */
3022: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3023:
3024: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3025:
3026: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3027: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3028: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3029: Ndum[ij]++;
3030: }
3031:
3032: ij=1;
3033: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3034: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3035: if((Ndum[i]!=0) && (i<=ncovcol)){
3036: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3037: Tvaraff[ij]=i; /*For printing (unclear) */
3038: ij++;
3039: }else
3040: Tvaraff[ij]=0;
3041: }
3042: ij--;
3043: cptcoveff=ij; /*Number of total covariates*/
3044:
3045: }
3046:
3047:
3048: /*********** Health Expectancies ****************/
3049:
3050: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3051:
3052: {
3053: /* Health expectancies, no variances */
3054: int i, j, nhstepm, hstepm, h, nstepm;
3055: int nhstepma, nstepma; /* Decreasing with age */
3056: double age, agelim, hf;
3057: double ***p3mat;
3058: double eip;
3059:
3060: pstamp(ficreseij);
3061: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3062: fprintf(ficreseij,"# Age");
3063: for(i=1; i<=nlstate;i++){
3064: for(j=1; j<=nlstate;j++){
3065: fprintf(ficreseij," e%1d%1d ",i,j);
3066: }
3067: fprintf(ficreseij," e%1d. ",i);
3068: }
3069: fprintf(ficreseij,"\n");
3070:
3071:
3072: if(estepm < stepm){
3073: printf ("Problem %d lower than %d\n",estepm, stepm);
3074: }
3075: else hstepm=estepm;
3076: /* We compute the life expectancy from trapezoids spaced every estepm months
3077: * This is mainly to measure the difference between two models: for example
3078: * if stepm=24 months pijx are given only every 2 years and by summing them
3079: * we are calculating an estimate of the Life Expectancy assuming a linear
3080: * progression in between and thus overestimating or underestimating according
3081: * to the curvature of the survival function. If, for the same date, we
3082: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3083: * to compare the new estimate of Life expectancy with the same linear
3084: * hypothesis. A more precise result, taking into account a more precise
3085: * curvature will be obtained if estepm is as small as stepm. */
3086:
3087: /* For example we decided to compute the life expectancy with the smallest unit */
3088: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3089: nhstepm is the number of hstepm from age to agelim
3090: nstepm is the number of stepm from age to agelin.
3091: Look at hpijx to understand the reason of that which relies in memory size
3092: and note for a fixed period like estepm months */
3093: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3094: survival function given by stepm (the optimization length). Unfortunately it
3095: means that if the survival funtion is printed only each two years of age and if
3096: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3097: results. So we changed our mind and took the option of the best precision.
3098: */
3099: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3100:
3101: agelim=AGESUP;
3102: /* If stepm=6 months */
3103: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3104: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3105:
3106: /* nhstepm age range expressed in number of stepm */
3107: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3108: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3109: /* if (stepm >= YEARM) hstepm=1;*/
3110: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3111: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3112:
3113: for (age=bage; age<=fage; age ++){
3114: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3115: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3116: /* if (stepm >= YEARM) hstepm=1;*/
3117: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3118:
3119: /* If stepm=6 months */
3120: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3121: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3122:
3123: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3124:
3125: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3126:
3127: printf("%d|",(int)age);fflush(stdout);
3128: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3129:
3130: /* Computing expectancies */
3131: for(i=1; i<=nlstate;i++)
3132: for(j=1; j<=nlstate;j++)
3133: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3134: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3135:
3136: /* 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]);*/
3137:
3138: }
3139:
3140: fprintf(ficreseij,"%3.0f",age );
3141: for(i=1; i<=nlstate;i++){
3142: eip=0;
3143: for(j=1; j<=nlstate;j++){
3144: eip +=eij[i][j][(int)age];
3145: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3146: }
3147: fprintf(ficreseij,"%9.4f", eip );
3148: }
3149: fprintf(ficreseij,"\n");
3150:
3151: }
3152: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3153: printf("\n");
3154: fprintf(ficlog,"\n");
3155:
3156: }
3157:
3158: 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[] )
3159:
3160: {
3161: /* Covariances of health expectancies eij and of total life expectancies according
3162: to initial status i, ei. .
3163: */
3164: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3165: int nhstepma, nstepma; /* Decreasing with age */
3166: double age, agelim, hf;
3167: double ***p3matp, ***p3matm, ***varhe;
3168: double **dnewm,**doldm;
3169: double *xp, *xm;
3170: double **gp, **gm;
3171: double ***gradg, ***trgradg;
3172: int theta;
3173:
3174: double eip, vip;
3175:
3176: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3177: xp=vector(1,npar);
3178: xm=vector(1,npar);
3179: dnewm=matrix(1,nlstate*nlstate,1,npar);
3180: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3181:
3182: pstamp(ficresstdeij);
3183: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3184: fprintf(ficresstdeij,"# Age");
3185: for(i=1; i<=nlstate;i++){
3186: for(j=1; j<=nlstate;j++)
3187: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3188: fprintf(ficresstdeij," e%1d. ",i);
3189: }
3190: fprintf(ficresstdeij,"\n");
3191:
3192: pstamp(ficrescveij);
3193: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3194: fprintf(ficrescveij,"# Age");
3195: for(i=1; i<=nlstate;i++)
3196: for(j=1; j<=nlstate;j++){
3197: cptj= (j-1)*nlstate+i;
3198: for(i2=1; i2<=nlstate;i2++)
3199: for(j2=1; j2<=nlstate;j2++){
3200: cptj2= (j2-1)*nlstate+i2;
3201: if(cptj2 <= cptj)
3202: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3203: }
3204: }
3205: fprintf(ficrescveij,"\n");
3206:
3207: if(estepm < stepm){
3208: printf ("Problem %d lower than %d\n",estepm, stepm);
3209: }
3210: else hstepm=estepm;
3211: /* We compute the life expectancy from trapezoids spaced every estepm months
3212: * This is mainly to measure the difference between two models: for example
3213: * if stepm=24 months pijx are given only every 2 years and by summing them
3214: * we are calculating an estimate of the Life Expectancy assuming a linear
3215: * progression in between and thus overestimating or underestimating according
3216: * to the curvature of the survival function. If, for the same date, we
3217: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3218: * to compare the new estimate of Life expectancy with the same linear
3219: * hypothesis. A more precise result, taking into account a more precise
3220: * curvature will be obtained if estepm is as small as stepm. */
3221:
3222: /* For example we decided to compute the life expectancy with the smallest unit */
3223: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3224: nhstepm is the number of hstepm from age to agelim
3225: nstepm is the number of stepm from age to agelin.
3226: Look at hpijx to understand the reason of that which relies in memory size
3227: and note for a fixed period like estepm months */
3228: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3229: survival function given by stepm (the optimization length). Unfortunately it
3230: means that if the survival funtion is printed only each two years of age and if
3231: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3232: results. So we changed our mind and took the option of the best precision.
3233: */
3234: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3235:
3236: /* If stepm=6 months */
3237: /* nhstepm age range expressed in number of stepm */
3238: agelim=AGESUP;
3239: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3240: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3241: /* if (stepm >= YEARM) hstepm=1;*/
3242: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3243:
3244: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3245: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3246: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3247: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3248: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3249: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3250:
3251: for (age=bage; age<=fage; age ++){
3252: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3253: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3254: /* if (stepm >= YEARM) hstepm=1;*/
3255: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3256:
3257: /* If stepm=6 months */
3258: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3259: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3260:
3261: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3262:
3263: /* Computing Variances of health expectancies */
3264: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3265: decrease memory allocation */
3266: for(theta=1; theta <=npar; theta++){
3267: for(i=1; i<=npar; i++){
3268: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3269: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3270: }
3271: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3272: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3273:
3274: for(j=1; j<= nlstate; j++){
3275: for(i=1; i<=nlstate; i++){
3276: for(h=0; h<=nhstepm-1; h++){
3277: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3278: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3279: }
3280: }
3281: }
3282:
3283: for(ij=1; ij<= nlstate*nlstate; ij++)
3284: for(h=0; h<=nhstepm-1; h++){
3285: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3286: }
3287: }/* End theta */
3288:
3289:
3290: for(h=0; h<=nhstepm-1; h++)
3291: for(j=1; j<=nlstate*nlstate;j++)
3292: for(theta=1; theta <=npar; theta++)
3293: trgradg[h][j][theta]=gradg[h][theta][j];
3294:
3295:
3296: for(ij=1;ij<=nlstate*nlstate;ij++)
3297: for(ji=1;ji<=nlstate*nlstate;ji++)
3298: varhe[ij][ji][(int)age] =0.;
3299:
3300: printf("%d|",(int)age);fflush(stdout);
3301: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3302: for(h=0;h<=nhstepm-1;h++){
3303: for(k=0;k<=nhstepm-1;k++){
3304: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3305: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3306: for(ij=1;ij<=nlstate*nlstate;ij++)
3307: for(ji=1;ji<=nlstate*nlstate;ji++)
3308: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3309: }
3310: }
3311:
3312: /* Computing expectancies */
3313: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3314: for(i=1; i<=nlstate;i++)
3315: for(j=1; j<=nlstate;j++)
3316: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3317: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3318:
3319: /* 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]);*/
3320:
3321: }
3322:
3323: fprintf(ficresstdeij,"%3.0f",age );
3324: for(i=1; i<=nlstate;i++){
3325: eip=0.;
3326: vip=0.;
3327: for(j=1; j<=nlstate;j++){
3328: eip += eij[i][j][(int)age];
3329: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3330: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3331: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3332: }
3333: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3334: }
3335: fprintf(ficresstdeij,"\n");
3336:
3337: fprintf(ficrescveij,"%3.0f",age );
3338: for(i=1; i<=nlstate;i++)
3339: for(j=1; j<=nlstate;j++){
3340: cptj= (j-1)*nlstate+i;
3341: for(i2=1; i2<=nlstate;i2++)
3342: for(j2=1; j2<=nlstate;j2++){
3343: cptj2= (j2-1)*nlstate+i2;
3344: if(cptj2 <= cptj)
3345: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3346: }
3347: }
3348: fprintf(ficrescveij,"\n");
3349:
3350: }
3351: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3352: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3353: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3354: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3355: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3356: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3357: printf("\n");
3358: fprintf(ficlog,"\n");
3359:
3360: free_vector(xm,1,npar);
3361: free_vector(xp,1,npar);
3362: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3363: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3364: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3365: }
3366:
3367: /************ Variance ******************/
3368: 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[])
3369: {
3370: /* Variance of health expectancies */
3371: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3372: /* double **newm;*/
3373: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3374:
3375: int movingaverage();
3376: double **dnewm,**doldm;
3377: double **dnewmp,**doldmp;
3378: int i, j, nhstepm, hstepm, h, nstepm ;
3379: int k;
3380: double *xp;
3381: double **gp, **gm; /* for var eij */
3382: double ***gradg, ***trgradg; /*for var eij */
3383: double **gradgp, **trgradgp; /* for var p point j */
3384: double *gpp, *gmp; /* for var p point j */
3385: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3386: double ***p3mat;
3387: double age,agelim, hf;
3388: double ***mobaverage;
3389: int theta;
3390: char digit[4];
3391: char digitp[25];
3392:
3393: char fileresprobmorprev[FILENAMELENGTH];
3394:
3395: if(popbased==1){
3396: if(mobilav!=0)
3397: strcpy(digitp,"-populbased-mobilav-");
3398: else strcpy(digitp,"-populbased-nomobil-");
3399: }
3400: else
3401: strcpy(digitp,"-stablbased-");
3402:
3403: if (mobilav!=0) {
3404: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3405: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3406: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3407: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3408: }
3409: }
3410:
3411: strcpy(fileresprobmorprev,"prmorprev");
3412: sprintf(digit,"%-d",ij);
3413: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3414: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3415: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3416: strcat(fileresprobmorprev,fileres);
3417: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3418: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3419: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3420: }
3421: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3422:
3423: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3424: pstamp(ficresprobmorprev);
3425: 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);
3426: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3427: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3428: fprintf(ficresprobmorprev," p.%-d SE",j);
3429: for(i=1; i<=nlstate;i++)
3430: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3431: }
3432: fprintf(ficresprobmorprev,"\n");
3433: fprintf(ficgp,"\n# Routine varevsij");
3434: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3435: 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");
3436: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3437: /* } */
3438: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3439: pstamp(ficresvij);
3440: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3441: if(popbased==1)
3442: 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);
3443: else
3444: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3445: fprintf(ficresvij,"# Age");
3446: for(i=1; i<=nlstate;i++)
3447: for(j=1; j<=nlstate;j++)
3448: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3449: fprintf(ficresvij,"\n");
3450:
3451: xp=vector(1,npar);
3452: dnewm=matrix(1,nlstate,1,npar);
3453: doldm=matrix(1,nlstate,1,nlstate);
3454: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3455: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3456:
3457: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3458: gpp=vector(nlstate+1,nlstate+ndeath);
3459: gmp=vector(nlstate+1,nlstate+ndeath);
3460: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3461:
3462: if(estepm < stepm){
3463: printf ("Problem %d lower than %d\n",estepm, stepm);
3464: }
3465: else hstepm=estepm;
3466: /* For example we decided to compute the life expectancy with the smallest unit */
3467: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3468: nhstepm is the number of hstepm from age to agelim
3469: nstepm is the number of stepm from age to agelin.
3470: Look at function hpijx to understand why (it is linked to memory size questions) */
3471: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3472: survival function given by stepm (the optimization length). Unfortunately it
3473: means that if the survival funtion is printed every two years of age and if
3474: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3475: results. So we changed our mind and took the option of the best precision.
3476: */
3477: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3478: agelim = AGESUP;
3479: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3480: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3481: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3482: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3483: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3484: gp=matrix(0,nhstepm,1,nlstate);
3485: gm=matrix(0,nhstepm,1,nlstate);
3486:
3487:
3488: for(theta=1; theta <=npar; theta++){
3489: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3490: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3491: }
3492: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3493: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3494:
3495: if (popbased==1) {
3496: if(mobilav ==0){
3497: for(i=1; i<=nlstate;i++)
3498: prlim[i][i]=probs[(int)age][i][ij];
3499: }else{ /* mobilav */
3500: for(i=1; i<=nlstate;i++)
3501: prlim[i][i]=mobaverage[(int)age][i][ij];
3502: }
3503: }
3504:
3505: for(j=1; j<= nlstate; j++){
3506: for(h=0; h<=nhstepm; h++){
3507: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3508: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3509: }
3510: }
3511: /* This for computing probability of death (h=1 means
3512: computed over hstepm matrices product = hstepm*stepm months)
3513: as a weighted average of prlim.
3514: */
3515: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3516: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3517: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3518: }
3519: /* end probability of death */
3520:
3521: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3522: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3523: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3524: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3525:
3526: if (popbased==1) {
3527: if(mobilav ==0){
3528: for(i=1; i<=nlstate;i++)
3529: prlim[i][i]=probs[(int)age][i][ij];
3530: }else{ /* mobilav */
3531: for(i=1; i<=nlstate;i++)
3532: prlim[i][i]=mobaverage[(int)age][i][ij];
3533: }
3534: }
3535:
3536: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3537: for(h=0; h<=nhstepm; h++){
3538: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3539: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3540: }
3541: }
3542: /* This for computing probability of death (h=1 means
3543: computed over hstepm matrices product = hstepm*stepm months)
3544: as a weighted average of prlim.
3545: */
3546: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3547: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3548: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3549: }
3550: /* end probability of death */
3551:
3552: for(j=1; j<= nlstate; j++) /* vareij */
3553: for(h=0; h<=nhstepm; h++){
3554: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3555: }
3556:
3557: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3558: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3559: }
3560:
3561: } /* End theta */
3562:
3563: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3564:
3565: for(h=0; h<=nhstepm; h++) /* veij */
3566: for(j=1; j<=nlstate;j++)
3567: for(theta=1; theta <=npar; theta++)
3568: trgradg[h][j][theta]=gradg[h][theta][j];
3569:
3570: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3571: for(theta=1; theta <=npar; theta++)
3572: trgradgp[j][theta]=gradgp[theta][j];
3573:
3574:
3575: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3576: for(i=1;i<=nlstate;i++)
3577: for(j=1;j<=nlstate;j++)
3578: vareij[i][j][(int)age] =0.;
3579:
3580: for(h=0;h<=nhstepm;h++){
3581: for(k=0;k<=nhstepm;k++){
3582: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3583: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3584: for(i=1;i<=nlstate;i++)
3585: for(j=1;j<=nlstate;j++)
3586: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3587: }
3588: }
3589:
3590: /* pptj */
3591: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3592: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3593: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3594: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3595: varppt[j][i]=doldmp[j][i];
3596: /* end ppptj */
3597: /* x centered again */
3598: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3599: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3600:
3601: if (popbased==1) {
3602: if(mobilav ==0){
3603: for(i=1; i<=nlstate;i++)
3604: prlim[i][i]=probs[(int)age][i][ij];
3605: }else{ /* mobilav */
3606: for(i=1; i<=nlstate;i++)
3607: prlim[i][i]=mobaverage[(int)age][i][ij];
3608: }
3609: }
3610:
3611: /* This for computing probability of death (h=1 means
3612: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3613: as a weighted average of prlim.
3614: */
3615: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3616: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3617: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3618: }
3619: /* end probability of death */
3620:
3621: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3622: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3623: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3624: for(i=1; i<=nlstate;i++){
3625: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3626: }
3627: }
3628: fprintf(ficresprobmorprev,"\n");
3629:
3630: fprintf(ficresvij,"%.0f ",age );
3631: for(i=1; i<=nlstate;i++)
3632: for(j=1; j<=nlstate;j++){
3633: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3634: }
3635: fprintf(ficresvij,"\n");
3636: free_matrix(gp,0,nhstepm,1,nlstate);
3637: free_matrix(gm,0,nhstepm,1,nlstate);
3638: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3639: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3640: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3641: } /* End age */
3642: free_vector(gpp,nlstate+1,nlstate+ndeath);
3643: free_vector(gmp,nlstate+1,nlstate+ndeath);
3644: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3645: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3646: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3647: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3648: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3649: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3650: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3651: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3652: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3653: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3654: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3655: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3656: 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);
3657: /* 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);
3658: */
3659: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3660: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3661:
3662: free_vector(xp,1,npar);
3663: free_matrix(doldm,1,nlstate,1,nlstate);
3664: free_matrix(dnewm,1,nlstate,1,npar);
3665: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3666: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3667: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3668: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3669: fclose(ficresprobmorprev);
3670: fflush(ficgp);
3671: fflush(fichtm);
3672: } /* end varevsij */
3673:
3674: /************ Variance of prevlim ******************/
3675: 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[])
3676: {
3677: /* Variance of prevalence limit */
3678: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3679:
3680: double **dnewm,**doldm;
3681: int i, j, nhstepm, hstepm;
3682: double *xp;
3683: double *gp, *gm;
3684: double **gradg, **trgradg;
3685: double age,agelim;
3686: int theta;
3687:
3688: pstamp(ficresvpl);
3689: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3690: fprintf(ficresvpl,"# Age");
3691: for(i=1; i<=nlstate;i++)
3692: fprintf(ficresvpl," %1d-%1d",i,i);
3693: fprintf(ficresvpl,"\n");
3694:
3695: xp=vector(1,npar);
3696: dnewm=matrix(1,nlstate,1,npar);
3697: doldm=matrix(1,nlstate,1,nlstate);
3698:
3699: hstepm=1*YEARM; /* Every year of age */
3700: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3701: agelim = AGESUP;
3702: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3703: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3704: if (stepm >= YEARM) hstepm=1;
3705: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3706: gradg=matrix(1,npar,1,nlstate);
3707: gp=vector(1,nlstate);
3708: gm=vector(1,nlstate);
3709:
3710: for(theta=1; theta <=npar; theta++){
3711: for(i=1; i<=npar; i++){ /* Computes gradient */
3712: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3713: }
3714: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3715: for(i=1;i<=nlstate;i++)
3716: gp[i] = prlim[i][i];
3717:
3718: for(i=1; i<=npar; i++) /* Computes gradient */
3719: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3720: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3721: for(i=1;i<=nlstate;i++)
3722: gm[i] = prlim[i][i];
3723:
3724: for(i=1;i<=nlstate;i++)
3725: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3726: } /* End theta */
3727:
3728: trgradg =matrix(1,nlstate,1,npar);
3729:
3730: for(j=1; j<=nlstate;j++)
3731: for(theta=1; theta <=npar; theta++)
3732: trgradg[j][theta]=gradg[theta][j];
3733:
3734: for(i=1;i<=nlstate;i++)
3735: varpl[i][(int)age] =0.;
3736: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3737: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3738: for(i=1;i<=nlstate;i++)
3739: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3740:
3741: fprintf(ficresvpl,"%.0f ",age );
3742: for(i=1; i<=nlstate;i++)
3743: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3744: fprintf(ficresvpl,"\n");
3745: free_vector(gp,1,nlstate);
3746: free_vector(gm,1,nlstate);
3747: free_matrix(gradg,1,npar,1,nlstate);
3748: free_matrix(trgradg,1,nlstate,1,npar);
3749: } /* End age */
3750:
3751: free_vector(xp,1,npar);
3752: free_matrix(doldm,1,nlstate,1,npar);
3753: free_matrix(dnewm,1,nlstate,1,nlstate);
3754:
3755: }
3756:
3757: /************ Variance of one-step probabilities ******************/
3758: 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[])
3759: {
3760: int i, j=0, k1, l1, tj;
3761: int k2, l2, j1, z1;
3762: int k=0, l;
3763: int first=1, first1, first2;
3764: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3765: double **dnewm,**doldm;
3766: double *xp;
3767: double *gp, *gm;
3768: double **gradg, **trgradg;
3769: double **mu;
3770: double age, cov[NCOVMAX+1];
3771: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3772: int theta;
3773: char fileresprob[FILENAMELENGTH];
3774: char fileresprobcov[FILENAMELENGTH];
3775: char fileresprobcor[FILENAMELENGTH];
3776: double ***varpij;
3777:
3778: strcpy(fileresprob,"prob");
3779: strcat(fileresprob,fileres);
3780: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3781: printf("Problem with resultfile: %s\n", fileresprob);
3782: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3783: }
3784: strcpy(fileresprobcov,"probcov");
3785: strcat(fileresprobcov,fileres);
3786: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3787: printf("Problem with resultfile: %s\n", fileresprobcov);
3788: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3789: }
3790: strcpy(fileresprobcor,"probcor");
3791: strcat(fileresprobcor,fileres);
3792: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3793: printf("Problem with resultfile: %s\n", fileresprobcor);
3794: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3795: }
3796: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3797: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3798: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3799: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3800: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3801: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3802: pstamp(ficresprob);
3803: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3804: fprintf(ficresprob,"# Age");
3805: pstamp(ficresprobcov);
3806: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3807: fprintf(ficresprobcov,"# Age");
3808: pstamp(ficresprobcor);
3809: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3810: fprintf(ficresprobcor,"# Age");
3811:
3812:
3813: for(i=1; i<=nlstate;i++)
3814: for(j=1; j<=(nlstate+ndeath);j++){
3815: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3816: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3817: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3818: }
3819: /* fprintf(ficresprob,"\n");
3820: fprintf(ficresprobcov,"\n");
3821: fprintf(ficresprobcor,"\n");
3822: */
3823: xp=vector(1,npar);
3824: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3825: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3826: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3827: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3828: first=1;
3829: fprintf(ficgp,"\n# Routine varprob");
3830: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3831: fprintf(fichtm,"\n");
3832:
3833: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3834: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3835: file %s<br>\n",optionfilehtmcov);
3836: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3837: and drawn. It helps understanding how is the covariance between two incidences.\
3838: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3839: 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. \
3840: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3841: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3842: standard deviations wide on each axis. <br>\
3843: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3844: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3845: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3846:
3847: cov[1]=1;
3848: /* tj=cptcoveff; */
3849: tj = (int) pow(2,cptcoveff);
3850: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3851: j1=0;
3852: for(j1=1; j1<=tj;j1++){
3853: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3854: /*j1++;*/
3855: if (cptcovn>0) {
3856: fprintf(ficresprob, "\n#********** Variable ");
3857: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3858: fprintf(ficresprob, "**********\n#\n");
3859: fprintf(ficresprobcov, "\n#********** Variable ");
3860: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3861: fprintf(ficresprobcov, "**********\n#\n");
3862:
3863: fprintf(ficgp, "\n#********** Variable ");
3864: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3865: fprintf(ficgp, "**********\n#\n");
3866:
3867:
3868: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3869: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3870: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3871:
3872: fprintf(ficresprobcor, "\n#********** Variable ");
3873: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3874: fprintf(ficresprobcor, "**********\n#");
3875: }
3876:
3877: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3878: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3879: gp=vector(1,(nlstate)*(nlstate+ndeath));
3880: gm=vector(1,(nlstate)*(nlstate+ndeath));
3881: for (age=bage; age<=fage; age ++){
3882: cov[2]=age;
3883: for (k=1; k<=cptcovn;k++) {
3884: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3885: * 1 1 1 1 1
3886: * 2 2 1 1 1
3887: * 3 1 2 1 1
3888: */
3889: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3890: }
3891: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3892: for (k=1; k<=cptcovprod;k++)
3893: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3894:
3895:
3896: for(theta=1; theta <=npar; theta++){
3897: for(i=1; i<=npar; i++)
3898: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3899:
3900: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3901:
3902: k=0;
3903: for(i=1; i<= (nlstate); i++){
3904: for(j=1; j<=(nlstate+ndeath);j++){
3905: k=k+1;
3906: gp[k]=pmmij[i][j];
3907: }
3908: }
3909:
3910: for(i=1; i<=npar; i++)
3911: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3912:
3913: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3914: k=0;
3915: for(i=1; i<=(nlstate); i++){
3916: for(j=1; j<=(nlstate+ndeath);j++){
3917: k=k+1;
3918: gm[k]=pmmij[i][j];
3919: }
3920: }
3921:
3922: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3923: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3924: }
3925:
3926: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3927: for(theta=1; theta <=npar; theta++)
3928: trgradg[j][theta]=gradg[theta][j];
3929:
3930: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3931: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3932:
3933: pmij(pmmij,cov,ncovmodel,x,nlstate);
3934:
3935: k=0;
3936: for(i=1; i<=(nlstate); i++){
3937: for(j=1; j<=(nlstate+ndeath);j++){
3938: k=k+1;
3939: mu[k][(int) age]=pmmij[i][j];
3940: }
3941: }
3942: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3943: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3944: varpij[i][j][(int)age] = doldm[i][j];
3945:
3946: /*printf("\n%d ",(int)age);
3947: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3948: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3949: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3950: }*/
3951:
3952: fprintf(ficresprob,"\n%d ",(int)age);
3953: fprintf(ficresprobcov,"\n%d ",(int)age);
3954: fprintf(ficresprobcor,"\n%d ",(int)age);
3955:
3956: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3957: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3958: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3959: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3960: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3961: }
3962: i=0;
3963: for (k=1; k<=(nlstate);k++){
3964: for (l=1; l<=(nlstate+ndeath);l++){
3965: i++;
3966: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3967: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3968: for (j=1; j<=i;j++){
3969: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3970: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3971: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3972: }
3973: }
3974: }/* end of loop for state */
3975: } /* end of loop for age */
3976: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3977: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3978: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3979: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3980:
3981: /* Confidence intervalle of pij */
3982: /*
3983: fprintf(ficgp,"\nunset parametric;unset label");
3984: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3985: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3986: 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);
3987: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3988: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3989: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3990: */
3991:
3992: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3993: first1=1;first2=2;
3994: for (k2=1; k2<=(nlstate);k2++){
3995: for (l2=1; l2<=(nlstate+ndeath);l2++){
3996: if(l2==k2) continue;
3997: j=(k2-1)*(nlstate+ndeath)+l2;
3998: for (k1=1; k1<=(nlstate);k1++){
3999: for (l1=1; l1<=(nlstate+ndeath);l1++){
4000: if(l1==k1) continue;
4001: i=(k1-1)*(nlstate+ndeath)+l1;
4002: if(i<=j) continue;
4003: for (age=bage; age<=fage; age ++){
4004: if ((int)age %5==0){
4005: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4006: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4007: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4008: mu1=mu[i][(int) age]/stepm*YEARM ;
4009: mu2=mu[j][(int) age]/stepm*YEARM;
4010: c12=cv12/sqrt(v1*v2);
4011: /* Computing eigen value of matrix of covariance */
4012: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4013: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4014: if ((lc2 <0) || (lc1 <0) ){
4015: if(first2==1){
4016: first1=0;
4017: 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);
4018: }
4019: 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);
4020: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4021: /* lc2=fabs(lc2); */
4022: }
4023:
4024: /* Eigen vectors */
4025: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4026: /*v21=sqrt(1.-v11*v11); *//* error */
4027: v21=(lc1-v1)/cv12*v11;
4028: v12=-v21;
4029: v22=v11;
4030: tnalp=v21/v11;
4031: if(first1==1){
4032: first1=0;
4033: 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);
4034: }
4035: 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);
4036: /*printf(fignu*/
4037: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4038: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4039: if(first==1){
4040: first=0;
4041: fprintf(ficgp,"\nset parametric;unset label");
4042: 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);
4043: fprintf(ficgp,"\nset ter png small size 320, 240");
4044: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4045: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4046: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4047: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4048: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4049: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4050: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4051: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4052: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4053: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4054: 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",\
4055: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4056: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4057: }else{
4058: first=0;
4059: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4060: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4061: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4062: 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",\
4063: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4064: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4065: }/* if first */
4066: } /* age mod 5 */
4067: } /* end loop age */
4068: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4069: first=1;
4070: } /*l12 */
4071: } /* k12 */
4072: } /*l1 */
4073: }/* k1 */
4074: /* } */ /* loop covariates */
4075: }
4076: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4077: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4078: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4079: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4080: free_vector(xp,1,npar);
4081: fclose(ficresprob);
4082: fclose(ficresprobcov);
4083: fclose(ficresprobcor);
4084: fflush(ficgp);
4085: fflush(fichtmcov);
4086: }
4087:
4088:
4089: /******************* Printing html file ***********/
4090: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4091: int lastpass, int stepm, int weightopt, char model[],\
4092: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4093: int popforecast, int estepm ,\
4094: double jprev1, double mprev1,double anprev1, \
4095: double jprev2, double mprev2,double anprev2){
4096: int jj1, k1, i1, cpt;
4097:
4098: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4099: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4100: </ul>");
4101: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4102: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4103: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4104: fprintf(fichtm,"\
4105: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4106: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4107: fprintf(fichtm,"\
4108: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4109: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4110: fprintf(fichtm,"\
4111: - (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): \
4112: <a href=\"%s\">%s</a> <br>\n",
4113: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4114: fprintf(fichtm,"\
4115: - Population projections by age and states: \
4116: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4117:
4118: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4119:
4120: m=pow(2,cptcoveff);
4121: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4122:
4123: jj1=0;
4124: for(k1=1; k1<=m;k1++){
4125: for(i1=1; i1<=ncodemax[k1];i1++){
4126: jj1++;
4127: if (cptcovn > 0) {
4128: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4129: for (cpt=1; cpt<=cptcoveff;cpt++)
4130: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4131: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4132: }
4133: /* Pij */
4134: 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> \
4135: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4136: /* Quasi-incidences */
4137: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4138: 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> \
4139: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4140: /* Period (stable) prevalence in each health state */
4141: for(cpt=1; cpt<=nlstate;cpt++){
4142: 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> \
4143: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4144: }
4145: for(cpt=1; cpt<=nlstate;cpt++) {
4146: 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> \
4147: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4148: }
4149: } /* end i1 */
4150: }/* End k1 */
4151: fprintf(fichtm,"</ul>");
4152:
4153:
4154: fprintf(fichtm,"\
4155: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4156: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4157:
4158: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4159: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4160: fprintf(fichtm,"\
4161: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4162: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4163:
4164: fprintf(fichtm,"\
4165: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4166: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4167: fprintf(fichtm,"\
4168: - 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): \
4169: <a href=\"%s\">%s</a> <br>\n</li>",
4170: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4171: fprintf(fichtm,"\
4172: - (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): \
4173: <a href=\"%s\">%s</a> <br>\n</li>",
4174: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4175: fprintf(fichtm,"\
4176: - 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",
4177: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4178: fprintf(fichtm,"\
4179: - 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",
4180: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4181: fprintf(fichtm,"\
4182: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4183: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4184:
4185: /* if(popforecast==1) fprintf(fichtm,"\n */
4186: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4187: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4188: /* <br>",fileres,fileres,fileres,fileres); */
4189: /* else */
4190: /* 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); */
4191: fflush(fichtm);
4192: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4193:
4194: m=pow(2,cptcoveff);
4195: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4196:
4197: jj1=0;
4198: for(k1=1; k1<=m;k1++){
4199: for(i1=1; i1<=ncodemax[k1];i1++){
4200: jj1++;
4201: if (cptcovn > 0) {
4202: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4203: for (cpt=1; cpt<=cptcoveff;cpt++)
4204: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4205: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4206: }
4207: for(cpt=1; cpt<=nlstate;cpt++) {
4208: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4209: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4210: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4211: }
4212: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4213: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4214: true period expectancies (those weighted with period prevalences are also\
4215: drawn in addition to the population based expectancies computed using\
4216: observed and cahotic prevalences: %s%d.png<br>\
4217: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4218: } /* end i1 */
4219: }/* End k1 */
4220: fprintf(fichtm,"</ul>");
4221: fflush(fichtm);
4222: }
4223:
4224: /******************* Gnuplot file **************/
4225: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4226:
4227: char dirfileres[132],optfileres[132];
4228: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4229: int ng=0;
4230: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4231: /* printf("Problem with file %s",optionfilegnuplot); */
4232: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4233: /* } */
4234:
4235: /*#ifdef windows */
4236: fprintf(ficgp,"cd \"%s\" \n",pathc);
4237: /*#endif */
4238: m=pow(2,cptcoveff);
4239:
4240: strcpy(dirfileres,optionfilefiname);
4241: strcpy(optfileres,"vpl");
4242: /* 1eme*/
4243: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4244: for (cpt=1; cpt<= nlstate ; cpt ++) {
4245: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4246: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4247: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4248: fprintf(ficgp,"set xlabel \"Age\" \n\
4249: set ylabel \"Probability\" \n\
4250: set ter png small size 320, 240\n\
4251: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4252:
4253: for (i=1; i<= nlstate ; i ++) {
4254: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4255: else fprintf(ficgp," %%*lf (%%*lf)");
4256: }
4257: 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);
4258: for (i=1; i<= nlstate ; i ++) {
4259: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4260: else fprintf(ficgp," %%*lf (%%*lf)");
4261: }
4262: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4263: for (i=1; i<= nlstate ; i ++) {
4264: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4265: else fprintf(ficgp," %%*lf (%%*lf)");
4266: }
4267: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4268: }
4269: }
4270: /*2 eme*/
4271: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4272: for (k1=1; k1<= m ; k1 ++) {
4273: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4274: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4275:
4276: for (i=1; i<= nlstate+1 ; i ++) {
4277: k=2*i;
4278: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4279: for (j=1; j<= nlstate+1 ; j ++) {
4280: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4281: else fprintf(ficgp," %%*lf (%%*lf)");
4282: }
4283: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4284: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4285: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4286: for (j=1; j<= nlstate+1 ; j ++) {
4287: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4288: else fprintf(ficgp," %%*lf (%%*lf)");
4289: }
4290: fprintf(ficgp,"\" t\"\" w l lt 0,");
4291: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4292: for (j=1; j<= nlstate+1 ; j ++) {
4293: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4294: else fprintf(ficgp," %%*lf (%%*lf)");
4295: }
4296: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4297: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4298: }
4299: }
4300:
4301: /*3eme*/
4302:
4303: for (k1=1; k1<= m ; k1 ++) {
4304: for (cpt=1; cpt<= nlstate ; cpt ++) {
4305: /* k=2+nlstate*(2*cpt-2); */
4306: k=2+(nlstate+1)*(cpt-1);
4307: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4308: fprintf(ficgp,"set ter png small size 320, 240\n\
4309: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4310: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4311: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4312: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4313: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4314: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4315: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4316:
4317: */
4318: for (i=1; i< nlstate ; i ++) {
4319: 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);
4320: /* 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);*/
4321:
4322: }
4323: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4324: }
4325: }
4326:
4327: /* CV preval stable (period) */
4328: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4329: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4330: k=3;
4331: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4332: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4333: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4334: set ter png small size 320, 240\n\
4335: unset log y\n\
4336: plot [%.f:%.f] ", ageminpar, agemaxpar);
4337: for (i=1; i<= nlstate ; i ++){
4338: if(i==1)
4339: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4340: else
4341: fprintf(ficgp,", '' ");
4342: l=(nlstate+ndeath)*(i-1)+1;
4343: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4344: for (j=1; j<= (nlstate-1) ; j ++)
4345: fprintf(ficgp,"+$%d",k+l+j);
4346: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4347: } /* nlstate */
4348: fprintf(ficgp,"\n");
4349: } /* end cpt state*/
4350: } /* end covariate */
4351:
4352: /* proba elementaires */
4353: for(i=1,jk=1; i <=nlstate; i++){
4354: for(k=1; k <=(nlstate+ndeath); k++){
4355: if (k != i) {
4356: for(j=1; j <=ncovmodel; j++){
4357: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4358: jk++;
4359: fprintf(ficgp,"\n");
4360: }
4361: }
4362: }
4363: }
4364: /*goto avoid;*/
4365: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4366: for(jk=1; jk <=m; jk++) {
4367: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4368: if (ng==2)
4369: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4370: else
4371: fprintf(ficgp,"\nset title \"Probability\"\n");
4372: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4373: i=1;
4374: for(k2=1; k2<=nlstate; k2++) {
4375: k3=i;
4376: for(k=1; k<=(nlstate+ndeath); k++) {
4377: if (k != k2){
4378: if(ng==2)
4379: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4380: else
4381: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4382: ij=1;/* To be checked else nbcode[0][0] wrong */
4383: for(j=3; j <=ncovmodel; j++) {
4384: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4385: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4386: /* ij++; */
4387: /* } */
4388: /* else */
4389: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4390: }
4391: fprintf(ficgp,")/(1");
4392:
4393: for(k1=1; k1 <=nlstate; k1++){
4394: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4395: ij=1;
4396: for(j=3; j <=ncovmodel; j++){
4397: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4398: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4399: /* ij++; */
4400: /* } */
4401: /* else */
4402: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4403: }
4404: fprintf(ficgp,")");
4405: }
4406: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4407: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4408: i=i+ncovmodel;
4409: }
4410: } /* end k */
4411: } /* end k2 */
4412: } /* end jk */
4413: } /* end ng */
4414: /* avoid: */
4415: fflush(ficgp);
4416: } /* end gnuplot */
4417:
4418:
4419: /*************** Moving average **************/
4420: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4421:
4422: int i, cpt, cptcod;
4423: int modcovmax =1;
4424: int mobilavrange, mob;
4425: double age;
4426:
4427: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4428: a covariate has 2 modalities */
4429: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4430:
4431: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4432: if(mobilav==1) mobilavrange=5; /* default */
4433: else mobilavrange=mobilav;
4434: for (age=bage; age<=fage; age++)
4435: for (i=1; i<=nlstate;i++)
4436: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4437: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4438: /* We keep the original values on the extreme ages bage, fage and for
4439: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4440: we use a 5 terms etc. until the borders are no more concerned.
4441: */
4442: for (mob=3;mob <=mobilavrange;mob=mob+2){
4443: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4444: for (i=1; i<=nlstate;i++){
4445: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4446: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4447: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4448: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4449: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4450: }
4451: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4452: }
4453: }
4454: }/* end age */
4455: }/* end mob */
4456: }else return -1;
4457: return 0;
4458: }/* End movingaverage */
4459:
4460:
4461: /************** Forecasting ******************/
4462: void 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){
4463: /* proj1, year, month, day of starting projection
4464: agemin, agemax range of age
4465: dateprev1 dateprev2 range of dates during which prevalence is computed
4466: anproj2 year of en of projection (same day and month as proj1).
4467: */
4468: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4469: double agec; /* generic age */
4470: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4471: double *popeffectif,*popcount;
4472: double ***p3mat;
4473: double ***mobaverage;
4474: char fileresf[FILENAMELENGTH];
4475:
4476: agelim=AGESUP;
4477: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4478:
4479: strcpy(fileresf,"f");
4480: strcat(fileresf,fileres);
4481: if((ficresf=fopen(fileresf,"w"))==NULL) {
4482: printf("Problem with forecast resultfile: %s\n", fileresf);
4483: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4484: }
4485: printf("Computing forecasting: result on file '%s' \n", fileresf);
4486: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4487:
4488: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4489:
4490: if (mobilav!=0) {
4491: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4492: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4493: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4494: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4495: }
4496: }
4497:
4498: stepsize=(int) (stepm+YEARM-1)/YEARM;
4499: if (stepm<=12) stepsize=1;
4500: if(estepm < stepm){
4501: printf ("Problem %d lower than %d\n",estepm, stepm);
4502: }
4503: else hstepm=estepm;
4504:
4505: hstepm=hstepm/stepm;
4506: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4507: fractional in yp1 */
4508: anprojmean=yp;
4509: yp2=modf((yp1*12),&yp);
4510: mprojmean=yp;
4511: yp1=modf((yp2*30.5),&yp);
4512: jprojmean=yp;
4513: if(jprojmean==0) jprojmean=1;
4514: if(mprojmean==0) jprojmean=1;
4515:
4516: i1=cptcoveff;
4517: if (cptcovn < 1){i1=1;}
4518:
4519: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4520:
4521: fprintf(ficresf,"#****** Routine prevforecast **\n");
4522:
4523: /* if (h==(int)(YEARM*yearp)){ */
4524: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4525: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4526: k=k+1;
4527: fprintf(ficresf,"\n#******");
4528: for(j=1;j<=cptcoveff;j++) {
4529: 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]]);
4530: }
4531: fprintf(ficresf,"******\n");
4532: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4533: for(j=1; j<=nlstate+ndeath;j++){
4534: for(i=1; i<=nlstate;i++)
4535: fprintf(ficresf," p%d%d",i,j);
4536: fprintf(ficresf," p.%d",j);
4537: }
4538: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4539: fprintf(ficresf,"\n");
4540: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4541:
4542: for (agec=fage; agec>=(ageminpar-1); agec--){
4543: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4544: nhstepm = nhstepm/hstepm;
4545: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4546: oldm=oldms;savm=savms;
4547: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4548:
4549: for (h=0; h<=nhstepm; h++){
4550: if (h*hstepm/YEARM*stepm ==yearp) {
4551: fprintf(ficresf,"\n");
4552: for(j=1;j<=cptcoveff;j++)
4553: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4554: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4555: }
4556: for(j=1; j<=nlstate+ndeath;j++) {
4557: ppij=0.;
4558: for(i=1; i<=nlstate;i++) {
4559: if (mobilav==1)
4560: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4561: else {
4562: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4563: }
4564: if (h*hstepm/YEARM*stepm== yearp) {
4565: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4566: }
4567: } /* end i */
4568: if (h*hstepm/YEARM*stepm==yearp) {
4569: fprintf(ficresf," %.3f", ppij);
4570: }
4571: }/* end j */
4572: } /* end h */
4573: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4574: } /* end agec */
4575: } /* end yearp */
4576: } /* end cptcod */
4577: } /* end cptcov */
4578:
4579: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4580:
4581: fclose(ficresf);
4582: }
4583:
4584: /************** Forecasting *****not tested NB*************/
4585: void 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){
4586:
4587: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4588: int *popage;
4589: double calagedatem, agelim, kk1, kk2;
4590: double *popeffectif,*popcount;
4591: double ***p3mat,***tabpop,***tabpopprev;
4592: double ***mobaverage;
4593: char filerespop[FILENAMELENGTH];
4594:
4595: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4596: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4597: agelim=AGESUP;
4598: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4599:
4600: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4601:
4602:
4603: strcpy(filerespop,"pop");
4604: strcat(filerespop,fileres);
4605: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4606: printf("Problem with forecast resultfile: %s\n", filerespop);
4607: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4608: }
4609: printf("Computing forecasting: result on file '%s' \n", filerespop);
4610: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4611:
4612: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4613:
4614: if (mobilav!=0) {
4615: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4616: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4617: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4618: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4619: }
4620: }
4621:
4622: stepsize=(int) (stepm+YEARM-1)/YEARM;
4623: if (stepm<=12) stepsize=1;
4624:
4625: agelim=AGESUP;
4626:
4627: hstepm=1;
4628: hstepm=hstepm/stepm;
4629:
4630: if (popforecast==1) {
4631: if((ficpop=fopen(popfile,"r"))==NULL) {
4632: printf("Problem with population file : %s\n",popfile);exit(0);
4633: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4634: }
4635: popage=ivector(0,AGESUP);
4636: popeffectif=vector(0,AGESUP);
4637: popcount=vector(0,AGESUP);
4638:
4639: i=1;
4640: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4641:
4642: imx=i;
4643: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4644: }
4645:
4646: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4647: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4648: k=k+1;
4649: fprintf(ficrespop,"\n#******");
4650: for(j=1;j<=cptcoveff;j++) {
4651: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4652: }
4653: fprintf(ficrespop,"******\n");
4654: fprintf(ficrespop,"# Age");
4655: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4656: if (popforecast==1) fprintf(ficrespop," [Population]");
4657:
4658: for (cpt=0; cpt<=0;cpt++) {
4659: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4660:
4661: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4662: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4663: nhstepm = nhstepm/hstepm;
4664:
4665: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4666: oldm=oldms;savm=savms;
4667: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4668:
4669: for (h=0; h<=nhstepm; h++){
4670: if (h==(int) (calagedatem+YEARM*cpt)) {
4671: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4672: }
4673: for(j=1; j<=nlstate+ndeath;j++) {
4674: kk1=0.;kk2=0;
4675: for(i=1; i<=nlstate;i++) {
4676: if (mobilav==1)
4677: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4678: else {
4679: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4680: }
4681: }
4682: if (h==(int)(calagedatem+12*cpt)){
4683: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4684: /*fprintf(ficrespop," %.3f", kk1);
4685: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4686: }
4687: }
4688: for(i=1; i<=nlstate;i++){
4689: kk1=0.;
4690: for(j=1; j<=nlstate;j++){
4691: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4692: }
4693: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4694: }
4695:
4696: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4697: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4698: }
4699: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4700: }
4701: }
4702:
4703: /******/
4704:
4705: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4706: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4707: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4708: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4709: nhstepm = nhstepm/hstepm;
4710:
4711: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4712: oldm=oldms;savm=savms;
4713: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4714: for (h=0; h<=nhstepm; h++){
4715: if (h==(int) (calagedatem+YEARM*cpt)) {
4716: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4717: }
4718: for(j=1; j<=nlstate+ndeath;j++) {
4719: kk1=0.;kk2=0;
4720: for(i=1; i<=nlstate;i++) {
4721: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4722: }
4723: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4724: }
4725: }
4726: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4727: }
4728: }
4729: }
4730: }
4731:
4732: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4733:
4734: if (popforecast==1) {
4735: free_ivector(popage,0,AGESUP);
4736: free_vector(popeffectif,0,AGESUP);
4737: free_vector(popcount,0,AGESUP);
4738: }
4739: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4740: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4741: fclose(ficrespop);
4742: } /* End of popforecast */
4743:
4744: int fileappend(FILE *fichier, char *optionfich)
4745: {
4746: if((fichier=fopen(optionfich,"a"))==NULL) {
4747: printf("Problem with file: %s\n", optionfich);
4748: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4749: return (0);
4750: }
4751: fflush(fichier);
4752: return (1);
4753: }
4754:
4755:
4756: /**************** function prwizard **********************/
4757: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4758: {
4759:
4760: /* Wizard to print covariance matrix template */
4761:
4762: char ca[32], cb[32];
4763: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4764: int numlinepar;
4765:
4766: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4767: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4768: for(i=1; i <=nlstate; i++){
4769: jj=0;
4770: for(j=1; j <=nlstate+ndeath; j++){
4771: if(j==i) continue;
4772: jj++;
4773: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4774: printf("%1d%1d",i,j);
4775: fprintf(ficparo,"%1d%1d",i,j);
4776: for(k=1; k<=ncovmodel;k++){
4777: /* printf(" %lf",param[i][j][k]); */
4778: /* fprintf(ficparo," %lf",param[i][j][k]); */
4779: printf(" 0.");
4780: fprintf(ficparo," 0.");
4781: }
4782: printf("\n");
4783: fprintf(ficparo,"\n");
4784: }
4785: }
4786: printf("# Scales (for hessian or gradient estimation)\n");
4787: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4788: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4789: for(i=1; i <=nlstate; i++){
4790: jj=0;
4791: for(j=1; j <=nlstate+ndeath; j++){
4792: if(j==i) continue;
4793: jj++;
4794: fprintf(ficparo,"%1d%1d",i,j);
4795: printf("%1d%1d",i,j);
4796: fflush(stdout);
4797: for(k=1; k<=ncovmodel;k++){
4798: /* printf(" %le",delti3[i][j][k]); */
4799: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4800: printf(" 0.");
4801: fprintf(ficparo," 0.");
4802: }
4803: numlinepar++;
4804: printf("\n");
4805: fprintf(ficparo,"\n");
4806: }
4807: }
4808: printf("# Covariance matrix\n");
4809: /* # 121 Var(a12)\n\ */
4810: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4811: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4812: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4813: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4814: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4815: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4816: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4817: fflush(stdout);
4818: fprintf(ficparo,"# Covariance matrix\n");
4819: /* # 121 Var(a12)\n\ */
4820: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4821: /* # ...\n\ */
4822: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4823:
4824: for(itimes=1;itimes<=2;itimes++){
4825: jj=0;
4826: for(i=1; i <=nlstate; i++){
4827: for(j=1; j <=nlstate+ndeath; j++){
4828: if(j==i) continue;
4829: for(k=1; k<=ncovmodel;k++){
4830: jj++;
4831: ca[0]= k+'a'-1;ca[1]='\0';
4832: if(itimes==1){
4833: printf("#%1d%1d%d",i,j,k);
4834: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4835: }else{
4836: printf("%1d%1d%d",i,j,k);
4837: fprintf(ficparo,"%1d%1d%d",i,j,k);
4838: /* printf(" %.5le",matcov[i][j]); */
4839: }
4840: ll=0;
4841: for(li=1;li <=nlstate; li++){
4842: for(lj=1;lj <=nlstate+ndeath; lj++){
4843: if(lj==li) continue;
4844: for(lk=1;lk<=ncovmodel;lk++){
4845: ll++;
4846: if(ll<=jj){
4847: cb[0]= lk +'a'-1;cb[1]='\0';
4848: if(ll<jj){
4849: if(itimes==1){
4850: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4851: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4852: }else{
4853: printf(" 0.");
4854: fprintf(ficparo," 0.");
4855: }
4856: }else{
4857: if(itimes==1){
4858: printf(" Var(%s%1d%1d)",ca,i,j);
4859: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4860: }else{
4861: printf(" 0.");
4862: fprintf(ficparo," 0.");
4863: }
4864: }
4865: }
4866: } /* end lk */
4867: } /* end lj */
4868: } /* end li */
4869: printf("\n");
4870: fprintf(ficparo,"\n");
4871: numlinepar++;
4872: } /* end k*/
4873: } /*end j */
4874: } /* end i */
4875: } /* end itimes */
4876:
4877: } /* end of prwizard */
4878: /******************* Gompertz Likelihood ******************************/
4879: double gompertz(double x[])
4880: {
4881: double A,B,L=0.0,sump=0.,num=0.;
4882: int i,n=0; /* n is the size of the sample */
4883:
4884: for (i=0;i<=imx-1 ; i++) {
4885: sump=sump+weight[i];
4886: /* sump=sump+1;*/
4887: num=num+1;
4888: }
4889:
4890:
4891: /* for (i=0; i<=imx; i++)
4892: 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]);*/
4893:
4894: for (i=1;i<=imx ; i++)
4895: {
4896: if (cens[i] == 1 && wav[i]>1)
4897: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4898:
4899: if (cens[i] == 0 && wav[i]>1)
4900: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4901: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4902:
4903: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4904: if (wav[i] > 1 ) { /* ??? */
4905: L=L+A*weight[i];
4906: /* 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]);*/
4907: }
4908: }
4909:
4910: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4911:
4912: return -2*L*num/sump;
4913: }
4914:
4915: #ifdef GSL
4916: /******************* Gompertz_f Likelihood ******************************/
4917: double gompertz_f(const gsl_vector *v, void *params)
4918: {
4919: double A,B,LL=0.0,sump=0.,num=0.;
4920: double *x= (double *) v->data;
4921: int i,n=0; /* n is the size of the sample */
4922:
4923: for (i=0;i<=imx-1 ; i++) {
4924: sump=sump+weight[i];
4925: /* sump=sump+1;*/
4926: num=num+1;
4927: }
4928:
4929:
4930: /* for (i=0; i<=imx; i++)
4931: 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]);*/
4932: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4933: for (i=1;i<=imx ; i++)
4934: {
4935: if (cens[i] == 1 && wav[i]>1)
4936: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4937:
4938: if (cens[i] == 0 && wav[i]>1)
4939: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4940: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4941:
4942: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4943: if (wav[i] > 1 ) { /* ??? */
4944: LL=LL+A*weight[i];
4945: /* 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]);*/
4946: }
4947: }
4948:
4949: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4950: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4951:
4952: return -2*LL*num/sump;
4953: }
4954: #endif
4955:
4956: /******************* Printing html file ***********/
4957: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4958: int lastpass, int stepm, int weightopt, char model[],\
4959: int imx, double p[],double **matcov,double agemortsup){
4960: int i,k;
4961:
4962: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4963: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4964: for (i=1;i<=2;i++)
4965: 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]));
4966: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4967: fprintf(fichtm,"</ul>");
4968:
4969: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4970:
4971: 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>");
4972:
4973: for (k=agegomp;k<(agemortsup-2);k++)
4974: 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]);
4975:
4976:
4977: fflush(fichtm);
4978: }
4979:
4980: /******************* Gnuplot file **************/
4981: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4982:
4983: char dirfileres[132],optfileres[132];
4984:
4985: int ng;
4986:
4987:
4988: /*#ifdef windows */
4989: fprintf(ficgp,"cd \"%s\" \n",pathc);
4990: /*#endif */
4991:
4992:
4993: strcpy(dirfileres,optionfilefiname);
4994: strcpy(optfileres,"vpl");
4995: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4996: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4997: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4998: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4999: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5000:
5001: }
5002:
5003: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5004: {
5005:
5006: /*-------- data file ----------*/
5007: FILE *fic;
5008: char dummy[]=" ";
5009: int i=0, j=0, n=0;
5010: int linei, month, year,iout;
5011: char line[MAXLINE], linetmp[MAXLINE];
5012: char stra[MAXLINE], strb[MAXLINE];
5013: char *stratrunc;
5014: int lstra;
5015:
5016:
5017: if((fic=fopen(datafile,"r"))==NULL) {
5018: printf("Problem while opening datafile: %s\n", datafile);return 1;
5019: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5020: }
5021:
5022: i=1;
5023: linei=0;
5024: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5025: linei=linei+1;
5026: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5027: if(line[j] == '\t')
5028: line[j] = ' ';
5029: }
5030: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5031: ;
5032: };
5033: line[j+1]=0; /* Trims blanks at end of line */
5034: if(line[0]=='#'){
5035: fprintf(ficlog,"Comment line\n%s\n",line);
5036: printf("Comment line\n%s\n",line);
5037: continue;
5038: }
5039: trimbb(linetmp,line); /* Trims multiple blanks in line */
5040: strcpy(line, linetmp);
5041:
5042:
5043: for (j=maxwav;j>=1;j--){
5044: cutv(stra, strb, line, ' ');
5045: if(strb[0]=='.') { /* Missing status */
5046: lval=-1;
5047: }else{
5048: errno=0;
5049: lval=strtol(strb,&endptr,10);
5050: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5051: if( strb[0]=='\0' || (*endptr != '\0')){
5052: 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);
5053: 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);
5054: return 1;
5055: }
5056: }
5057: s[j][i]=lval;
5058:
5059: strcpy(line,stra);
5060: cutv(stra, strb,line,' ');
5061: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5062: }
5063: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5064: month=99;
5065: year=9999;
5066: }else{
5067: 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);
5068: 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);
5069: return 1;
5070: }
5071: anint[j][i]= (double) year;
5072: mint[j][i]= (double)month;
5073: strcpy(line,stra);
5074: } /* ENd Waves */
5075:
5076: cutv(stra, strb,line,' ');
5077: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5078: }
5079: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5080: month=99;
5081: year=9999;
5082: }else{
5083: 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);
5084: 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);
5085: return 1;
5086: }
5087: andc[i]=(double) year;
5088: moisdc[i]=(double) month;
5089: strcpy(line,stra);
5090:
5091: cutv(stra, strb,line,' ');
5092: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5093: }
5094: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5095: month=99;
5096: year=9999;
5097: }else{
5098: 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);
5099: 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);
5100: return 1;
5101: }
5102: if (year==9999) {
5103: 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);
5104: 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);
5105: return 1;
5106:
5107: }
5108: annais[i]=(double)(year);
5109: moisnais[i]=(double)(month);
5110: strcpy(line,stra);
5111:
5112: cutv(stra, strb,line,' ');
5113: errno=0;
5114: dval=strtod(strb,&endptr);
5115: if( strb[0]=='\0' || (*endptr != '\0')){
5116: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5117: 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);
5118: fflush(ficlog);
5119: return 1;
5120: }
5121: weight[i]=dval;
5122: strcpy(line,stra);
5123:
5124: for (j=ncovcol;j>=1;j--){
5125: cutv(stra, strb,line,' ');
5126: if(strb[0]=='.') { /* Missing status */
5127: lval=-1;
5128: }else{
5129: errno=0;
5130: lval=strtol(strb,&endptr,10);
5131: if( strb[0]=='\0' || (*endptr != '\0')){
5132: 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);
5133: 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);
5134: return 1;
5135: }
5136: }
5137: if(lval <-1 || lval >1){
5138: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5139: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5140: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5141: For example, for multinomial values like 1, 2 and 3,\n \
5142: build V1=0 V2=0 for the reference value (1),\n \
5143: V1=1 V2=0 for (2) \n \
5144: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5145: output of IMaCh is often meaningless.\n \
5146: Exiting.\n",lval,linei, i,line,j);
5147: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5148: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5149: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5150: For example, for multinomial values like 1, 2 and 3,\n \
5151: build V1=0 V2=0 for the reference value (1),\n \
5152: V1=1 V2=0 for (2) \n \
5153: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5154: output of IMaCh is often meaningless.\n \
5155: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5156: return 1;
5157: }
5158: covar[j][i]=(double)(lval);
5159: strcpy(line,stra);
5160: }
5161: lstra=strlen(stra);
5162:
5163: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5164: stratrunc = &(stra[lstra-9]);
5165: num[i]=atol(stratrunc);
5166: }
5167: else
5168: num[i]=atol(stra);
5169: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5170: 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;}*/
5171:
5172: i=i+1;
5173: } /* End loop reading data */
5174:
5175: *imax=i-1; /* Number of individuals */
5176: fclose(fic);
5177:
5178: return (0);
5179: /* endread: */
5180: printf("Exiting readdata: ");
5181: fclose(fic);
5182: return (1);
5183:
5184:
5185:
5186: }
5187: void removespace(char *str) {
5188: char *p1 = str, *p2 = str;
5189: do
5190: while (*p2 == ' ')
5191: p2++;
5192: while (*p1++ == *p2++);
5193: }
5194:
5195: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5196: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5197: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5198: * - cptcovn or number of covariates k of the models excluding age*products =6
5199: * - cptcovage number of covariates with age*products =2
5200: * - cptcovs number of simple covariates
5201: * - 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
5202: * which is a new column after the 9 (ncovcol) variables.
5203: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5204: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5205: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5206: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5207: */
5208: {
5209: int i, j, k, ks;
5210: int j1, k1, k2;
5211: char modelsav[80];
5212: char stra[80], strb[80], strc[80], strd[80],stre[80];
5213:
5214: /*removespace(model);*/
5215: if (strlen(model) >1){ /* If there is at least 1 covariate */
5216: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5217: j=nbocc(model,'+'); /**< j=Number of '+' */
5218: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5219: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5220: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5221: /* including age products which are counted in cptcovage.
5222: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5223: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5224: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5225: strcpy(modelsav,model);
5226: if (strstr(model,"AGE") !=0){
5227: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5228: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5229: return 1;
5230: }
5231: if (strstr(model,"v") !=0){
5232: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5233: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5234: return 1;
5235: }
5236:
5237: /* Design
5238: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5239: * < ncovcol=8 >
5240: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5241: * k= 1 2 3 4 5 6 7 8
5242: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5243: * covar[k,i], value of kth covariate if not including age for individual i:
5244: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5245: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5246: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5247: * Tage[++cptcovage]=k
5248: * if products, new covar are created after ncovcol with k1
5249: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5250: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5251: * 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
5252: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5253: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5254: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5255: * < ncovcol=8 >
5256: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5257: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5258: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5259: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5260: * p Tprod[1]@2={ 6, 5}
5261: *p Tvard[1][1]@4= {7, 8, 5, 6}
5262: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5263: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5264: *How to reorganize?
5265: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5266: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5267: * {2, 1, 4, 8, 5, 6, 3, 7}
5268: * Struct []
5269: */
5270:
5271: /* This loop fills the array Tvar from the string 'model'.*/
5272: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5273: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5274: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5275: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5276: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5277: /* k=1 Tvar[1]=2 (from V2) */
5278: /* k=5 Tvar[5] */
5279: /* for (k=1; k<=cptcovn;k++) { */
5280: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5281: /* } */
5282: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5283: /*
5284: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5285: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5286: Tvar[k]=0;
5287: cptcovage=0;
5288: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5289: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5290: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5291: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5292: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5293: /*scanf("%d",i);*/
5294: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5295: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5296: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5297: /* covar is not filled and then is empty */
5298: cptcovprod--;
5299: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5300: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5301: cptcovage++; /* Sums the number of covariates which include age as a product */
5302: Tage[cptcovage]=k; /* Tage[1] = 4 */
5303: /*printf("stre=%s ", stre);*/
5304: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5305: cptcovprod--;
5306: cutl(stre,strb,strc,'V');
5307: Tvar[k]=atoi(stre);
5308: cptcovage++;
5309: Tage[cptcovage]=k;
5310: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5311: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5312: cptcovn++;
5313: cptcovprodnoage++;k1++;
5314: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5315: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5316: because this model-covariate is a construction we invent a new column
5317: ncovcol + k1
5318: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5319: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5320: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5321: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5322: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5323: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5324: k2=k2+2;
5325: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5326: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5327: for (i=1; i<=lastobs;i++){
5328: /* Computes the new covariate which is a product of
5329: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5330: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5331: }
5332: } /* End age is not in the model */
5333: } /* End if model includes a product */
5334: else { /* no more sum */
5335: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5336: /* scanf("%d",i);*/
5337: cutl(strd,strc,strb,'V');
5338: ks++; /**< Number of simple covariates */
5339: cptcovn++;
5340: Tvar[k]=atoi(strd);
5341: }
5342: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5343: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5344: scanf("%d",i);*/
5345: } /* end of loop + */
5346: } /* end model */
5347:
5348: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5349: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5350:
5351: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5352: printf("cptcovprod=%d ", cptcovprod);
5353: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5354:
5355: scanf("%d ",i);*/
5356:
5357:
5358: return (0); /* with covar[new additional covariate if product] and Tage if age */
5359: /*endread:*/
5360: printf("Exiting decodemodel: ");
5361: return (1);
5362: }
5363:
5364: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5365: {
5366: int i, m;
5367:
5368: for (i=1; i<=imx; i++) {
5369: for(m=2; (m<= maxwav); m++) {
5370: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5371: anint[m][i]=9999;
5372: s[m][i]=-1;
5373: }
5374: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5375: *nberr = *nberr + 1;
5376: 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5377: 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5378: s[m][i]=-1;
5379: }
5380: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5381: (*nberr)++;
5382: 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]);
5383: 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]);
5384: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5385: }
5386: }
5387: }
5388:
5389: for (i=1; i<=imx; i++) {
5390: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5391: for(m=firstpass; (m<= lastpass); m++){
5392: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5393: if (s[m][i] >= nlstate+1) {
5394: if(agedc[i]>0){
5395: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5396: agev[m][i]=agedc[i];
5397: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5398: }else {
5399: if ((int)andc[i]!=9999){
5400: nbwarn++;
5401: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5402: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5403: agev[m][i]=-1;
5404: }
5405: }
5406: } /* agedc > 0 */
5407: }
5408: else if(s[m][i] !=9){ /* Standard case, age in fractional
5409: years but with the precision of a month */
5410: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5411: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5412: agev[m][i]=1;
5413: else if(agev[m][i] < *agemin){
5414: *agemin=agev[m][i];
5415: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5416: }
5417: else if(agev[m][i] >*agemax){
5418: *agemax=agev[m][i];
5419: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5420: }
5421: /*agev[m][i]=anint[m][i]-annais[i];*/
5422: /* agev[m][i] = age[i]+2*m;*/
5423: }
5424: else { /* =9 */
5425: agev[m][i]=1;
5426: s[m][i]=-1;
5427: }
5428: }
5429: else /*= 0 Unknown */
5430: agev[m][i]=1;
5431: }
5432:
5433: }
5434: for (i=1; i<=imx; i++) {
5435: for(m=firstpass; (m<=lastpass); m++){
5436: if (s[m][i] > (nlstate+ndeath)) {
5437: (*nberr)++;
5438: 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);
5439: 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);
5440: return 1;
5441: }
5442: }
5443: }
5444:
5445: /*for (i=1; i<=imx; i++){
5446: for (m=firstpass; (m<lastpass); m++){
5447: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5448: }
5449:
5450: }*/
5451:
5452:
5453: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5454: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5455:
5456: return (0);
5457: /* endread:*/
5458: printf("Exiting calandcheckages: ");
5459: return (1);
5460: }
5461:
5462: #if defined(_MSC_VER)
5463: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5464: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5465: //#include "stdafx.h"
5466: //#include <stdio.h>
5467: //#include <tchar.h>
5468: //#include <windows.h>
5469: //#include <iostream>
5470: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5471:
5472: LPFN_ISWOW64PROCESS fnIsWow64Process;
5473:
5474: BOOL IsWow64()
5475: {
5476: BOOL bIsWow64 = FALSE;
5477:
5478: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5479: // (HANDLE, PBOOL);
5480:
5481: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5482:
5483: HMODULE module = GetModuleHandle(_T("kernel32"));
5484: const char funcName[] = "IsWow64Process";
5485: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5486: GetProcAddress(module, funcName);
5487:
5488: if (NULL != fnIsWow64Process)
5489: {
5490: if (!fnIsWow64Process(GetCurrentProcess(),
5491: &bIsWow64))
5492: //throw std::exception("Unknown error");
5493: printf("Unknown error\n");
5494: }
5495: return bIsWow64 != FALSE;
5496: }
5497: #endif
5498: void syscompilerinfo()
5499: {
5500: /* #include "syscompilerinfo.h"*/
5501: /* #include <gnu/libc-version.h> */ /* Only on gnu */
5502: #include <stdint.h>
5503: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5504: #if defined(__clang__)
5505: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5506: #endif
5507: #if defined(__ICC) || defined(__INTEL_COMPILER)
5508: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5509: #endif
5510: #if defined(__GNUC__) || defined(__GNUG__)
5511: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5512: #endif
5513: #if defined(__HP_cc) || defined(__HP_aCC)
5514: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5515: #endif
5516: #if defined(__IBMC__) || defined(__IBMCPP__)
5517: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5518: #endif
5519: #if defined(_MSC_VER)
5520: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5521: #endif
5522: #if defined(__PGI)
5523: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5524: #endif
5525: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5526: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5527: #endif
5528: printf(". ");fprintf(ficlog,". ");
5529:
5530: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5531: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5532: // Windows (x64 and x86)
5533: printf("Windows (x64 and x86). ");fprintf(ficlog,"Windows (x64 and x86). ");
5534: #elif __unix__ // all unices, not all compilers
5535: // Unix
5536: printf("Unix. ");fprintf(ficlog,"Unix. ");
5537: #elif __linux__
5538: // linux
5539: printf("linux. ");fprintf(ficlog,"linux. ");
5540: #elif __APPLE__
5541: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5542: printf("Mac OS. ");fprintf(ficlog,"Mac OS. ");
5543: #endif
5544:
5545: /* __MINGW32__ */
5546: /* __CYGWIN__ */
5547: /* __MINGW64__ */
5548: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5549: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5550: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5551: /* _WIN64 // Defined for applications for Win64. */
5552: /* _M_X64 // Defined for compilations that target x64 processors. */
5553: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5554:
5555: #if UINTPTR_MAX == 0xffffffff
5556: printf(" 32-bit.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
5557: #elif UINTPTR_MAX == 0xffffffffffffffff
5558: printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
5559: #else
5560: printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* wtf */
5561: #endif
5562:
5563: /* struct utsname sysInfo;
5564:
5565: if (uname(&sysInfo) != -1) {
5566: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5567: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5568: }
5569: else
5570: perror("uname() error");
5571: */
5572: #if defined(__GNUC__)
5573: # if defined(__GNUC_PATCHLEVEL__)
5574: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5575: + __GNUC_MINOR__ * 100 \
5576: + __GNUC_PATCHLEVEL__)
5577: # else
5578: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5579: + __GNUC_MINOR__ * 100)
5580: # endif
5581: printf("GNU C version %d.\n", __GNUC_VERSION__);
5582: fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
5583: #endif
5584:
5585: // void main()
5586: // {
5587: #if defined(_MSC_VER)
5588: if (IsWow64())
5589: printf("The process is running under WOW64.\n");
5590: else
5591: printf("The process is not running under WOW64.\n");
5592:
5593: // printf("\nPress Enter to continue...");
5594: // getchar();
5595: // }
5596:
5597: #endif
5598:
5599: /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
5600:
5601: }
5602:
5603: /***********************************************/
5604: /**************** Main Program *****************/
5605: /***********************************************/
5606:
5607: int main(int argc, char *argv[])
5608: {
5609: #ifdef GSL
5610: const gsl_multimin_fminimizer_type *T;
5611: size_t iteri = 0, it;
5612: int rval = GSL_CONTINUE;
5613: int status = GSL_SUCCESS;
5614: double ssval;
5615: #endif
5616: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5617: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5618:
5619: int jj, ll, li, lj, lk;
5620: int numlinepar=0; /* Current linenumber of parameter file */
5621: int itimes;
5622: int NDIM=2;
5623: int vpopbased=0;
5624:
5625: char ca[32], cb[32];
5626: /* FILE *fichtm; *//* Html File */
5627: /* FILE *ficgp;*/ /*Gnuplot File */
5628: struct stat info;
5629: double agedeb;
5630: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5631:
5632: double fret;
5633: double dum; /* Dummy variable */
5634: double ***p3mat;
5635: double ***mobaverage;
5636:
5637: char line[MAXLINE];
5638: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5639: char pathr[MAXLINE], pathimach[MAXLINE];
5640: char *tok, *val; /* pathtot */
5641: int firstobs=1, lastobs=10;
5642: int c, h , cpt;
5643: int jl;
5644: int i1, j1, jk, stepsize;
5645: int *tab;
5646: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5647: int mobilav=0,popforecast=0;
5648: int hstepm, nhstepm;
5649: int agemortsup;
5650: float sumlpop=0.;
5651: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5652: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5653:
5654: double bage=0, fage=110, age, agelim, agebase;
5655: double ftolpl=FTOL;
5656: double **prlim;
5657: double ***param; /* Matrix of parameters */
5658: double *p;
5659: double **matcov; /* Matrix of covariance */
5660: double ***delti3; /* Scale */
5661: double *delti; /* Scale */
5662: double ***eij, ***vareij;
5663: double **varpl; /* Variances of prevalence limits by age */
5664: double *epj, vepp;
5665:
5666: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5667: double **ximort;
5668: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5669: int *dcwave;
5670:
5671: char z[1]="c";
5672:
5673: /*char *strt;*/
5674: char strtend[80];
5675:
5676:
5677: /* setlocale (LC_ALL, ""); */
5678: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5679: /* textdomain (PACKAGE); */
5680: /* setlocale (LC_CTYPE, ""); */
5681: /* setlocale (LC_MESSAGES, ""); */
5682:
5683: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5684: rstart_time = time(NULL);
5685: /* (void) gettimeofday(&start_time,&tzp);*/
5686: start_time = *localtime(&rstart_time);
5687: curr_time=start_time;
5688: /*tml = *localtime(&start_time.tm_sec);*/
5689: /* strcpy(strstart,asctime(&tml)); */
5690: strcpy(strstart,asctime(&start_time));
5691:
5692: /* printf("Localtime (at start)=%s",strstart); */
5693: /* tp.tm_sec = tp.tm_sec +86400; */
5694: /* tm = *localtime(&start_time.tm_sec); */
5695: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5696: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5697: /* tmg.tm_hour=tmg.tm_hour + 1; */
5698: /* tp.tm_sec = mktime(&tmg); */
5699: /* strt=asctime(&tmg); */
5700: /* printf("Time(after) =%s",strstart); */
5701: /* (void) time (&time_value);
5702: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5703: * tm = *localtime(&time_value);
5704: * strstart=asctime(&tm);
5705: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5706: */
5707:
5708: nberr=0; /* Number of errors and warnings */
5709: nbwarn=0;
5710: getcwd(pathcd, size);
5711:
5712: printf("\n%s\n%s",version,fullversion);
5713: if(argc <=1){
5714: printf("\nEnter the parameter file name: ");
5715: fgets(pathr,FILENAMELENGTH,stdin);
5716: i=strlen(pathr);
5717: if(pathr[i-1]=='\n')
5718: pathr[i-1]='\0';
5719: i=strlen(pathr);
5720: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5721: pathr[i-1]='\0';
5722: for (tok = pathr; tok != NULL; ){
5723: printf("Pathr |%s|\n",pathr);
5724: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5725: printf("val= |%s| pathr=%s\n",val,pathr);
5726: strcpy (pathtot, val);
5727: if(pathr[0] == '\0') break; /* Dirty */
5728: }
5729: }
5730: else{
5731: strcpy(pathtot,argv[1]);
5732: }
5733: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5734: /*cygwin_split_path(pathtot,path,optionfile);
5735: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5736: /* cutv(path,optionfile,pathtot,'\\');*/
5737:
5738: /* Split argv[0], imach program to get pathimach */
5739: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5740: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5741: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5742: /* strcpy(pathimach,argv[0]); */
5743: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5744: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5745: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5746: chdir(path); /* Can be a relative path */
5747: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5748: printf("Current directory %s!\n",pathcd);
5749: strcpy(command,"mkdir ");
5750: strcat(command,optionfilefiname);
5751: if((outcmd=system(command)) != 0){
5752: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5753: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5754: /* fclose(ficlog); */
5755: /* exit(1); */
5756: }
5757: /* if((imk=mkdir(optionfilefiname))<0){ */
5758: /* perror("mkdir"); */
5759: /* } */
5760:
5761: /*-------- arguments in the command line --------*/
5762:
5763: /* Log file */
5764: strcat(filelog, optionfilefiname);
5765: strcat(filelog,".log"); /* */
5766: if((ficlog=fopen(filelog,"w"))==NULL) {
5767: printf("Problem with logfile %s\n",filelog);
5768: goto end;
5769: }
5770: fprintf(ficlog,"Log filename:%s\n",filelog);
5771: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5772: fprintf(ficlog,"\nEnter the parameter file name: \n");
5773: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5774: path=%s \n\
5775: optionfile=%s\n\
5776: optionfilext=%s\n\
5777: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5778:
5779: syscompilerinfo();
5780:
5781: printf("Local time (at start):%s",strstart);
5782: fprintf(ficlog,"Local time (at start): %s",strstart);
5783: fflush(ficlog);
5784: /* (void) gettimeofday(&curr_time,&tzp); */
5785: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5786:
5787: /* */
5788: strcpy(fileres,"r");
5789: strcat(fileres, optionfilefiname);
5790: strcat(fileres,".txt"); /* Other files have txt extension */
5791:
5792: /*---------arguments file --------*/
5793:
5794: if((ficpar=fopen(optionfile,"r"))==NULL) {
5795: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5796: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5797: fflush(ficlog);
5798: /* goto end; */
5799: exit(70);
5800: }
5801:
5802:
5803:
5804: strcpy(filereso,"o");
5805: strcat(filereso,fileres);
5806: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5807: printf("Problem with Output resultfile: %s\n", filereso);
5808: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5809: fflush(ficlog);
5810: goto end;
5811: }
5812:
5813: /* Reads comments: lines beginning with '#' */
5814: numlinepar=0;
5815: while((c=getc(ficpar))=='#' && c!= EOF){
5816: ungetc(c,ficpar);
5817: fgets(line, MAXLINE, ficpar);
5818: numlinepar++;
5819: fputs(line,stdout);
5820: fputs(line,ficparo);
5821: fputs(line,ficlog);
5822: }
5823: ungetc(c,ficpar);
5824:
5825: 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);
5826: numlinepar++;
5827: 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);
5828: 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);
5829: 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);
5830: fflush(ficlog);
5831: while((c=getc(ficpar))=='#' && c!= EOF){
5832: ungetc(c,ficpar);
5833: fgets(line, MAXLINE, ficpar);
5834: numlinepar++;
5835: fputs(line, stdout);
5836: //puts(line);
5837: fputs(line,ficparo);
5838: fputs(line,ficlog);
5839: }
5840: ungetc(c,ficpar);
5841:
5842:
5843: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5844: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5845: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5846: v1+v2*age+v2*v3 makes cptcovn = 3
5847: */
5848: if (strlen(model)>1)
5849: 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*/
5850: else
5851: ncovmodel=2;
5852: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5853: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5854: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5855: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5856: 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);
5857: 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);
5858: fflush(stdout);
5859: fclose (ficlog);
5860: goto end;
5861: }
5862: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5863: delti=delti3[1][1];
5864: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5865: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5866: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5867: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5868: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5869: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5870: fclose (ficparo);
5871: fclose (ficlog);
5872: goto end;
5873: exit(0);
5874: }
5875: else if(mle==-3) {
5876: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5877: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5878: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5879: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5880: matcov=matrix(1,npar,1,npar);
5881: }
5882: else{
5883: /* Read guessed parameters */
5884: /* Reads comments: lines beginning with '#' */
5885: while((c=getc(ficpar))=='#' && c!= EOF){
5886: ungetc(c,ficpar);
5887: fgets(line, MAXLINE, ficpar);
5888: numlinepar++;
5889: fputs(line,stdout);
5890: fputs(line,ficparo);
5891: fputs(line,ficlog);
5892: }
5893: ungetc(c,ficpar);
5894:
5895: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5896: for(i=1; i <=nlstate; i++){
5897: j=0;
5898: for(jj=1; jj <=nlstate+ndeath; jj++){
5899: if(jj==i) continue;
5900: j++;
5901: fscanf(ficpar,"%1d%1d",&i1,&j1);
5902: if ((i1 != i) && (j1 != j)){
5903: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5904: It might be a problem of design; if ncovcol and the model are correct\n \
5905: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5906: exit(1);
5907: }
5908: fprintf(ficparo,"%1d%1d",i1,j1);
5909: if(mle==1)
5910: printf("%1d%1d",i,j);
5911: fprintf(ficlog,"%1d%1d",i,j);
5912: for(k=1; k<=ncovmodel;k++){
5913: fscanf(ficpar," %lf",¶m[i][j][k]);
5914: if(mle==1){
5915: printf(" %lf",param[i][j][k]);
5916: fprintf(ficlog," %lf",param[i][j][k]);
5917: }
5918: else
5919: fprintf(ficlog," %lf",param[i][j][k]);
5920: fprintf(ficparo," %lf",param[i][j][k]);
5921: }
5922: fscanf(ficpar,"\n");
5923: numlinepar++;
5924: if(mle==1)
5925: printf("\n");
5926: fprintf(ficlog,"\n");
5927: fprintf(ficparo,"\n");
5928: }
5929: }
5930: fflush(ficlog);
5931:
5932: /* Reads scales values */
5933: p=param[1][1];
5934:
5935: /* Reads comments: lines beginning with '#' */
5936: while((c=getc(ficpar))=='#' && c!= EOF){
5937: ungetc(c,ficpar);
5938: fgets(line, MAXLINE, ficpar);
5939: numlinepar++;
5940: fputs(line,stdout);
5941: fputs(line,ficparo);
5942: fputs(line,ficlog);
5943: }
5944: ungetc(c,ficpar);
5945:
5946: for(i=1; i <=nlstate; i++){
5947: for(j=1; j <=nlstate+ndeath-1; j++){
5948: fscanf(ficpar,"%1d%1d",&i1,&j1);
5949: if ( (i1-i) * (j1-j) != 0){
5950: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5951: exit(1);
5952: }
5953: printf("%1d%1d",i,j);
5954: fprintf(ficparo,"%1d%1d",i1,j1);
5955: fprintf(ficlog,"%1d%1d",i1,j1);
5956: for(k=1; k<=ncovmodel;k++){
5957: fscanf(ficpar,"%le",&delti3[i][j][k]);
5958: printf(" %le",delti3[i][j][k]);
5959: fprintf(ficparo," %le",delti3[i][j][k]);
5960: fprintf(ficlog," %le",delti3[i][j][k]);
5961: }
5962: fscanf(ficpar,"\n");
5963: numlinepar++;
5964: printf("\n");
5965: fprintf(ficparo,"\n");
5966: fprintf(ficlog,"\n");
5967: }
5968: }
5969: fflush(ficlog);
5970:
5971: /* Reads covariance matrix */
5972: delti=delti3[1][1];
5973:
5974:
5975: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5976:
5977: /* Reads comments: lines beginning with '#' */
5978: while((c=getc(ficpar))=='#' && c!= EOF){
5979: ungetc(c,ficpar);
5980: fgets(line, MAXLINE, ficpar);
5981: numlinepar++;
5982: fputs(line,stdout);
5983: fputs(line,ficparo);
5984: fputs(line,ficlog);
5985: }
5986: ungetc(c,ficpar);
5987:
5988: matcov=matrix(1,npar,1,npar);
5989: for(i=1; i <=npar; i++)
5990: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5991:
5992: for(i=1; i <=npar; i++){
5993: fscanf(ficpar,"%s",str);
5994: if(mle==1)
5995: printf("%s",str);
5996: fprintf(ficlog,"%s",str);
5997: fprintf(ficparo,"%s",str);
5998: for(j=1; j <=i; j++){
5999: fscanf(ficpar," %le",&matcov[i][j]);
6000: if(mle==1){
6001: printf(" %.5le",matcov[i][j]);
6002: }
6003: fprintf(ficlog," %.5le",matcov[i][j]);
6004: fprintf(ficparo," %.5le",matcov[i][j]);
6005: }
6006: fscanf(ficpar,"\n");
6007: numlinepar++;
6008: if(mle==1)
6009: printf("\n");
6010: fprintf(ficlog,"\n");
6011: fprintf(ficparo,"\n");
6012: }
6013: for(i=1; i <=npar; i++)
6014: for(j=i+1;j<=npar;j++)
6015: matcov[i][j]=matcov[j][i];
6016:
6017: if(mle==1)
6018: printf("\n");
6019: fprintf(ficlog,"\n");
6020:
6021: fflush(ficlog);
6022:
6023: /*-------- Rewriting parameter file ----------*/
6024: strcpy(rfileres,"r"); /* "Rparameterfile */
6025: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6026: strcat(rfileres,"."); /* */
6027: strcat(rfileres,optionfilext); /* Other files have txt extension */
6028: if((ficres =fopen(rfileres,"w"))==NULL) {
6029: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6030: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6031: }
6032: fprintf(ficres,"#%s\n",version);
6033: } /* End of mle != -3 */
6034:
6035:
6036: n= lastobs;
6037: num=lvector(1,n);
6038: moisnais=vector(1,n);
6039: annais=vector(1,n);
6040: moisdc=vector(1,n);
6041: andc=vector(1,n);
6042: agedc=vector(1,n);
6043: cod=ivector(1,n);
6044: weight=vector(1,n);
6045: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6046: mint=matrix(1,maxwav,1,n);
6047: anint=matrix(1,maxwav,1,n);
6048: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6049: tab=ivector(1,NCOVMAX);
6050: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6051:
6052: /* Reads data from file datafile */
6053: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6054: goto end;
6055:
6056: /* Calculation of the number of parameters from char model */
6057: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6058: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6059: k=3 V4 Tvar[k=3]= 4 (from V4)
6060: k=2 V1 Tvar[k=2]= 1 (from V1)
6061: k=1 Tvar[1]=2 (from V2)
6062: */
6063: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6064: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6065: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6066: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6067: */
6068: /* For model-covariate k tells which data-covariate to use but
6069: because this model-covariate is a construction we invent a new column
6070: ncovcol + k1
6071: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6072: Tvar[3=V1*V4]=4+1 etc */
6073: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6074: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6075: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6076: */
6077: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6078: 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
6079: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6080: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6081: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6082: 4 covariates (3 plus signs)
6083: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6084: */
6085:
6086: if(decodemodel(model, lastobs) == 1)
6087: goto end;
6088:
6089: if((double)(lastobs-imx)/(double)imx > 1.10){
6090: nbwarn++;
6091: 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);
6092: 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);
6093: }
6094: /* if(mle==1){*/
6095: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6096: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6097: }
6098:
6099: /*-calculation of age at interview from date of interview and age at death -*/
6100: agev=matrix(1,maxwav,1,imx);
6101:
6102: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6103: goto end;
6104:
6105:
6106: agegomp=(int)agemin;
6107: free_vector(moisnais,1,n);
6108: free_vector(annais,1,n);
6109: /* free_matrix(mint,1,maxwav,1,n);
6110: free_matrix(anint,1,maxwav,1,n);*/
6111: free_vector(moisdc,1,n);
6112: free_vector(andc,1,n);
6113: /* */
6114:
6115: wav=ivector(1,imx);
6116: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6117: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6118: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6119:
6120: /* Concatenates waves */
6121: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6122: /* */
6123:
6124: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6125:
6126: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6127: ncodemax[1]=1;
6128: Ndum =ivector(-1,NCOVMAX);
6129: if (ncovmodel > 2)
6130: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6131:
6132: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6133: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6134: h=0;
6135:
6136:
6137: /*if (cptcovn > 0) */
6138:
6139:
6140: m=pow(2,cptcoveff);
6141:
6142: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6143: 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 */
6144: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6145: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6146: h++;
6147: if (h>m)
6148: h=1;
6149: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6150: * h 1 2 3 4
6151: *______________________________
6152: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6153: * 2 2 1 1 1
6154: * 3 i=2 1 2 1 1
6155: * 4 2 2 1 1
6156: * 5 i=3 1 i=2 1 2 1
6157: * 6 2 1 2 1
6158: * 7 i=4 1 2 2 1
6159: * 8 2 2 2 1
6160: * 9 i=5 1 i=3 1 i=2 1 1
6161: * 10 2 1 1 1
6162: * 11 i=6 1 2 1 1
6163: * 12 2 2 1 1
6164: * 13 i=7 1 i=4 1 2 1
6165: * 14 2 1 2 1
6166: * 15 i=8 1 2 2 1
6167: * 16 2 2 2 1
6168: */
6169: codtab[h][k]=j;
6170: /*codtab[h][Tvar[k]]=j;*/
6171: 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]]);
6172: }
6173: }
6174: }
6175: }
6176: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6177: codtab[1][2]=1;codtab[2][2]=2; */
6178: /* for(i=1; i <=m ;i++){
6179: for(k=1; k <=cptcovn; k++){
6180: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6181: }
6182: printf("\n");
6183: }
6184: scanf("%d",i);*/
6185:
6186: free_ivector(Ndum,-1,NCOVMAX);
6187:
6188:
6189:
6190: /*------------ gnuplot -------------*/
6191: strcpy(optionfilegnuplot,optionfilefiname);
6192: if(mle==-3)
6193: strcat(optionfilegnuplot,"-mort");
6194: strcat(optionfilegnuplot,".gp");
6195:
6196: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6197: printf("Problem with file %s",optionfilegnuplot);
6198: }
6199: else{
6200: fprintf(ficgp,"\n# %s\n", version);
6201: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6202: //fprintf(ficgp,"set missing 'NaNq'\n");
6203: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6204: }
6205: /* fclose(ficgp);*/
6206: /*--------- index.htm --------*/
6207:
6208: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6209: if(mle==-3)
6210: strcat(optionfilehtm,"-mort");
6211: strcat(optionfilehtm,".htm");
6212: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6213: printf("Problem with %s \n",optionfilehtm);
6214: exit(0);
6215: }
6216:
6217: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6218: strcat(optionfilehtmcov,"-cov.htm");
6219: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6220: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6221: }
6222: else{
6223: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6224: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6225: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6226: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6227: }
6228:
6229: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6230: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6231: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6232: \n\
6233: <hr size=\"2\" color=\"#EC5E5E\">\
6234: <ul><li><h4>Parameter files</h4>\n\
6235: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6236: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6237: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6238: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6239: - Date and time at start: %s</ul>\n",\
6240: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6241: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6242: fileres,fileres,\
6243: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6244: fflush(fichtm);
6245:
6246: strcpy(pathr,path);
6247: strcat(pathr,optionfilefiname);
6248: chdir(optionfilefiname); /* Move to directory named optionfile */
6249:
6250: /* Calculates basic frequencies. Computes observed prevalence at single age
6251: and prints on file fileres'p'. */
6252: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6253:
6254: fprintf(fichtm,"\n");
6255: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6256: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6257: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6258: imx,agemin,agemax,jmin,jmax,jmean);
6259: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6260: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6261: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6262: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6263: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6264:
6265:
6266: /* For Powell, parameters are in a vector p[] starting at p[1]
6267: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6268: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6269:
6270: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6271:
6272: if (mle==-3){
6273: ximort=matrix(1,NDIM,1,NDIM);
6274: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6275: cens=ivector(1,n);
6276: ageexmed=vector(1,n);
6277: agecens=vector(1,n);
6278: dcwave=ivector(1,n);
6279:
6280: for (i=1; i<=imx; i++){
6281: dcwave[i]=-1;
6282: for (m=firstpass; m<=lastpass; m++)
6283: if (s[m][i]>nlstate) {
6284: dcwave[i]=m;
6285: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6286: break;
6287: }
6288: }
6289:
6290: for (i=1; i<=imx; i++) {
6291: if (wav[i]>0){
6292: ageexmed[i]=agev[mw[1][i]][i];
6293: j=wav[i];
6294: agecens[i]=1.;
6295:
6296: if (ageexmed[i]> 1 && wav[i] > 0){
6297: agecens[i]=agev[mw[j][i]][i];
6298: cens[i]= 1;
6299: }else if (ageexmed[i]< 1)
6300: cens[i]= -1;
6301: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6302: cens[i]=0 ;
6303: }
6304: else cens[i]=-1;
6305: }
6306:
6307: for (i=1;i<=NDIM;i++) {
6308: for (j=1;j<=NDIM;j++)
6309: ximort[i][j]=(i == j ? 1.0 : 0.0);
6310: }
6311:
6312: /*p[1]=0.0268; p[NDIM]=0.083;*/
6313: /*printf("%lf %lf", p[1], p[2]);*/
6314:
6315:
6316: #ifdef GSL
6317: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6318: #else
6319: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6320: #endif
6321: strcpy(filerespow,"pow-mort");
6322: strcat(filerespow,fileres);
6323: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6324: printf("Problem with resultfile: %s\n", filerespow);
6325: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6326: }
6327: #ifdef GSL
6328: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6329: #else
6330: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6331: #endif
6332: /* for (i=1;i<=nlstate;i++)
6333: for(j=1;j<=nlstate+ndeath;j++)
6334: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6335: */
6336: fprintf(ficrespow,"\n");
6337: #ifdef GSL
6338: /* gsl starts here */
6339: T = gsl_multimin_fminimizer_nmsimplex;
6340: gsl_multimin_fminimizer *sfm = NULL;
6341: gsl_vector *ss, *x;
6342: gsl_multimin_function minex_func;
6343:
6344: /* Initial vertex size vector */
6345: ss = gsl_vector_alloc (NDIM);
6346:
6347: if (ss == NULL){
6348: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6349: }
6350: /* Set all step sizes to 1 */
6351: gsl_vector_set_all (ss, 0.001);
6352:
6353: /* Starting point */
6354:
6355: x = gsl_vector_alloc (NDIM);
6356:
6357: if (x == NULL){
6358: gsl_vector_free(ss);
6359: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6360: }
6361:
6362: /* Initialize method and iterate */
6363: /* p[1]=0.0268; p[NDIM]=0.083; */
6364: /* gsl_vector_set(x, 0, 0.0268); */
6365: /* gsl_vector_set(x, 1, 0.083); */
6366: gsl_vector_set(x, 0, p[1]);
6367: gsl_vector_set(x, 1, p[2]);
6368:
6369: minex_func.f = &gompertz_f;
6370: minex_func.n = NDIM;
6371: minex_func.params = (void *)&p; /* ??? */
6372:
6373: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6374: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6375:
6376: printf("Iterations beginning .....\n\n");
6377: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6378:
6379: iteri=0;
6380: while (rval == GSL_CONTINUE){
6381: iteri++;
6382: status = gsl_multimin_fminimizer_iterate(sfm);
6383:
6384: if (status) printf("error: %s\n", gsl_strerror (status));
6385: fflush(0);
6386:
6387: if (status)
6388: break;
6389:
6390: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6391: ssval = gsl_multimin_fminimizer_size (sfm);
6392:
6393: if (rval == GSL_SUCCESS)
6394: printf ("converged to a local maximum at\n");
6395:
6396: printf("%5d ", iteri);
6397: for (it = 0; it < NDIM; it++){
6398: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6399: }
6400: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6401: }
6402:
6403: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6404:
6405: gsl_vector_free(x); /* initial values */
6406: gsl_vector_free(ss); /* inital step size */
6407: for (it=0; it<NDIM; it++){
6408: p[it+1]=gsl_vector_get(sfm->x,it);
6409: fprintf(ficrespow," %.12lf", p[it]);
6410: }
6411: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6412: #endif
6413: #ifdef POWELL
6414: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6415: #endif
6416: fclose(ficrespow);
6417:
6418: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6419:
6420: for(i=1; i <=NDIM; i++)
6421: for(j=i+1;j<=NDIM;j++)
6422: matcov[i][j]=matcov[j][i];
6423:
6424: printf("\nCovariance matrix\n ");
6425: for(i=1; i <=NDIM; i++) {
6426: for(j=1;j<=NDIM;j++){
6427: printf("%f ",matcov[i][j]);
6428: }
6429: printf("\n ");
6430: }
6431:
6432: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6433: for (i=1;i<=NDIM;i++)
6434: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6435:
6436: lsurv=vector(1,AGESUP);
6437: lpop=vector(1,AGESUP);
6438: tpop=vector(1,AGESUP);
6439: lsurv[agegomp]=100000;
6440:
6441: for (k=agegomp;k<=AGESUP;k++) {
6442: agemortsup=k;
6443: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6444: }
6445:
6446: for (k=agegomp;k<agemortsup;k++)
6447: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6448:
6449: for (k=agegomp;k<agemortsup;k++){
6450: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6451: sumlpop=sumlpop+lpop[k];
6452: }
6453:
6454: tpop[agegomp]=sumlpop;
6455: for (k=agegomp;k<(agemortsup-3);k++){
6456: /* tpop[k+1]=2;*/
6457: tpop[k+1]=tpop[k]-lpop[k];
6458: }
6459:
6460:
6461: printf("\nAge lx qx dx Lx Tx e(x)\n");
6462: for (k=agegomp;k<(agemortsup-2);k++)
6463: 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]);
6464:
6465:
6466: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6467: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6468:
6469: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6470: stepm, weightopt,\
6471: model,imx,p,matcov,agemortsup);
6472:
6473: free_vector(lsurv,1,AGESUP);
6474: free_vector(lpop,1,AGESUP);
6475: free_vector(tpop,1,AGESUP);
6476: #ifdef GSL
6477: free_ivector(cens,1,n);
6478: free_vector(agecens,1,n);
6479: free_ivector(dcwave,1,n);
6480: free_matrix(ximort,1,NDIM,1,NDIM);
6481: #endif
6482: } /* Endof if mle==-3 */
6483:
6484: else{ /* For mle >=1 */
6485: globpr=0;/* debug */
6486: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6487: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6488: for (k=1; k<=npar;k++)
6489: printf(" %d %8.5f",k,p[k]);
6490: printf("\n");
6491: globpr=1; /* to print the contributions */
6492: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6493: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6494: for (k=1; k<=npar;k++)
6495: printf(" %d %8.5f",k,p[k]);
6496: printf("\n");
6497: if(mle>=1){ /* Could be 1 or 2 */
6498: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6499: }
6500:
6501: /*--------- results files --------------*/
6502: 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);
6503:
6504:
6505: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6506: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6507: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6508: for(i=1,jk=1; i <=nlstate; i++){
6509: for(k=1; k <=(nlstate+ndeath); k++){
6510: if (k != i) {
6511: printf("%d%d ",i,k);
6512: fprintf(ficlog,"%d%d ",i,k);
6513: fprintf(ficres,"%1d%1d ",i,k);
6514: for(j=1; j <=ncovmodel; j++){
6515: printf("%lf ",p[jk]);
6516: fprintf(ficlog,"%lf ",p[jk]);
6517: fprintf(ficres,"%lf ",p[jk]);
6518: jk++;
6519: }
6520: printf("\n");
6521: fprintf(ficlog,"\n");
6522: fprintf(ficres,"\n");
6523: }
6524: }
6525: }
6526: if(mle!=0){
6527: /* Computing hessian and covariance matrix */
6528: ftolhess=ftol; /* Usually correct */
6529: hesscov(matcov, p, npar, delti, ftolhess, func);
6530: }
6531: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6532: printf("# Scales (for hessian or gradient estimation)\n");
6533: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6534: for(i=1,jk=1; i <=nlstate; i++){
6535: for(j=1; j <=nlstate+ndeath; j++){
6536: if (j!=i) {
6537: fprintf(ficres,"%1d%1d",i,j);
6538: printf("%1d%1d",i,j);
6539: fprintf(ficlog,"%1d%1d",i,j);
6540: for(k=1; k<=ncovmodel;k++){
6541: printf(" %.5e",delti[jk]);
6542: fprintf(ficlog," %.5e",delti[jk]);
6543: fprintf(ficres," %.5e",delti[jk]);
6544: jk++;
6545: }
6546: printf("\n");
6547: fprintf(ficlog,"\n");
6548: fprintf(ficres,"\n");
6549: }
6550: }
6551: }
6552:
6553: 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");
6554: if(mle>=1)
6555: 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");
6556: 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");
6557: /* # 121 Var(a12)\n\ */
6558: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6559: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6560: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6561: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6562: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6563: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6564: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6565:
6566:
6567: /* Just to have a covariance matrix which will be more understandable
6568: even is we still don't want to manage dictionary of variables
6569: */
6570: for(itimes=1;itimes<=2;itimes++){
6571: jj=0;
6572: for(i=1; i <=nlstate; i++){
6573: for(j=1; j <=nlstate+ndeath; j++){
6574: if(j==i) continue;
6575: for(k=1; k<=ncovmodel;k++){
6576: jj++;
6577: ca[0]= k+'a'-1;ca[1]='\0';
6578: if(itimes==1){
6579: if(mle>=1)
6580: printf("#%1d%1d%d",i,j,k);
6581: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6582: fprintf(ficres,"#%1d%1d%d",i,j,k);
6583: }else{
6584: if(mle>=1)
6585: printf("%1d%1d%d",i,j,k);
6586: fprintf(ficlog,"%1d%1d%d",i,j,k);
6587: fprintf(ficres,"%1d%1d%d",i,j,k);
6588: }
6589: ll=0;
6590: for(li=1;li <=nlstate; li++){
6591: for(lj=1;lj <=nlstate+ndeath; lj++){
6592: if(lj==li) continue;
6593: for(lk=1;lk<=ncovmodel;lk++){
6594: ll++;
6595: if(ll<=jj){
6596: cb[0]= lk +'a'-1;cb[1]='\0';
6597: if(ll<jj){
6598: if(itimes==1){
6599: if(mle>=1)
6600: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6601: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6602: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6603: }else{
6604: if(mle>=1)
6605: printf(" %.5e",matcov[jj][ll]);
6606: fprintf(ficlog," %.5e",matcov[jj][ll]);
6607: fprintf(ficres," %.5e",matcov[jj][ll]);
6608: }
6609: }else{
6610: if(itimes==1){
6611: if(mle>=1)
6612: printf(" Var(%s%1d%1d)",ca,i,j);
6613: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6614: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6615: }else{
6616: if(mle>=1)
6617: printf(" %.5e",matcov[jj][ll]);
6618: fprintf(ficlog," %.5e",matcov[jj][ll]);
6619: fprintf(ficres," %.5e",matcov[jj][ll]);
6620: }
6621: }
6622: }
6623: } /* end lk */
6624: } /* end lj */
6625: } /* end li */
6626: if(mle>=1)
6627: printf("\n");
6628: fprintf(ficlog,"\n");
6629: fprintf(ficres,"\n");
6630: numlinepar++;
6631: } /* end k*/
6632: } /*end j */
6633: } /* end i */
6634: } /* end itimes */
6635:
6636: fflush(ficlog);
6637: fflush(ficres);
6638:
6639: while((c=getc(ficpar))=='#' && c!= EOF){
6640: ungetc(c,ficpar);
6641: fgets(line, MAXLINE, ficpar);
6642: fputs(line,stdout);
6643: fputs(line,ficparo);
6644: }
6645: ungetc(c,ficpar);
6646:
6647: estepm=0;
6648: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6649: if (estepm==0 || estepm < stepm) estepm=stepm;
6650: if (fage <= 2) {
6651: bage = ageminpar;
6652: fage = agemaxpar;
6653: }
6654:
6655: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6656: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6657: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6658:
6659: while((c=getc(ficpar))=='#' && c!= EOF){
6660: ungetc(c,ficpar);
6661: fgets(line, MAXLINE, ficpar);
6662: fputs(line,stdout);
6663: fputs(line,ficparo);
6664: }
6665: ungetc(c,ficpar);
6666:
6667: 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);
6668: 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);
6669: 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);
6670: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6671: 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);
6672:
6673: while((c=getc(ficpar))=='#' && c!= EOF){
6674: ungetc(c,ficpar);
6675: fgets(line, MAXLINE, ficpar);
6676: fputs(line,stdout);
6677: fputs(line,ficparo);
6678: }
6679: ungetc(c,ficpar);
6680:
6681:
6682: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6683: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6684:
6685: fscanf(ficpar,"pop_based=%d\n",&popbased);
6686: fprintf(ficparo,"pop_based=%d\n",popbased);
6687: fprintf(ficres,"pop_based=%d\n",popbased);
6688:
6689: while((c=getc(ficpar))=='#' && c!= EOF){
6690: ungetc(c,ficpar);
6691: fgets(line, MAXLINE, ficpar);
6692: fputs(line,stdout);
6693: fputs(line,ficparo);
6694: }
6695: ungetc(c,ficpar);
6696:
6697: 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);
6698: 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);
6699: 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);
6700: 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);
6701: 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);
6702: /* day and month of proj2 are not used but only year anproj2.*/
6703:
6704:
6705:
6706: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6707: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6708:
6709: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6710: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6711:
6712: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6713: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6714: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6715:
6716: /*------------ free_vector -------------*/
6717: /* chdir(path); */
6718:
6719: free_ivector(wav,1,imx);
6720: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6721: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6722: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6723: free_lvector(num,1,n);
6724: free_vector(agedc,1,n);
6725: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6726: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6727: fclose(ficparo);
6728: fclose(ficres);
6729:
6730:
6731: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6732: #include "prevlim.h" /* Use ficrespl, ficlog */
6733: fclose(ficrespl);
6734:
6735: #ifdef FREEEXIT2
6736: #include "freeexit2.h"
6737: #endif
6738:
6739: /*------------- h Pij x at various ages ------------*/
6740: #include "hpijx.h"
6741: fclose(ficrespij);
6742:
6743: /*-------------- Variance of one-step probabilities---*/
6744: k=1;
6745: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6746:
6747:
6748: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6749: for(i=1;i<=AGESUP;i++)
6750: for(j=1;j<=NCOVMAX;j++)
6751: for(k=1;k<=NCOVMAX;k++)
6752: probs[i][j][k]=0.;
6753:
6754: /*---------- Forecasting ------------------*/
6755: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6756: if(prevfcast==1){
6757: /* if(stepm ==1){*/
6758: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6759: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6760: /* } */
6761: /* else{ */
6762: /* erreur=108; */
6763: /* 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); */
6764: /* 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); */
6765: /* } */
6766: }
6767:
6768:
6769: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6770:
6771: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6772: /* 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",\
6773: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6774: */
6775:
6776: if (mobilav!=0) {
6777: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6778: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6779: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6780: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6781: }
6782: }
6783:
6784:
6785: /*---------- Health expectancies, no variances ------------*/
6786:
6787: strcpy(filerese,"e");
6788: strcat(filerese,fileres);
6789: if((ficreseij=fopen(filerese,"w"))==NULL) {
6790: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6791: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6792: }
6793: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6794: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6795: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6796: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6797:
6798: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6799: fprintf(ficreseij,"\n#****** ");
6800: for(j=1;j<=cptcoveff;j++) {
6801: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6802: }
6803: fprintf(ficreseij,"******\n");
6804:
6805: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6806: oldm=oldms;savm=savms;
6807: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6808:
6809: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6810: /*}*/
6811: }
6812: fclose(ficreseij);
6813:
6814:
6815: /*---------- Health expectancies and variances ------------*/
6816:
6817:
6818: strcpy(filerest,"t");
6819: strcat(filerest,fileres);
6820: if((ficrest=fopen(filerest,"w"))==NULL) {
6821: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6822: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6823: }
6824: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6825: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6826:
6827:
6828: strcpy(fileresstde,"stde");
6829: strcat(fileresstde,fileres);
6830: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6831: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6832: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6833: }
6834: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6835: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6836:
6837: strcpy(filerescve,"cve");
6838: strcat(filerescve,fileres);
6839: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6840: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6841: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6842: }
6843: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6844: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6845:
6846: strcpy(fileresv,"v");
6847: strcat(fileresv,fileres);
6848: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6849: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6850: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6851: }
6852: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6853: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6854:
6855: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6856: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6857:
6858: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6859: fprintf(ficrest,"\n#****** ");
6860: for(j=1;j<=cptcoveff;j++)
6861: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6862: fprintf(ficrest,"******\n");
6863:
6864: fprintf(ficresstdeij,"\n#****** ");
6865: fprintf(ficrescveij,"\n#****** ");
6866: for(j=1;j<=cptcoveff;j++) {
6867: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6868: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6869: }
6870: fprintf(ficresstdeij,"******\n");
6871: fprintf(ficrescveij,"******\n");
6872:
6873: fprintf(ficresvij,"\n#****** ");
6874: for(j=1;j<=cptcoveff;j++)
6875: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6876: fprintf(ficresvij,"******\n");
6877:
6878: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6879: oldm=oldms;savm=savms;
6880: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6881: /*
6882: */
6883: /* goto endfree; */
6884:
6885: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6886: pstamp(ficrest);
6887:
6888:
6889: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6890: oldm=oldms;savm=savms; /* Segmentation fault */
6891: cptcod= 0; /* To be deleted */
6892: 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 */
6893: 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 ");
6894: if(vpopbased==1)
6895: 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);
6896: else
6897: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6898: fprintf(ficrest,"# Age e.. (std) ");
6899: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6900: fprintf(ficrest,"\n");
6901:
6902: epj=vector(1,nlstate+1);
6903: for(age=bage; age <=fage ;age++){
6904: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6905: if (vpopbased==1) {
6906: if(mobilav ==0){
6907: for(i=1; i<=nlstate;i++)
6908: prlim[i][i]=probs[(int)age][i][k];
6909: }else{ /* mobilav */
6910: for(i=1; i<=nlstate;i++)
6911: prlim[i][i]=mobaverage[(int)age][i][k];
6912: }
6913: }
6914:
6915: fprintf(ficrest," %4.0f",age);
6916: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6917: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6918: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6919: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6920: }
6921: epj[nlstate+1] +=epj[j];
6922: }
6923:
6924: for(i=1, vepp=0.;i <=nlstate;i++)
6925: for(j=1;j <=nlstate;j++)
6926: vepp += vareij[i][j][(int)age];
6927: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6928: for(j=1;j <=nlstate;j++){
6929: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6930: }
6931: fprintf(ficrest,"\n");
6932: }
6933: }
6934: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6935: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6936: free_vector(epj,1,nlstate+1);
6937: /*}*/
6938: }
6939: free_vector(weight,1,n);
6940: free_imatrix(Tvard,1,NCOVMAX,1,2);
6941: free_imatrix(s,1,maxwav+1,1,n);
6942: free_matrix(anint,1,maxwav,1,n);
6943: free_matrix(mint,1,maxwav,1,n);
6944: free_ivector(cod,1,n);
6945: free_ivector(tab,1,NCOVMAX);
6946: fclose(ficresstdeij);
6947: fclose(ficrescveij);
6948: fclose(ficresvij);
6949: fclose(ficrest);
6950: fclose(ficpar);
6951:
6952: /*------- Variance of period (stable) prevalence------*/
6953:
6954: strcpy(fileresvpl,"vpl");
6955: strcat(fileresvpl,fileres);
6956: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6957: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6958: exit(0);
6959: }
6960: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6961:
6962: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6963: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6964:
6965: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6966: fprintf(ficresvpl,"\n#****** ");
6967: for(j=1;j<=cptcoveff;j++)
6968: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6969: fprintf(ficresvpl,"******\n");
6970:
6971: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6972: oldm=oldms;savm=savms;
6973: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6974: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6975: /*}*/
6976: }
6977:
6978: fclose(ficresvpl);
6979:
6980: /*---------- End : free ----------------*/
6981: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6982: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6983: } /* mle==-3 arrives here for freeing */
6984: /* endfree:*/
6985: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6986: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6987: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6988: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6989: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6990: free_matrix(covar,0,NCOVMAX,1,n);
6991: free_matrix(matcov,1,npar,1,npar);
6992: /*free_vector(delti,1,npar);*/
6993: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6994: free_matrix(agev,1,maxwav,1,imx);
6995: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6996:
6997: free_ivector(ncodemax,1,NCOVMAX);
6998: free_ivector(Tvar,1,NCOVMAX);
6999: free_ivector(Tprod,1,NCOVMAX);
7000: free_ivector(Tvaraff,1,NCOVMAX);
7001: free_ivector(Tage,1,NCOVMAX);
7002:
7003: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7004: free_imatrix(codtab,1,100,1,10);
7005: fflush(fichtm);
7006: fflush(ficgp);
7007:
7008:
7009: if((nberr >0) || (nbwarn>0)){
7010: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7011: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7012: }else{
7013: printf("End of Imach\n");
7014: fprintf(ficlog,"End of Imach\n");
7015: }
7016: printf("See log file on %s\n",filelog);
7017: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7018: /*(void) gettimeofday(&end_time,&tzp);*/
7019: rend_time = time(NULL);
7020: end_time = *localtime(&rend_time);
7021: /* tml = *localtime(&end_time.tm_sec); */
7022: strcpy(strtend,asctime(&end_time));
7023: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7024: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7025: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7026:
7027: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7028: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7029: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7030: /* printf("Total time was %d uSec.\n", total_usecs);*/
7031: /* if(fileappend(fichtm,optionfilehtm)){ */
7032: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7033: fclose(fichtm);
7034: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7035: fclose(fichtmcov);
7036: fclose(ficgp);
7037: fclose(ficlog);
7038: /*------ End -----------*/
7039:
7040:
7041: printf("Before Current directory %s!\n",pathcd);
7042: if(chdir(pathcd) != 0)
7043: printf("Can't move to directory %s!\n",path);
7044: if(getcwd(pathcd,MAXLINE) > 0)
7045: printf("Current directory %s!\n",pathcd);
7046: /*strcat(plotcmd,CHARSEPARATOR);*/
7047: sprintf(plotcmd,"gnuplot");
7048: #ifdef _WIN32
7049: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7050: #endif
7051: if(!stat(plotcmd,&info)){
7052: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7053: if(!stat(getenv("GNUPLOTBIN"),&info)){
7054: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7055: }else
7056: strcpy(pplotcmd,plotcmd);
7057: #ifdef __unix
7058: strcpy(plotcmd,GNUPLOTPROGRAM);
7059: if(!stat(plotcmd,&info)){
7060: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7061: }else
7062: strcpy(pplotcmd,plotcmd);
7063: #endif
7064: }else
7065: strcpy(pplotcmd,plotcmd);
7066:
7067: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7068: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7069:
7070: if((outcmd=system(plotcmd)) != 0){
7071: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7072: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7073: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7074: if((outcmd=system(plotcmd)) != 0)
7075: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7076: }
7077: printf(" Successful, please wait...");
7078: while (z[0] != 'q') {
7079: /* chdir(path); */
7080: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7081: scanf("%s",z);
7082: /* if (z[0] == 'c') system("./imach"); */
7083: if (z[0] == 'e') {
7084: #ifdef __APPLE__
7085: sprintf(pplotcmd, "open %s", optionfilehtm);
7086: #elif __linux
7087: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7088: #else
7089: sprintf(pplotcmd, "%s", optionfilehtm);
7090: #endif
7091: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7092: system(pplotcmd);
7093: }
7094: else if (z[0] == 'g') system(plotcmd);
7095: else if (z[0] == 'q') exit(0);
7096: }
7097: end:
7098: while (z[0] != 'q') {
7099: printf("\nType q for exiting: ");
7100: scanf("%s",z);
7101: }
7102: }
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