1: /* $Id: imach.c,v 1.174 2015/01/03 16:15:49 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.174 2015/01/03 16:15:49 brouard
5: Summary: Still in cross-compilation
6:
7: Revision 1.173 2015/01/03 12:06:26 brouard
8: Summary: trying to detect cross-compilation
9:
10: Revision 1.172 2014/12/27 12:07:47 brouard
11: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
12:
13: Revision 1.171 2014/12/23 13:26:59 brouard
14: Summary: Back from Visual C
15:
16: Still problem with utsname.h on Windows
17:
18: Revision 1.170 2014/12/23 11:17:12 brouard
19: Summary: Cleaning some \%% back to %%
20:
21: The escape was mandatory for a specific compiler (which one?), but too many warnings.
22:
23: Revision 1.169 2014/12/22 23:08:31 brouard
24: Summary: 0.98p
25:
26: Outputs some informations on compiler used, OS etc. Testing on different platforms.
27:
28: Revision 1.168 2014/12/22 15:17:42 brouard
29: Summary: update
30:
31: Revision 1.167 2014/12/22 13:50:56 brouard
32: Summary: Testing uname and compiler version and if compiled 32 or 64
33:
34: Testing on Linux 64
35:
36: Revision 1.166 2014/12/22 11:40:47 brouard
37: *** empty log message ***
38:
39: Revision 1.165 2014/12/16 11:20:36 brouard
40: Summary: After compiling on Visual C
41:
42: * imach.c (Module): Merging 1.61 to 1.162
43:
44: Revision 1.164 2014/12/16 10:52:11 brouard
45: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
46:
47: * imach.c (Module): Merging 1.61 to 1.162
48:
49: Revision 1.163 2014/12/16 10:30:11 brouard
50: * imach.c (Module): Merging 1.61 to 1.162
51:
52: Revision 1.162 2014/09/25 11:43:39 brouard
53: Summary: temporary backup 0.99!
54:
55: Revision 1.1 2014/09/16 11:06:58 brouard
56: Summary: With some code (wrong) for nlopt
57:
58: Author:
59:
60: Revision 1.161 2014/09/15 20:41:41 brouard
61: Summary: Problem with macro SQR on Intel compiler
62:
63: Revision 1.160 2014/09/02 09:24:05 brouard
64: *** empty log message ***
65:
66: Revision 1.159 2014/09/01 10:34:10 brouard
67: Summary: WIN32
68: Author: Brouard
69:
70: Revision 1.158 2014/08/27 17:11:51 brouard
71: *** empty log message ***
72:
73: Revision 1.157 2014/08/27 16:26:55 brouard
74: Summary: Preparing windows Visual studio version
75: Author: Brouard
76:
77: In order to compile on Visual studio, time.h is now correct and time_t
78: and tm struct should be used. difftime should be used but sometimes I
79: just make the differences in raw time format (time(&now).
80: Trying to suppress #ifdef LINUX
81: Add xdg-open for __linux in order to open default browser.
82:
83: Revision 1.156 2014/08/25 20:10:10 brouard
84: *** empty log message ***
85:
86: Revision 1.155 2014/08/25 18:32:34 brouard
87: Summary: New compile, minor changes
88: Author: Brouard
89:
90: Revision 1.154 2014/06/20 17:32:08 brouard
91: Summary: Outputs now all graphs of convergence to period prevalence
92:
93: Revision 1.153 2014/06/20 16:45:46 brouard
94: Summary: If 3 live state, convergence to period prevalence on same graph
95: Author: Brouard
96:
97: Revision 1.152 2014/06/18 17:54:09 brouard
98: Summary: open browser, use gnuplot on same dir than imach if not found in the path
99:
100: Revision 1.151 2014/06/18 16:43:30 brouard
101: *** empty log message ***
102:
103: Revision 1.150 2014/06/18 16:42:35 brouard
104: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
105: Author: brouard
106:
107: Revision 1.149 2014/06/18 15:51:14 brouard
108: Summary: Some fixes in parameter files errors
109: Author: Nicolas Brouard
110:
111: Revision 1.148 2014/06/17 17:38:48 brouard
112: Summary: Nothing new
113: Author: Brouard
114:
115: Just a new packaging for OS/X version 0.98nS
116:
117: Revision 1.147 2014/06/16 10:33:11 brouard
118: *** empty log message ***
119:
120: Revision 1.146 2014/06/16 10:20:28 brouard
121: Summary: Merge
122: Author: Brouard
123:
124: Merge, before building revised version.
125:
126: Revision 1.145 2014/06/10 21:23:15 brouard
127: Summary: Debugging with valgrind
128: Author: Nicolas Brouard
129:
130: Lot of changes in order to output the results with some covariates
131: After the Edimburgh REVES conference 2014, it seems mandatory to
132: improve the code.
133: No more memory valgrind error but a lot has to be done in order to
134: continue the work of splitting the code into subroutines.
135: Also, decodemodel has been improved. Tricode is still not
136: optimal. nbcode should be improved. Documentation has been added in
137: the source code.
138:
139: Revision 1.143 2014/01/26 09:45:38 brouard
140: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
141:
142: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
143: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
144:
145: Revision 1.142 2014/01/26 03:57:36 brouard
146: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
147:
148: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
149:
150: Revision 1.141 2014/01/26 02:42:01 brouard
151: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
152:
153: Revision 1.140 2011/09/02 10:37:54 brouard
154: Summary: times.h is ok with mingw32 now.
155:
156: Revision 1.139 2010/06/14 07:50:17 brouard
157: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
158: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
159:
160: Revision 1.138 2010/04/30 18:19:40 brouard
161: *** empty log message ***
162:
163: Revision 1.137 2010/04/29 18:11:38 brouard
164: (Module): Checking covariates for more complex models
165: than V1+V2. A lot of change to be done. Unstable.
166:
167: Revision 1.136 2010/04/26 20:30:53 brouard
168: (Module): merging some libgsl code. Fixing computation
169: of likelione (using inter/intrapolation if mle = 0) in order to
170: get same likelihood as if mle=1.
171: Some cleaning of code and comments added.
172:
173: Revision 1.135 2009/10/29 15:33:14 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 1.134 2009/10/29 13:18:53 brouard
177: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
178:
179: Revision 1.133 2009/07/06 10:21:25 brouard
180: just nforces
181:
182: Revision 1.132 2009/07/06 08:22:05 brouard
183: Many tings
184:
185: Revision 1.131 2009/06/20 16:22:47 brouard
186: Some dimensions resccaled
187:
188: Revision 1.130 2009/05/26 06:44:34 brouard
189: (Module): Max Covariate is now set to 20 instead of 8. A
190: lot of cleaning with variables initialized to 0. Trying to make
191: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
192:
193: Revision 1.129 2007/08/31 13:49:27 lievre
194: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
195:
196: Revision 1.128 2006/06/30 13:02:05 brouard
197: (Module): Clarifications on computing e.j
198:
199: Revision 1.127 2006/04/28 18:11:50 brouard
200: (Module): Yes the sum of survivors was wrong since
201: imach-114 because nhstepm was no more computed in the age
202: loop. Now we define nhstepma in the age loop.
203: (Module): In order to speed up (in case of numerous covariates) we
204: compute health expectancies (without variances) in a first step
205: and then all the health expectancies with variances or standard
206: deviation (needs data from the Hessian matrices) which slows the
207: computation.
208: In the future we should be able to stop the program is only health
209: expectancies and graph are needed without standard deviations.
210:
211: Revision 1.126 2006/04/28 17:23:28 brouard
212: (Module): Yes the sum of survivors was wrong since
213: imach-114 because nhstepm was no more computed in the age
214: loop. Now we define nhstepma in the age loop.
215: Version 0.98h
216:
217: Revision 1.125 2006/04/04 15:20:31 lievre
218: Errors in calculation of health expectancies. Age was not initialized.
219: Forecasting file added.
220:
221: Revision 1.124 2006/03/22 17:13:53 lievre
222: Parameters are printed with %lf instead of %f (more numbers after the comma).
223: The log-likelihood is printed in the log file
224:
225: Revision 1.123 2006/03/20 10:52:43 brouard
226: * imach.c (Module): <title> changed, corresponds to .htm file
227: name. <head> headers where missing.
228:
229: * imach.c (Module): Weights can have a decimal point as for
230: English (a comma might work with a correct LC_NUMERIC environment,
231: otherwise the weight is truncated).
232: Modification of warning when the covariates values are not 0 or
233: 1.
234: Version 0.98g
235:
236: Revision 1.122 2006/03/20 09:45:41 brouard
237: (Module): Weights can have a decimal point as for
238: English (a comma might work with a correct LC_NUMERIC environment,
239: otherwise the weight is truncated).
240: Modification of warning when the covariates values are not 0 or
241: 1.
242: Version 0.98g
243:
244: Revision 1.121 2006/03/16 17:45:01 lievre
245: * imach.c (Module): Comments concerning covariates added
246:
247: * imach.c (Module): refinements in the computation of lli if
248: status=-2 in order to have more reliable computation if stepm is
249: not 1 month. Version 0.98f
250:
251: Revision 1.120 2006/03/16 15:10:38 lievre
252: (Module): refinements in the computation of lli if
253: status=-2 in order to have more reliable computation if stepm is
254: not 1 month. Version 0.98f
255:
256: Revision 1.119 2006/03/15 17:42:26 brouard
257: (Module): Bug if status = -2, the loglikelihood was
258: computed as likelihood omitting the logarithm. Version O.98e
259:
260: Revision 1.118 2006/03/14 18:20:07 brouard
261: (Module): varevsij Comments added explaining the second
262: table of variances if popbased=1 .
263: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
264: (Module): Function pstamp added
265: (Module): Version 0.98d
266:
267: Revision 1.117 2006/03/14 17:16:22 brouard
268: (Module): varevsij Comments added explaining the second
269: table of variances if popbased=1 .
270: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
271: (Module): Function pstamp added
272: (Module): Version 0.98d
273:
274: Revision 1.116 2006/03/06 10:29:27 brouard
275: (Module): Variance-covariance wrong links and
276: varian-covariance of ej. is needed (Saito).
277:
278: Revision 1.115 2006/02/27 12:17:45 brouard
279: (Module): One freematrix added in mlikeli! 0.98c
280:
281: Revision 1.114 2006/02/26 12:57:58 brouard
282: (Module): Some improvements in processing parameter
283: filename with strsep.
284:
285: Revision 1.113 2006/02/24 14:20:24 brouard
286: (Module): Memory leaks checks with valgrind and:
287: datafile was not closed, some imatrix were not freed and on matrix
288: allocation too.
289:
290: Revision 1.112 2006/01/30 09:55:26 brouard
291: (Module): Back to gnuplot.exe instead of wgnuplot.exe
292:
293: Revision 1.111 2006/01/25 20:38:18 brouard
294: (Module): Lots of cleaning and bugs added (Gompertz)
295: (Module): Comments can be added in data file. Missing date values
296: can be a simple dot '.'.
297:
298: Revision 1.110 2006/01/25 00:51:50 brouard
299: (Module): Lots of cleaning and bugs added (Gompertz)
300:
301: Revision 1.109 2006/01/24 19:37:15 brouard
302: (Module): Comments (lines starting with a #) are allowed in data.
303:
304: Revision 1.108 2006/01/19 18:05:42 lievre
305: Gnuplot problem appeared...
306: To be fixed
307:
308: Revision 1.107 2006/01/19 16:20:37 brouard
309: Test existence of gnuplot in imach path
310:
311: Revision 1.106 2006/01/19 13:24:36 brouard
312: Some cleaning and links added in html output
313:
314: Revision 1.105 2006/01/05 20:23:19 lievre
315: *** empty log message ***
316:
317: Revision 1.104 2005/09/30 16:11:43 lievre
318: (Module): sump fixed, loop imx fixed, and simplifications.
319: (Module): If the status is missing at the last wave but we know
320: that the person is alive, then we can code his/her status as -2
321: (instead of missing=-1 in earlier versions) and his/her
322: contributions to the likelihood is 1 - Prob of dying from last
323: health status (= 1-p13= p11+p12 in the easiest case of somebody in
324: the healthy state at last known wave). Version is 0.98
325:
326: Revision 1.103 2005/09/30 15:54:49 lievre
327: (Module): sump fixed, loop imx fixed, and simplifications.
328:
329: Revision 1.102 2004/09/15 17:31:30 brouard
330: Add the possibility to read data file including tab characters.
331:
332: Revision 1.101 2004/09/15 10:38:38 brouard
333: Fix on curr_time
334:
335: Revision 1.100 2004/07/12 18:29:06 brouard
336: Add version for Mac OS X. Just define UNIX in Makefile
337:
338: Revision 1.99 2004/06/05 08:57:40 brouard
339: *** empty log message ***
340:
341: Revision 1.98 2004/05/16 15:05:56 brouard
342: New version 0.97 . First attempt to estimate force of mortality
343: directly from the data i.e. without the need of knowing the health
344: state at each age, but using a Gompertz model: log u =a + b*age .
345: This is the basic analysis of mortality and should be done before any
346: other analysis, in order to test if the mortality estimated from the
347: cross-longitudinal survey is different from the mortality estimated
348: from other sources like vital statistic data.
349:
350: The same imach parameter file can be used but the option for mle should be -3.
351:
352: Agnès, who wrote this part of the code, tried to keep most of the
353: former routines in order to include the new code within the former code.
354:
355: The output is very simple: only an estimate of the intercept and of
356: the slope with 95% confident intervals.
357:
358: Current limitations:
359: A) Even if you enter covariates, i.e. with the
360: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
361: B) There is no computation of Life Expectancy nor Life Table.
362:
363: Revision 1.97 2004/02/20 13:25:42 lievre
364: Version 0.96d. Population forecasting command line is (temporarily)
365: suppressed.
366:
367: Revision 1.96 2003/07/15 15:38:55 brouard
368: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
369: rewritten within the same printf. Workaround: many printfs.
370:
371: Revision 1.95 2003/07/08 07:54:34 brouard
372: * imach.c (Repository):
373: (Repository): Using imachwizard code to output a more meaningful covariance
374: matrix (cov(a12,c31) instead of numbers.
375:
376: Revision 1.94 2003/06/27 13:00:02 brouard
377: Just cleaning
378:
379: Revision 1.93 2003/06/25 16:33:55 brouard
380: (Module): On windows (cygwin) function asctime_r doesn't
381: exist so I changed back to asctime which exists.
382: (Module): Version 0.96b
383:
384: Revision 1.92 2003/06/25 16:30:45 brouard
385: (Module): On windows (cygwin) function asctime_r doesn't
386: exist so I changed back to asctime which exists.
387:
388: Revision 1.91 2003/06/25 15:30:29 brouard
389: * imach.c (Repository): Duplicated warning errors corrected.
390: (Repository): Elapsed time after each iteration is now output. It
391: helps to forecast when convergence will be reached. Elapsed time
392: is stamped in powell. We created a new html file for the graphs
393: concerning matrix of covariance. It has extension -cov.htm.
394:
395: Revision 1.90 2003/06/24 12:34:15 brouard
396: (Module): Some bugs corrected for windows. Also, when
397: mle=-1 a template is output in file "or"mypar.txt with the design
398: of the covariance matrix to be input.
399:
400: Revision 1.89 2003/06/24 12:30:52 brouard
401: (Module): Some bugs corrected for windows. Also, when
402: mle=-1 a template is output in file "or"mypar.txt with the design
403: of the covariance matrix to be input.
404:
405: Revision 1.88 2003/06/23 17:54:56 brouard
406: * 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.
407:
408: Revision 1.87 2003/06/18 12:26:01 brouard
409: Version 0.96
410:
411: Revision 1.86 2003/06/17 20:04:08 brouard
412: (Module): Change position of html and gnuplot routines and added
413: routine fileappend.
414:
415: Revision 1.85 2003/06/17 13:12:43 brouard
416: * imach.c (Repository): Check when date of death was earlier that
417: current date of interview. It may happen when the death was just
418: prior to the death. In this case, dh was negative and likelihood
419: was wrong (infinity). We still send an "Error" but patch by
420: assuming that the date of death was just one stepm after the
421: interview.
422: (Repository): Because some people have very long ID (first column)
423: we changed int to long in num[] and we added a new lvector for
424: memory allocation. But we also truncated to 8 characters (left
425: truncation)
426: (Repository): No more line truncation errors.
427:
428: Revision 1.84 2003/06/13 21:44:43 brouard
429: * imach.c (Repository): Replace "freqsummary" at a correct
430: place. It differs from routine "prevalence" which may be called
431: many times. Probs is memory consuming and must be used with
432: parcimony.
433: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
434:
435: Revision 1.83 2003/06/10 13:39:11 lievre
436: *** empty log message ***
437:
438: Revision 1.82 2003/06/05 15:57:20 brouard
439: Add log in imach.c and fullversion number is now printed.
440:
441: */
442: /*
443: Interpolated Markov Chain
444:
445: Short summary of the programme:
446:
447: This program computes Healthy Life Expectancies from
448: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
449: first survey ("cross") where individuals from different ages are
450: interviewed on their health status or degree of disability (in the
451: case of a health survey which is our main interest) -2- at least a
452: second wave of interviews ("longitudinal") which measure each change
453: (if any) in individual health status. Health expectancies are
454: computed from the time spent in each health state according to a
455: model. More health states you consider, more time is necessary to reach the
456: Maximum Likelihood of the parameters involved in the model. The
457: simplest model is the multinomial logistic model where pij is the
458: probability to be observed in state j at the second wave
459: conditional to be observed in state i at the first wave. Therefore
460: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
461: 'age' is age and 'sex' is a covariate. If you want to have a more
462: complex model than "constant and age", you should modify the program
463: where the markup *Covariates have to be included here again* invites
464: you to do it. More covariates you add, slower the
465: convergence.
466:
467: The advantage of this computer programme, compared to a simple
468: multinomial logistic model, is clear when the delay between waves is not
469: identical for each individual. Also, if a individual missed an
470: intermediate interview, the information is lost, but taken into
471: account using an interpolation or extrapolation.
472:
473: hPijx is the probability to be observed in state i at age x+h
474: conditional to the observed state i at age x. The delay 'h' can be
475: split into an exact number (nh*stepm) of unobserved intermediate
476: states. This elementary transition (by month, quarter,
477: semester or year) is modelled as a multinomial logistic. The hPx
478: matrix is simply the matrix product of nh*stepm elementary matrices
479: and the contribution of each individual to the likelihood is simply
480: hPijx.
481:
482: Also this programme outputs the covariance matrix of the parameters but also
483: of the life expectancies. It also computes the period (stable) prevalence.
484:
485: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
486: Institut national d'études démographiques, Paris.
487: This software have been partly granted by Euro-REVES, a concerted action
488: from the European Union.
489: It is copyrighted identically to a GNU software product, ie programme and
490: software can be distributed freely for non commercial use. Latest version
491: can be accessed at http://euroreves.ined.fr/imach .
492:
493: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
494: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
495:
496: **********************************************************************/
497: /*
498: main
499: read parameterfile
500: read datafile
501: concatwav
502: freqsummary
503: if (mle >= 1)
504: mlikeli
505: print results files
506: if mle==1
507: computes hessian
508: read end of parameter file: agemin, agemax, bage, fage, estepm
509: begin-prev-date,...
510: open gnuplot file
511: open html file
512: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
513: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
514: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
515: freexexit2 possible for memory heap.
516:
517: h Pij x | pij_nom ficrestpij
518: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
519: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
520: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
521:
522: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
523: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
524: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
525: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
526: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
527:
528: forecasting if prevfcast==1 prevforecast call prevalence()
529: health expectancies
530: Variance-covariance of DFLE
531: prevalence()
532: movingaverage()
533: varevsij()
534: if popbased==1 varevsij(,popbased)
535: total life expectancies
536: Variance of period (stable) prevalence
537: end
538: */
539:
540: #define POWELL /* Instead of NLOPT */
541:
542: #include <math.h>
543: #include <stdio.h>
544: #include <stdlib.h>
545: #include <string.h>
546:
547: #ifdef _WIN32
548: #include <io.h>
549: #include <windows.h>
550: #include <tchar.h>
551: #else
552: #include <unistd.h>
553: #endif
554:
555: #include <limits.h>
556: #include <sys/types.h>
557:
558: #if defined(__GNUC__)
559: #include <sys/utsname.h> /* Doesn't work on Windows */
560: #endif
561:
562: #include <sys/stat.h>
563: #include <errno.h>
564: /* extern int errno; */
565:
566: /* #ifdef LINUX */
567: /* #include <time.h> */
568: /* #include "timeval.h" */
569: /* #else */
570: /* #include <sys/time.h> */
571: /* #endif */
572:
573: #include <time.h>
574:
575: #ifdef GSL
576: #include <gsl/gsl_errno.h>
577: #include <gsl/gsl_multimin.h>
578: #endif
579:
580:
581: #ifdef NLOPT
582: #include <nlopt.h>
583: typedef struct {
584: double (* function)(double [] );
585: } myfunc_data ;
586: #endif
587:
588: /* #include <libintl.h> */
589: /* #define _(String) gettext (String) */
590:
591: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
592:
593: #define GNUPLOTPROGRAM "gnuplot"
594: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
595: #define FILENAMELENGTH 132
596:
597: #define GLOCK_ERROR_NOPATH -1 /* empty path */
598: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
599:
600: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
601: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
602:
603: #define NINTERVMAX 8
604: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
605: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
606: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
607: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
608: #define MAXN 20000
609: #define YEARM 12. /**< Number of months per year */
610: #define AGESUP 130
611: #define AGEBASE 40
612: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
613: #ifdef _WIN32
614: #define DIRSEPARATOR '\\'
615: #define CHARSEPARATOR "\\"
616: #define ODIRSEPARATOR '/'
617: #else
618: #define DIRSEPARATOR '/'
619: #define CHARSEPARATOR "/"
620: #define ODIRSEPARATOR '\\'
621: #endif
622:
623: /* $Id: imach.c,v 1.174 2015/01/03 16:15:49 brouard Exp $ */
624: /* $State: Exp $ */
625:
626: 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";
627: char fullversion[]="$Revision: 1.174 $ $Date: 2015/01/03 16:15:49 $";
628: char strstart[80];
629: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
630: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
631: int nvar=0, nforce=0; /* Number of variables, number of forces */
632: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
633: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
634: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
635: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
636: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
637: int cptcovprodnoage=0; /**< Number of covariate products without age */
638: int cptcoveff=0; /* Total number of covariates to vary for printing results */
639: int cptcov=0; /* Working variable */
640: int npar=NPARMAX;
641: int nlstate=2; /* Number of live states */
642: int ndeath=1; /* Number of dead states */
643: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
644: int popbased=0;
645:
646: int *wav; /* Number of waves for this individuual 0 is possible */
647: int maxwav=0; /* Maxim number of waves */
648: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
649: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
650: int gipmx=0, gsw=0; /* Global variables on the number of contributions
651: to the likelihood and the sum of weights (done by funcone)*/
652: int mle=1, weightopt=0;
653: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
654: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
655: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
656: * wave mi and wave mi+1 is not an exact multiple of stepm. */
657: int countcallfunc=0; /* Count the number of calls to func */
658: double jmean=1; /* Mean space between 2 waves */
659: double **matprod2(); /* test */
660: double **oldm, **newm, **savm; /* Working pointers to matrices */
661: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
662: /*FILE *fic ; */ /* Used in readdata only */
663: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
664: FILE *ficlog, *ficrespow;
665: int globpr=0; /* Global variable for printing or not */
666: double fretone; /* Only one call to likelihood */
667: long ipmx=0; /* Number of contributions */
668: double sw; /* Sum of weights */
669: char filerespow[FILENAMELENGTH];
670: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
671: FILE *ficresilk;
672: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
673: FILE *ficresprobmorprev;
674: FILE *fichtm, *fichtmcov; /* Html File */
675: FILE *ficreseij;
676: char filerese[FILENAMELENGTH];
677: FILE *ficresstdeij;
678: char fileresstde[FILENAMELENGTH];
679: FILE *ficrescveij;
680: char filerescve[FILENAMELENGTH];
681: FILE *ficresvij;
682: char fileresv[FILENAMELENGTH];
683: FILE *ficresvpl;
684: char fileresvpl[FILENAMELENGTH];
685: char title[MAXLINE];
686: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
687: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
688: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
689: char command[FILENAMELENGTH];
690: int outcmd=0;
691:
692: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
693:
694: char filelog[FILENAMELENGTH]; /* Log file */
695: char filerest[FILENAMELENGTH];
696: char fileregp[FILENAMELENGTH];
697: char popfile[FILENAMELENGTH];
698:
699: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
700:
701: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
702: /* struct timezone tzp; */
703: /* extern int gettimeofday(); */
704: struct tm tml, *gmtime(), *localtime();
705:
706: extern time_t time();
707:
708: struct tm start_time, end_time, curr_time, last_time, forecast_time;
709: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
710: struct tm tm;
711:
712: char strcurr[80], strfor[80];
713:
714: char *endptr;
715: long lval;
716: double dval;
717:
718: #define NR_END 1
719: #define FREE_ARG char*
720: #define FTOL 1.0e-10
721:
722: #define NRANSI
723: #define ITMAX 200
724:
725: #define TOL 2.0e-4
726:
727: #define CGOLD 0.3819660
728: #define ZEPS 1.0e-10
729: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
730:
731: #define GOLD 1.618034
732: #define GLIMIT 100.0
733: #define TINY 1.0e-20
734:
735: static double maxarg1,maxarg2;
736: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
737: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
738:
739: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
740: #define rint(a) floor(a+0.5)
741: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
742: /* #define mytinydouble 1.0e-16 */
743: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
744: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
745: /* static double dsqrarg; */
746: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
747: static double sqrarg;
748: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
749: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
750: int agegomp= AGEGOMP;
751:
752: int imx;
753: int stepm=1;
754: /* Stepm, step in month: minimum step interpolation*/
755:
756: int estepm;
757: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
758:
759: int m,nb;
760: long *num;
761: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
762: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
763: double **pmmij, ***probs;
764: double *ageexmed,*agecens;
765: double dateintmean=0;
766:
767: double *weight;
768: int **s; /* Status */
769: double *agedc;
770: double **covar; /**< covar[j,i], value of jth covariate for individual i,
771: * covar=matrix(0,NCOVMAX,1,n);
772: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
773: double idx;
774: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
775: int *Ndum; /** Freq of modality (tricode */
776: int **codtab; /**< codtab=imatrix(1,100,1,10); */
777: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
778: double *lsurv, *lpop, *tpop;
779:
780: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
781: double ftolhess; /**< Tolerance for computing hessian */
782:
783: /**************** split *************************/
784: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
785: {
786: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
787: the name of the file (name), its extension only (ext) and its first part of the name (finame)
788: */
789: char *ss; /* pointer */
790: int l1, l2; /* length counters */
791:
792: l1 = strlen(path ); /* length of path */
793: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
794: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
795: if ( ss == NULL ) { /* no directory, so determine current directory */
796: strcpy( name, path ); /* we got the fullname name because no directory */
797: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
798: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
799: /* get current working directory */
800: /* extern char* getcwd ( char *buf , int len);*/
801: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
802: return( GLOCK_ERROR_GETCWD );
803: }
804: /* got dirc from getcwd*/
805: printf(" DIRC = %s \n",dirc);
806: } else { /* strip direcotry from path */
807: ss++; /* after this, the filename */
808: l2 = strlen( ss ); /* length of filename */
809: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
810: strcpy( name, ss ); /* save file name */
811: strncpy( dirc, path, l1 - l2 ); /* now the directory */
812: dirc[l1-l2] = 0; /* add zero */
813: printf(" DIRC2 = %s \n",dirc);
814: }
815: /* We add a separator at the end of dirc if not exists */
816: l1 = strlen( dirc ); /* length of directory */
817: if( dirc[l1-1] != DIRSEPARATOR ){
818: dirc[l1] = DIRSEPARATOR;
819: dirc[l1+1] = 0;
820: printf(" DIRC3 = %s \n",dirc);
821: }
822: ss = strrchr( name, '.' ); /* find last / */
823: if (ss >0){
824: ss++;
825: strcpy(ext,ss); /* save extension */
826: l1= strlen( name);
827: l2= strlen(ss)+1;
828: strncpy( finame, name, l1-l2);
829: finame[l1-l2]= 0;
830: }
831:
832: return( 0 ); /* we're done */
833: }
834:
835:
836: /******************************************/
837:
838: void replace_back_to_slash(char *s, char*t)
839: {
840: int i;
841: int lg=0;
842: i=0;
843: lg=strlen(t);
844: for(i=0; i<= lg; i++) {
845: (s[i] = t[i]);
846: if (t[i]== '\\') s[i]='/';
847: }
848: }
849:
850: char *trimbb(char *out, char *in)
851: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
852: char *s;
853: s=out;
854: while (*in != '\0'){
855: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
856: in++;
857: }
858: *out++ = *in++;
859: }
860: *out='\0';
861: return s;
862: }
863:
864: char *cutl(char *blocc, char *alocc, char *in, char occ)
865: {
866: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
867: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
868: gives blocc="abcdef2ghi" and alocc="j".
869: If occ is not found blocc is null and alocc is equal to in. Returns blocc
870: */
871: char *s, *t;
872: t=in;s=in;
873: while ((*in != occ) && (*in != '\0')){
874: *alocc++ = *in++;
875: }
876: if( *in == occ){
877: *(alocc)='\0';
878: s=++in;
879: }
880:
881: if (s == t) {/* occ not found */
882: *(alocc-(in-s))='\0';
883: in=s;
884: }
885: while ( *in != '\0'){
886: *blocc++ = *in++;
887: }
888:
889: *blocc='\0';
890: return t;
891: }
892: char *cutv(char *blocc, char *alocc, char *in, char occ)
893: {
894: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
895: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
896: gives blocc="abcdef2ghi" and alocc="j".
897: If occ is not found blocc is null and alocc is equal to in. Returns alocc
898: */
899: char *s, *t;
900: t=in;s=in;
901: while (*in != '\0'){
902: while( *in == occ){
903: *blocc++ = *in++;
904: s=in;
905: }
906: *blocc++ = *in++;
907: }
908: if (s == t) /* occ not found */
909: *(blocc-(in-s))='\0';
910: else
911: *(blocc-(in-s)-1)='\0';
912: in=s;
913: while ( *in != '\0'){
914: *alocc++ = *in++;
915: }
916:
917: *alocc='\0';
918: return s;
919: }
920:
921: int nbocc(char *s, char occ)
922: {
923: int i,j=0;
924: int lg=20;
925: i=0;
926: lg=strlen(s);
927: for(i=0; i<= lg; i++) {
928: if (s[i] == occ ) j++;
929: }
930: return j;
931: }
932:
933: /* void cutv(char *u,char *v, char*t, char occ) */
934: /* { */
935: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
936: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
937: /* gives u="abcdef2ghi" and v="j" *\/ */
938: /* int i,lg,j,p=0; */
939: /* i=0; */
940: /* lg=strlen(t); */
941: /* for(j=0; j<=lg-1; j++) { */
942: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
943: /* } */
944:
945: /* for(j=0; j<p; j++) { */
946: /* (u[j] = t[j]); */
947: /* } */
948: /* u[p]='\0'; */
949:
950: /* for(j=0; j<= lg; j++) { */
951: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
952: /* } */
953: /* } */
954:
955: #ifdef _WIN32
956: char * strsep(char **pp, const char *delim)
957: {
958: char *p, *q;
959:
960: if ((p = *pp) == NULL)
961: return 0;
962: if ((q = strpbrk (p, delim)) != NULL)
963: {
964: *pp = q + 1;
965: *q = '\0';
966: }
967: else
968: *pp = 0;
969: return p;
970: }
971: #endif
972:
973: /********************** nrerror ********************/
974:
975: void nrerror(char error_text[])
976: {
977: fprintf(stderr,"ERREUR ...\n");
978: fprintf(stderr,"%s\n",error_text);
979: exit(EXIT_FAILURE);
980: }
981: /*********************** vector *******************/
982: double *vector(int nl, int nh)
983: {
984: double *v;
985: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
986: if (!v) nrerror("allocation failure in vector");
987: return v-nl+NR_END;
988: }
989:
990: /************************ free vector ******************/
991: void free_vector(double*v, int nl, int nh)
992: {
993: free((FREE_ARG)(v+nl-NR_END));
994: }
995:
996: /************************ivector *******************************/
997: int *ivector(long nl,long nh)
998: {
999: int *v;
1000: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1001: if (!v) nrerror("allocation failure in ivector");
1002: return v-nl+NR_END;
1003: }
1004:
1005: /******************free ivector **************************/
1006: void free_ivector(int *v, long nl, long nh)
1007: {
1008: free((FREE_ARG)(v+nl-NR_END));
1009: }
1010:
1011: /************************lvector *******************************/
1012: long *lvector(long nl,long nh)
1013: {
1014: long *v;
1015: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1016: if (!v) nrerror("allocation failure in ivector");
1017: return v-nl+NR_END;
1018: }
1019:
1020: /******************free lvector **************************/
1021: void free_lvector(long *v, long nl, long nh)
1022: {
1023: free((FREE_ARG)(v+nl-NR_END));
1024: }
1025:
1026: /******************* imatrix *******************************/
1027: int **imatrix(long nrl, long nrh, long ncl, long nch)
1028: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1029: {
1030: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1031: int **m;
1032:
1033: /* allocate pointers to rows */
1034: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1035: if (!m) nrerror("allocation failure 1 in matrix()");
1036: m += NR_END;
1037: m -= nrl;
1038:
1039:
1040: /* allocate rows and set pointers to them */
1041: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1042: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1043: m[nrl] += NR_END;
1044: m[nrl] -= ncl;
1045:
1046: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1047:
1048: /* return pointer to array of pointers to rows */
1049: return m;
1050: }
1051:
1052: /****************** free_imatrix *************************/
1053: void free_imatrix(m,nrl,nrh,ncl,nch)
1054: int **m;
1055: long nch,ncl,nrh,nrl;
1056: /* free an int matrix allocated by imatrix() */
1057: {
1058: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1059: free((FREE_ARG) (m+nrl-NR_END));
1060: }
1061:
1062: /******************* matrix *******************************/
1063: double **matrix(long nrl, long nrh, long ncl, long nch)
1064: {
1065: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1066: double **m;
1067:
1068: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1069: if (!m) nrerror("allocation failure 1 in matrix()");
1070: m += NR_END;
1071: m -= nrl;
1072:
1073: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1074: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1075: m[nrl] += NR_END;
1076: m[nrl] -= ncl;
1077:
1078: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1079: return m;
1080: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1081: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1082: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1083: */
1084: }
1085:
1086: /*************************free matrix ************************/
1087: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1088: {
1089: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1090: free((FREE_ARG)(m+nrl-NR_END));
1091: }
1092:
1093: /******************* ma3x *******************************/
1094: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1095: {
1096: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1097: double ***m;
1098:
1099: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1100: if (!m) nrerror("allocation failure 1 in matrix()");
1101: m += NR_END;
1102: m -= nrl;
1103:
1104: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1105: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1106: m[nrl] += NR_END;
1107: m[nrl] -= ncl;
1108:
1109: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1110:
1111: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1112: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1113: m[nrl][ncl] += NR_END;
1114: m[nrl][ncl] -= nll;
1115: for (j=ncl+1; j<=nch; j++)
1116: m[nrl][j]=m[nrl][j-1]+nlay;
1117:
1118: for (i=nrl+1; i<=nrh; i++) {
1119: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1120: for (j=ncl+1; j<=nch; j++)
1121: m[i][j]=m[i][j-1]+nlay;
1122: }
1123: return m;
1124: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1125: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1126: */
1127: }
1128:
1129: /*************************free ma3x ************************/
1130: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1131: {
1132: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1133: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1134: free((FREE_ARG)(m+nrl-NR_END));
1135: }
1136:
1137: /*************** function subdirf ***********/
1138: char *subdirf(char fileres[])
1139: {
1140: /* Caution optionfilefiname is hidden */
1141: strcpy(tmpout,optionfilefiname);
1142: strcat(tmpout,"/"); /* Add to the right */
1143: strcat(tmpout,fileres);
1144: return tmpout;
1145: }
1146:
1147: /*************** function subdirf2 ***********/
1148: char *subdirf2(char fileres[], char *preop)
1149: {
1150:
1151: /* Caution optionfilefiname is hidden */
1152: strcpy(tmpout,optionfilefiname);
1153: strcat(tmpout,"/");
1154: strcat(tmpout,preop);
1155: strcat(tmpout,fileres);
1156: return tmpout;
1157: }
1158:
1159: /*************** function subdirf3 ***********/
1160: char *subdirf3(char fileres[], char *preop, char *preop2)
1161: {
1162:
1163: /* Caution optionfilefiname is hidden */
1164: strcpy(tmpout,optionfilefiname);
1165: strcat(tmpout,"/");
1166: strcat(tmpout,preop);
1167: strcat(tmpout,preop2);
1168: strcat(tmpout,fileres);
1169: return tmpout;
1170: }
1171:
1172: char *asc_diff_time(long time_sec, char ascdiff[])
1173: {
1174: long sec_left, days, hours, minutes;
1175: days = (time_sec) / (60*60*24);
1176: sec_left = (time_sec) % (60*60*24);
1177: hours = (sec_left) / (60*60) ;
1178: sec_left = (sec_left) %(60*60);
1179: minutes = (sec_left) /60;
1180: sec_left = (sec_left) % (60);
1181: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1182: return ascdiff;
1183: }
1184:
1185: /***************** f1dim *************************/
1186: extern int ncom;
1187: extern double *pcom,*xicom;
1188: extern double (*nrfunc)(double []);
1189:
1190: double f1dim(double x)
1191: {
1192: int j;
1193: double f;
1194: double *xt;
1195:
1196: xt=vector(1,ncom);
1197: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1198: f=(*nrfunc)(xt);
1199: free_vector(xt,1,ncom);
1200: return f;
1201: }
1202:
1203: /*****************brent *************************/
1204: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1205: {
1206: int iter;
1207: double a,b,d,etemp;
1208: double fu=0,fv,fw,fx;
1209: double ftemp=0.;
1210: double p,q,r,tol1,tol2,u,v,w,x,xm;
1211: double e=0.0;
1212:
1213: a=(ax < cx ? ax : cx);
1214: b=(ax > cx ? ax : cx);
1215: x=w=v=bx;
1216: fw=fv=fx=(*f)(x);
1217: for (iter=1;iter<=ITMAX;iter++) {
1218: xm=0.5*(a+b);
1219: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1220: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1221: printf(".");fflush(stdout);
1222: fprintf(ficlog,".");fflush(ficlog);
1223: #ifdef DEBUGBRENT
1224: 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);
1225: 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);
1226: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1227: #endif
1228: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1229: *xmin=x;
1230: return fx;
1231: }
1232: ftemp=fu;
1233: if (fabs(e) > tol1) {
1234: r=(x-w)*(fx-fv);
1235: q=(x-v)*(fx-fw);
1236: p=(x-v)*q-(x-w)*r;
1237: q=2.0*(q-r);
1238: if (q > 0.0) p = -p;
1239: q=fabs(q);
1240: etemp=e;
1241: e=d;
1242: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1243: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1244: else {
1245: d=p/q;
1246: u=x+d;
1247: if (u-a < tol2 || b-u < tol2)
1248: d=SIGN(tol1,xm-x);
1249: }
1250: } else {
1251: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1252: }
1253: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1254: fu=(*f)(u);
1255: if (fu <= fx) {
1256: if (u >= x) a=x; else b=x;
1257: SHFT(v,w,x,u)
1258: SHFT(fv,fw,fx,fu)
1259: } else {
1260: if (u < x) a=u; else b=u;
1261: if (fu <= fw || w == x) {
1262: v=w;
1263: w=u;
1264: fv=fw;
1265: fw=fu;
1266: } else if (fu <= fv || v == x || v == w) {
1267: v=u;
1268: fv=fu;
1269: }
1270: }
1271: }
1272: nrerror("Too many iterations in brent");
1273: *xmin=x;
1274: return fx;
1275: }
1276:
1277: /****************** mnbrak ***********************/
1278:
1279: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1280: double (*func)(double))
1281: {
1282: double ulim,u,r,q, dum;
1283: double fu;
1284:
1285: *fa=(*func)(*ax);
1286: *fb=(*func)(*bx);
1287: if (*fb > *fa) {
1288: SHFT(dum,*ax,*bx,dum)
1289: SHFT(dum,*fb,*fa,dum)
1290: }
1291: *cx=(*bx)+GOLD*(*bx-*ax);
1292: *fc=(*func)(*cx);
1293: while (*fb > *fc) { /* Declining fa, fb, fc */
1294: r=(*bx-*ax)*(*fb-*fc);
1295: q=(*bx-*cx)*(*fb-*fa);
1296: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1297: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1298: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1299: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1300: fu=(*func)(u);
1301: #ifdef DEBUG
1302: /* f(x)=A(x-u)**2+f(u) */
1303: double A, fparabu;
1304: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1305: fparabu= *fa - A*(*ax-u)*(*ax-u);
1306: 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);
1307: 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);
1308: #endif
1309: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1310: fu=(*func)(u);
1311: if (fu < *fc) {
1312: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1313: SHFT(*fb,*fc,fu,(*func)(u))
1314: }
1315: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1316: u=ulim;
1317: fu=(*func)(u);
1318: } else {
1319: u=(*cx)+GOLD*(*cx-*bx);
1320: fu=(*func)(u);
1321: }
1322: SHFT(*ax,*bx,*cx,u)
1323: SHFT(*fa,*fb,*fc,fu)
1324: }
1325: }
1326:
1327: /*************** linmin ************************/
1328: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1329: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1330: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1331: the value of func at the returned location p . This is actually all accomplished by calling the
1332: routines mnbrak and brent .*/
1333: int ncom;
1334: double *pcom,*xicom;
1335: double (*nrfunc)(double []);
1336:
1337: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1338: {
1339: double brent(double ax, double bx, double cx,
1340: double (*f)(double), double tol, double *xmin);
1341: double f1dim(double x);
1342: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1343: double *fc, double (*func)(double));
1344: int j;
1345: double xx,xmin,bx,ax;
1346: double fx,fb,fa;
1347:
1348: ncom=n;
1349: pcom=vector(1,n);
1350: xicom=vector(1,n);
1351: nrfunc=func;
1352: for (j=1;j<=n;j++) {
1353: pcom[j]=p[j];
1354: xicom[j]=xi[j];
1355: }
1356: ax=0.0;
1357: xx=1.0;
1358: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1359: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1360: #ifdef DEBUG
1361: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1362: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1363: #endif
1364: for (j=1;j<=n;j++) {
1365: xi[j] *= xmin;
1366: p[j] += xi[j];
1367: }
1368: free_vector(xicom,1,n);
1369: free_vector(pcom,1,n);
1370: }
1371:
1372:
1373: /*************** powell ************************/
1374: /*
1375: Minimization of a function func of n variables. Input consists of an initial starting point
1376: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1377: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1378: such that failure to decrease by more than this amount on one iteration signals doneness. On
1379: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1380: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1381: */
1382: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1383: double (*func)(double []))
1384: {
1385: void linmin(double p[], double xi[], int n, double *fret,
1386: double (*func)(double []));
1387: int i,ibig,j;
1388: double del,t,*pt,*ptt,*xit;
1389: double fp,fptt;
1390: double *xits;
1391: int niterf, itmp;
1392:
1393: pt=vector(1,n);
1394: ptt=vector(1,n);
1395: xit=vector(1,n);
1396: xits=vector(1,n);
1397: *fret=(*func)(p);
1398: for (j=1;j<=n;j++) pt[j]=p[j];
1399: rcurr_time = time(NULL);
1400: for (*iter=1;;++(*iter)) {
1401: fp=(*fret);
1402: ibig=0;
1403: del=0.0;
1404: rlast_time=rcurr_time;
1405: /* (void) gettimeofday(&curr_time,&tzp); */
1406: rcurr_time = time(NULL);
1407: curr_time = *localtime(&rcurr_time);
1408: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1409: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1410: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1411: for (i=1;i<=n;i++) {
1412: printf(" %d %.12f",i, p[i]);
1413: fprintf(ficlog," %d %.12lf",i, p[i]);
1414: fprintf(ficrespow," %.12lf", p[i]);
1415: }
1416: printf("\n");
1417: fprintf(ficlog,"\n");
1418: fprintf(ficrespow,"\n");fflush(ficrespow);
1419: if(*iter <=3){
1420: tml = *localtime(&rcurr_time);
1421: strcpy(strcurr,asctime(&tml));
1422: rforecast_time=rcurr_time;
1423: itmp = strlen(strcurr);
1424: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1425: strcurr[itmp-1]='\0';
1426: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1427: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1428: for(niterf=10;niterf<=30;niterf+=10){
1429: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1430: forecast_time = *localtime(&rforecast_time);
1431: strcpy(strfor,asctime(&forecast_time));
1432: itmp = strlen(strfor);
1433: if(strfor[itmp-1]=='\n')
1434: strfor[itmp-1]='\0';
1435: 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);
1436: 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);
1437: }
1438: }
1439: for (i=1;i<=n;i++) {
1440: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1441: fptt=(*fret);
1442: #ifdef DEBUG
1443: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1444: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1445: #endif
1446: printf("%d",i);fflush(stdout);
1447: fprintf(ficlog,"%d",i);fflush(ficlog);
1448: linmin(p,xit,n,fret,func);
1449: if (fabs(fptt-(*fret)) > del) {
1450: del=fabs(fptt-(*fret));
1451: ibig=i;
1452: }
1453: #ifdef DEBUG
1454: printf("%d %.12e",i,(*fret));
1455: fprintf(ficlog,"%d %.12e",i,(*fret));
1456: for (j=1;j<=n;j++) {
1457: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1458: printf(" x(%d)=%.12e",j,xit[j]);
1459: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1460: }
1461: for(j=1;j<=n;j++) {
1462: printf(" p(%d)=%.12e",j,p[j]);
1463: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1464: }
1465: printf("\n");
1466: fprintf(ficlog,"\n");
1467: #endif
1468: } /* end i */
1469: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1470: #ifdef DEBUG
1471: int k[2],l;
1472: k[0]=1;
1473: k[1]=-1;
1474: printf("Max: %.12e",(*func)(p));
1475: fprintf(ficlog,"Max: %.12e",(*func)(p));
1476: for (j=1;j<=n;j++) {
1477: printf(" %.12e",p[j]);
1478: fprintf(ficlog," %.12e",p[j]);
1479: }
1480: printf("\n");
1481: fprintf(ficlog,"\n");
1482: for(l=0;l<=1;l++) {
1483: for (j=1;j<=n;j++) {
1484: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1485: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1486: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1487: }
1488: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1489: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1490: }
1491: #endif
1492:
1493:
1494: free_vector(xit,1,n);
1495: free_vector(xits,1,n);
1496: free_vector(ptt,1,n);
1497: free_vector(pt,1,n);
1498: return;
1499: }
1500: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1501: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1502: ptt[j]=2.0*p[j]-pt[j];
1503: xit[j]=p[j]-pt[j];
1504: pt[j]=p[j];
1505: }
1506: fptt=(*func)(ptt);
1507: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1508: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1509: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1510: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1511: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1512: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1513: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1514: /* Thus we compare delta(2h) with observed f1-f3 */
1515: /* or best gain on one ancient line 'del' with total */
1516: /* gain f1-f2 = f1 - f2 - 'del' with del */
1517: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1518:
1519: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1520: t= t- del*SQR(fp-fptt);
1521: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1522: 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);
1523: #ifdef DEBUG
1524: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1525: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1526: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1527: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1528: 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);
1529: 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);
1530: #endif
1531: if (t < 0.0) { /* Then we use it for last direction */
1532: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1533: for (j=1;j<=n;j++) {
1534: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1535: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1536: }
1537: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1538: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1539:
1540: #ifdef DEBUG
1541: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1542: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1543: for(j=1;j<=n;j++){
1544: printf(" %.12e",xit[j]);
1545: fprintf(ficlog," %.12e",xit[j]);
1546: }
1547: printf("\n");
1548: fprintf(ficlog,"\n");
1549: #endif
1550: } /* end of t negative */
1551: } /* end if (fptt < fp) */
1552: }
1553: }
1554:
1555: /**** Prevalence limit (stable or period prevalence) ****************/
1556:
1557: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1558: {
1559: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1560: matrix by transitions matrix until convergence is reached */
1561:
1562: int i, ii,j,k;
1563: double min, max, maxmin, maxmax,sumnew=0.;
1564: /* double **matprod2(); */ /* test */
1565: double **out, cov[NCOVMAX+1], **pmij();
1566: double **newm;
1567: double agefin, delaymax=50 ; /* Max number of years to converge */
1568:
1569: for (ii=1;ii<=nlstate+ndeath;ii++)
1570: for (j=1;j<=nlstate+ndeath;j++){
1571: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1572: }
1573:
1574: cov[1]=1.;
1575:
1576: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1577: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1578: newm=savm;
1579: /* Covariates have to be included here again */
1580: cov[2]=agefin;
1581:
1582: for (k=1; k<=cptcovn;k++) {
1583: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1584: /*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]]);*/
1585: }
1586: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1587: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1588: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1589:
1590: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1591: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1592: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1593: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1594: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1595: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1596:
1597: savm=oldm;
1598: oldm=newm;
1599: maxmax=0.;
1600: for(j=1;j<=nlstate;j++){
1601: min=1.;
1602: max=0.;
1603: for(i=1; i<=nlstate; i++) {
1604: sumnew=0;
1605: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1606: prlim[i][j]= newm[i][j]/(1-sumnew);
1607: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1608: max=FMAX(max,prlim[i][j]);
1609: min=FMIN(min,prlim[i][j]);
1610: }
1611: maxmin=max-min;
1612: maxmax=FMAX(maxmax,maxmin);
1613: } /* j loop */
1614: if(maxmax < ftolpl){
1615: return prlim;
1616: }
1617: } /* age loop */
1618: return prlim; /* should not reach here */
1619: }
1620:
1621: /*************** transition probabilities ***************/
1622:
1623: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1624: {
1625: /* According to parameters values stored in x and the covariate's values stored in cov,
1626: computes the probability to be observed in state j being in state i by appying the
1627: model to the ncovmodel covariates (including constant and age).
1628: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1629: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1630: ncth covariate in the global vector x is given by the formula:
1631: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1632: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1633: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1634: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1635: Outputs ps[i][j] the probability to be observed in j being in j according to
1636: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1637: */
1638: double s1, lnpijopii;
1639: /*double t34;*/
1640: int i,j, nc, ii, jj;
1641:
1642: for(i=1; i<= nlstate; i++){
1643: for(j=1; j<i;j++){
1644: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1645: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1646: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1647: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1648: }
1649: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1650: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1651: }
1652: for(j=i+1; j<=nlstate+ndeath;j++){
1653: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1654: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1655: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1656: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1657: }
1658: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1659: }
1660: }
1661:
1662: for(i=1; i<= nlstate; i++){
1663: s1=0;
1664: for(j=1; j<i; j++){
1665: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1666: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1667: }
1668: for(j=i+1; j<=nlstate+ndeath; j++){
1669: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1670: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1671: }
1672: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1673: ps[i][i]=1./(s1+1.);
1674: /* Computing other pijs */
1675: for(j=1; j<i; j++)
1676: ps[i][j]= exp(ps[i][j])*ps[i][i];
1677: for(j=i+1; j<=nlstate+ndeath; j++)
1678: ps[i][j]= exp(ps[i][j])*ps[i][i];
1679: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1680: } /* end i */
1681:
1682: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1683: for(jj=1; jj<= nlstate+ndeath; jj++){
1684: ps[ii][jj]=0;
1685: ps[ii][ii]=1;
1686: }
1687: }
1688:
1689:
1690: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1691: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1692: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1693: /* } */
1694: /* printf("\n "); */
1695: /* } */
1696: /* printf("\n ");printf("%lf ",cov[2]);*/
1697: /*
1698: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1699: goto end;*/
1700: return ps;
1701: }
1702:
1703: /**************** Product of 2 matrices ******************/
1704:
1705: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1706: {
1707: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1708: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1709: /* in, b, out are matrice of pointers which should have been initialized
1710: before: only the contents of out is modified. The function returns
1711: a pointer to pointers identical to out */
1712: int i, j, k;
1713: for(i=nrl; i<= nrh; i++)
1714: for(k=ncolol; k<=ncoloh; k++){
1715: out[i][k]=0.;
1716: for(j=ncl; j<=nch; j++)
1717: out[i][k] +=in[i][j]*b[j][k];
1718: }
1719: return out;
1720: }
1721:
1722:
1723: /************* Higher Matrix Product ***************/
1724:
1725: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1726: {
1727: /* Computes the transition matrix starting at age 'age' over
1728: 'nhstepm*hstepm*stepm' months (i.e. until
1729: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1730: nhstepm*hstepm matrices.
1731: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1732: (typically every 2 years instead of every month which is too big
1733: for the memory).
1734: Model is determined by parameters x and covariates have to be
1735: included manually here.
1736:
1737: */
1738:
1739: int i, j, d, h, k;
1740: double **out, cov[NCOVMAX+1];
1741: double **newm;
1742:
1743: /* Hstepm could be zero and should return the unit matrix */
1744: for (i=1;i<=nlstate+ndeath;i++)
1745: for (j=1;j<=nlstate+ndeath;j++){
1746: oldm[i][j]=(i==j ? 1.0 : 0.0);
1747: po[i][j][0]=(i==j ? 1.0 : 0.0);
1748: }
1749: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1750: for(h=1; h <=nhstepm; h++){
1751: for(d=1; d <=hstepm; d++){
1752: newm=savm;
1753: /* Covariates have to be included here again */
1754: cov[1]=1.;
1755: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1756: for (k=1; k<=cptcovn;k++)
1757: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1758: for (k=1; k<=cptcovage;k++)
1759: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1760: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1761: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1762:
1763:
1764: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1765: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1766: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1767: pmij(pmmij,cov,ncovmodel,x,nlstate));
1768: savm=oldm;
1769: oldm=newm;
1770: }
1771: for(i=1; i<=nlstate+ndeath; i++)
1772: for(j=1;j<=nlstate+ndeath;j++) {
1773: po[i][j][h]=newm[i][j];
1774: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1775: }
1776: /*printf("h=%d ",h);*/
1777: } /* end h */
1778: /* printf("\n H=%d \n",h); */
1779: return po;
1780: }
1781:
1782: #ifdef NLOPT
1783: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1784: double fret;
1785: double *xt;
1786: int j;
1787: myfunc_data *d2 = (myfunc_data *) pd;
1788: /* xt = (p1-1); */
1789: xt=vector(1,n);
1790: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1791:
1792: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1793: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1794: printf("Function = %.12lf ",fret);
1795: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1796: printf("\n");
1797: free_vector(xt,1,n);
1798: return fret;
1799: }
1800: #endif
1801:
1802: /*************** log-likelihood *************/
1803: double func( double *x)
1804: {
1805: int i, ii, j, k, mi, d, kk;
1806: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1807: double **out;
1808: double sw; /* Sum of weights */
1809: double lli; /* Individual log likelihood */
1810: int s1, s2;
1811: double bbh, survp;
1812: long ipmx;
1813: /*extern weight */
1814: /* We are differentiating ll according to initial status */
1815: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1816: /*for(i=1;i<imx;i++)
1817: printf(" %d\n",s[4][i]);
1818: */
1819:
1820: ++countcallfunc;
1821:
1822: cov[1]=1.;
1823:
1824: for(k=1; k<=nlstate; k++) ll[k]=0.;
1825:
1826: if(mle==1){
1827: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1828: /* Computes the values of the ncovmodel covariates of the model
1829: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1830: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1831: to be observed in j being in i according to the model.
1832: */
1833: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1834: cov[2+k]=covar[Tvar[k]][i];
1835: }
1836: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1837: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1838: has been calculated etc */
1839: for(mi=1; mi<= wav[i]-1; mi++){
1840: for (ii=1;ii<=nlstate+ndeath;ii++)
1841: for (j=1;j<=nlstate+ndeath;j++){
1842: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1843: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1844: }
1845: for(d=0; d<dh[mi][i]; d++){
1846: newm=savm;
1847: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1848: for (kk=1; kk<=cptcovage;kk++) {
1849: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1850: }
1851: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1852: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1853: savm=oldm;
1854: oldm=newm;
1855: } /* end mult */
1856:
1857: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1858: /* But now since version 0.9 we anticipate for bias at large stepm.
1859: * If stepm is larger than one month (smallest stepm) and if the exact delay
1860: * (in months) between two waves is not a multiple of stepm, we rounded to
1861: * the nearest (and in case of equal distance, to the lowest) interval but now
1862: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1863: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1864: * probability in order to take into account the bias as a fraction of the way
1865: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1866: * -stepm/2 to stepm/2 .
1867: * For stepm=1 the results are the same as for previous versions of Imach.
1868: * For stepm > 1 the results are less biased than in previous versions.
1869: */
1870: s1=s[mw[mi][i]][i];
1871: s2=s[mw[mi+1][i]][i];
1872: bbh=(double)bh[mi][i]/(double)stepm;
1873: /* bias bh is positive if real duration
1874: * is higher than the multiple of stepm and negative otherwise.
1875: */
1876: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1877: if( s2 > nlstate){
1878: /* i.e. if s2 is a death state and if the date of death is known
1879: then the contribution to the likelihood is the probability to
1880: die between last step unit time and current step unit time,
1881: which is also equal to probability to die before dh
1882: minus probability to die before dh-stepm .
1883: In version up to 0.92 likelihood was computed
1884: as if date of death was unknown. Death was treated as any other
1885: health state: the date of the interview describes the actual state
1886: and not the date of a change in health state. The former idea was
1887: to consider that at each interview the state was recorded
1888: (healthy, disable or death) and IMaCh was corrected; but when we
1889: introduced the exact date of death then we should have modified
1890: the contribution of an exact death to the likelihood. This new
1891: contribution is smaller and very dependent of the step unit
1892: stepm. It is no more the probability to die between last interview
1893: and month of death but the probability to survive from last
1894: interview up to one month before death multiplied by the
1895: probability to die within a month. Thanks to Chris
1896: Jackson for correcting this bug. Former versions increased
1897: mortality artificially. The bad side is that we add another loop
1898: which slows down the processing. The difference can be up to 10%
1899: lower mortality.
1900: */
1901: lli=log(out[s1][s2] - savm[s1][s2]);
1902:
1903:
1904: } else if (s2==-2) {
1905: for (j=1,survp=0. ; j<=nlstate; j++)
1906: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1907: /*survp += out[s1][j]; */
1908: lli= log(survp);
1909: }
1910:
1911: else if (s2==-4) {
1912: for (j=3,survp=0. ; j<=nlstate; j++)
1913: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1914: lli= log(survp);
1915: }
1916:
1917: else if (s2==-5) {
1918: for (j=1,survp=0. ; j<=2; j++)
1919: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1920: lli= log(survp);
1921: }
1922:
1923: else{
1924: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1925: /* 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 */
1926: }
1927: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1928: /*if(lli ==000.0)*/
1929: /*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); */
1930: ipmx +=1;
1931: sw += weight[i];
1932: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1933: } /* end of wave */
1934: } /* end of individual */
1935: } else if(mle==2){
1936: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1937: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1938: for(mi=1; mi<= wav[i]-1; mi++){
1939: for (ii=1;ii<=nlstate+ndeath;ii++)
1940: for (j=1;j<=nlstate+ndeath;j++){
1941: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1942: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1943: }
1944: for(d=0; d<=dh[mi][i]; d++){
1945: newm=savm;
1946: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1947: for (kk=1; kk<=cptcovage;kk++) {
1948: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1949: }
1950: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1951: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1952: savm=oldm;
1953: oldm=newm;
1954: } /* end mult */
1955:
1956: s1=s[mw[mi][i]][i];
1957: s2=s[mw[mi+1][i]][i];
1958: bbh=(double)bh[mi][i]/(double)stepm;
1959: 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 */
1960: ipmx +=1;
1961: sw += weight[i];
1962: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1963: } /* end of wave */
1964: } /* end of individual */
1965: } else if(mle==3){ /* exponential inter-extrapolation */
1966: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1967: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1968: for(mi=1; mi<= wav[i]-1; mi++){
1969: for (ii=1;ii<=nlstate+ndeath;ii++)
1970: for (j=1;j<=nlstate+ndeath;j++){
1971: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1972: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1973: }
1974: for(d=0; d<dh[mi][i]; d++){
1975: newm=savm;
1976: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1977: for (kk=1; kk<=cptcovage;kk++) {
1978: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1979: }
1980: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1981: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1982: savm=oldm;
1983: oldm=newm;
1984: } /* end mult */
1985:
1986: s1=s[mw[mi][i]][i];
1987: s2=s[mw[mi+1][i]][i];
1988: bbh=(double)bh[mi][i]/(double)stepm;
1989: 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 */
1990: ipmx +=1;
1991: sw += weight[i];
1992: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1993: } /* end of wave */
1994: } /* end of individual */
1995: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1996: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1997: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1998: for(mi=1; mi<= wav[i]-1; mi++){
1999: for (ii=1;ii<=nlstate+ndeath;ii++)
2000: for (j=1;j<=nlstate+ndeath;j++){
2001: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2002: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2003: }
2004: for(d=0; d<dh[mi][i]; d++){
2005: newm=savm;
2006: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2007: for (kk=1; kk<=cptcovage;kk++) {
2008: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2009: }
2010:
2011: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2012: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2013: savm=oldm;
2014: oldm=newm;
2015: } /* end mult */
2016:
2017: s1=s[mw[mi][i]][i];
2018: s2=s[mw[mi+1][i]][i];
2019: if( s2 > nlstate){
2020: lli=log(out[s1][s2] - savm[s1][s2]);
2021: }else{
2022: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2023: }
2024: ipmx +=1;
2025: sw += weight[i];
2026: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2027: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
2028: } /* end of wave */
2029: } /* end of individual */
2030: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2031: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2032: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2033: for(mi=1; mi<= wav[i]-1; mi++){
2034: for (ii=1;ii<=nlstate+ndeath;ii++)
2035: for (j=1;j<=nlstate+ndeath;j++){
2036: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2037: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2038: }
2039: for(d=0; d<dh[mi][i]; d++){
2040: newm=savm;
2041: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2042: for (kk=1; kk<=cptcovage;kk++) {
2043: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2044: }
2045:
2046: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2047: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2048: savm=oldm;
2049: oldm=newm;
2050: } /* end mult */
2051:
2052: s1=s[mw[mi][i]][i];
2053: s2=s[mw[mi+1][i]][i];
2054: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2055: ipmx +=1;
2056: sw += weight[i];
2057: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2058: /*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]);*/
2059: } /* end of wave */
2060: } /* end of individual */
2061: } /* End of if */
2062: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2063: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2064: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2065: return -l;
2066: }
2067:
2068: /*************** log-likelihood *************/
2069: double funcone( double *x)
2070: {
2071: /* Same as likeli but slower because of a lot of printf and if */
2072: int i, ii, j, k, mi, d, kk;
2073: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2074: double **out;
2075: double lli; /* Individual log likelihood */
2076: double llt;
2077: int s1, s2;
2078: double bbh, survp;
2079: /*extern weight */
2080: /* We are differentiating ll according to initial status */
2081: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2082: /*for(i=1;i<imx;i++)
2083: printf(" %d\n",s[4][i]);
2084: */
2085: cov[1]=1.;
2086:
2087: for(k=1; k<=nlstate; k++) ll[k]=0.;
2088:
2089: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2090: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2091: for(mi=1; mi<= wav[i]-1; mi++){
2092: for (ii=1;ii<=nlstate+ndeath;ii++)
2093: for (j=1;j<=nlstate+ndeath;j++){
2094: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2095: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2096: }
2097: for(d=0; d<dh[mi][i]; d++){
2098: newm=savm;
2099: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2100: for (kk=1; kk<=cptcovage;kk++) {
2101: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2102: }
2103: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2104: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2105: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2106: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2107: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2108: savm=oldm;
2109: oldm=newm;
2110: } /* end mult */
2111:
2112: s1=s[mw[mi][i]][i];
2113: s2=s[mw[mi+1][i]][i];
2114: bbh=(double)bh[mi][i]/(double)stepm;
2115: /* bias is positive if real duration
2116: * is higher than the multiple of stepm and negative otherwise.
2117: */
2118: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2119: lli=log(out[s1][s2] - savm[s1][s2]);
2120: } else if (s2==-2) {
2121: for (j=1,survp=0. ; j<=nlstate; j++)
2122: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2123: lli= log(survp);
2124: }else if (mle==1){
2125: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2126: } else if(mle==2){
2127: 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 */
2128: } else if(mle==3){ /* exponential inter-extrapolation */
2129: 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 */
2130: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2131: lli=log(out[s1][s2]); /* Original formula */
2132: } else{ /* mle=0 back to 1 */
2133: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2134: /*lli=log(out[s1][s2]); */ /* Original formula */
2135: } /* End of if */
2136: ipmx +=1;
2137: sw += weight[i];
2138: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2139: /*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]); */
2140: if(globpr){
2141: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2142: %11.6f %11.6f %11.6f ", \
2143: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2144: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2145: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2146: llt +=ll[k]*gipmx/gsw;
2147: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2148: }
2149: fprintf(ficresilk," %10.6f\n", -llt);
2150: }
2151: } /* end of wave */
2152: } /* end of individual */
2153: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2154: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2155: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2156: if(globpr==0){ /* First time we count the contributions and weights */
2157: gipmx=ipmx;
2158: gsw=sw;
2159: }
2160: return -l;
2161: }
2162:
2163:
2164: /*************** function likelione ***********/
2165: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2166: {
2167: /* This routine should help understanding what is done with
2168: the selection of individuals/waves and
2169: to check the exact contribution to the likelihood.
2170: Plotting could be done.
2171: */
2172: int k;
2173:
2174: if(*globpri !=0){ /* Just counts and sums, no printings */
2175: strcpy(fileresilk,"ilk");
2176: strcat(fileresilk,fileres);
2177: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2178: printf("Problem with resultfile: %s\n", fileresilk);
2179: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2180: }
2181: 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");
2182: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2183: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2184: for(k=1; k<=nlstate; k++)
2185: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2186: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2187: }
2188:
2189: *fretone=(*funcone)(p);
2190: if(*globpri !=0){
2191: fclose(ficresilk);
2192: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2193: fflush(fichtm);
2194: }
2195: return;
2196: }
2197:
2198:
2199: /*********** Maximum Likelihood Estimation ***************/
2200:
2201: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2202: {
2203: int i,j, iter=0;
2204: double **xi;
2205: double fret;
2206: double fretone; /* Only one call to likelihood */
2207: /* char filerespow[FILENAMELENGTH];*/
2208:
2209: #ifdef NLOPT
2210: int creturn;
2211: nlopt_opt opt;
2212: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2213: double *lb;
2214: double minf; /* the minimum objective value, upon return */
2215: double * p1; /* Shifted parameters from 0 instead of 1 */
2216: myfunc_data dinst, *d = &dinst;
2217: #endif
2218:
2219:
2220: xi=matrix(1,npar,1,npar);
2221: for (i=1;i<=npar;i++)
2222: for (j=1;j<=npar;j++)
2223: xi[i][j]=(i==j ? 1.0 : 0.0);
2224: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2225: strcpy(filerespow,"pow");
2226: strcat(filerespow,fileres);
2227: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2228: printf("Problem with resultfile: %s\n", filerespow);
2229: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2230: }
2231: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2232: for (i=1;i<=nlstate;i++)
2233: for(j=1;j<=nlstate+ndeath;j++)
2234: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2235: fprintf(ficrespow,"\n");
2236: #ifdef POWELL
2237: powell(p,xi,npar,ftol,&iter,&fret,func);
2238: #endif
2239:
2240: #ifdef NLOPT
2241: #ifdef NEWUOA
2242: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2243: #else
2244: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2245: #endif
2246: lb=vector(0,npar-1);
2247: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2248: nlopt_set_lower_bounds(opt, lb);
2249: nlopt_set_initial_step1(opt, 0.1);
2250:
2251: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2252: d->function = func;
2253: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2254: nlopt_set_min_objective(opt, myfunc, d);
2255: nlopt_set_xtol_rel(opt, ftol);
2256: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2257: printf("nlopt failed! %d\n",creturn);
2258: }
2259: else {
2260: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2261: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2262: iter=1; /* not equal */
2263: }
2264: nlopt_destroy(opt);
2265: #endif
2266: free_matrix(xi,1,npar,1,npar);
2267: fclose(ficrespow);
2268: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2269: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2270: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2271:
2272: }
2273:
2274: /**** Computes Hessian and covariance matrix ***/
2275: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2276: {
2277: double **a,**y,*x,pd;
2278: double **hess;
2279: int i, j;
2280: int *indx;
2281:
2282: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2283: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2284: void lubksb(double **a, int npar, int *indx, double b[]) ;
2285: void ludcmp(double **a, int npar, int *indx, double *d) ;
2286: double gompertz(double p[]);
2287: hess=matrix(1,npar,1,npar);
2288:
2289: printf("\nCalculation of the hessian matrix. Wait...\n");
2290: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2291: for (i=1;i<=npar;i++){
2292: printf("%d",i);fflush(stdout);
2293: fprintf(ficlog,"%d",i);fflush(ficlog);
2294:
2295: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2296:
2297: /* printf(" %f ",p[i]);
2298: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2299: }
2300:
2301: for (i=1;i<=npar;i++) {
2302: for (j=1;j<=npar;j++) {
2303: if (j>i) {
2304: printf(".%d%d",i,j);fflush(stdout);
2305: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2306: hess[i][j]=hessij(p,delti,i,j,func,npar);
2307:
2308: hess[j][i]=hess[i][j];
2309: /*printf(" %lf ",hess[i][j]);*/
2310: }
2311: }
2312: }
2313: printf("\n");
2314: fprintf(ficlog,"\n");
2315:
2316: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2317: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2318:
2319: a=matrix(1,npar,1,npar);
2320: y=matrix(1,npar,1,npar);
2321: x=vector(1,npar);
2322: indx=ivector(1,npar);
2323: for (i=1;i<=npar;i++)
2324: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2325: ludcmp(a,npar,indx,&pd);
2326:
2327: for (j=1;j<=npar;j++) {
2328: for (i=1;i<=npar;i++) x[i]=0;
2329: x[j]=1;
2330: lubksb(a,npar,indx,x);
2331: for (i=1;i<=npar;i++){
2332: matcov[i][j]=x[i];
2333: }
2334: }
2335:
2336: printf("\n#Hessian matrix#\n");
2337: fprintf(ficlog,"\n#Hessian matrix#\n");
2338: for (i=1;i<=npar;i++) {
2339: for (j=1;j<=npar;j++) {
2340: printf("%.3e ",hess[i][j]);
2341: fprintf(ficlog,"%.3e ",hess[i][j]);
2342: }
2343: printf("\n");
2344: fprintf(ficlog,"\n");
2345: }
2346:
2347: /* Recompute Inverse */
2348: for (i=1;i<=npar;i++)
2349: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2350: ludcmp(a,npar,indx,&pd);
2351:
2352: /* printf("\n#Hessian matrix recomputed#\n");
2353:
2354: for (j=1;j<=npar;j++) {
2355: for (i=1;i<=npar;i++) x[i]=0;
2356: x[j]=1;
2357: lubksb(a,npar,indx,x);
2358: for (i=1;i<=npar;i++){
2359: y[i][j]=x[i];
2360: printf("%.3e ",y[i][j]);
2361: fprintf(ficlog,"%.3e ",y[i][j]);
2362: }
2363: printf("\n");
2364: fprintf(ficlog,"\n");
2365: }
2366: */
2367:
2368: free_matrix(a,1,npar,1,npar);
2369: free_matrix(y,1,npar,1,npar);
2370: free_vector(x,1,npar);
2371: free_ivector(indx,1,npar);
2372: free_matrix(hess,1,npar,1,npar);
2373:
2374:
2375: }
2376:
2377: /*************** hessian matrix ****************/
2378: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2379: {
2380: int i;
2381: int l=1, lmax=20;
2382: double k1,k2;
2383: double p2[MAXPARM+1]; /* identical to x */
2384: double res;
2385: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2386: double fx;
2387: int k=0,kmax=10;
2388: double l1;
2389:
2390: fx=func(x);
2391: for (i=1;i<=npar;i++) p2[i]=x[i];
2392: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2393: l1=pow(10,l);
2394: delts=delt;
2395: for(k=1 ; k <kmax; k=k+1){
2396: delt = delta*(l1*k);
2397: p2[theta]=x[theta] +delt;
2398: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2399: p2[theta]=x[theta]-delt;
2400: k2=func(p2)-fx;
2401: /*res= (k1-2.0*fx+k2)/delt/delt; */
2402: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2403:
2404: #ifdef DEBUGHESS
2405: 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);
2406: 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);
2407: #endif
2408: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2409: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2410: k=kmax;
2411: }
2412: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2413: k=kmax; l=lmax*10;
2414: }
2415: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2416: delts=delt;
2417: }
2418: }
2419: }
2420: delti[theta]=delts;
2421: return res;
2422:
2423: }
2424:
2425: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2426: {
2427: int i;
2428: int l=1, lmax=20;
2429: double k1,k2,k3,k4,res,fx;
2430: double p2[MAXPARM+1];
2431: int k;
2432:
2433: fx=func(x);
2434: for (k=1; k<=2; k++) {
2435: for (i=1;i<=npar;i++) p2[i]=x[i];
2436: p2[thetai]=x[thetai]+delti[thetai]/k;
2437: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2438: k1=func(p2)-fx;
2439:
2440: p2[thetai]=x[thetai]+delti[thetai]/k;
2441: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2442: k2=func(p2)-fx;
2443:
2444: p2[thetai]=x[thetai]-delti[thetai]/k;
2445: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2446: k3=func(p2)-fx;
2447:
2448: p2[thetai]=x[thetai]-delti[thetai]/k;
2449: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2450: k4=func(p2)-fx;
2451: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2452: #ifdef DEBUG
2453: 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);
2454: 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);
2455: #endif
2456: }
2457: return res;
2458: }
2459:
2460: /************** Inverse of matrix **************/
2461: void ludcmp(double **a, int n, int *indx, double *d)
2462: {
2463: int i,imax,j,k;
2464: double big,dum,sum,temp;
2465: double *vv;
2466:
2467: vv=vector(1,n);
2468: *d=1.0;
2469: for (i=1;i<=n;i++) {
2470: big=0.0;
2471: for (j=1;j<=n;j++)
2472: if ((temp=fabs(a[i][j])) > big) big=temp;
2473: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2474: vv[i]=1.0/big;
2475: }
2476: for (j=1;j<=n;j++) {
2477: for (i=1;i<j;i++) {
2478: sum=a[i][j];
2479: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2480: a[i][j]=sum;
2481: }
2482: big=0.0;
2483: for (i=j;i<=n;i++) {
2484: sum=a[i][j];
2485: for (k=1;k<j;k++)
2486: sum -= a[i][k]*a[k][j];
2487: a[i][j]=sum;
2488: if ( (dum=vv[i]*fabs(sum)) >= big) {
2489: big=dum;
2490: imax=i;
2491: }
2492: }
2493: if (j != imax) {
2494: for (k=1;k<=n;k++) {
2495: dum=a[imax][k];
2496: a[imax][k]=a[j][k];
2497: a[j][k]=dum;
2498: }
2499: *d = -(*d);
2500: vv[imax]=vv[j];
2501: }
2502: indx[j]=imax;
2503: if (a[j][j] == 0.0) a[j][j]=TINY;
2504: if (j != n) {
2505: dum=1.0/(a[j][j]);
2506: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2507: }
2508: }
2509: free_vector(vv,1,n); /* Doesn't work */
2510: ;
2511: }
2512:
2513: void lubksb(double **a, int n, int *indx, double b[])
2514: {
2515: int i,ii=0,ip,j;
2516: double sum;
2517:
2518: for (i=1;i<=n;i++) {
2519: ip=indx[i];
2520: sum=b[ip];
2521: b[ip]=b[i];
2522: if (ii)
2523: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2524: else if (sum) ii=i;
2525: b[i]=sum;
2526: }
2527: for (i=n;i>=1;i--) {
2528: sum=b[i];
2529: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2530: b[i]=sum/a[i][i];
2531: }
2532: }
2533:
2534: void pstamp(FILE *fichier)
2535: {
2536: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2537: }
2538:
2539: /************ Frequencies ********************/
2540: 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[])
2541: { /* Some frequencies */
2542:
2543: int i, m, jk, j1, bool, z1,j;
2544: int first;
2545: double ***freq; /* Frequencies */
2546: double *pp, **prop;
2547: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2548: char fileresp[FILENAMELENGTH];
2549:
2550: pp=vector(1,nlstate);
2551: prop=matrix(1,nlstate,iagemin,iagemax+3);
2552: strcpy(fileresp,"p");
2553: strcat(fileresp,fileres);
2554: if((ficresp=fopen(fileresp,"w"))==NULL) {
2555: printf("Problem with prevalence resultfile: %s\n", fileresp);
2556: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2557: exit(0);
2558: }
2559: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2560: j1=0;
2561:
2562: j=cptcoveff;
2563: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2564:
2565: first=1;
2566:
2567: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2568: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2569: /* j1++; */
2570: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2571: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2572: scanf("%d", i);*/
2573: for (i=-5; i<=nlstate+ndeath; i++)
2574: for (jk=-5; jk<=nlstate+ndeath; jk++)
2575: for(m=iagemin; m <= iagemax+3; m++)
2576: freq[i][jk][m]=0;
2577:
2578: for (i=1; i<=nlstate; i++)
2579: for(m=iagemin; m <= iagemax+3; m++)
2580: prop[i][m]=0;
2581:
2582: dateintsum=0;
2583: k2cpt=0;
2584: for (i=1; i<=imx; i++) {
2585: bool=1;
2586: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2587: for (z1=1; z1<=cptcoveff; z1++)
2588: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2589: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2590: bool=0;
2591: /* 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",
2592: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2593: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2594: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2595: }
2596: }
2597:
2598: if (bool==1){
2599: for(m=firstpass; m<=lastpass; m++){
2600: k2=anint[m][i]+(mint[m][i]/12.);
2601: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2602: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2603: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2604: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2605: if (m<lastpass) {
2606: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2607: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2608: }
2609:
2610: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2611: dateintsum=dateintsum+k2;
2612: k2cpt++;
2613: }
2614: /*}*/
2615: }
2616: }
2617: } /* end i */
2618:
2619: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2620: pstamp(ficresp);
2621: if (cptcovn>0) {
2622: fprintf(ficresp, "\n#********** Variable ");
2623: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2624: fprintf(ficresp, "**********\n#");
2625: fprintf(ficlog, "\n#********** Variable ");
2626: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2627: fprintf(ficlog, "**********\n#");
2628: }
2629: for(i=1; i<=nlstate;i++)
2630: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2631: fprintf(ficresp, "\n");
2632:
2633: for(i=iagemin; i <= iagemax+3; i++){
2634: if(i==iagemax+3){
2635: fprintf(ficlog,"Total");
2636: }else{
2637: if(first==1){
2638: first=0;
2639: printf("See log file for details...\n");
2640: }
2641: fprintf(ficlog,"Age %d", i);
2642: }
2643: for(jk=1; jk <=nlstate ; jk++){
2644: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2645: pp[jk] += freq[jk][m][i];
2646: }
2647: for(jk=1; jk <=nlstate ; jk++){
2648: for(m=-1, pos=0; m <=0 ; m++)
2649: pos += freq[jk][m][i];
2650: if(pp[jk]>=1.e-10){
2651: if(first==1){
2652: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2653: }
2654: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2655: }else{
2656: if(first==1)
2657: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2658: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2659: }
2660: }
2661:
2662: for(jk=1; jk <=nlstate ; jk++){
2663: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2664: pp[jk] += freq[jk][m][i];
2665: }
2666: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2667: pos += pp[jk];
2668: posprop += prop[jk][i];
2669: }
2670: for(jk=1; jk <=nlstate ; jk++){
2671: if(pos>=1.e-5){
2672: if(first==1)
2673: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2674: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2675: }else{
2676: if(first==1)
2677: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2678: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2679: }
2680: if( i <= iagemax){
2681: if(pos>=1.e-5){
2682: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2683: /*probs[i][jk][j1]= pp[jk]/pos;*/
2684: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2685: }
2686: else
2687: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2688: }
2689: }
2690:
2691: for(jk=-1; jk <=nlstate+ndeath; jk++)
2692: for(m=-1; m <=nlstate+ndeath; m++)
2693: if(freq[jk][m][i] !=0 ) {
2694: if(first==1)
2695: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2696: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2697: }
2698: if(i <= iagemax)
2699: fprintf(ficresp,"\n");
2700: if(first==1)
2701: printf("Others in log...\n");
2702: fprintf(ficlog,"\n");
2703: }
2704: /*}*/
2705: }
2706: dateintmean=dateintsum/k2cpt;
2707:
2708: fclose(ficresp);
2709: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2710: free_vector(pp,1,nlstate);
2711: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2712: /* End of Freq */
2713: }
2714:
2715: /************ Prevalence ********************/
2716: 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)
2717: {
2718: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2719: in each health status at the date of interview (if between dateprev1 and dateprev2).
2720: We still use firstpass and lastpass as another selection.
2721: */
2722:
2723: int i, m, jk, j1, bool, z1,j;
2724:
2725: double **prop;
2726: double posprop;
2727: double y2; /* in fractional years */
2728: int iagemin, iagemax;
2729: int first; /** to stop verbosity which is redirected to log file */
2730:
2731: iagemin= (int) agemin;
2732: iagemax= (int) agemax;
2733: /*pp=vector(1,nlstate);*/
2734: prop=matrix(1,nlstate,iagemin,iagemax+3);
2735: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2736: j1=0;
2737:
2738: /*j=cptcoveff;*/
2739: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2740:
2741: first=1;
2742: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2743: /*for(i1=1; i1<=ncodemax[k1];i1++){
2744: j1++;*/
2745:
2746: for (i=1; i<=nlstate; i++)
2747: for(m=iagemin; m <= iagemax+3; m++)
2748: prop[i][m]=0.0;
2749:
2750: for (i=1; i<=imx; i++) { /* Each individual */
2751: bool=1;
2752: if (cptcovn>0) {
2753: for (z1=1; z1<=cptcoveff; z1++)
2754: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2755: bool=0;
2756: }
2757: if (bool==1) {
2758: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2759: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2760: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2761: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2762: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2763: 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);
2764: if (s[m][i]>0 && s[m][i]<=nlstate) {
2765: /*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]]);*/
2766: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2767: prop[s[m][i]][iagemax+3] += weight[i];
2768: }
2769: }
2770: } /* end selection of waves */
2771: }
2772: }
2773: for(i=iagemin; i <= iagemax+3; i++){
2774: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2775: posprop += prop[jk][i];
2776: }
2777:
2778: for(jk=1; jk <=nlstate ; jk++){
2779: if( i <= iagemax){
2780: if(posprop>=1.e-5){
2781: probs[i][jk][j1]= prop[jk][i]/posprop;
2782: } else{
2783: if(first==1){
2784: first=0;
2785: 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]);
2786: }
2787: }
2788: }
2789: }/* end jk */
2790: }/* end i */
2791: /*} *//* end i1 */
2792: } /* end j1 */
2793:
2794: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2795: /*free_vector(pp,1,nlstate);*/
2796: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2797: } /* End of prevalence */
2798:
2799: /************* Waves Concatenation ***************/
2800:
2801: 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)
2802: {
2803: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2804: Death is a valid wave (if date is known).
2805: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2806: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2807: and mw[mi+1][i]. dh depends on stepm.
2808: */
2809:
2810: int i, mi, m;
2811: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2812: double sum=0., jmean=0.;*/
2813: int first;
2814: int j, k=0,jk, ju, jl;
2815: double sum=0.;
2816: first=0;
2817: jmin=100000;
2818: jmax=-1;
2819: jmean=0.;
2820: for(i=1; i<=imx; i++){
2821: mi=0;
2822: m=firstpass;
2823: while(s[m][i] <= nlstate){
2824: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2825: mw[++mi][i]=m;
2826: if(m >=lastpass)
2827: break;
2828: else
2829: m++;
2830: }/* end while */
2831: if (s[m][i] > nlstate){
2832: mi++; /* Death is another wave */
2833: /* if(mi==0) never been interviewed correctly before death */
2834: /* Only death is a correct wave */
2835: mw[mi][i]=m;
2836: }
2837:
2838: wav[i]=mi;
2839: if(mi==0){
2840: nbwarn++;
2841: if(first==0){
2842: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2843: first=1;
2844: }
2845: if(first==1){
2846: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2847: }
2848: } /* end mi==0 */
2849: } /* End individuals */
2850:
2851: for(i=1; i<=imx; i++){
2852: for(mi=1; mi<wav[i];mi++){
2853: if (stepm <=0)
2854: dh[mi][i]=1;
2855: else{
2856: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2857: if (agedc[i] < 2*AGESUP) {
2858: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2859: if(j==0) j=1; /* Survives at least one month after exam */
2860: else if(j<0){
2861: nberr++;
2862: 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]);
2863: j=1; /* Temporary Dangerous patch */
2864: 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);
2865: 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]);
2866: 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);
2867: }
2868: k=k+1;
2869: if (j >= jmax){
2870: jmax=j;
2871: ijmax=i;
2872: }
2873: if (j <= jmin){
2874: jmin=j;
2875: ijmin=i;
2876: }
2877: sum=sum+j;
2878: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2879: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2880: }
2881: }
2882: else{
2883: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2884: /* 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]); */
2885:
2886: k=k+1;
2887: if (j >= jmax) {
2888: jmax=j;
2889: ijmax=i;
2890: }
2891: else if (j <= jmin){
2892: jmin=j;
2893: ijmin=i;
2894: }
2895: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2896: /*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]);*/
2897: if(j<0){
2898: nberr++;
2899: 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]);
2900: 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]);
2901: }
2902: sum=sum+j;
2903: }
2904: jk= j/stepm;
2905: jl= j -jk*stepm;
2906: ju= j -(jk+1)*stepm;
2907: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2908: if(jl==0){
2909: dh[mi][i]=jk;
2910: bh[mi][i]=0;
2911: }else{ /* We want a negative bias in order to only have interpolation ie
2912: * to avoid the price of an extra matrix product in likelihood */
2913: dh[mi][i]=jk+1;
2914: bh[mi][i]=ju;
2915: }
2916: }else{
2917: if(jl <= -ju){
2918: dh[mi][i]=jk;
2919: bh[mi][i]=jl; /* bias is positive if real duration
2920: * is higher than the multiple of stepm and negative otherwise.
2921: */
2922: }
2923: else{
2924: dh[mi][i]=jk+1;
2925: bh[mi][i]=ju;
2926: }
2927: if(dh[mi][i]==0){
2928: dh[mi][i]=1; /* At least one step */
2929: bh[mi][i]=ju; /* At least one step */
2930: /* 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);*/
2931: }
2932: } /* end if mle */
2933: }
2934: } /* end wave */
2935: }
2936: jmean=sum/k;
2937: 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);
2938: 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);
2939: }
2940:
2941: /*********** Tricode ****************************/
2942: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2943: {
2944: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2945: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2946: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2947: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2948: * nbcode[Tvar[j]][1]=
2949: */
2950:
2951: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2952: int modmaxcovj=0; /* Modality max of covariates j */
2953: int cptcode=0; /* Modality max of covariates j */
2954: int modmincovj=0; /* Modality min of covariates j */
2955:
2956:
2957: cptcoveff=0;
2958:
2959: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2960: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2961:
2962: /* Loop on covariates without age and products */
2963: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2964: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2965: modality of this covariate Vj*/
2966: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2967: * If product of Vn*Vm, still boolean *:
2968: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2969: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2970: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2971: modality of the nth covariate of individual i. */
2972: if (ij > modmaxcovj)
2973: modmaxcovj=ij;
2974: else if (ij < modmincovj)
2975: modmincovj=ij;
2976: if ((ij < -1) && (ij > NCOVMAX)){
2977: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2978: exit(1);
2979: }else
2980: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2981: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2982: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2983: /* getting the maximum value of the modality of the covariate
2984: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2985: female is 1, then modmaxcovj=1.*/
2986: }
2987: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2988: cptcode=modmaxcovj;
2989: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2990: /*for (i=0; i<=cptcode; i++) {*/
2991: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2992: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2993: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2994: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2995: }
2996: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2997: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2998: } /* Ndum[-1] number of undefined modalities */
2999:
3000: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3001: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3002: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3003: modmincovj=3; modmaxcovj = 7;
3004: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3005: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3006: variables V1_1 and V1_2.
3007: nbcode[Tvar[j]][ij]=k;
3008: nbcode[Tvar[j]][1]=0;
3009: nbcode[Tvar[j]][2]=1;
3010: nbcode[Tvar[j]][3]=2;
3011: */
3012: ij=1; /* ij is similar to i but can jumps over null modalities */
3013: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3014: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3015: /*recode from 0 */
3016: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3017: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3018: k is a modality. If we have model=V1+V1*sex
3019: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3020: ij++;
3021: }
3022: if (ij > ncodemax[j]) break;
3023: } /* end of loop on */
3024: } /* end of loop on modality */
3025: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3026:
3027: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3028:
3029: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3030: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3031: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3032: Ndum[ij]++;
3033: }
3034:
3035: ij=1;
3036: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3037: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3038: if((Ndum[i]!=0) && (i<=ncovcol)){
3039: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3040: Tvaraff[ij]=i; /*For printing (unclear) */
3041: ij++;
3042: }else
3043: Tvaraff[ij]=0;
3044: }
3045: ij--;
3046: cptcoveff=ij; /*Number of total covariates*/
3047:
3048: }
3049:
3050:
3051: /*********** Health Expectancies ****************/
3052:
3053: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3054:
3055: {
3056: /* Health expectancies, no variances */
3057: int i, j, nhstepm, hstepm, h, nstepm;
3058: int nhstepma, nstepma; /* Decreasing with age */
3059: double age, agelim, hf;
3060: double ***p3mat;
3061: double eip;
3062:
3063: pstamp(ficreseij);
3064: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3065: fprintf(ficreseij,"# Age");
3066: for(i=1; i<=nlstate;i++){
3067: for(j=1; j<=nlstate;j++){
3068: fprintf(ficreseij," e%1d%1d ",i,j);
3069: }
3070: fprintf(ficreseij," e%1d. ",i);
3071: }
3072: fprintf(ficreseij,"\n");
3073:
3074:
3075: if(estepm < stepm){
3076: printf ("Problem %d lower than %d\n",estepm, stepm);
3077: }
3078: else hstepm=estepm;
3079: /* We compute the life expectancy from trapezoids spaced every estepm months
3080: * This is mainly to measure the difference between two models: for example
3081: * if stepm=24 months pijx are given only every 2 years and by summing them
3082: * we are calculating an estimate of the Life Expectancy assuming a linear
3083: * progression in between and thus overestimating or underestimating according
3084: * to the curvature of the survival function. If, for the same date, we
3085: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3086: * to compare the new estimate of Life expectancy with the same linear
3087: * hypothesis. A more precise result, taking into account a more precise
3088: * curvature will be obtained if estepm is as small as stepm. */
3089:
3090: /* For example we decided to compute the life expectancy with the smallest unit */
3091: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3092: nhstepm is the number of hstepm from age to agelim
3093: nstepm is the number of stepm from age to agelin.
3094: Look at hpijx to understand the reason of that which relies in memory size
3095: and note for a fixed period like estepm months */
3096: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3097: survival function given by stepm (the optimization length). Unfortunately it
3098: means that if the survival funtion is printed only each two years of age and if
3099: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3100: results. So we changed our mind and took the option of the best precision.
3101: */
3102: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3103:
3104: agelim=AGESUP;
3105: /* If stepm=6 months */
3106: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3107: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3108:
3109: /* nhstepm age range expressed in number of stepm */
3110: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3111: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3112: /* if (stepm >= YEARM) hstepm=1;*/
3113: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3114: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3115:
3116: for (age=bage; age<=fage; age ++){
3117: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3118: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3119: /* if (stepm >= YEARM) hstepm=1;*/
3120: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3121:
3122: /* If stepm=6 months */
3123: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3124: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3125:
3126: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3127:
3128: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3129:
3130: printf("%d|",(int)age);fflush(stdout);
3131: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3132:
3133: /* Computing expectancies */
3134: for(i=1; i<=nlstate;i++)
3135: for(j=1; j<=nlstate;j++)
3136: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3137: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3138:
3139: /* 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]);*/
3140:
3141: }
3142:
3143: fprintf(ficreseij,"%3.0f",age );
3144: for(i=1; i<=nlstate;i++){
3145: eip=0;
3146: for(j=1; j<=nlstate;j++){
3147: eip +=eij[i][j][(int)age];
3148: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3149: }
3150: fprintf(ficreseij,"%9.4f", eip );
3151: }
3152: fprintf(ficreseij,"\n");
3153:
3154: }
3155: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3156: printf("\n");
3157: fprintf(ficlog,"\n");
3158:
3159: }
3160:
3161: 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[] )
3162:
3163: {
3164: /* Covariances of health expectancies eij and of total life expectancies according
3165: to initial status i, ei. .
3166: */
3167: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3168: int nhstepma, nstepma; /* Decreasing with age */
3169: double age, agelim, hf;
3170: double ***p3matp, ***p3matm, ***varhe;
3171: double **dnewm,**doldm;
3172: double *xp, *xm;
3173: double **gp, **gm;
3174: double ***gradg, ***trgradg;
3175: int theta;
3176:
3177: double eip, vip;
3178:
3179: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3180: xp=vector(1,npar);
3181: xm=vector(1,npar);
3182: dnewm=matrix(1,nlstate*nlstate,1,npar);
3183: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3184:
3185: pstamp(ficresstdeij);
3186: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3187: fprintf(ficresstdeij,"# Age");
3188: for(i=1; i<=nlstate;i++){
3189: for(j=1; j<=nlstate;j++)
3190: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3191: fprintf(ficresstdeij," e%1d. ",i);
3192: }
3193: fprintf(ficresstdeij,"\n");
3194:
3195: pstamp(ficrescveij);
3196: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3197: fprintf(ficrescveij,"# Age");
3198: for(i=1; i<=nlstate;i++)
3199: for(j=1; j<=nlstate;j++){
3200: cptj= (j-1)*nlstate+i;
3201: for(i2=1; i2<=nlstate;i2++)
3202: for(j2=1; j2<=nlstate;j2++){
3203: cptj2= (j2-1)*nlstate+i2;
3204: if(cptj2 <= cptj)
3205: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3206: }
3207: }
3208: fprintf(ficrescveij,"\n");
3209:
3210: if(estepm < stepm){
3211: printf ("Problem %d lower than %d\n",estepm, stepm);
3212: }
3213: else hstepm=estepm;
3214: /* We compute the life expectancy from trapezoids spaced every estepm months
3215: * This is mainly to measure the difference between two models: for example
3216: * if stepm=24 months pijx are given only every 2 years and by summing them
3217: * we are calculating an estimate of the Life Expectancy assuming a linear
3218: * progression in between and thus overestimating or underestimating according
3219: * to the curvature of the survival function. If, for the same date, we
3220: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3221: * to compare the new estimate of Life expectancy with the same linear
3222: * hypothesis. A more precise result, taking into account a more precise
3223: * curvature will be obtained if estepm is as small as stepm. */
3224:
3225: /* For example we decided to compute the life expectancy with the smallest unit */
3226: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3227: nhstepm is the number of hstepm from age to agelim
3228: nstepm is the number of stepm from age to agelin.
3229: Look at hpijx to understand the reason of that which relies in memory size
3230: and note for a fixed period like estepm months */
3231: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3232: survival function given by stepm (the optimization length). Unfortunately it
3233: means that if the survival funtion is printed only each two years of age and if
3234: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3235: results. So we changed our mind and took the option of the best precision.
3236: */
3237: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3238:
3239: /* If stepm=6 months */
3240: /* nhstepm age range expressed in number of stepm */
3241: agelim=AGESUP;
3242: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3243: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3244: /* if (stepm >= YEARM) hstepm=1;*/
3245: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3246:
3247: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3248: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3249: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3250: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3251: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3252: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3253:
3254: for (age=bage; age<=fage; age ++){
3255: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3256: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3257: /* if (stepm >= YEARM) hstepm=1;*/
3258: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3259:
3260: /* If stepm=6 months */
3261: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3262: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3263:
3264: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3265:
3266: /* Computing Variances of health expectancies */
3267: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3268: decrease memory allocation */
3269: for(theta=1; theta <=npar; theta++){
3270: for(i=1; i<=npar; i++){
3271: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3272: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3273: }
3274: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3275: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3276:
3277: for(j=1; j<= nlstate; j++){
3278: for(i=1; i<=nlstate; i++){
3279: for(h=0; h<=nhstepm-1; h++){
3280: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3281: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3282: }
3283: }
3284: }
3285:
3286: for(ij=1; ij<= nlstate*nlstate; ij++)
3287: for(h=0; h<=nhstepm-1; h++){
3288: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3289: }
3290: }/* End theta */
3291:
3292:
3293: for(h=0; h<=nhstepm-1; h++)
3294: for(j=1; j<=nlstate*nlstate;j++)
3295: for(theta=1; theta <=npar; theta++)
3296: trgradg[h][j][theta]=gradg[h][theta][j];
3297:
3298:
3299: for(ij=1;ij<=nlstate*nlstate;ij++)
3300: for(ji=1;ji<=nlstate*nlstate;ji++)
3301: varhe[ij][ji][(int)age] =0.;
3302:
3303: printf("%d|",(int)age);fflush(stdout);
3304: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3305: for(h=0;h<=nhstepm-1;h++){
3306: for(k=0;k<=nhstepm-1;k++){
3307: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3308: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3309: for(ij=1;ij<=nlstate*nlstate;ij++)
3310: for(ji=1;ji<=nlstate*nlstate;ji++)
3311: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3312: }
3313: }
3314:
3315: /* Computing expectancies */
3316: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3317: for(i=1; i<=nlstate;i++)
3318: for(j=1; j<=nlstate;j++)
3319: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3320: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3321:
3322: /* 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]);*/
3323:
3324: }
3325:
3326: fprintf(ficresstdeij,"%3.0f",age );
3327: for(i=1; i<=nlstate;i++){
3328: eip=0.;
3329: vip=0.;
3330: for(j=1; j<=nlstate;j++){
3331: eip += eij[i][j][(int)age];
3332: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3333: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3334: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3335: }
3336: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3337: }
3338: fprintf(ficresstdeij,"\n");
3339:
3340: fprintf(ficrescveij,"%3.0f",age );
3341: for(i=1; i<=nlstate;i++)
3342: for(j=1; j<=nlstate;j++){
3343: cptj= (j-1)*nlstate+i;
3344: for(i2=1; i2<=nlstate;i2++)
3345: for(j2=1; j2<=nlstate;j2++){
3346: cptj2= (j2-1)*nlstate+i2;
3347: if(cptj2 <= cptj)
3348: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3349: }
3350: }
3351: fprintf(ficrescveij,"\n");
3352:
3353: }
3354: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3355: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3356: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3357: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3358: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3359: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3360: printf("\n");
3361: fprintf(ficlog,"\n");
3362:
3363: free_vector(xm,1,npar);
3364: free_vector(xp,1,npar);
3365: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3366: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3367: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3368: }
3369:
3370: /************ Variance ******************/
3371: 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[])
3372: {
3373: /* Variance of health expectancies */
3374: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3375: /* double **newm;*/
3376: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3377:
3378: int movingaverage();
3379: double **dnewm,**doldm;
3380: double **dnewmp,**doldmp;
3381: int i, j, nhstepm, hstepm, h, nstepm ;
3382: int k;
3383: double *xp;
3384: double **gp, **gm; /* for var eij */
3385: double ***gradg, ***trgradg; /*for var eij */
3386: double **gradgp, **trgradgp; /* for var p point j */
3387: double *gpp, *gmp; /* for var p point j */
3388: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3389: double ***p3mat;
3390: double age,agelim, hf;
3391: double ***mobaverage;
3392: int theta;
3393: char digit[4];
3394: char digitp[25];
3395:
3396: char fileresprobmorprev[FILENAMELENGTH];
3397:
3398: if(popbased==1){
3399: if(mobilav!=0)
3400: strcpy(digitp,"-populbased-mobilav-");
3401: else strcpy(digitp,"-populbased-nomobil-");
3402: }
3403: else
3404: strcpy(digitp,"-stablbased-");
3405:
3406: if (mobilav!=0) {
3407: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3408: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3409: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3410: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3411: }
3412: }
3413:
3414: strcpy(fileresprobmorprev,"prmorprev");
3415: sprintf(digit,"%-d",ij);
3416: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3417: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3418: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3419: strcat(fileresprobmorprev,fileres);
3420: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3421: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3422: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3423: }
3424: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3425:
3426: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3427: pstamp(ficresprobmorprev);
3428: 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);
3429: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3430: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3431: fprintf(ficresprobmorprev," p.%-d SE",j);
3432: for(i=1; i<=nlstate;i++)
3433: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3434: }
3435: fprintf(ficresprobmorprev,"\n");
3436: fprintf(ficgp,"\n# Routine varevsij");
3437: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3438: 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");
3439: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3440: /* } */
3441: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3442: pstamp(ficresvij);
3443: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3444: if(popbased==1)
3445: 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);
3446: else
3447: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3448: fprintf(ficresvij,"# Age");
3449: for(i=1; i<=nlstate;i++)
3450: for(j=1; j<=nlstate;j++)
3451: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3452: fprintf(ficresvij,"\n");
3453:
3454: xp=vector(1,npar);
3455: dnewm=matrix(1,nlstate,1,npar);
3456: doldm=matrix(1,nlstate,1,nlstate);
3457: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3458: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3459:
3460: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3461: gpp=vector(nlstate+1,nlstate+ndeath);
3462: gmp=vector(nlstate+1,nlstate+ndeath);
3463: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3464:
3465: if(estepm < stepm){
3466: printf ("Problem %d lower than %d\n",estepm, stepm);
3467: }
3468: else hstepm=estepm;
3469: /* For example we decided to compute the life expectancy with the smallest unit */
3470: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3471: nhstepm is the number of hstepm from age to agelim
3472: nstepm is the number of stepm from age to agelin.
3473: Look at function hpijx to understand why (it is linked to memory size questions) */
3474: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3475: survival function given by stepm (the optimization length). Unfortunately it
3476: means that if the survival funtion is printed every two years of age and if
3477: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3478: results. So we changed our mind and took the option of the best precision.
3479: */
3480: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3481: agelim = AGESUP;
3482: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3483: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3484: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3485: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3486: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3487: gp=matrix(0,nhstepm,1,nlstate);
3488: gm=matrix(0,nhstepm,1,nlstate);
3489:
3490:
3491: for(theta=1; theta <=npar; theta++){
3492: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3493: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3494: }
3495: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3496: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3497:
3498: if (popbased==1) {
3499: if(mobilav ==0){
3500: for(i=1; i<=nlstate;i++)
3501: prlim[i][i]=probs[(int)age][i][ij];
3502: }else{ /* mobilav */
3503: for(i=1; i<=nlstate;i++)
3504: prlim[i][i]=mobaverage[(int)age][i][ij];
3505: }
3506: }
3507:
3508: for(j=1; j<= nlstate; j++){
3509: for(h=0; h<=nhstepm; h++){
3510: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3511: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3512: }
3513: }
3514: /* This for computing probability of death (h=1 means
3515: computed over hstepm matrices product = hstepm*stepm months)
3516: as a weighted average of prlim.
3517: */
3518: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3519: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3520: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3521: }
3522: /* end probability of death */
3523:
3524: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3525: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3526: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3527: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3528:
3529: if (popbased==1) {
3530: if(mobilav ==0){
3531: for(i=1; i<=nlstate;i++)
3532: prlim[i][i]=probs[(int)age][i][ij];
3533: }else{ /* mobilav */
3534: for(i=1; i<=nlstate;i++)
3535: prlim[i][i]=mobaverage[(int)age][i][ij];
3536: }
3537: }
3538:
3539: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3540: for(h=0; h<=nhstepm; h++){
3541: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3542: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3543: }
3544: }
3545: /* This for computing probability of death (h=1 means
3546: computed over hstepm matrices product = hstepm*stepm months)
3547: as a weighted average of prlim.
3548: */
3549: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3550: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3551: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3552: }
3553: /* end probability of death */
3554:
3555: for(j=1; j<= nlstate; j++) /* vareij */
3556: for(h=0; h<=nhstepm; h++){
3557: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3558: }
3559:
3560: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3561: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3562: }
3563:
3564: } /* End theta */
3565:
3566: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3567:
3568: for(h=0; h<=nhstepm; h++) /* veij */
3569: for(j=1; j<=nlstate;j++)
3570: for(theta=1; theta <=npar; theta++)
3571: trgradg[h][j][theta]=gradg[h][theta][j];
3572:
3573: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3574: for(theta=1; theta <=npar; theta++)
3575: trgradgp[j][theta]=gradgp[theta][j];
3576:
3577:
3578: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3579: for(i=1;i<=nlstate;i++)
3580: for(j=1;j<=nlstate;j++)
3581: vareij[i][j][(int)age] =0.;
3582:
3583: for(h=0;h<=nhstepm;h++){
3584: for(k=0;k<=nhstepm;k++){
3585: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3586: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3587: for(i=1;i<=nlstate;i++)
3588: for(j=1;j<=nlstate;j++)
3589: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3590: }
3591: }
3592:
3593: /* pptj */
3594: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3595: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3596: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3597: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3598: varppt[j][i]=doldmp[j][i];
3599: /* end ppptj */
3600: /* x centered again */
3601: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3602: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3603:
3604: if (popbased==1) {
3605: if(mobilav ==0){
3606: for(i=1; i<=nlstate;i++)
3607: prlim[i][i]=probs[(int)age][i][ij];
3608: }else{ /* mobilav */
3609: for(i=1; i<=nlstate;i++)
3610: prlim[i][i]=mobaverage[(int)age][i][ij];
3611: }
3612: }
3613:
3614: /* This for computing probability of death (h=1 means
3615: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3616: as a weighted average of prlim.
3617: */
3618: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3619: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3620: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3621: }
3622: /* end probability of death */
3623:
3624: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3625: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3626: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3627: for(i=1; i<=nlstate;i++){
3628: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3629: }
3630: }
3631: fprintf(ficresprobmorprev,"\n");
3632:
3633: fprintf(ficresvij,"%.0f ",age );
3634: for(i=1; i<=nlstate;i++)
3635: for(j=1; j<=nlstate;j++){
3636: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3637: }
3638: fprintf(ficresvij,"\n");
3639: free_matrix(gp,0,nhstepm,1,nlstate);
3640: free_matrix(gm,0,nhstepm,1,nlstate);
3641: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3642: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3643: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3644: } /* End age */
3645: free_vector(gpp,nlstate+1,nlstate+ndeath);
3646: free_vector(gmp,nlstate+1,nlstate+ndeath);
3647: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3648: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3649: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3650: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3651: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3652: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3653: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3654: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3655: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3656: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3657: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3658: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3659: 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);
3660: /* 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);
3661: */
3662: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3663: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3664:
3665: free_vector(xp,1,npar);
3666: free_matrix(doldm,1,nlstate,1,nlstate);
3667: free_matrix(dnewm,1,nlstate,1,npar);
3668: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3669: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3670: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3671: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3672: fclose(ficresprobmorprev);
3673: fflush(ficgp);
3674: fflush(fichtm);
3675: } /* end varevsij */
3676:
3677: /************ Variance of prevlim ******************/
3678: 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[])
3679: {
3680: /* Variance of prevalence limit */
3681: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3682:
3683: double **dnewm,**doldm;
3684: int i, j, nhstepm, hstepm;
3685: double *xp;
3686: double *gp, *gm;
3687: double **gradg, **trgradg;
3688: double age,agelim;
3689: int theta;
3690:
3691: pstamp(ficresvpl);
3692: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3693: fprintf(ficresvpl,"# Age");
3694: for(i=1; i<=nlstate;i++)
3695: fprintf(ficresvpl," %1d-%1d",i,i);
3696: fprintf(ficresvpl,"\n");
3697:
3698: xp=vector(1,npar);
3699: dnewm=matrix(1,nlstate,1,npar);
3700: doldm=matrix(1,nlstate,1,nlstate);
3701:
3702: hstepm=1*YEARM; /* Every year of age */
3703: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3704: agelim = AGESUP;
3705: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3706: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3707: if (stepm >= YEARM) hstepm=1;
3708: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3709: gradg=matrix(1,npar,1,nlstate);
3710: gp=vector(1,nlstate);
3711: gm=vector(1,nlstate);
3712:
3713: for(theta=1; theta <=npar; theta++){
3714: for(i=1; i<=npar; i++){ /* Computes gradient */
3715: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3716: }
3717: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3718: for(i=1;i<=nlstate;i++)
3719: gp[i] = prlim[i][i];
3720:
3721: for(i=1; i<=npar; i++) /* Computes gradient */
3722: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3723: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3724: for(i=1;i<=nlstate;i++)
3725: gm[i] = prlim[i][i];
3726:
3727: for(i=1;i<=nlstate;i++)
3728: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3729: } /* End theta */
3730:
3731: trgradg =matrix(1,nlstate,1,npar);
3732:
3733: for(j=1; j<=nlstate;j++)
3734: for(theta=1; theta <=npar; theta++)
3735: trgradg[j][theta]=gradg[theta][j];
3736:
3737: for(i=1;i<=nlstate;i++)
3738: varpl[i][(int)age] =0.;
3739: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3740: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3741: for(i=1;i<=nlstate;i++)
3742: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3743:
3744: fprintf(ficresvpl,"%.0f ",age );
3745: for(i=1; i<=nlstate;i++)
3746: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3747: fprintf(ficresvpl,"\n");
3748: free_vector(gp,1,nlstate);
3749: free_vector(gm,1,nlstate);
3750: free_matrix(gradg,1,npar,1,nlstate);
3751: free_matrix(trgradg,1,nlstate,1,npar);
3752: } /* End age */
3753:
3754: free_vector(xp,1,npar);
3755: free_matrix(doldm,1,nlstate,1,npar);
3756: free_matrix(dnewm,1,nlstate,1,nlstate);
3757:
3758: }
3759:
3760: /************ Variance of one-step probabilities ******************/
3761: 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[])
3762: {
3763: int i, j=0, k1, l1, tj;
3764: int k2, l2, j1, z1;
3765: int k=0, l;
3766: int first=1, first1, first2;
3767: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3768: double **dnewm,**doldm;
3769: double *xp;
3770: double *gp, *gm;
3771: double **gradg, **trgradg;
3772: double **mu;
3773: double age, cov[NCOVMAX+1];
3774: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3775: int theta;
3776: char fileresprob[FILENAMELENGTH];
3777: char fileresprobcov[FILENAMELENGTH];
3778: char fileresprobcor[FILENAMELENGTH];
3779: double ***varpij;
3780:
3781: strcpy(fileresprob,"prob");
3782: strcat(fileresprob,fileres);
3783: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3784: printf("Problem with resultfile: %s\n", fileresprob);
3785: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3786: }
3787: strcpy(fileresprobcov,"probcov");
3788: strcat(fileresprobcov,fileres);
3789: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3790: printf("Problem with resultfile: %s\n", fileresprobcov);
3791: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3792: }
3793: strcpy(fileresprobcor,"probcor");
3794: strcat(fileresprobcor,fileres);
3795: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3796: printf("Problem with resultfile: %s\n", fileresprobcor);
3797: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3798: }
3799: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3800: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3801: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3802: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3803: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3804: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3805: pstamp(ficresprob);
3806: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3807: fprintf(ficresprob,"# Age");
3808: pstamp(ficresprobcov);
3809: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3810: fprintf(ficresprobcov,"# Age");
3811: pstamp(ficresprobcor);
3812: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3813: fprintf(ficresprobcor,"# Age");
3814:
3815:
3816: for(i=1; i<=nlstate;i++)
3817: for(j=1; j<=(nlstate+ndeath);j++){
3818: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3819: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3820: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3821: }
3822: /* fprintf(ficresprob,"\n");
3823: fprintf(ficresprobcov,"\n");
3824: fprintf(ficresprobcor,"\n");
3825: */
3826: xp=vector(1,npar);
3827: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3828: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3829: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3830: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3831: first=1;
3832: fprintf(ficgp,"\n# Routine varprob");
3833: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3834: fprintf(fichtm,"\n");
3835:
3836: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3837: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3838: file %s<br>\n",optionfilehtmcov);
3839: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3840: and drawn. It helps understanding how is the covariance between two incidences.\
3841: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3842: 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. \
3843: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3844: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3845: standard deviations wide on each axis. <br>\
3846: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3847: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3848: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3849:
3850: cov[1]=1;
3851: /* tj=cptcoveff; */
3852: tj = (int) pow(2,cptcoveff);
3853: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3854: j1=0;
3855: for(j1=1; j1<=tj;j1++){
3856: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3857: /*j1++;*/
3858: if (cptcovn>0) {
3859: fprintf(ficresprob, "\n#********** Variable ");
3860: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3861: fprintf(ficresprob, "**********\n#\n");
3862: fprintf(ficresprobcov, "\n#********** Variable ");
3863: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3864: fprintf(ficresprobcov, "**********\n#\n");
3865:
3866: fprintf(ficgp, "\n#********** Variable ");
3867: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3868: fprintf(ficgp, "**********\n#\n");
3869:
3870:
3871: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3872: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3873: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3874:
3875: fprintf(ficresprobcor, "\n#********** Variable ");
3876: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3877: fprintf(ficresprobcor, "**********\n#");
3878: }
3879:
3880: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3881: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3882: gp=vector(1,(nlstate)*(nlstate+ndeath));
3883: gm=vector(1,(nlstate)*(nlstate+ndeath));
3884: for (age=bage; age<=fage; age ++){
3885: cov[2]=age;
3886: for (k=1; k<=cptcovn;k++) {
3887: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3888: * 1 1 1 1 1
3889: * 2 2 1 1 1
3890: * 3 1 2 1 1
3891: */
3892: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3893: }
3894: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3895: for (k=1; k<=cptcovprod;k++)
3896: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3897:
3898:
3899: for(theta=1; theta <=npar; theta++){
3900: for(i=1; i<=npar; i++)
3901: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3902:
3903: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3904:
3905: k=0;
3906: for(i=1; i<= (nlstate); i++){
3907: for(j=1; j<=(nlstate+ndeath);j++){
3908: k=k+1;
3909: gp[k]=pmmij[i][j];
3910: }
3911: }
3912:
3913: for(i=1; i<=npar; i++)
3914: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3915:
3916: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3917: k=0;
3918: for(i=1; i<=(nlstate); i++){
3919: for(j=1; j<=(nlstate+ndeath);j++){
3920: k=k+1;
3921: gm[k]=pmmij[i][j];
3922: }
3923: }
3924:
3925: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3926: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3927: }
3928:
3929: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3930: for(theta=1; theta <=npar; theta++)
3931: trgradg[j][theta]=gradg[theta][j];
3932:
3933: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3934: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3935:
3936: pmij(pmmij,cov,ncovmodel,x,nlstate);
3937:
3938: k=0;
3939: for(i=1; i<=(nlstate); i++){
3940: for(j=1; j<=(nlstate+ndeath);j++){
3941: k=k+1;
3942: mu[k][(int) age]=pmmij[i][j];
3943: }
3944: }
3945: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3946: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3947: varpij[i][j][(int)age] = doldm[i][j];
3948:
3949: /*printf("\n%d ",(int)age);
3950: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3951: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3952: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3953: }*/
3954:
3955: fprintf(ficresprob,"\n%d ",(int)age);
3956: fprintf(ficresprobcov,"\n%d ",(int)age);
3957: fprintf(ficresprobcor,"\n%d ",(int)age);
3958:
3959: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3960: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3961: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3962: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3963: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3964: }
3965: i=0;
3966: for (k=1; k<=(nlstate);k++){
3967: for (l=1; l<=(nlstate+ndeath);l++){
3968: i++;
3969: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3970: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3971: for (j=1; j<=i;j++){
3972: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3973: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3974: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3975: }
3976: }
3977: }/* end of loop for state */
3978: } /* end of loop for age */
3979: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3980: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3981: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3982: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3983:
3984: /* Confidence intervalle of pij */
3985: /*
3986: fprintf(ficgp,"\nunset parametric;unset label");
3987: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3988: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3989: 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);
3990: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3991: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3992: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3993: */
3994:
3995: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3996: first1=1;first2=2;
3997: for (k2=1; k2<=(nlstate);k2++){
3998: for (l2=1; l2<=(nlstate+ndeath);l2++){
3999: if(l2==k2) continue;
4000: j=(k2-1)*(nlstate+ndeath)+l2;
4001: for (k1=1; k1<=(nlstate);k1++){
4002: for (l1=1; l1<=(nlstate+ndeath);l1++){
4003: if(l1==k1) continue;
4004: i=(k1-1)*(nlstate+ndeath)+l1;
4005: if(i<=j) continue;
4006: for (age=bage; age<=fage; age ++){
4007: if ((int)age %5==0){
4008: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4009: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4010: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4011: mu1=mu[i][(int) age]/stepm*YEARM ;
4012: mu2=mu[j][(int) age]/stepm*YEARM;
4013: c12=cv12/sqrt(v1*v2);
4014: /* Computing eigen value of matrix of covariance */
4015: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4016: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4017: if ((lc2 <0) || (lc1 <0) ){
4018: if(first2==1){
4019: first1=0;
4020: 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);
4021: }
4022: 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);
4023: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4024: /* lc2=fabs(lc2); */
4025: }
4026:
4027: /* Eigen vectors */
4028: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4029: /*v21=sqrt(1.-v11*v11); *//* error */
4030: v21=(lc1-v1)/cv12*v11;
4031: v12=-v21;
4032: v22=v11;
4033: tnalp=v21/v11;
4034: if(first1==1){
4035: first1=0;
4036: 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);
4037: }
4038: 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);
4039: /*printf(fignu*/
4040: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4041: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4042: if(first==1){
4043: first=0;
4044: fprintf(ficgp,"\nset parametric;unset label");
4045: 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);
4046: fprintf(ficgp,"\nset ter png small size 320, 240");
4047: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4048: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4049: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4050: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4051: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4052: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4053: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4054: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4055: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4056: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4057: 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",\
4058: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4059: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4060: }else{
4061: first=0;
4062: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4063: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4064: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4065: 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",\
4066: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4067: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4068: }/* if first */
4069: } /* age mod 5 */
4070: } /* end loop age */
4071: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4072: first=1;
4073: } /*l12 */
4074: } /* k12 */
4075: } /*l1 */
4076: }/* k1 */
4077: /* } */ /* loop covariates */
4078: }
4079: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4080: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4081: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4082: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4083: free_vector(xp,1,npar);
4084: fclose(ficresprob);
4085: fclose(ficresprobcov);
4086: fclose(ficresprobcor);
4087: fflush(ficgp);
4088: fflush(fichtmcov);
4089: }
4090:
4091:
4092: /******************* Printing html file ***********/
4093: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4094: int lastpass, int stepm, int weightopt, char model[],\
4095: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4096: int popforecast, int estepm ,\
4097: double jprev1, double mprev1,double anprev1, \
4098: double jprev2, double mprev2,double anprev2){
4099: int jj1, k1, i1, cpt;
4100:
4101: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4102: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4103: </ul>");
4104: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4105: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4106: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4107: fprintf(fichtm,"\
4108: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4109: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4110: fprintf(fichtm,"\
4111: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4112: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4113: fprintf(fichtm,"\
4114: - (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): \
4115: <a href=\"%s\">%s</a> <br>\n",
4116: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4117: fprintf(fichtm,"\
4118: - Population projections by age and states: \
4119: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4120:
4121: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4122:
4123: m=pow(2,cptcoveff);
4124: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4125:
4126: jj1=0;
4127: for(k1=1; k1<=m;k1++){
4128: for(i1=1; i1<=ncodemax[k1];i1++){
4129: jj1++;
4130: if (cptcovn > 0) {
4131: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4132: for (cpt=1; cpt<=cptcoveff;cpt++)
4133: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4134: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4135: }
4136: /* Pij */
4137: 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> \
4138: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4139: /* Quasi-incidences */
4140: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4141: 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> \
4142: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4143: /* Period (stable) prevalence in each health state */
4144: for(cpt=1; cpt<=nlstate;cpt++){
4145: 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> \
4146: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4147: }
4148: for(cpt=1; cpt<=nlstate;cpt++) {
4149: 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> \
4150: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4151: }
4152: } /* end i1 */
4153: }/* End k1 */
4154: fprintf(fichtm,"</ul>");
4155:
4156:
4157: fprintf(fichtm,"\
4158: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4159: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4160:
4161: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4162: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4163: fprintf(fichtm,"\
4164: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4165: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4166:
4167: fprintf(fichtm,"\
4168: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4169: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4170: fprintf(fichtm,"\
4171: - 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): \
4172: <a href=\"%s\">%s</a> <br>\n</li>",
4173: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4174: fprintf(fichtm,"\
4175: - (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): \
4176: <a href=\"%s\">%s</a> <br>\n</li>",
4177: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4178: fprintf(fichtm,"\
4179: - 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",
4180: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4181: fprintf(fichtm,"\
4182: - 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",
4183: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4184: fprintf(fichtm,"\
4185: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4186: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4187:
4188: /* if(popforecast==1) fprintf(fichtm,"\n */
4189: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4190: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4191: /* <br>",fileres,fileres,fileres,fileres); */
4192: /* else */
4193: /* 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); */
4194: fflush(fichtm);
4195: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4196:
4197: m=pow(2,cptcoveff);
4198: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4199:
4200: jj1=0;
4201: for(k1=1; k1<=m;k1++){
4202: for(i1=1; i1<=ncodemax[k1];i1++){
4203: jj1++;
4204: if (cptcovn > 0) {
4205: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4206: for (cpt=1; cpt<=cptcoveff;cpt++)
4207: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4208: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4209: }
4210: for(cpt=1; cpt<=nlstate;cpt++) {
4211: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4212: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4213: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4214: }
4215: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4216: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4217: true period expectancies (those weighted with period prevalences are also\
4218: drawn in addition to the population based expectancies computed using\
4219: observed and cahotic prevalences: %s%d.png<br>\
4220: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4221: } /* end i1 */
4222: }/* End k1 */
4223: fprintf(fichtm,"</ul>");
4224: fflush(fichtm);
4225: }
4226:
4227: /******************* Gnuplot file **************/
4228: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4229:
4230: char dirfileres[132],optfileres[132];
4231: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4232: int ng=0;
4233: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4234: /* printf("Problem with file %s",optionfilegnuplot); */
4235: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4236: /* } */
4237:
4238: /*#ifdef windows */
4239: fprintf(ficgp,"cd \"%s\" \n",pathc);
4240: /*#endif */
4241: m=pow(2,cptcoveff);
4242:
4243: strcpy(dirfileres,optionfilefiname);
4244: strcpy(optfileres,"vpl");
4245: /* 1eme*/
4246: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4247: for (cpt=1; cpt<= nlstate ; cpt ++) {
4248: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4249: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4250: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4251: fprintf(ficgp,"set xlabel \"Age\" \n\
4252: set ylabel \"Probability\" \n\
4253: set ter png small size 320, 240\n\
4254: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4255:
4256: for (i=1; i<= nlstate ; i ++) {
4257: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4258: else fprintf(ficgp," %%*lf (%%*lf)");
4259: }
4260: 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);
4261: for (i=1; i<= nlstate ; i ++) {
4262: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4263: else fprintf(ficgp," %%*lf (%%*lf)");
4264: }
4265: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4266: for (i=1; i<= nlstate ; i ++) {
4267: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4268: else fprintf(ficgp," %%*lf (%%*lf)");
4269: }
4270: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4271: }
4272: }
4273: /*2 eme*/
4274: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4275: for (k1=1; k1<= m ; k1 ++) {
4276: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4277: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4278:
4279: for (i=1; i<= nlstate+1 ; i ++) {
4280: k=2*i;
4281: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4282: for (j=1; j<= nlstate+1 ; j ++) {
4283: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4284: else fprintf(ficgp," %%*lf (%%*lf)");
4285: }
4286: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4287: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4288: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4289: for (j=1; j<= nlstate+1 ; j ++) {
4290: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4291: else fprintf(ficgp," %%*lf (%%*lf)");
4292: }
4293: fprintf(ficgp,"\" t\"\" w l lt 0,");
4294: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4295: for (j=1; j<= nlstate+1 ; j ++) {
4296: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4297: else fprintf(ficgp," %%*lf (%%*lf)");
4298: }
4299: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4300: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4301: }
4302: }
4303:
4304: /*3eme*/
4305:
4306: for (k1=1; k1<= m ; k1 ++) {
4307: for (cpt=1; cpt<= nlstate ; cpt ++) {
4308: /* k=2+nlstate*(2*cpt-2); */
4309: k=2+(nlstate+1)*(cpt-1);
4310: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4311: fprintf(ficgp,"set ter png small size 320, 240\n\
4312: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4313: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4314: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4315: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4316: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4317: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4318: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4319:
4320: */
4321: for (i=1; i< nlstate ; i ++) {
4322: 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);
4323: /* 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);*/
4324:
4325: }
4326: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4327: }
4328: }
4329:
4330: /* CV preval stable (period) */
4331: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4332: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4333: k=3;
4334: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4335: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4336: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4337: set ter png small size 320, 240\n\
4338: unset log y\n\
4339: plot [%.f:%.f] ", ageminpar, agemaxpar);
4340: for (i=1; i<= nlstate ; i ++){
4341: if(i==1)
4342: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4343: else
4344: fprintf(ficgp,", '' ");
4345: l=(nlstate+ndeath)*(i-1)+1;
4346: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4347: for (j=1; j<= (nlstate-1) ; j ++)
4348: fprintf(ficgp,"+$%d",k+l+j);
4349: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4350: } /* nlstate */
4351: fprintf(ficgp,"\n");
4352: } /* end cpt state*/
4353: } /* end covariate */
4354:
4355: /* proba elementaires */
4356: for(i=1,jk=1; i <=nlstate; i++){
4357: for(k=1; k <=(nlstate+ndeath); k++){
4358: if (k != i) {
4359: for(j=1; j <=ncovmodel; j++){
4360: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4361: jk++;
4362: fprintf(ficgp,"\n");
4363: }
4364: }
4365: }
4366: }
4367: /*goto avoid;*/
4368: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4369: for(jk=1; jk <=m; jk++) {
4370: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4371: if (ng==2)
4372: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4373: else
4374: fprintf(ficgp,"\nset title \"Probability\"\n");
4375: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4376: i=1;
4377: for(k2=1; k2<=nlstate; k2++) {
4378: k3=i;
4379: for(k=1; k<=(nlstate+ndeath); k++) {
4380: if (k != k2){
4381: if(ng==2)
4382: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4383: else
4384: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4385: ij=1;/* To be checked else nbcode[0][0] wrong */
4386: for(j=3; j <=ncovmodel; j++) {
4387: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4388: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4389: /* ij++; */
4390: /* } */
4391: /* else */
4392: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4393: }
4394: fprintf(ficgp,")/(1");
4395:
4396: for(k1=1; k1 <=nlstate; k1++){
4397: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4398: ij=1;
4399: for(j=3; j <=ncovmodel; j++){
4400: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4401: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4402: /* ij++; */
4403: /* } */
4404: /* else */
4405: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4406: }
4407: fprintf(ficgp,")");
4408: }
4409: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4410: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4411: i=i+ncovmodel;
4412: }
4413: } /* end k */
4414: } /* end k2 */
4415: } /* end jk */
4416: } /* end ng */
4417: /* avoid: */
4418: fflush(ficgp);
4419: } /* end gnuplot */
4420:
4421:
4422: /*************** Moving average **************/
4423: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4424:
4425: int i, cpt, cptcod;
4426: int modcovmax =1;
4427: int mobilavrange, mob;
4428: double age;
4429:
4430: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4431: a covariate has 2 modalities */
4432: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4433:
4434: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4435: if(mobilav==1) mobilavrange=5; /* default */
4436: else mobilavrange=mobilav;
4437: for (age=bage; age<=fage; age++)
4438: for (i=1; i<=nlstate;i++)
4439: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4440: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4441: /* We keep the original values on the extreme ages bage, fage and for
4442: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4443: we use a 5 terms etc. until the borders are no more concerned.
4444: */
4445: for (mob=3;mob <=mobilavrange;mob=mob+2){
4446: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4447: for (i=1; i<=nlstate;i++){
4448: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4449: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4450: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4451: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4452: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4453: }
4454: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4455: }
4456: }
4457: }/* end age */
4458: }/* end mob */
4459: }else return -1;
4460: return 0;
4461: }/* End movingaverage */
4462:
4463:
4464: /************** Forecasting ******************/
4465: 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){
4466: /* proj1, year, month, day of starting projection
4467: agemin, agemax range of age
4468: dateprev1 dateprev2 range of dates during which prevalence is computed
4469: anproj2 year of en of projection (same day and month as proj1).
4470: */
4471: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4472: double agec; /* generic age */
4473: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4474: double *popeffectif,*popcount;
4475: double ***p3mat;
4476: double ***mobaverage;
4477: char fileresf[FILENAMELENGTH];
4478:
4479: agelim=AGESUP;
4480: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4481:
4482: strcpy(fileresf,"f");
4483: strcat(fileresf,fileres);
4484: if((ficresf=fopen(fileresf,"w"))==NULL) {
4485: printf("Problem with forecast resultfile: %s\n", fileresf);
4486: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4487: }
4488: printf("Computing forecasting: result on file '%s' \n", fileresf);
4489: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4490:
4491: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4492:
4493: if (mobilav!=0) {
4494: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4495: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4496: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4497: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4498: }
4499: }
4500:
4501: stepsize=(int) (stepm+YEARM-1)/YEARM;
4502: if (stepm<=12) stepsize=1;
4503: if(estepm < stepm){
4504: printf ("Problem %d lower than %d\n",estepm, stepm);
4505: }
4506: else hstepm=estepm;
4507:
4508: hstepm=hstepm/stepm;
4509: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4510: fractional in yp1 */
4511: anprojmean=yp;
4512: yp2=modf((yp1*12),&yp);
4513: mprojmean=yp;
4514: yp1=modf((yp2*30.5),&yp);
4515: jprojmean=yp;
4516: if(jprojmean==0) jprojmean=1;
4517: if(mprojmean==0) jprojmean=1;
4518:
4519: i1=cptcoveff;
4520: if (cptcovn < 1){i1=1;}
4521:
4522: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4523:
4524: fprintf(ficresf,"#****** Routine prevforecast **\n");
4525:
4526: /* if (h==(int)(YEARM*yearp)){ */
4527: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4528: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4529: k=k+1;
4530: fprintf(ficresf,"\n#******");
4531: for(j=1;j<=cptcoveff;j++) {
4532: 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]]);
4533: }
4534: fprintf(ficresf,"******\n");
4535: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4536: for(j=1; j<=nlstate+ndeath;j++){
4537: for(i=1; i<=nlstate;i++)
4538: fprintf(ficresf," p%d%d",i,j);
4539: fprintf(ficresf," p.%d",j);
4540: }
4541: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4542: fprintf(ficresf,"\n");
4543: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4544:
4545: for (agec=fage; agec>=(ageminpar-1); agec--){
4546: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4547: nhstepm = nhstepm/hstepm;
4548: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4549: oldm=oldms;savm=savms;
4550: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4551:
4552: for (h=0; h<=nhstepm; h++){
4553: if (h*hstepm/YEARM*stepm ==yearp) {
4554: fprintf(ficresf,"\n");
4555: for(j=1;j<=cptcoveff;j++)
4556: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4557: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4558: }
4559: for(j=1; j<=nlstate+ndeath;j++) {
4560: ppij=0.;
4561: for(i=1; i<=nlstate;i++) {
4562: if (mobilav==1)
4563: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4564: else {
4565: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4566: }
4567: if (h*hstepm/YEARM*stepm== yearp) {
4568: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4569: }
4570: } /* end i */
4571: if (h*hstepm/YEARM*stepm==yearp) {
4572: fprintf(ficresf," %.3f", ppij);
4573: }
4574: }/* end j */
4575: } /* end h */
4576: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4577: } /* end agec */
4578: } /* end yearp */
4579: } /* end cptcod */
4580: } /* end cptcov */
4581:
4582: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4583:
4584: fclose(ficresf);
4585: }
4586:
4587: /************** Forecasting *****not tested NB*************/
4588: 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){
4589:
4590: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4591: int *popage;
4592: double calagedatem, agelim, kk1, kk2;
4593: double *popeffectif,*popcount;
4594: double ***p3mat,***tabpop,***tabpopprev;
4595: double ***mobaverage;
4596: char filerespop[FILENAMELENGTH];
4597:
4598: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4599: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4600: agelim=AGESUP;
4601: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4602:
4603: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4604:
4605:
4606: strcpy(filerespop,"pop");
4607: strcat(filerespop,fileres);
4608: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4609: printf("Problem with forecast resultfile: %s\n", filerespop);
4610: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4611: }
4612: printf("Computing forecasting: result on file '%s' \n", filerespop);
4613: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4614:
4615: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4616:
4617: if (mobilav!=0) {
4618: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4619: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4620: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4621: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4622: }
4623: }
4624:
4625: stepsize=(int) (stepm+YEARM-1)/YEARM;
4626: if (stepm<=12) stepsize=1;
4627:
4628: agelim=AGESUP;
4629:
4630: hstepm=1;
4631: hstepm=hstepm/stepm;
4632:
4633: if (popforecast==1) {
4634: if((ficpop=fopen(popfile,"r"))==NULL) {
4635: printf("Problem with population file : %s\n",popfile);exit(0);
4636: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4637: }
4638: popage=ivector(0,AGESUP);
4639: popeffectif=vector(0,AGESUP);
4640: popcount=vector(0,AGESUP);
4641:
4642: i=1;
4643: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4644:
4645: imx=i;
4646: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4647: }
4648:
4649: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4650: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4651: k=k+1;
4652: fprintf(ficrespop,"\n#******");
4653: for(j=1;j<=cptcoveff;j++) {
4654: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4655: }
4656: fprintf(ficrespop,"******\n");
4657: fprintf(ficrespop,"# Age");
4658: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4659: if (popforecast==1) fprintf(ficrespop," [Population]");
4660:
4661: for (cpt=0; cpt<=0;cpt++) {
4662: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4663:
4664: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4665: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4666: nhstepm = nhstepm/hstepm;
4667:
4668: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4669: oldm=oldms;savm=savms;
4670: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4671:
4672: for (h=0; h<=nhstepm; h++){
4673: if (h==(int) (calagedatem+YEARM*cpt)) {
4674: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4675: }
4676: for(j=1; j<=nlstate+ndeath;j++) {
4677: kk1=0.;kk2=0;
4678: for(i=1; i<=nlstate;i++) {
4679: if (mobilav==1)
4680: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4681: else {
4682: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4683: }
4684: }
4685: if (h==(int)(calagedatem+12*cpt)){
4686: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4687: /*fprintf(ficrespop," %.3f", kk1);
4688: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4689: }
4690: }
4691: for(i=1; i<=nlstate;i++){
4692: kk1=0.;
4693: for(j=1; j<=nlstate;j++){
4694: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4695: }
4696: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4697: }
4698:
4699: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4700: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4701: }
4702: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4703: }
4704: }
4705:
4706: /******/
4707:
4708: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4709: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4710: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4711: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4712: nhstepm = nhstepm/hstepm;
4713:
4714: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4715: oldm=oldms;savm=savms;
4716: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4717: for (h=0; h<=nhstepm; h++){
4718: if (h==(int) (calagedatem+YEARM*cpt)) {
4719: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4720: }
4721: for(j=1; j<=nlstate+ndeath;j++) {
4722: kk1=0.;kk2=0;
4723: for(i=1; i<=nlstate;i++) {
4724: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4725: }
4726: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4727: }
4728: }
4729: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4730: }
4731: }
4732: }
4733: }
4734:
4735: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4736:
4737: if (popforecast==1) {
4738: free_ivector(popage,0,AGESUP);
4739: free_vector(popeffectif,0,AGESUP);
4740: free_vector(popcount,0,AGESUP);
4741: }
4742: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4743: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4744: fclose(ficrespop);
4745: } /* End of popforecast */
4746:
4747: int fileappend(FILE *fichier, char *optionfich)
4748: {
4749: if((fichier=fopen(optionfich,"a"))==NULL) {
4750: printf("Problem with file: %s\n", optionfich);
4751: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4752: return (0);
4753: }
4754: fflush(fichier);
4755: return (1);
4756: }
4757:
4758:
4759: /**************** function prwizard **********************/
4760: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4761: {
4762:
4763: /* Wizard to print covariance matrix template */
4764:
4765: char ca[32], cb[32];
4766: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4767: int numlinepar;
4768:
4769: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4770: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4771: for(i=1; i <=nlstate; i++){
4772: jj=0;
4773: for(j=1; j <=nlstate+ndeath; j++){
4774: if(j==i) continue;
4775: jj++;
4776: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4777: printf("%1d%1d",i,j);
4778: fprintf(ficparo,"%1d%1d",i,j);
4779: for(k=1; k<=ncovmodel;k++){
4780: /* printf(" %lf",param[i][j][k]); */
4781: /* fprintf(ficparo," %lf",param[i][j][k]); */
4782: printf(" 0.");
4783: fprintf(ficparo," 0.");
4784: }
4785: printf("\n");
4786: fprintf(ficparo,"\n");
4787: }
4788: }
4789: printf("# Scales (for hessian or gradient estimation)\n");
4790: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4791: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4792: for(i=1; i <=nlstate; i++){
4793: jj=0;
4794: for(j=1; j <=nlstate+ndeath; j++){
4795: if(j==i) continue;
4796: jj++;
4797: fprintf(ficparo,"%1d%1d",i,j);
4798: printf("%1d%1d",i,j);
4799: fflush(stdout);
4800: for(k=1; k<=ncovmodel;k++){
4801: /* printf(" %le",delti3[i][j][k]); */
4802: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4803: printf(" 0.");
4804: fprintf(ficparo," 0.");
4805: }
4806: numlinepar++;
4807: printf("\n");
4808: fprintf(ficparo,"\n");
4809: }
4810: }
4811: printf("# Covariance matrix\n");
4812: /* # 121 Var(a12)\n\ */
4813: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4814: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4815: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4816: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4817: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4818: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4819: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4820: fflush(stdout);
4821: fprintf(ficparo,"# Covariance matrix\n");
4822: /* # 121 Var(a12)\n\ */
4823: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4824: /* # ...\n\ */
4825: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4826:
4827: for(itimes=1;itimes<=2;itimes++){
4828: jj=0;
4829: for(i=1; i <=nlstate; i++){
4830: for(j=1; j <=nlstate+ndeath; j++){
4831: if(j==i) continue;
4832: for(k=1; k<=ncovmodel;k++){
4833: jj++;
4834: ca[0]= k+'a'-1;ca[1]='\0';
4835: if(itimes==1){
4836: printf("#%1d%1d%d",i,j,k);
4837: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4838: }else{
4839: printf("%1d%1d%d",i,j,k);
4840: fprintf(ficparo,"%1d%1d%d",i,j,k);
4841: /* printf(" %.5le",matcov[i][j]); */
4842: }
4843: ll=0;
4844: for(li=1;li <=nlstate; li++){
4845: for(lj=1;lj <=nlstate+ndeath; lj++){
4846: if(lj==li) continue;
4847: for(lk=1;lk<=ncovmodel;lk++){
4848: ll++;
4849: if(ll<=jj){
4850: cb[0]= lk +'a'-1;cb[1]='\0';
4851: if(ll<jj){
4852: if(itimes==1){
4853: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4854: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4855: }else{
4856: printf(" 0.");
4857: fprintf(ficparo," 0.");
4858: }
4859: }else{
4860: if(itimes==1){
4861: printf(" Var(%s%1d%1d)",ca,i,j);
4862: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4863: }else{
4864: printf(" 0.");
4865: fprintf(ficparo," 0.");
4866: }
4867: }
4868: }
4869: } /* end lk */
4870: } /* end lj */
4871: } /* end li */
4872: printf("\n");
4873: fprintf(ficparo,"\n");
4874: numlinepar++;
4875: } /* end k*/
4876: } /*end j */
4877: } /* end i */
4878: } /* end itimes */
4879:
4880: } /* end of prwizard */
4881: /******************* Gompertz Likelihood ******************************/
4882: double gompertz(double x[])
4883: {
4884: double A,B,L=0.0,sump=0.,num=0.;
4885: int i,n=0; /* n is the size of the sample */
4886:
4887: for (i=0;i<=imx-1 ; i++) {
4888: sump=sump+weight[i];
4889: /* sump=sump+1;*/
4890: num=num+1;
4891: }
4892:
4893:
4894: /* for (i=0; i<=imx; i++)
4895: 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]);*/
4896:
4897: for (i=1;i<=imx ; i++)
4898: {
4899: if (cens[i] == 1 && wav[i]>1)
4900: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4901:
4902: if (cens[i] == 0 && wav[i]>1)
4903: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4904: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4905:
4906: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4907: if (wav[i] > 1 ) { /* ??? */
4908: L=L+A*weight[i];
4909: /* 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]);*/
4910: }
4911: }
4912:
4913: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4914:
4915: return -2*L*num/sump;
4916: }
4917:
4918: #ifdef GSL
4919: /******************* Gompertz_f Likelihood ******************************/
4920: double gompertz_f(const gsl_vector *v, void *params)
4921: {
4922: double A,B,LL=0.0,sump=0.,num=0.;
4923: double *x= (double *) v->data;
4924: int i,n=0; /* n is the size of the sample */
4925:
4926: for (i=0;i<=imx-1 ; i++) {
4927: sump=sump+weight[i];
4928: /* sump=sump+1;*/
4929: num=num+1;
4930: }
4931:
4932:
4933: /* for (i=0; i<=imx; i++)
4934: 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]);*/
4935: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4936: for (i=1;i<=imx ; i++)
4937: {
4938: if (cens[i] == 1 && wav[i]>1)
4939: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4940:
4941: if (cens[i] == 0 && wav[i]>1)
4942: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4943: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4944:
4945: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4946: if (wav[i] > 1 ) { /* ??? */
4947: LL=LL+A*weight[i];
4948: /* 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]);*/
4949: }
4950: }
4951:
4952: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4953: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4954:
4955: return -2*LL*num/sump;
4956: }
4957: #endif
4958:
4959: /******************* Printing html file ***********/
4960: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4961: int lastpass, int stepm, int weightopt, char model[],\
4962: int imx, double p[],double **matcov,double agemortsup){
4963: int i,k;
4964:
4965: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4966: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4967: for (i=1;i<=2;i++)
4968: 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]));
4969: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4970: fprintf(fichtm,"</ul>");
4971:
4972: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4973:
4974: 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>");
4975:
4976: for (k=agegomp;k<(agemortsup-2);k++)
4977: 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]);
4978:
4979:
4980: fflush(fichtm);
4981: }
4982:
4983: /******************* Gnuplot file **************/
4984: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4985:
4986: char dirfileres[132],optfileres[132];
4987:
4988: int ng;
4989:
4990:
4991: /*#ifdef windows */
4992: fprintf(ficgp,"cd \"%s\" \n",pathc);
4993: /*#endif */
4994:
4995:
4996: strcpy(dirfileres,optionfilefiname);
4997: strcpy(optfileres,"vpl");
4998: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4999: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5000: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5001: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5002: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5003:
5004: }
5005:
5006: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5007: {
5008:
5009: /*-------- data file ----------*/
5010: FILE *fic;
5011: char dummy[]=" ";
5012: int i=0, j=0, n=0;
5013: int linei, month, year,iout;
5014: char line[MAXLINE], linetmp[MAXLINE];
5015: char stra[MAXLINE], strb[MAXLINE];
5016: char *stratrunc;
5017: int lstra;
5018:
5019:
5020: if((fic=fopen(datafile,"r"))==NULL) {
5021: printf("Problem while opening datafile: %s\n", datafile);return 1;
5022: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5023: }
5024:
5025: i=1;
5026: linei=0;
5027: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5028: linei=linei+1;
5029: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5030: if(line[j] == '\t')
5031: line[j] = ' ';
5032: }
5033: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5034: ;
5035: };
5036: line[j+1]=0; /* Trims blanks at end of line */
5037: if(line[0]=='#'){
5038: fprintf(ficlog,"Comment line\n%s\n",line);
5039: printf("Comment line\n%s\n",line);
5040: continue;
5041: }
5042: trimbb(linetmp,line); /* Trims multiple blanks in line */
5043: strcpy(line, linetmp);
5044:
5045:
5046: for (j=maxwav;j>=1;j--){
5047: cutv(stra, strb, line, ' ');
5048: if(strb[0]=='.') { /* Missing status */
5049: lval=-1;
5050: }else{
5051: errno=0;
5052: lval=strtol(strb,&endptr,10);
5053: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5054: if( strb[0]=='\0' || (*endptr != '\0')){
5055: 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);
5056: 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);
5057: return 1;
5058: }
5059: }
5060: s[j][i]=lval;
5061:
5062: strcpy(line,stra);
5063: cutv(stra, strb,line,' ');
5064: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5065: }
5066: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5067: month=99;
5068: year=9999;
5069: }else{
5070: 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);
5071: 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);
5072: return 1;
5073: }
5074: anint[j][i]= (double) year;
5075: mint[j][i]= (double)month;
5076: strcpy(line,stra);
5077: } /* ENd Waves */
5078:
5079: cutv(stra, strb,line,' ');
5080: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5081: }
5082: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5083: month=99;
5084: year=9999;
5085: }else{
5086: 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);
5087: 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);
5088: return 1;
5089: }
5090: andc[i]=(double) year;
5091: moisdc[i]=(double) month;
5092: strcpy(line,stra);
5093:
5094: cutv(stra, strb,line,' ');
5095: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5096: }
5097: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5098: month=99;
5099: year=9999;
5100: }else{
5101: 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);
5102: 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);
5103: return 1;
5104: }
5105: if (year==9999) {
5106: 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);
5107: 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);
5108: return 1;
5109:
5110: }
5111: annais[i]=(double)(year);
5112: moisnais[i]=(double)(month);
5113: strcpy(line,stra);
5114:
5115: cutv(stra, strb,line,' ');
5116: errno=0;
5117: dval=strtod(strb,&endptr);
5118: if( strb[0]=='\0' || (*endptr != '\0')){
5119: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5120: 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);
5121: fflush(ficlog);
5122: return 1;
5123: }
5124: weight[i]=dval;
5125: strcpy(line,stra);
5126:
5127: for (j=ncovcol;j>=1;j--){
5128: cutv(stra, strb,line,' ');
5129: if(strb[0]=='.') { /* Missing status */
5130: lval=-1;
5131: }else{
5132: errno=0;
5133: lval=strtol(strb,&endptr,10);
5134: if( strb[0]=='\0' || (*endptr != '\0')){
5135: 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);
5136: 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);
5137: return 1;
5138: }
5139: }
5140: if(lval <-1 || lval >1){
5141: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5142: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5143: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5144: For example, for multinomial values like 1, 2 and 3,\n \
5145: build V1=0 V2=0 for the reference value (1),\n \
5146: V1=1 V2=0 for (2) \n \
5147: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5148: output of IMaCh is often meaningless.\n \
5149: Exiting.\n",lval,linei, i,line,j);
5150: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5151: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5152: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5153: For example, for multinomial values like 1, 2 and 3,\n \
5154: build V1=0 V2=0 for the reference value (1),\n \
5155: V1=1 V2=0 for (2) \n \
5156: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5157: output of IMaCh is often meaningless.\n \
5158: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5159: return 1;
5160: }
5161: covar[j][i]=(double)(lval);
5162: strcpy(line,stra);
5163: }
5164: lstra=strlen(stra);
5165:
5166: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5167: stratrunc = &(stra[lstra-9]);
5168: num[i]=atol(stratrunc);
5169: }
5170: else
5171: num[i]=atol(stra);
5172: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5173: 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;}*/
5174:
5175: i=i+1;
5176: } /* End loop reading data */
5177:
5178: *imax=i-1; /* Number of individuals */
5179: fclose(fic);
5180:
5181: return (0);
5182: /* endread: */
5183: printf("Exiting readdata: ");
5184: fclose(fic);
5185: return (1);
5186:
5187:
5188:
5189: }
5190: void removespace(char *str) {
5191: char *p1 = str, *p2 = str;
5192: do
5193: while (*p2 == ' ')
5194: p2++;
5195: while (*p1++ == *p2++);
5196: }
5197:
5198: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5199: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5200: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5201: * - cptcovn or number of covariates k of the models excluding age*products =6
5202: * - cptcovage number of covariates with age*products =2
5203: * - cptcovs number of simple covariates
5204: * - 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
5205: * which is a new column after the 9 (ncovcol) variables.
5206: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5207: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5208: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5209: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5210: */
5211: {
5212: int i, j, k, ks;
5213: int j1, k1, k2;
5214: char modelsav[80];
5215: char stra[80], strb[80], strc[80], strd[80],stre[80];
5216:
5217: /*removespace(model);*/
5218: if (strlen(model) >1){ /* If there is at least 1 covariate */
5219: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5220: j=nbocc(model,'+'); /**< j=Number of '+' */
5221: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5222: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5223: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5224: /* including age products which are counted in cptcovage.
5225: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5226: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5227: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5228: strcpy(modelsav,model);
5229: if (strstr(model,"AGE") !=0){
5230: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5231: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5232: return 1;
5233: }
5234: if (strstr(model,"v") !=0){
5235: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5236: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5237: return 1;
5238: }
5239:
5240: /* Design
5241: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5242: * < ncovcol=8 >
5243: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5244: * k= 1 2 3 4 5 6 7 8
5245: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5246: * covar[k,i], value of kth covariate if not including age for individual i:
5247: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5248: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5249: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5250: * Tage[++cptcovage]=k
5251: * if products, new covar are created after ncovcol with k1
5252: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5253: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5254: * 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
5255: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5256: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5257: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5258: * < ncovcol=8 >
5259: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5260: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5261: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5262: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5263: * p Tprod[1]@2={ 6, 5}
5264: *p Tvard[1][1]@4= {7, 8, 5, 6}
5265: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5266: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5267: *How to reorganize?
5268: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5269: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5270: * {2, 1, 4, 8, 5, 6, 3, 7}
5271: * Struct []
5272: */
5273:
5274: /* This loop fills the array Tvar from the string 'model'.*/
5275: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5276: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5277: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5278: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5279: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5280: /* k=1 Tvar[1]=2 (from V2) */
5281: /* k=5 Tvar[5] */
5282: /* for (k=1; k<=cptcovn;k++) { */
5283: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5284: /* } */
5285: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5286: /*
5287: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5288: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5289: Tvar[k]=0;
5290: cptcovage=0;
5291: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5292: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5293: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5294: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5295: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5296: /*scanf("%d",i);*/
5297: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5298: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5299: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5300: /* covar is not filled and then is empty */
5301: cptcovprod--;
5302: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5303: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5304: cptcovage++; /* Sums the number of covariates which include age as a product */
5305: Tage[cptcovage]=k; /* Tage[1] = 4 */
5306: /*printf("stre=%s ", stre);*/
5307: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5308: cptcovprod--;
5309: cutl(stre,strb,strc,'V');
5310: Tvar[k]=atoi(stre);
5311: cptcovage++;
5312: Tage[cptcovage]=k;
5313: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5314: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5315: cptcovn++;
5316: cptcovprodnoage++;k1++;
5317: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5318: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5319: because this model-covariate is a construction we invent a new column
5320: ncovcol + k1
5321: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5322: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5323: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5324: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5325: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5326: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5327: k2=k2+2;
5328: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5329: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5330: for (i=1; i<=lastobs;i++){
5331: /* Computes the new covariate which is a product of
5332: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5333: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5334: }
5335: } /* End age is not in the model */
5336: } /* End if model includes a product */
5337: else { /* no more sum */
5338: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5339: /* scanf("%d",i);*/
5340: cutl(strd,strc,strb,'V');
5341: ks++; /**< Number of simple covariates */
5342: cptcovn++;
5343: Tvar[k]=atoi(strd);
5344: }
5345: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5346: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5347: scanf("%d",i);*/
5348: } /* end of loop + */
5349: } /* end model */
5350:
5351: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5352: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5353:
5354: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5355: printf("cptcovprod=%d ", cptcovprod);
5356: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5357:
5358: scanf("%d ",i);*/
5359:
5360:
5361: return (0); /* with covar[new additional covariate if product] and Tage if age */
5362: /*endread:*/
5363: printf("Exiting decodemodel: ");
5364: return (1);
5365: }
5366:
5367: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5368: {
5369: int i, m;
5370:
5371: for (i=1; i<=imx; i++) {
5372: for(m=2; (m<= maxwav); m++) {
5373: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5374: anint[m][i]=9999;
5375: s[m][i]=-1;
5376: }
5377: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5378: *nberr = *nberr + 1;
5379: 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);
5380: 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);
5381: s[m][i]=-1;
5382: }
5383: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5384: (*nberr)++;
5385: 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]);
5386: 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]);
5387: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5388: }
5389: }
5390: }
5391:
5392: for (i=1; i<=imx; i++) {
5393: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5394: for(m=firstpass; (m<= lastpass); m++){
5395: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5396: if (s[m][i] >= nlstate+1) {
5397: if(agedc[i]>0){
5398: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5399: agev[m][i]=agedc[i];
5400: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5401: }else {
5402: if ((int)andc[i]!=9999){
5403: nbwarn++;
5404: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5405: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5406: agev[m][i]=-1;
5407: }
5408: }
5409: } /* agedc > 0 */
5410: }
5411: else if(s[m][i] !=9){ /* Standard case, age in fractional
5412: years but with the precision of a month */
5413: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5414: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5415: agev[m][i]=1;
5416: else if(agev[m][i] < *agemin){
5417: *agemin=agev[m][i];
5418: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5419: }
5420: else if(agev[m][i] >*agemax){
5421: *agemax=agev[m][i];
5422: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5423: }
5424: /*agev[m][i]=anint[m][i]-annais[i];*/
5425: /* agev[m][i] = age[i]+2*m;*/
5426: }
5427: else { /* =9 */
5428: agev[m][i]=1;
5429: s[m][i]=-1;
5430: }
5431: }
5432: else /*= 0 Unknown */
5433: agev[m][i]=1;
5434: }
5435:
5436: }
5437: for (i=1; i<=imx; i++) {
5438: for(m=firstpass; (m<=lastpass); m++){
5439: if (s[m][i] > (nlstate+ndeath)) {
5440: (*nberr)++;
5441: 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);
5442: 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);
5443: return 1;
5444: }
5445: }
5446: }
5447:
5448: /*for (i=1; i<=imx; i++){
5449: for (m=firstpass; (m<lastpass); m++){
5450: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5451: }
5452:
5453: }*/
5454:
5455:
5456: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5457: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5458:
5459: return (0);
5460: /* endread:*/
5461: printf("Exiting calandcheckages: ");
5462: return (1);
5463: }
5464:
5465: #if defined(_MSC_VER)
5466: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5467: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5468: //#include "stdafx.h"
5469: //#include <stdio.h>
5470: //#include <tchar.h>
5471: //#include <windows.h>
5472: //#include <iostream>
5473: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5474:
5475: LPFN_ISWOW64PROCESS fnIsWow64Process;
5476:
5477: BOOL IsWow64()
5478: {
5479: BOOL bIsWow64 = FALSE;
5480:
5481: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5482: // (HANDLE, PBOOL);
5483:
5484: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5485:
5486: HMODULE module = GetModuleHandle(_T("kernel32"));
5487: const char funcName[] = "IsWow64Process";
5488: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5489: GetProcAddress(module, funcName);
5490:
5491: if (NULL != fnIsWow64Process)
5492: {
5493: if (!fnIsWow64Process(GetCurrentProcess(),
5494: &bIsWow64))
5495: //throw std::exception("Unknown error");
5496: printf("Unknown error\n");
5497: }
5498: return bIsWow64 != FALSE;
5499: }
5500: #endif
5501: void syscompilerinfo()
5502: {
5503: /* #include "syscompilerinfo.h"*/
5504: #if defined(__GNUC__)
5505: #include <gnu/libc-version.h> /* Only on gnu */
5506: #endif
5507:
5508: #include <stdint.h>
5509: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5510: #if defined(__clang__)
5511: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5512: #endif
5513: #if defined(__ICC) || defined(__INTEL_COMPILER)
5514: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5515: #endif
5516: #if defined(__GNUC__) || defined(__GNUG__)
5517: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5518: #endif
5519: #if defined(__HP_cc) || defined(__HP_aCC)
5520: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5521: #endif
5522: #if defined(__IBMC__) || defined(__IBMCPP__)
5523: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5524: #endif
5525: #if defined(_MSC_VER)
5526: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5527: #endif
5528: #if defined(__PGI)
5529: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5530: #endif
5531: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5532: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5533: #endif
5534: printf(" for ");fprintf(ficlog," for ");
5535:
5536: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5537: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5538: // Windows (x64 and x86)
5539: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5540: #elif __unix__ // all unices, not all compilers
5541: // Unix
5542: printf("Unix ");fprintf(ficlog,"Unix ");
5543: #elif __linux__
5544: // linux
5545: printf("linux ");fprintf(ficlog,"linux ");
5546: #elif __APPLE__
5547: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5548: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5549: #endif
5550:
5551: /* __MINGW32__ */
5552: /* __CYGWIN__ */
5553: /* __MINGW64__ */
5554: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5555: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5556: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5557: /* _WIN64 // Defined for applications for Win64. */
5558: /* _M_X64 // Defined for compilations that target x64 processors. */
5559: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5560:
5561: #if UINTPTR_MAX == 0xffffffff
5562: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5563: #elif UINTPTR_MAX == 0xffffffffffffffff
5564: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5565: #else
5566: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5567: #endif
5568:
5569: /* struct utsname sysInfo;
5570:
5571: if (uname(&sysInfo) != -1) {
5572: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5573: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5574: }
5575: else
5576: perror("uname() error");
5577: */
5578: #if defined(__GNUC__)
5579: # if defined(__GNUC_PATCHLEVEL__)
5580: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5581: + __GNUC_MINOR__ * 100 \
5582: + __GNUC_PATCHLEVEL__)
5583: # else
5584: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5585: + __GNUC_MINOR__ * 100)
5586: # endif
5587: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5588: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5589: printf("GNU libc version: %s\n", gnu_get_libc_version());
5590: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5591:
5592: #endif
5593:
5594: // void main()
5595: // {
5596: #if defined(_MSC_VER)
5597: if (IsWow64()){
5598: printf("The program (probably compile for 32bit) is running under WOW64 (64bit) emulation.\n");
5599: fprintf(ficlog, "The program (ie 32bit) is running under WOW64 (64bit) emulation.\n");
5600: }
5601: else{
5602: printf("The process is not running under WOW64 (i.e probably on a 64bits windows).\n");
5603: frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bits windows).\n");
5604: }
5605: // printf("\nPress Enter to continue...");
5606: // getchar();
5607: // }
5608:
5609: #endif
5610:
5611:
5612: }
5613:
5614: /***********************************************/
5615: /**************** Main Program *****************/
5616: /***********************************************/
5617:
5618: int main(int argc, char *argv[])
5619: {
5620: #ifdef GSL
5621: const gsl_multimin_fminimizer_type *T;
5622: size_t iteri = 0, it;
5623: int rval = GSL_CONTINUE;
5624: int status = GSL_SUCCESS;
5625: double ssval;
5626: #endif
5627: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5628: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5629:
5630: int jj, ll, li, lj, lk;
5631: int numlinepar=0; /* Current linenumber of parameter file */
5632: int itimes;
5633: int NDIM=2;
5634: int vpopbased=0;
5635:
5636: char ca[32], cb[32];
5637: /* FILE *fichtm; *//* Html File */
5638: /* FILE *ficgp;*/ /*Gnuplot File */
5639: struct stat info;
5640: double agedeb;
5641: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5642:
5643: double fret;
5644: double dum; /* Dummy variable */
5645: double ***p3mat;
5646: double ***mobaverage;
5647:
5648: char line[MAXLINE];
5649: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5650: char pathr[MAXLINE], pathimach[MAXLINE];
5651: char *tok, *val; /* pathtot */
5652: int firstobs=1, lastobs=10;
5653: int c, h , cpt;
5654: int jl;
5655: int i1, j1, jk, stepsize;
5656: int *tab;
5657: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5658: int mobilav=0,popforecast=0;
5659: int hstepm, nhstepm;
5660: int agemortsup;
5661: float sumlpop=0.;
5662: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5663: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5664:
5665: double bage=0, fage=110, age, agelim, agebase;
5666: double ftolpl=FTOL;
5667: double **prlim;
5668: double ***param; /* Matrix of parameters */
5669: double *p;
5670: double **matcov; /* Matrix of covariance */
5671: double ***delti3; /* Scale */
5672: double *delti; /* Scale */
5673: double ***eij, ***vareij;
5674: double **varpl; /* Variances of prevalence limits by age */
5675: double *epj, vepp;
5676:
5677: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5678: double **ximort;
5679: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5680: int *dcwave;
5681:
5682: char z[1]="c";
5683:
5684: /*char *strt;*/
5685: char strtend[80];
5686:
5687:
5688: /* setlocale (LC_ALL, ""); */
5689: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5690: /* textdomain (PACKAGE); */
5691: /* setlocale (LC_CTYPE, ""); */
5692: /* setlocale (LC_MESSAGES, ""); */
5693:
5694: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5695: rstart_time = time(NULL);
5696: /* (void) gettimeofday(&start_time,&tzp);*/
5697: start_time = *localtime(&rstart_time);
5698: curr_time=start_time;
5699: /*tml = *localtime(&start_time.tm_sec);*/
5700: /* strcpy(strstart,asctime(&tml)); */
5701: strcpy(strstart,asctime(&start_time));
5702:
5703: /* printf("Localtime (at start)=%s",strstart); */
5704: /* tp.tm_sec = tp.tm_sec +86400; */
5705: /* tm = *localtime(&start_time.tm_sec); */
5706: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5707: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5708: /* tmg.tm_hour=tmg.tm_hour + 1; */
5709: /* tp.tm_sec = mktime(&tmg); */
5710: /* strt=asctime(&tmg); */
5711: /* printf("Time(after) =%s",strstart); */
5712: /* (void) time (&time_value);
5713: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5714: * tm = *localtime(&time_value);
5715: * strstart=asctime(&tm);
5716: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5717: */
5718:
5719: nberr=0; /* Number of errors and warnings */
5720: nbwarn=0;
5721: getcwd(pathcd, size);
5722:
5723: printf("\n%s\n%s",version,fullversion);
5724: if(argc <=1){
5725: printf("\nEnter the parameter file name: ");
5726: fgets(pathr,FILENAMELENGTH,stdin);
5727: i=strlen(pathr);
5728: if(pathr[i-1]=='\n')
5729: pathr[i-1]='\0';
5730: i=strlen(pathr);
5731: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5732: pathr[i-1]='\0';
5733: for (tok = pathr; tok != NULL; ){
5734: printf("Pathr |%s|\n",pathr);
5735: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5736: printf("val= |%s| pathr=%s\n",val,pathr);
5737: strcpy (pathtot, val);
5738: if(pathr[0] == '\0') break; /* Dirty */
5739: }
5740: }
5741: else{
5742: strcpy(pathtot,argv[1]);
5743: }
5744: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5745: /*cygwin_split_path(pathtot,path,optionfile);
5746: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5747: /* cutv(path,optionfile,pathtot,'\\');*/
5748:
5749: /* Split argv[0], imach program to get pathimach */
5750: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5751: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5752: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5753: /* strcpy(pathimach,argv[0]); */
5754: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5755: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5756: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5757: chdir(path); /* Can be a relative path */
5758: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5759: printf("Current directory %s!\n",pathcd);
5760: strcpy(command,"mkdir ");
5761: strcat(command,optionfilefiname);
5762: if((outcmd=system(command)) != 0){
5763: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5764: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5765: /* fclose(ficlog); */
5766: /* exit(1); */
5767: }
5768: /* if((imk=mkdir(optionfilefiname))<0){ */
5769: /* perror("mkdir"); */
5770: /* } */
5771:
5772: /*-------- arguments in the command line --------*/
5773:
5774: /* Log file */
5775: strcat(filelog, optionfilefiname);
5776: strcat(filelog,".log"); /* */
5777: if((ficlog=fopen(filelog,"w"))==NULL) {
5778: printf("Problem with logfile %s\n",filelog);
5779: goto end;
5780: }
5781: fprintf(ficlog,"Log filename:%s\n",filelog);
5782: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5783: fprintf(ficlog,"\nEnter the parameter file name: \n");
5784: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5785: path=%s \n\
5786: optionfile=%s\n\
5787: optionfilext=%s\n\
5788: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5789:
5790: syscompilerinfo();
5791:
5792: printf("Local time (at start):%s",strstart);
5793: fprintf(ficlog,"Local time (at start): %s",strstart);
5794: fflush(ficlog);
5795: /* (void) gettimeofday(&curr_time,&tzp); */
5796: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5797:
5798: /* */
5799: strcpy(fileres,"r");
5800: strcat(fileres, optionfilefiname);
5801: strcat(fileres,".txt"); /* Other files have txt extension */
5802:
5803: /*---------arguments file --------*/
5804:
5805: if((ficpar=fopen(optionfile,"r"))==NULL) {
5806: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5807: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5808: fflush(ficlog);
5809: /* goto end; */
5810: exit(70);
5811: }
5812:
5813:
5814:
5815: strcpy(filereso,"o");
5816: strcat(filereso,fileres);
5817: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5818: printf("Problem with Output resultfile: %s\n", filereso);
5819: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5820: fflush(ficlog);
5821: goto end;
5822: }
5823:
5824: /* Reads comments: lines beginning with '#' */
5825: numlinepar=0;
5826: while((c=getc(ficpar))=='#' && c!= EOF){
5827: ungetc(c,ficpar);
5828: fgets(line, MAXLINE, ficpar);
5829: numlinepar++;
5830: fputs(line,stdout);
5831: fputs(line,ficparo);
5832: fputs(line,ficlog);
5833: }
5834: ungetc(c,ficpar);
5835:
5836: 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);
5837: numlinepar++;
5838: 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);
5839: 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);
5840: 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);
5841: fflush(ficlog);
5842: while((c=getc(ficpar))=='#' && c!= EOF){
5843: ungetc(c,ficpar);
5844: fgets(line, MAXLINE, ficpar);
5845: numlinepar++;
5846: fputs(line, stdout);
5847: //puts(line);
5848: fputs(line,ficparo);
5849: fputs(line,ficlog);
5850: }
5851: ungetc(c,ficpar);
5852:
5853:
5854: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5855: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5856: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5857: v1+v2*age+v2*v3 makes cptcovn = 3
5858: */
5859: if (strlen(model)>1)
5860: 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*/
5861: else
5862: ncovmodel=2;
5863: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5864: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5865: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5866: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5867: 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);
5868: 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);
5869: fflush(stdout);
5870: fclose (ficlog);
5871: goto end;
5872: }
5873: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5874: delti=delti3[1][1];
5875: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5876: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5877: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5878: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5879: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5880: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5881: fclose (ficparo);
5882: fclose (ficlog);
5883: goto end;
5884: exit(0);
5885: }
5886: else if(mle==-3) {
5887: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5888: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5889: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5890: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5891: matcov=matrix(1,npar,1,npar);
5892: }
5893: else{
5894: /* Read guessed parameters */
5895: /* Reads comments: lines beginning with '#' */
5896: while((c=getc(ficpar))=='#' && c!= EOF){
5897: ungetc(c,ficpar);
5898: fgets(line, MAXLINE, ficpar);
5899: numlinepar++;
5900: fputs(line,stdout);
5901: fputs(line,ficparo);
5902: fputs(line,ficlog);
5903: }
5904: ungetc(c,ficpar);
5905:
5906: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5907: for(i=1; i <=nlstate; i++){
5908: j=0;
5909: for(jj=1; jj <=nlstate+ndeath; jj++){
5910: if(jj==i) continue;
5911: j++;
5912: fscanf(ficpar,"%1d%1d",&i1,&j1);
5913: if ((i1 != i) && (j1 != j)){
5914: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5915: It might be a problem of design; if ncovcol and the model are correct\n \
5916: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5917: exit(1);
5918: }
5919: fprintf(ficparo,"%1d%1d",i1,j1);
5920: if(mle==1)
5921: printf("%1d%1d",i,j);
5922: fprintf(ficlog,"%1d%1d",i,j);
5923: for(k=1; k<=ncovmodel;k++){
5924: fscanf(ficpar," %lf",¶m[i][j][k]);
5925: if(mle==1){
5926: printf(" %lf",param[i][j][k]);
5927: fprintf(ficlog," %lf",param[i][j][k]);
5928: }
5929: else
5930: fprintf(ficlog," %lf",param[i][j][k]);
5931: fprintf(ficparo," %lf",param[i][j][k]);
5932: }
5933: fscanf(ficpar,"\n");
5934: numlinepar++;
5935: if(mle==1)
5936: printf("\n");
5937: fprintf(ficlog,"\n");
5938: fprintf(ficparo,"\n");
5939: }
5940: }
5941: fflush(ficlog);
5942:
5943: /* Reads scales values */
5944: p=param[1][1];
5945:
5946: /* Reads comments: lines beginning with '#' */
5947: while((c=getc(ficpar))=='#' && c!= EOF){
5948: ungetc(c,ficpar);
5949: fgets(line, MAXLINE, ficpar);
5950: numlinepar++;
5951: fputs(line,stdout);
5952: fputs(line,ficparo);
5953: fputs(line,ficlog);
5954: }
5955: ungetc(c,ficpar);
5956:
5957: for(i=1; i <=nlstate; i++){
5958: for(j=1; j <=nlstate+ndeath-1; j++){
5959: fscanf(ficpar,"%1d%1d",&i1,&j1);
5960: if ( (i1-i) * (j1-j) != 0){
5961: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5962: exit(1);
5963: }
5964: printf("%1d%1d",i,j);
5965: fprintf(ficparo,"%1d%1d",i1,j1);
5966: fprintf(ficlog,"%1d%1d",i1,j1);
5967: for(k=1; k<=ncovmodel;k++){
5968: fscanf(ficpar,"%le",&delti3[i][j][k]);
5969: printf(" %le",delti3[i][j][k]);
5970: fprintf(ficparo," %le",delti3[i][j][k]);
5971: fprintf(ficlog," %le",delti3[i][j][k]);
5972: }
5973: fscanf(ficpar,"\n");
5974: numlinepar++;
5975: printf("\n");
5976: fprintf(ficparo,"\n");
5977: fprintf(ficlog,"\n");
5978: }
5979: }
5980: fflush(ficlog);
5981:
5982: /* Reads covariance matrix */
5983: delti=delti3[1][1];
5984:
5985:
5986: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5987:
5988: /* Reads comments: lines beginning with '#' */
5989: while((c=getc(ficpar))=='#' && c!= EOF){
5990: ungetc(c,ficpar);
5991: fgets(line, MAXLINE, ficpar);
5992: numlinepar++;
5993: fputs(line,stdout);
5994: fputs(line,ficparo);
5995: fputs(line,ficlog);
5996: }
5997: ungetc(c,ficpar);
5998:
5999: matcov=matrix(1,npar,1,npar);
6000: for(i=1; i <=npar; i++)
6001: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6002:
6003: for(i=1; i <=npar; i++){
6004: fscanf(ficpar,"%s",str);
6005: if(mle==1)
6006: printf("%s",str);
6007: fprintf(ficlog,"%s",str);
6008: fprintf(ficparo,"%s",str);
6009: for(j=1; j <=i; j++){
6010: fscanf(ficpar," %le",&matcov[i][j]);
6011: if(mle==1){
6012: printf(" %.5le",matcov[i][j]);
6013: }
6014: fprintf(ficlog," %.5le",matcov[i][j]);
6015: fprintf(ficparo," %.5le",matcov[i][j]);
6016: }
6017: fscanf(ficpar,"\n");
6018: numlinepar++;
6019: if(mle==1)
6020: printf("\n");
6021: fprintf(ficlog,"\n");
6022: fprintf(ficparo,"\n");
6023: }
6024: for(i=1; i <=npar; i++)
6025: for(j=i+1;j<=npar;j++)
6026: matcov[i][j]=matcov[j][i];
6027:
6028: if(mle==1)
6029: printf("\n");
6030: fprintf(ficlog,"\n");
6031:
6032: fflush(ficlog);
6033:
6034: /*-------- Rewriting parameter file ----------*/
6035: strcpy(rfileres,"r"); /* "Rparameterfile */
6036: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6037: strcat(rfileres,"."); /* */
6038: strcat(rfileres,optionfilext); /* Other files have txt extension */
6039: if((ficres =fopen(rfileres,"w"))==NULL) {
6040: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6041: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6042: }
6043: fprintf(ficres,"#%s\n",version);
6044: } /* End of mle != -3 */
6045:
6046:
6047: n= lastobs;
6048: num=lvector(1,n);
6049: moisnais=vector(1,n);
6050: annais=vector(1,n);
6051: moisdc=vector(1,n);
6052: andc=vector(1,n);
6053: agedc=vector(1,n);
6054: cod=ivector(1,n);
6055: weight=vector(1,n);
6056: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6057: mint=matrix(1,maxwav,1,n);
6058: anint=matrix(1,maxwav,1,n);
6059: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6060: tab=ivector(1,NCOVMAX);
6061: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6062:
6063: /* Reads data from file datafile */
6064: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6065: goto end;
6066:
6067: /* Calculation of the number of parameters from char model */
6068: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6069: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6070: k=3 V4 Tvar[k=3]= 4 (from V4)
6071: k=2 V1 Tvar[k=2]= 1 (from V1)
6072: k=1 Tvar[1]=2 (from V2)
6073: */
6074: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6075: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6076: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6077: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6078: */
6079: /* For model-covariate k tells which data-covariate to use but
6080: because this model-covariate is a construction we invent a new column
6081: ncovcol + k1
6082: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6083: Tvar[3=V1*V4]=4+1 etc */
6084: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6085: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6086: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6087: */
6088: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6089: 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
6090: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6091: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6092: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6093: 4 covariates (3 plus signs)
6094: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6095: */
6096:
6097: if(decodemodel(model, lastobs) == 1)
6098: goto end;
6099:
6100: if((double)(lastobs-imx)/(double)imx > 1.10){
6101: nbwarn++;
6102: 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);
6103: 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);
6104: }
6105: /* if(mle==1){*/
6106: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6107: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6108: }
6109:
6110: /*-calculation of age at interview from date of interview and age at death -*/
6111: agev=matrix(1,maxwav,1,imx);
6112:
6113: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6114: goto end;
6115:
6116:
6117: agegomp=(int)agemin;
6118: free_vector(moisnais,1,n);
6119: free_vector(annais,1,n);
6120: /* free_matrix(mint,1,maxwav,1,n);
6121: free_matrix(anint,1,maxwav,1,n);*/
6122: free_vector(moisdc,1,n);
6123: free_vector(andc,1,n);
6124: /* */
6125:
6126: wav=ivector(1,imx);
6127: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6128: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6129: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6130:
6131: /* Concatenates waves */
6132: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6133: /* */
6134:
6135: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6136:
6137: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6138: ncodemax[1]=1;
6139: Ndum =ivector(-1,NCOVMAX);
6140: if (ncovmodel > 2)
6141: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6142:
6143: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6144: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6145: h=0;
6146:
6147:
6148: /*if (cptcovn > 0) */
6149:
6150:
6151: m=pow(2,cptcoveff);
6152:
6153: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6154: 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 */
6155: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6156: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6157: h++;
6158: if (h>m)
6159: h=1;
6160: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6161: * h 1 2 3 4
6162: *______________________________
6163: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6164: * 2 2 1 1 1
6165: * 3 i=2 1 2 1 1
6166: * 4 2 2 1 1
6167: * 5 i=3 1 i=2 1 2 1
6168: * 6 2 1 2 1
6169: * 7 i=4 1 2 2 1
6170: * 8 2 2 2 1
6171: * 9 i=5 1 i=3 1 i=2 1 1
6172: * 10 2 1 1 1
6173: * 11 i=6 1 2 1 1
6174: * 12 2 2 1 1
6175: * 13 i=7 1 i=4 1 2 1
6176: * 14 2 1 2 1
6177: * 15 i=8 1 2 2 1
6178: * 16 2 2 2 1
6179: */
6180: codtab[h][k]=j;
6181: /*codtab[h][Tvar[k]]=j;*/
6182: 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]]);
6183: }
6184: }
6185: }
6186: }
6187: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6188: codtab[1][2]=1;codtab[2][2]=2; */
6189: /* for(i=1; i <=m ;i++){
6190: for(k=1; k <=cptcovn; k++){
6191: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6192: }
6193: printf("\n");
6194: }
6195: scanf("%d",i);*/
6196:
6197: free_ivector(Ndum,-1,NCOVMAX);
6198:
6199:
6200:
6201: /*------------ gnuplot -------------*/
6202: strcpy(optionfilegnuplot,optionfilefiname);
6203: if(mle==-3)
6204: strcat(optionfilegnuplot,"-mort");
6205: strcat(optionfilegnuplot,".gp");
6206:
6207: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6208: printf("Problem with file %s",optionfilegnuplot);
6209: }
6210: else{
6211: fprintf(ficgp,"\n# %s\n", version);
6212: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6213: //fprintf(ficgp,"set missing 'NaNq'\n");
6214: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6215: }
6216: /* fclose(ficgp);*/
6217: /*--------- index.htm --------*/
6218:
6219: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6220: if(mle==-3)
6221: strcat(optionfilehtm,"-mort");
6222: strcat(optionfilehtm,".htm");
6223: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6224: printf("Problem with %s \n",optionfilehtm);
6225: exit(0);
6226: }
6227:
6228: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6229: strcat(optionfilehtmcov,"-cov.htm");
6230: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6231: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6232: }
6233: else{
6234: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6235: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6236: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6237: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6238: }
6239:
6240: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6241: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6242: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6243: \n\
6244: <hr size=\"2\" color=\"#EC5E5E\">\
6245: <ul><li><h4>Parameter files</h4>\n\
6246: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6247: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6248: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6249: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6250: - Date and time at start: %s</ul>\n",\
6251: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6252: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6253: fileres,fileres,\
6254: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6255: fflush(fichtm);
6256:
6257: strcpy(pathr,path);
6258: strcat(pathr,optionfilefiname);
6259: chdir(optionfilefiname); /* Move to directory named optionfile */
6260:
6261: /* Calculates basic frequencies. Computes observed prevalence at single age
6262: and prints on file fileres'p'. */
6263: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6264:
6265: fprintf(fichtm,"\n");
6266: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6267: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6268: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6269: imx,agemin,agemax,jmin,jmax,jmean);
6270: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6271: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6272: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6273: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6274: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6275:
6276:
6277: /* For Powell, parameters are in a vector p[] starting at p[1]
6278: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6279: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6280:
6281: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6282:
6283: if (mle==-3){
6284: ximort=matrix(1,NDIM,1,NDIM);
6285: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6286: cens=ivector(1,n);
6287: ageexmed=vector(1,n);
6288: agecens=vector(1,n);
6289: dcwave=ivector(1,n);
6290:
6291: for (i=1; i<=imx; i++){
6292: dcwave[i]=-1;
6293: for (m=firstpass; m<=lastpass; m++)
6294: if (s[m][i]>nlstate) {
6295: dcwave[i]=m;
6296: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6297: break;
6298: }
6299: }
6300:
6301: for (i=1; i<=imx; i++) {
6302: if (wav[i]>0){
6303: ageexmed[i]=agev[mw[1][i]][i];
6304: j=wav[i];
6305: agecens[i]=1.;
6306:
6307: if (ageexmed[i]> 1 && wav[i] > 0){
6308: agecens[i]=agev[mw[j][i]][i];
6309: cens[i]= 1;
6310: }else if (ageexmed[i]< 1)
6311: cens[i]= -1;
6312: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6313: cens[i]=0 ;
6314: }
6315: else cens[i]=-1;
6316: }
6317:
6318: for (i=1;i<=NDIM;i++) {
6319: for (j=1;j<=NDIM;j++)
6320: ximort[i][j]=(i == j ? 1.0 : 0.0);
6321: }
6322:
6323: /*p[1]=0.0268; p[NDIM]=0.083;*/
6324: /*printf("%lf %lf", p[1], p[2]);*/
6325:
6326:
6327: #ifdef GSL
6328: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6329: #else
6330: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6331: #endif
6332: strcpy(filerespow,"pow-mort");
6333: strcat(filerespow,fileres);
6334: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6335: printf("Problem with resultfile: %s\n", filerespow);
6336: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6337: }
6338: #ifdef GSL
6339: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6340: #else
6341: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6342: #endif
6343: /* for (i=1;i<=nlstate;i++)
6344: for(j=1;j<=nlstate+ndeath;j++)
6345: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6346: */
6347: fprintf(ficrespow,"\n");
6348: #ifdef GSL
6349: /* gsl starts here */
6350: T = gsl_multimin_fminimizer_nmsimplex;
6351: gsl_multimin_fminimizer *sfm = NULL;
6352: gsl_vector *ss, *x;
6353: gsl_multimin_function minex_func;
6354:
6355: /* Initial vertex size vector */
6356: ss = gsl_vector_alloc (NDIM);
6357:
6358: if (ss == NULL){
6359: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6360: }
6361: /* Set all step sizes to 1 */
6362: gsl_vector_set_all (ss, 0.001);
6363:
6364: /* Starting point */
6365:
6366: x = gsl_vector_alloc (NDIM);
6367:
6368: if (x == NULL){
6369: gsl_vector_free(ss);
6370: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6371: }
6372:
6373: /* Initialize method and iterate */
6374: /* p[1]=0.0268; p[NDIM]=0.083; */
6375: /* gsl_vector_set(x, 0, 0.0268); */
6376: /* gsl_vector_set(x, 1, 0.083); */
6377: gsl_vector_set(x, 0, p[1]);
6378: gsl_vector_set(x, 1, p[2]);
6379:
6380: minex_func.f = &gompertz_f;
6381: minex_func.n = NDIM;
6382: minex_func.params = (void *)&p; /* ??? */
6383:
6384: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6385: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6386:
6387: printf("Iterations beginning .....\n\n");
6388: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6389:
6390: iteri=0;
6391: while (rval == GSL_CONTINUE){
6392: iteri++;
6393: status = gsl_multimin_fminimizer_iterate(sfm);
6394:
6395: if (status) printf("error: %s\n", gsl_strerror (status));
6396: fflush(0);
6397:
6398: if (status)
6399: break;
6400:
6401: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6402: ssval = gsl_multimin_fminimizer_size (sfm);
6403:
6404: if (rval == GSL_SUCCESS)
6405: printf ("converged to a local maximum at\n");
6406:
6407: printf("%5d ", iteri);
6408: for (it = 0; it < NDIM; it++){
6409: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6410: }
6411: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6412: }
6413:
6414: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6415:
6416: gsl_vector_free(x); /* initial values */
6417: gsl_vector_free(ss); /* inital step size */
6418: for (it=0; it<NDIM; it++){
6419: p[it+1]=gsl_vector_get(sfm->x,it);
6420: fprintf(ficrespow," %.12lf", p[it]);
6421: }
6422: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6423: #endif
6424: #ifdef POWELL
6425: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6426: #endif
6427: fclose(ficrespow);
6428:
6429: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6430:
6431: for(i=1; i <=NDIM; i++)
6432: for(j=i+1;j<=NDIM;j++)
6433: matcov[i][j]=matcov[j][i];
6434:
6435: printf("\nCovariance matrix\n ");
6436: for(i=1; i <=NDIM; i++) {
6437: for(j=1;j<=NDIM;j++){
6438: printf("%f ",matcov[i][j]);
6439: }
6440: printf("\n ");
6441: }
6442:
6443: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6444: for (i=1;i<=NDIM;i++)
6445: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6446:
6447: lsurv=vector(1,AGESUP);
6448: lpop=vector(1,AGESUP);
6449: tpop=vector(1,AGESUP);
6450: lsurv[agegomp]=100000;
6451:
6452: for (k=agegomp;k<=AGESUP;k++) {
6453: agemortsup=k;
6454: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6455: }
6456:
6457: for (k=agegomp;k<agemortsup;k++)
6458: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6459:
6460: for (k=agegomp;k<agemortsup;k++){
6461: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6462: sumlpop=sumlpop+lpop[k];
6463: }
6464:
6465: tpop[agegomp]=sumlpop;
6466: for (k=agegomp;k<(agemortsup-3);k++){
6467: /* tpop[k+1]=2;*/
6468: tpop[k+1]=tpop[k]-lpop[k];
6469: }
6470:
6471:
6472: printf("\nAge lx qx dx Lx Tx e(x)\n");
6473: for (k=agegomp;k<(agemortsup-2);k++)
6474: 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]);
6475:
6476:
6477: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6478: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6479:
6480: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6481: stepm, weightopt,\
6482: model,imx,p,matcov,agemortsup);
6483:
6484: free_vector(lsurv,1,AGESUP);
6485: free_vector(lpop,1,AGESUP);
6486: free_vector(tpop,1,AGESUP);
6487: #ifdef GSL
6488: free_ivector(cens,1,n);
6489: free_vector(agecens,1,n);
6490: free_ivector(dcwave,1,n);
6491: free_matrix(ximort,1,NDIM,1,NDIM);
6492: #endif
6493: } /* Endof if mle==-3 */
6494:
6495: else{ /* For mle >=1 */
6496: globpr=0;/* debug */
6497: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6498: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6499: for (k=1; k<=npar;k++)
6500: printf(" %d %8.5f",k,p[k]);
6501: printf("\n");
6502: globpr=1; /* to print the contributions */
6503: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6504: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6505: for (k=1; k<=npar;k++)
6506: printf(" %d %8.5f",k,p[k]);
6507: printf("\n");
6508: if(mle>=1){ /* Could be 1 or 2 */
6509: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6510: }
6511:
6512: /*--------- results files --------------*/
6513: 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);
6514:
6515:
6516: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6517: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6518: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6519: for(i=1,jk=1; i <=nlstate; i++){
6520: for(k=1; k <=(nlstate+ndeath); k++){
6521: if (k != i) {
6522: printf("%d%d ",i,k);
6523: fprintf(ficlog,"%d%d ",i,k);
6524: fprintf(ficres,"%1d%1d ",i,k);
6525: for(j=1; j <=ncovmodel; j++){
6526: printf("%lf ",p[jk]);
6527: fprintf(ficlog,"%lf ",p[jk]);
6528: fprintf(ficres,"%lf ",p[jk]);
6529: jk++;
6530: }
6531: printf("\n");
6532: fprintf(ficlog,"\n");
6533: fprintf(ficres,"\n");
6534: }
6535: }
6536: }
6537: if(mle!=0){
6538: /* Computing hessian and covariance matrix */
6539: ftolhess=ftol; /* Usually correct */
6540: hesscov(matcov, p, npar, delti, ftolhess, func);
6541: }
6542: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6543: printf("# Scales (for hessian or gradient estimation)\n");
6544: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6545: for(i=1,jk=1; i <=nlstate; i++){
6546: for(j=1; j <=nlstate+ndeath; j++){
6547: if (j!=i) {
6548: fprintf(ficres,"%1d%1d",i,j);
6549: printf("%1d%1d",i,j);
6550: fprintf(ficlog,"%1d%1d",i,j);
6551: for(k=1; k<=ncovmodel;k++){
6552: printf(" %.5e",delti[jk]);
6553: fprintf(ficlog," %.5e",delti[jk]);
6554: fprintf(ficres," %.5e",delti[jk]);
6555: jk++;
6556: }
6557: printf("\n");
6558: fprintf(ficlog,"\n");
6559: fprintf(ficres,"\n");
6560: }
6561: }
6562: }
6563:
6564: 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");
6565: if(mle>=1)
6566: 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");
6567: 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");
6568: /* # 121 Var(a12)\n\ */
6569: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6570: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6571: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6572: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6573: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6574: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6575: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6576:
6577:
6578: /* Just to have a covariance matrix which will be more understandable
6579: even is we still don't want to manage dictionary of variables
6580: */
6581: for(itimes=1;itimes<=2;itimes++){
6582: jj=0;
6583: for(i=1; i <=nlstate; i++){
6584: for(j=1; j <=nlstate+ndeath; j++){
6585: if(j==i) continue;
6586: for(k=1; k<=ncovmodel;k++){
6587: jj++;
6588: ca[0]= k+'a'-1;ca[1]='\0';
6589: if(itimes==1){
6590: if(mle>=1)
6591: printf("#%1d%1d%d",i,j,k);
6592: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6593: fprintf(ficres,"#%1d%1d%d",i,j,k);
6594: }else{
6595: if(mle>=1)
6596: printf("%1d%1d%d",i,j,k);
6597: fprintf(ficlog,"%1d%1d%d",i,j,k);
6598: fprintf(ficres,"%1d%1d%d",i,j,k);
6599: }
6600: ll=0;
6601: for(li=1;li <=nlstate; li++){
6602: for(lj=1;lj <=nlstate+ndeath; lj++){
6603: if(lj==li) continue;
6604: for(lk=1;lk<=ncovmodel;lk++){
6605: ll++;
6606: if(ll<=jj){
6607: cb[0]= lk +'a'-1;cb[1]='\0';
6608: if(ll<jj){
6609: if(itimes==1){
6610: if(mle>=1)
6611: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6612: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6613: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6614: }else{
6615: if(mle>=1)
6616: printf(" %.5e",matcov[jj][ll]);
6617: fprintf(ficlog," %.5e",matcov[jj][ll]);
6618: fprintf(ficres," %.5e",matcov[jj][ll]);
6619: }
6620: }else{
6621: if(itimes==1){
6622: if(mle>=1)
6623: printf(" Var(%s%1d%1d)",ca,i,j);
6624: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6625: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6626: }else{
6627: if(mle>=1)
6628: printf(" %.5e",matcov[jj][ll]);
6629: fprintf(ficlog," %.5e",matcov[jj][ll]);
6630: fprintf(ficres," %.5e",matcov[jj][ll]);
6631: }
6632: }
6633: }
6634: } /* end lk */
6635: } /* end lj */
6636: } /* end li */
6637: if(mle>=1)
6638: printf("\n");
6639: fprintf(ficlog,"\n");
6640: fprintf(ficres,"\n");
6641: numlinepar++;
6642: } /* end k*/
6643: } /*end j */
6644: } /* end i */
6645: } /* end itimes */
6646:
6647: fflush(ficlog);
6648: fflush(ficres);
6649:
6650: while((c=getc(ficpar))=='#' && c!= EOF){
6651: ungetc(c,ficpar);
6652: fgets(line, MAXLINE, ficpar);
6653: fputs(line,stdout);
6654: fputs(line,ficparo);
6655: }
6656: ungetc(c,ficpar);
6657:
6658: estepm=0;
6659: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6660: if (estepm==0 || estepm < stepm) estepm=stepm;
6661: if (fage <= 2) {
6662: bage = ageminpar;
6663: fage = agemaxpar;
6664: }
6665:
6666: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6667: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6668: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6669:
6670: while((c=getc(ficpar))=='#' && c!= EOF){
6671: ungetc(c,ficpar);
6672: fgets(line, MAXLINE, ficpar);
6673: fputs(line,stdout);
6674: fputs(line,ficparo);
6675: }
6676: ungetc(c,ficpar);
6677:
6678: 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);
6679: 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);
6680: 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);
6681: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6682: 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);
6683:
6684: while((c=getc(ficpar))=='#' && c!= EOF){
6685: ungetc(c,ficpar);
6686: fgets(line, MAXLINE, ficpar);
6687: fputs(line,stdout);
6688: fputs(line,ficparo);
6689: }
6690: ungetc(c,ficpar);
6691:
6692:
6693: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6694: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6695:
6696: fscanf(ficpar,"pop_based=%d\n",&popbased);
6697: fprintf(ficparo,"pop_based=%d\n",popbased);
6698: fprintf(ficres,"pop_based=%d\n",popbased);
6699:
6700: while((c=getc(ficpar))=='#' && c!= EOF){
6701: ungetc(c,ficpar);
6702: fgets(line, MAXLINE, ficpar);
6703: fputs(line,stdout);
6704: fputs(line,ficparo);
6705: }
6706: ungetc(c,ficpar);
6707:
6708: 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);
6709: 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);
6710: 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);
6711: 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);
6712: 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);
6713: /* day and month of proj2 are not used but only year anproj2.*/
6714:
6715:
6716:
6717: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6718: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6719:
6720: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6721: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6722:
6723: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6724: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6725: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6726:
6727: /*------------ free_vector -------------*/
6728: /* chdir(path); */
6729:
6730: free_ivector(wav,1,imx);
6731: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6732: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6733: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6734: free_lvector(num,1,n);
6735: free_vector(agedc,1,n);
6736: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6737: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6738: fclose(ficparo);
6739: fclose(ficres);
6740:
6741:
6742: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6743: #include "prevlim.h" /* Use ficrespl, ficlog */
6744: fclose(ficrespl);
6745:
6746: #ifdef FREEEXIT2
6747: #include "freeexit2.h"
6748: #endif
6749:
6750: /*------------- h Pij x at various ages ------------*/
6751: #include "hpijx.h"
6752: fclose(ficrespij);
6753:
6754: /*-------------- Variance of one-step probabilities---*/
6755: k=1;
6756: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6757:
6758:
6759: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6760: for(i=1;i<=AGESUP;i++)
6761: for(j=1;j<=NCOVMAX;j++)
6762: for(k=1;k<=NCOVMAX;k++)
6763: probs[i][j][k]=0.;
6764:
6765: /*---------- Forecasting ------------------*/
6766: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6767: if(prevfcast==1){
6768: /* if(stepm ==1){*/
6769: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6770: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6771: /* } */
6772: /* else{ */
6773: /* erreur=108; */
6774: /* 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); */
6775: /* 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); */
6776: /* } */
6777: }
6778:
6779:
6780: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6781:
6782: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6783: /* 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",\
6784: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6785: */
6786:
6787: if (mobilav!=0) {
6788: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6789: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6790: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6791: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6792: }
6793: }
6794:
6795:
6796: /*---------- Health expectancies, no variances ------------*/
6797:
6798: strcpy(filerese,"e");
6799: strcat(filerese,fileres);
6800: if((ficreseij=fopen(filerese,"w"))==NULL) {
6801: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6802: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6803: }
6804: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6805: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6806: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6807: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6808:
6809: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6810: fprintf(ficreseij,"\n#****** ");
6811: for(j=1;j<=cptcoveff;j++) {
6812: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6813: }
6814: fprintf(ficreseij,"******\n");
6815:
6816: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6817: oldm=oldms;savm=savms;
6818: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6819:
6820: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6821: /*}*/
6822: }
6823: fclose(ficreseij);
6824:
6825:
6826: /*---------- Health expectancies and variances ------------*/
6827:
6828:
6829: strcpy(filerest,"t");
6830: strcat(filerest,fileres);
6831: if((ficrest=fopen(filerest,"w"))==NULL) {
6832: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6833: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6834: }
6835: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6836: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6837:
6838:
6839: strcpy(fileresstde,"stde");
6840: strcat(fileresstde,fileres);
6841: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6842: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6843: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6844: }
6845: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6846: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6847:
6848: strcpy(filerescve,"cve");
6849: strcat(filerescve,fileres);
6850: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6851: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6852: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6853: }
6854: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6855: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6856:
6857: strcpy(fileresv,"v");
6858: strcat(fileresv,fileres);
6859: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6860: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6861: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6862: }
6863: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6864: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6865:
6866: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6867: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6868:
6869: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6870: fprintf(ficrest,"\n#****** ");
6871: for(j=1;j<=cptcoveff;j++)
6872: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6873: fprintf(ficrest,"******\n");
6874:
6875: fprintf(ficresstdeij,"\n#****** ");
6876: fprintf(ficrescveij,"\n#****** ");
6877: for(j=1;j<=cptcoveff;j++) {
6878: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6879: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6880: }
6881: fprintf(ficresstdeij,"******\n");
6882: fprintf(ficrescveij,"******\n");
6883:
6884: fprintf(ficresvij,"\n#****** ");
6885: for(j=1;j<=cptcoveff;j++)
6886: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6887: fprintf(ficresvij,"******\n");
6888:
6889: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6890: oldm=oldms;savm=savms;
6891: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6892: /*
6893: */
6894: /* goto endfree; */
6895:
6896: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6897: pstamp(ficrest);
6898:
6899:
6900: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6901: oldm=oldms;savm=savms; /* Segmentation fault */
6902: cptcod= 0; /* To be deleted */
6903: 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 */
6904: 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 ");
6905: if(vpopbased==1)
6906: 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);
6907: else
6908: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6909: fprintf(ficrest,"# Age e.. (std) ");
6910: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6911: fprintf(ficrest,"\n");
6912:
6913: epj=vector(1,nlstate+1);
6914: for(age=bage; age <=fage ;age++){
6915: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6916: if (vpopbased==1) {
6917: if(mobilav ==0){
6918: for(i=1; i<=nlstate;i++)
6919: prlim[i][i]=probs[(int)age][i][k];
6920: }else{ /* mobilav */
6921: for(i=1; i<=nlstate;i++)
6922: prlim[i][i]=mobaverage[(int)age][i][k];
6923: }
6924: }
6925:
6926: fprintf(ficrest," %4.0f",age);
6927: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6928: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6929: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6930: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6931: }
6932: epj[nlstate+1] +=epj[j];
6933: }
6934:
6935: for(i=1, vepp=0.;i <=nlstate;i++)
6936: for(j=1;j <=nlstate;j++)
6937: vepp += vareij[i][j][(int)age];
6938: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6939: for(j=1;j <=nlstate;j++){
6940: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6941: }
6942: fprintf(ficrest,"\n");
6943: }
6944: }
6945: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6946: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6947: free_vector(epj,1,nlstate+1);
6948: /*}*/
6949: }
6950: free_vector(weight,1,n);
6951: free_imatrix(Tvard,1,NCOVMAX,1,2);
6952: free_imatrix(s,1,maxwav+1,1,n);
6953: free_matrix(anint,1,maxwav,1,n);
6954: free_matrix(mint,1,maxwav,1,n);
6955: free_ivector(cod,1,n);
6956: free_ivector(tab,1,NCOVMAX);
6957: fclose(ficresstdeij);
6958: fclose(ficrescveij);
6959: fclose(ficresvij);
6960: fclose(ficrest);
6961: fclose(ficpar);
6962:
6963: /*------- Variance of period (stable) prevalence------*/
6964:
6965: strcpy(fileresvpl,"vpl");
6966: strcat(fileresvpl,fileres);
6967: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6968: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6969: exit(0);
6970: }
6971: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6972:
6973: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6974: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6975:
6976: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6977: fprintf(ficresvpl,"\n#****** ");
6978: for(j=1;j<=cptcoveff;j++)
6979: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6980: fprintf(ficresvpl,"******\n");
6981:
6982: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6983: oldm=oldms;savm=savms;
6984: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6985: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6986: /*}*/
6987: }
6988:
6989: fclose(ficresvpl);
6990:
6991: /*---------- End : free ----------------*/
6992: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6993: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6994: } /* mle==-3 arrives here for freeing */
6995: /* endfree:*/
6996: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6997: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6998: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6999: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7000: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7001: free_matrix(covar,0,NCOVMAX,1,n);
7002: free_matrix(matcov,1,npar,1,npar);
7003: /*free_vector(delti,1,npar);*/
7004: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7005: free_matrix(agev,1,maxwav,1,imx);
7006: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7007:
7008: free_ivector(ncodemax,1,NCOVMAX);
7009: free_ivector(Tvar,1,NCOVMAX);
7010: free_ivector(Tprod,1,NCOVMAX);
7011: free_ivector(Tvaraff,1,NCOVMAX);
7012: free_ivector(Tage,1,NCOVMAX);
7013:
7014: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7015: free_imatrix(codtab,1,100,1,10);
7016: fflush(fichtm);
7017: fflush(ficgp);
7018:
7019:
7020: if((nberr >0) || (nbwarn>0)){
7021: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7022: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7023: }else{
7024: printf("End of Imach\n");
7025: fprintf(ficlog,"End of Imach\n");
7026: }
7027: printf("See log file on %s\n",filelog);
7028: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7029: /*(void) gettimeofday(&end_time,&tzp);*/
7030: rend_time = time(NULL);
7031: end_time = *localtime(&rend_time);
7032: /* tml = *localtime(&end_time.tm_sec); */
7033: strcpy(strtend,asctime(&end_time));
7034: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7035: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7036: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7037:
7038: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7039: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7040: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7041: /* printf("Total time was %d uSec.\n", total_usecs);*/
7042: /* if(fileappend(fichtm,optionfilehtm)){ */
7043: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7044: fclose(fichtm);
7045: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7046: fclose(fichtmcov);
7047: fclose(ficgp);
7048: fclose(ficlog);
7049: /*------ End -----------*/
7050:
7051:
7052: printf("Before Current directory %s!\n",pathcd);
7053: if(chdir(pathcd) != 0)
7054: printf("Can't move to directory %s!\n",path);
7055: if(getcwd(pathcd,MAXLINE) > 0)
7056: printf("Current directory %s!\n",pathcd);
7057: /*strcat(plotcmd,CHARSEPARATOR);*/
7058: sprintf(plotcmd,"gnuplot");
7059: #ifdef _WIN32
7060: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7061: #endif
7062: if(!stat(plotcmd,&info)){
7063: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7064: if(!stat(getenv("GNUPLOTBIN"),&info)){
7065: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7066: }else
7067: strcpy(pplotcmd,plotcmd);
7068: #ifdef __unix
7069: strcpy(plotcmd,GNUPLOTPROGRAM);
7070: if(!stat(plotcmd,&info)){
7071: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7072: }else
7073: strcpy(pplotcmd,plotcmd);
7074: #endif
7075: }else
7076: strcpy(pplotcmd,plotcmd);
7077:
7078: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7079: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7080:
7081: if((outcmd=system(plotcmd)) != 0){
7082: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7083: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7084: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7085: if((outcmd=system(plotcmd)) != 0)
7086: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7087: }
7088: printf(" Successful, please wait...");
7089: while (z[0] != 'q') {
7090: /* chdir(path); */
7091: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7092: scanf("%s",z);
7093: /* if (z[0] == 'c') system("./imach"); */
7094: if (z[0] == 'e') {
7095: #ifdef __APPLE__
7096: sprintf(pplotcmd, "open %s", optionfilehtm);
7097: #elif __linux
7098: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7099: #else
7100: sprintf(pplotcmd, "%s", optionfilehtm);
7101: #endif
7102: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7103: system(pplotcmd);
7104: }
7105: else if (z[0] == 'g') system(plotcmd);
7106: else if (z[0] == 'q') exit(0);
7107: }
7108: end:
7109: while (z[0] != 'q') {
7110: printf("\nType q for exiting: ");
7111: scanf("%s",z);
7112: }
7113: }
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