1: /* $Id: imach.c,v 1.190 2015/05/05 08:51:13 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.190 2015/05/05 08:51:13 brouard
5: Summary: Adding digits in output parameters (7 digits instead of 6)
6:
7: Fix 1+age+.
8:
9: Revision 1.189 2015/04/30 14:45:16 brouard
10: Summary: 0.98q2
11:
12: Revision 1.188 2015/04/30 08:27:53 brouard
13: *** empty log message ***
14:
15: Revision 1.187 2015/04/29 09:11:15 brouard
16: *** empty log message ***
17:
18: Revision 1.186 2015/04/23 12:01:52 brouard
19: Summary: V1*age is working now, version 0.98q1
20:
21: Some codes had been disabled in order to simplify and Vn*age was
22: working in the optimization phase, ie, giving correct MLE parameters,
23: but, as usual, outputs were not correct and program core dumped.
24:
25: Revision 1.185 2015/03/11 13:26:42 brouard
26: Summary: Inclusion of compile and links command line for Intel Compiler
27:
28: Revision 1.184 2015/03/11 11:52:39 brouard
29: Summary: Back from Windows 8. Intel Compiler
30:
31: Revision 1.183 2015/03/10 20:34:32 brouard
32: Summary: 0.98q0, trying with directest, mnbrak fixed
33:
34: We use directest instead of original Powell test; probably no
35: incidence on the results, but better justifications;
36: We fixed Numerical Recipes mnbrak routine which was wrong and gave
37: wrong results.
38:
39: Revision 1.182 2015/02/12 08:19:57 brouard
40: Summary: Trying to keep directest which seems simpler and more general
41: Author: Nicolas Brouard
42:
43: Revision 1.181 2015/02/11 23:22:24 brouard
44: Summary: Comments on Powell added
45:
46: Author:
47:
48: Revision 1.180 2015/02/11 17:33:45 brouard
49: Summary: Finishing move from main to function (hpijx and prevalence_limit)
50:
51: Revision 1.179 2015/01/04 09:57:06 brouard
52: Summary: back to OS/X
53:
54: Revision 1.178 2015/01/04 09:35:48 brouard
55: *** empty log message ***
56:
57: Revision 1.177 2015/01/03 18:40:56 brouard
58: Summary: Still testing ilc32 on OSX
59:
60: Revision 1.176 2015/01/03 16:45:04 brouard
61: *** empty log message ***
62:
63: Revision 1.175 2015/01/03 16:33:42 brouard
64: *** empty log message ***
65:
66: Revision 1.174 2015/01/03 16:15:49 brouard
67: Summary: Still in cross-compilation
68:
69: Revision 1.173 2015/01/03 12:06:26 brouard
70: Summary: trying to detect cross-compilation
71:
72: Revision 1.172 2014/12/27 12:07:47 brouard
73: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
74:
75: Revision 1.171 2014/12/23 13:26:59 brouard
76: Summary: Back from Visual C
77:
78: Still problem with utsname.h on Windows
79:
80: Revision 1.170 2014/12/23 11:17:12 brouard
81: Summary: Cleaning some \%% back to %%
82:
83: The escape was mandatory for a specific compiler (which one?), but too many warnings.
84:
85: Revision 1.169 2014/12/22 23:08:31 brouard
86: Summary: 0.98p
87:
88: Outputs some informations on compiler used, OS etc. Testing on different platforms.
89:
90: Revision 1.168 2014/12/22 15:17:42 brouard
91: Summary: update
92:
93: Revision 1.167 2014/12/22 13:50:56 brouard
94: Summary: Testing uname and compiler version and if compiled 32 or 64
95:
96: Testing on Linux 64
97:
98: Revision 1.166 2014/12/22 11:40:47 brouard
99: *** empty log message ***
100:
101: Revision 1.165 2014/12/16 11:20:36 brouard
102: Summary: After compiling on Visual C
103:
104: * imach.c (Module): Merging 1.61 to 1.162
105:
106: Revision 1.164 2014/12/16 10:52:11 brouard
107: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
108:
109: * imach.c (Module): Merging 1.61 to 1.162
110:
111: Revision 1.163 2014/12/16 10:30:11 brouard
112: * imach.c (Module): Merging 1.61 to 1.162
113:
114: Revision 1.162 2014/09/25 11:43:39 brouard
115: Summary: temporary backup 0.99!
116:
117: Revision 1.1 2014/09/16 11:06:58 brouard
118: Summary: With some code (wrong) for nlopt
119:
120: Author:
121:
122: Revision 1.161 2014/09/15 20:41:41 brouard
123: Summary: Problem with macro SQR on Intel compiler
124:
125: Revision 1.160 2014/09/02 09:24:05 brouard
126: *** empty log message ***
127:
128: Revision 1.159 2014/09/01 10:34:10 brouard
129: Summary: WIN32
130: Author: Brouard
131:
132: Revision 1.158 2014/08/27 17:11:51 brouard
133: *** empty log message ***
134:
135: Revision 1.157 2014/08/27 16:26:55 brouard
136: Summary: Preparing windows Visual studio version
137: Author: Brouard
138:
139: In order to compile on Visual studio, time.h is now correct and time_t
140: and tm struct should be used. difftime should be used but sometimes I
141: just make the differences in raw time format (time(&now).
142: Trying to suppress #ifdef LINUX
143: Add xdg-open for __linux in order to open default browser.
144:
145: Revision 1.156 2014/08/25 20:10:10 brouard
146: *** empty log message ***
147:
148: Revision 1.155 2014/08/25 18:32:34 brouard
149: Summary: New compile, minor changes
150: Author: Brouard
151:
152: Revision 1.154 2014/06/20 17:32:08 brouard
153: Summary: Outputs now all graphs of convergence to period prevalence
154:
155: Revision 1.153 2014/06/20 16:45:46 brouard
156: Summary: If 3 live state, convergence to period prevalence on same graph
157: Author: Brouard
158:
159: Revision 1.152 2014/06/18 17:54:09 brouard
160: Summary: open browser, use gnuplot on same dir than imach if not found in the path
161:
162: Revision 1.151 2014/06/18 16:43:30 brouard
163: *** empty log message ***
164:
165: Revision 1.150 2014/06/18 16:42:35 brouard
166: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
167: Author: brouard
168:
169: Revision 1.149 2014/06/18 15:51:14 brouard
170: Summary: Some fixes in parameter files errors
171: Author: Nicolas Brouard
172:
173: Revision 1.148 2014/06/17 17:38:48 brouard
174: Summary: Nothing new
175: Author: Brouard
176:
177: Just a new packaging for OS/X version 0.98nS
178:
179: Revision 1.147 2014/06/16 10:33:11 brouard
180: *** empty log message ***
181:
182: Revision 1.146 2014/06/16 10:20:28 brouard
183: Summary: Merge
184: Author: Brouard
185:
186: Merge, before building revised version.
187:
188: Revision 1.145 2014/06/10 21:23:15 brouard
189: Summary: Debugging with valgrind
190: Author: Nicolas Brouard
191:
192: Lot of changes in order to output the results with some covariates
193: After the Edimburgh REVES conference 2014, it seems mandatory to
194: improve the code.
195: No more memory valgrind error but a lot has to be done in order to
196: continue the work of splitting the code into subroutines.
197: Also, decodemodel has been improved. Tricode is still not
198: optimal. nbcode should be improved. Documentation has been added in
199: the source code.
200:
201: Revision 1.143 2014/01/26 09:45:38 brouard
202: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
203:
204: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
205: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
206:
207: Revision 1.142 2014/01/26 03:57:36 brouard
208: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
209:
210: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
211:
212: Revision 1.141 2014/01/26 02:42:01 brouard
213: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
214:
215: Revision 1.140 2011/09/02 10:37:54 brouard
216: Summary: times.h is ok with mingw32 now.
217:
218: Revision 1.139 2010/06/14 07:50:17 brouard
219: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
220: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
221:
222: Revision 1.138 2010/04/30 18:19:40 brouard
223: *** empty log message ***
224:
225: Revision 1.137 2010/04/29 18:11:38 brouard
226: (Module): Checking covariates for more complex models
227: than V1+V2. A lot of change to be done. Unstable.
228:
229: Revision 1.136 2010/04/26 20:30:53 brouard
230: (Module): merging some libgsl code. Fixing computation
231: of likelione (using inter/intrapolation if mle = 0) in order to
232: get same likelihood as if mle=1.
233: Some cleaning of code and comments added.
234:
235: Revision 1.135 2009/10/29 15:33:14 brouard
236: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
237:
238: Revision 1.134 2009/10/29 13:18:53 brouard
239: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
240:
241: Revision 1.133 2009/07/06 10:21:25 brouard
242: just nforces
243:
244: Revision 1.132 2009/07/06 08:22:05 brouard
245: Many tings
246:
247: Revision 1.131 2009/06/20 16:22:47 brouard
248: Some dimensions resccaled
249:
250: Revision 1.130 2009/05/26 06:44:34 brouard
251: (Module): Max Covariate is now set to 20 instead of 8. A
252: lot of cleaning with variables initialized to 0. Trying to make
253: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
254:
255: Revision 1.129 2007/08/31 13:49:27 lievre
256: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
257:
258: Revision 1.128 2006/06/30 13:02:05 brouard
259: (Module): Clarifications on computing e.j
260:
261: Revision 1.127 2006/04/28 18:11:50 brouard
262: (Module): Yes the sum of survivors was wrong since
263: imach-114 because nhstepm was no more computed in the age
264: loop. Now we define nhstepma in the age loop.
265: (Module): In order to speed up (in case of numerous covariates) we
266: compute health expectancies (without variances) in a first step
267: and then all the health expectancies with variances or standard
268: deviation (needs data from the Hessian matrices) which slows the
269: computation.
270: In the future we should be able to stop the program is only health
271: expectancies and graph are needed without standard deviations.
272:
273: Revision 1.126 2006/04/28 17:23:28 brouard
274: (Module): Yes the sum of survivors was wrong since
275: imach-114 because nhstepm was no more computed in the age
276: loop. Now we define nhstepma in the age loop.
277: Version 0.98h
278:
279: Revision 1.125 2006/04/04 15:20:31 lievre
280: Errors in calculation of health expectancies. Age was not initialized.
281: Forecasting file added.
282:
283: Revision 1.124 2006/03/22 17:13:53 lievre
284: Parameters are printed with %lf instead of %f (more numbers after the comma).
285: The log-likelihood is printed in the log file
286:
287: Revision 1.123 2006/03/20 10:52:43 brouard
288: * imach.c (Module): <title> changed, corresponds to .htm file
289: name. <head> headers where missing.
290:
291: * imach.c (Module): Weights can have a decimal point as for
292: English (a comma might work with a correct LC_NUMERIC environment,
293: otherwise the weight is truncated).
294: Modification of warning when the covariates values are not 0 or
295: 1.
296: Version 0.98g
297:
298: Revision 1.122 2006/03/20 09:45:41 brouard
299: (Module): Weights can have a decimal point as for
300: English (a comma might work with a correct LC_NUMERIC environment,
301: otherwise the weight is truncated).
302: Modification of warning when the covariates values are not 0 or
303: 1.
304: Version 0.98g
305:
306: Revision 1.121 2006/03/16 17:45:01 lievre
307: * imach.c (Module): Comments concerning covariates added
308:
309: * imach.c (Module): refinements in the computation of lli if
310: status=-2 in order to have more reliable computation if stepm is
311: not 1 month. Version 0.98f
312:
313: Revision 1.120 2006/03/16 15:10:38 lievre
314: (Module): refinements in the computation of lli if
315: status=-2 in order to have more reliable computation if stepm is
316: not 1 month. Version 0.98f
317:
318: Revision 1.119 2006/03/15 17:42:26 brouard
319: (Module): Bug if status = -2, the loglikelihood was
320: computed as likelihood omitting the logarithm. Version O.98e
321:
322: Revision 1.118 2006/03/14 18:20:07 brouard
323: (Module): varevsij Comments added explaining the second
324: table of variances if popbased=1 .
325: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
326: (Module): Function pstamp added
327: (Module): Version 0.98d
328:
329: Revision 1.117 2006/03/14 17:16:22 brouard
330: (Module): varevsij Comments added explaining the second
331: table of variances if popbased=1 .
332: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
333: (Module): Function pstamp added
334: (Module): Version 0.98d
335:
336: Revision 1.116 2006/03/06 10:29:27 brouard
337: (Module): Variance-covariance wrong links and
338: varian-covariance of ej. is needed (Saito).
339:
340: Revision 1.115 2006/02/27 12:17:45 brouard
341: (Module): One freematrix added in mlikeli! 0.98c
342:
343: Revision 1.114 2006/02/26 12:57:58 brouard
344: (Module): Some improvements in processing parameter
345: filename with strsep.
346:
347: Revision 1.113 2006/02/24 14:20:24 brouard
348: (Module): Memory leaks checks with valgrind and:
349: datafile was not closed, some imatrix were not freed and on matrix
350: allocation too.
351:
352: Revision 1.112 2006/01/30 09:55:26 brouard
353: (Module): Back to gnuplot.exe instead of wgnuplot.exe
354:
355: Revision 1.111 2006/01/25 20:38:18 brouard
356: (Module): Lots of cleaning and bugs added (Gompertz)
357: (Module): Comments can be added in data file. Missing date values
358: can be a simple dot '.'.
359:
360: Revision 1.110 2006/01/25 00:51:50 brouard
361: (Module): Lots of cleaning and bugs added (Gompertz)
362:
363: Revision 1.109 2006/01/24 19:37:15 brouard
364: (Module): Comments (lines starting with a #) are allowed in data.
365:
366: Revision 1.108 2006/01/19 18:05:42 lievre
367: Gnuplot problem appeared...
368: To be fixed
369:
370: Revision 1.107 2006/01/19 16:20:37 brouard
371: Test existence of gnuplot in imach path
372:
373: Revision 1.106 2006/01/19 13:24:36 brouard
374: Some cleaning and links added in html output
375:
376: Revision 1.105 2006/01/05 20:23:19 lievre
377: *** empty log message ***
378:
379: Revision 1.104 2005/09/30 16:11:43 lievre
380: (Module): sump fixed, loop imx fixed, and simplifications.
381: (Module): If the status is missing at the last wave but we know
382: that the person is alive, then we can code his/her status as -2
383: (instead of missing=-1 in earlier versions) and his/her
384: contributions to the likelihood is 1 - Prob of dying from last
385: health status (= 1-p13= p11+p12 in the easiest case of somebody in
386: the healthy state at last known wave). Version is 0.98
387:
388: Revision 1.103 2005/09/30 15:54:49 lievre
389: (Module): sump fixed, loop imx fixed, and simplifications.
390:
391: Revision 1.102 2004/09/15 17:31:30 brouard
392: Add the possibility to read data file including tab characters.
393:
394: Revision 1.101 2004/09/15 10:38:38 brouard
395: Fix on curr_time
396:
397: Revision 1.100 2004/07/12 18:29:06 brouard
398: Add version for Mac OS X. Just define UNIX in Makefile
399:
400: Revision 1.99 2004/06/05 08:57:40 brouard
401: *** empty log message ***
402:
403: Revision 1.98 2004/05/16 15:05:56 brouard
404: New version 0.97 . First attempt to estimate force of mortality
405: directly from the data i.e. without the need of knowing the health
406: state at each age, but using a Gompertz model: log u =a + b*age .
407: This is the basic analysis of mortality and should be done before any
408: other analysis, in order to test if the mortality estimated from the
409: cross-longitudinal survey is different from the mortality estimated
410: from other sources like vital statistic data.
411:
412: The same imach parameter file can be used but the option for mle should be -3.
413:
414: Agnès, who wrote this part of the code, tried to keep most of the
415: former routines in order to include the new code within the former code.
416:
417: The output is very simple: only an estimate of the intercept and of
418: the slope with 95% confident intervals.
419:
420: Current limitations:
421: A) Even if you enter covariates, i.e. with the
422: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
423: B) There is no computation of Life Expectancy nor Life Table.
424:
425: Revision 1.97 2004/02/20 13:25:42 lievre
426: Version 0.96d. Population forecasting command line is (temporarily)
427: suppressed.
428:
429: Revision 1.96 2003/07/15 15:38:55 brouard
430: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
431: rewritten within the same printf. Workaround: many printfs.
432:
433: Revision 1.95 2003/07/08 07:54:34 brouard
434: * imach.c (Repository):
435: (Repository): Using imachwizard code to output a more meaningful covariance
436: matrix (cov(a12,c31) instead of numbers.
437:
438: Revision 1.94 2003/06/27 13:00:02 brouard
439: Just cleaning
440:
441: Revision 1.93 2003/06/25 16:33:55 brouard
442: (Module): On windows (cygwin) function asctime_r doesn't
443: exist so I changed back to asctime which exists.
444: (Module): Version 0.96b
445:
446: Revision 1.92 2003/06/25 16:30:45 brouard
447: (Module): On windows (cygwin) function asctime_r doesn't
448: exist so I changed back to asctime which exists.
449:
450: Revision 1.91 2003/06/25 15:30:29 brouard
451: * imach.c (Repository): Duplicated warning errors corrected.
452: (Repository): Elapsed time after each iteration is now output. It
453: helps to forecast when convergence will be reached. Elapsed time
454: is stamped in powell. We created a new html file for the graphs
455: concerning matrix of covariance. It has extension -cov.htm.
456:
457: Revision 1.90 2003/06/24 12:34:15 brouard
458: (Module): Some bugs corrected for windows. Also, when
459: mle=-1 a template is output in file "or"mypar.txt with the design
460: of the covariance matrix to be input.
461:
462: Revision 1.89 2003/06/24 12:30:52 brouard
463: (Module): Some bugs corrected for windows. Also, when
464: mle=-1 a template is output in file "or"mypar.txt with the design
465: of the covariance matrix to be input.
466:
467: Revision 1.88 2003/06/23 17:54:56 brouard
468: * 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.
469:
470: Revision 1.87 2003/06/18 12:26:01 brouard
471: Version 0.96
472:
473: Revision 1.86 2003/06/17 20:04:08 brouard
474: (Module): Change position of html and gnuplot routines and added
475: routine fileappend.
476:
477: Revision 1.85 2003/06/17 13:12:43 brouard
478: * imach.c (Repository): Check when date of death was earlier that
479: current date of interview. It may happen when the death was just
480: prior to the death. In this case, dh was negative and likelihood
481: was wrong (infinity). We still send an "Error" but patch by
482: assuming that the date of death was just one stepm after the
483: interview.
484: (Repository): Because some people have very long ID (first column)
485: we changed int to long in num[] and we added a new lvector for
486: memory allocation. But we also truncated to 8 characters (left
487: truncation)
488: (Repository): No more line truncation errors.
489:
490: Revision 1.84 2003/06/13 21:44:43 brouard
491: * imach.c (Repository): Replace "freqsummary" at a correct
492: place. It differs from routine "prevalence" which may be called
493: many times. Probs is memory consuming and must be used with
494: parcimony.
495: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
496:
497: Revision 1.83 2003/06/10 13:39:11 lievre
498: *** empty log message ***
499:
500: Revision 1.82 2003/06/05 15:57:20 brouard
501: Add log in imach.c and fullversion number is now printed.
502:
503: */
504: /*
505: Interpolated Markov Chain
506:
507: Short summary of the programme:
508:
509: This program computes Healthy Life Expectancies from
510: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
511: first survey ("cross") where individuals from different ages are
512: interviewed on their health status or degree of disability (in the
513: case of a health survey which is our main interest) -2- at least a
514: second wave of interviews ("longitudinal") which measure each change
515: (if any) in individual health status. Health expectancies are
516: computed from the time spent in each health state according to a
517: model. More health states you consider, more time is necessary to reach the
518: Maximum Likelihood of the parameters involved in the model. The
519: simplest model is the multinomial logistic model where pij is the
520: probability to be observed in state j at the second wave
521: conditional to be observed in state i at the first wave. Therefore
522: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
523: 'age' is age and 'sex' is a covariate. If you want to have a more
524: complex model than "constant and age", you should modify the program
525: where the markup *Covariates have to be included here again* invites
526: you to do it. More covariates you add, slower the
527: convergence.
528:
529: The advantage of this computer programme, compared to a simple
530: multinomial logistic model, is clear when the delay between waves is not
531: identical for each individual. Also, if a individual missed an
532: intermediate interview, the information is lost, but taken into
533: account using an interpolation or extrapolation.
534:
535: hPijx is the probability to be observed in state i at age x+h
536: conditional to the observed state i at age x. The delay 'h' can be
537: split into an exact number (nh*stepm) of unobserved intermediate
538: states. This elementary transition (by month, quarter,
539: semester or year) is modelled as a multinomial logistic. The hPx
540: matrix is simply the matrix product of nh*stepm elementary matrices
541: and the contribution of each individual to the likelihood is simply
542: hPijx.
543:
544: Also this programme outputs the covariance matrix of the parameters but also
545: of the life expectancies. It also computes the period (stable) prevalence.
546:
547: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
548: Institut national d'études démographiques, Paris.
549: This software have been partly granted by Euro-REVES, a concerted action
550: from the European Union.
551: It is copyrighted identically to a GNU software product, ie programme and
552: software can be distributed freely for non commercial use. Latest version
553: can be accessed at http://euroreves.ined.fr/imach .
554:
555: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
556: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
557:
558: **********************************************************************/
559: /*
560: main
561: read parameterfile
562: read datafile
563: concatwav
564: freqsummary
565: if (mle >= 1)
566: mlikeli
567: print results files
568: if mle==1
569: computes hessian
570: read end of parameter file: agemin, agemax, bage, fage, estepm
571: begin-prev-date,...
572: open gnuplot file
573: open html file
574: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
575: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
576: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
577: freexexit2 possible for memory heap.
578:
579: h Pij x | pij_nom ficrestpij
580: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
581: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
582: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
583:
584: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
585: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
586: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
587: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
588: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
589:
590: forecasting if prevfcast==1 prevforecast call prevalence()
591: health expectancies
592: Variance-covariance of DFLE
593: prevalence()
594: movingaverage()
595: varevsij()
596: if popbased==1 varevsij(,popbased)
597: total life expectancies
598: Variance of period (stable) prevalence
599: end
600: */
601:
602: /* #define DEBUG */
603: /* #define DEBUGBRENT */
604: #define POWELL /* Instead of NLOPT */
605: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
606: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
607:
608: #include <math.h>
609: #include <stdio.h>
610: #include <stdlib.h>
611: #include <string.h>
612:
613: #ifdef _WIN32
614: #include <io.h>
615: #include <windows.h>
616: #include <tchar.h>
617: #else
618: #include <unistd.h>
619: #endif
620:
621: #include <limits.h>
622: #include <sys/types.h>
623:
624: #if defined(__GNUC__)
625: #include <sys/utsname.h> /* Doesn't work on Windows */
626: #endif
627:
628: #include <sys/stat.h>
629: #include <errno.h>
630: /* extern int errno; */
631:
632: /* #ifdef LINUX */
633: /* #include <time.h> */
634: /* #include "timeval.h" */
635: /* #else */
636: /* #include <sys/time.h> */
637: /* #endif */
638:
639: #include <time.h>
640:
641: #ifdef GSL
642: #include <gsl/gsl_errno.h>
643: #include <gsl/gsl_multimin.h>
644: #endif
645:
646:
647: #ifdef NLOPT
648: #include <nlopt.h>
649: typedef struct {
650: double (* function)(double [] );
651: } myfunc_data ;
652: #endif
653:
654: /* #include <libintl.h> */
655: /* #define _(String) gettext (String) */
656:
657: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
658:
659: #define GNUPLOTPROGRAM "gnuplot"
660: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
661: #define FILENAMELENGTH 132
662:
663: #define GLOCK_ERROR_NOPATH -1 /* empty path */
664: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
665:
666: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
667: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
668:
669: #define NINTERVMAX 8
670: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
671: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
672: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
673: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
674: #define MAXN 20000
675: #define YEARM 12. /**< Number of months per year */
676: #define AGESUP 130
677: #define AGEBASE 40
678: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
679: #ifdef _WIN32
680: #define DIRSEPARATOR '\\'
681: #define CHARSEPARATOR "\\"
682: #define ODIRSEPARATOR '/'
683: #else
684: #define DIRSEPARATOR '/'
685: #define CHARSEPARATOR "/"
686: #define ODIRSEPARATOR '\\'
687: #endif
688:
689: /* $Id: imach.c,v 1.190 2015/05/05 08:51:13 brouard Exp $ */
690: /* $State: Exp $ */
691:
692: char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
693: char fullversion[]="$Revision: 1.190 $ $Date: 2015/05/05 08:51:13 $";
694: char strstart[80];
695: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
696: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
697: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
698: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
699: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
700: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
701: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
702: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
703: int cptcovprodnoage=0; /**< Number of covariate products without age */
704: int cptcoveff=0; /* Total number of covariates to vary for printing results */
705: int cptcov=0; /* Working variable */
706: int npar=NPARMAX;
707: int nlstate=2; /* Number of live states */
708: int ndeath=1; /* Number of dead states */
709: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
710: int popbased=0;
711:
712: int *wav; /* Number of waves for this individuual 0 is possible */
713: int maxwav=0; /* Maxim number of waves */
714: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
715: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
716: int gipmx=0, gsw=0; /* Global variables on the number of contributions
717: to the likelihood and the sum of weights (done by funcone)*/
718: int mle=1, weightopt=0;
719: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
720: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
721: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
722: * wave mi and wave mi+1 is not an exact multiple of stepm. */
723: int countcallfunc=0; /* Count the number of calls to func */
724: double jmean=1; /* Mean space between 2 waves */
725: double **matprod2(); /* test */
726: double **oldm, **newm, **savm; /* Working pointers to matrices */
727: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
728: /*FILE *fic ; */ /* Used in readdata only */
729: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
730: FILE *ficlog, *ficrespow;
731: int globpr=0; /* Global variable for printing or not */
732: double fretone; /* Only one call to likelihood */
733: long ipmx=0; /* Number of contributions */
734: double sw; /* Sum of weights */
735: char filerespow[FILENAMELENGTH];
736: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
737: FILE *ficresilk;
738: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
739: FILE *ficresprobmorprev;
740: FILE *fichtm, *fichtmcov; /* Html File */
741: FILE *ficreseij;
742: char filerese[FILENAMELENGTH];
743: FILE *ficresstdeij;
744: char fileresstde[FILENAMELENGTH];
745: FILE *ficrescveij;
746: char filerescve[FILENAMELENGTH];
747: FILE *ficresvij;
748: char fileresv[FILENAMELENGTH];
749: FILE *ficresvpl;
750: char fileresvpl[FILENAMELENGTH];
751: char title[MAXLINE];
752: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
753: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
754: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
755: char command[FILENAMELENGTH];
756: int outcmd=0;
757:
758: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
759:
760: char filelog[FILENAMELENGTH]; /* Log file */
761: char filerest[FILENAMELENGTH];
762: char fileregp[FILENAMELENGTH];
763: char popfile[FILENAMELENGTH];
764:
765: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
766:
767: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
768: /* struct timezone tzp; */
769: /* extern int gettimeofday(); */
770: struct tm tml, *gmtime(), *localtime();
771:
772: extern time_t time();
773:
774: struct tm start_time, end_time, curr_time, last_time, forecast_time;
775: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
776: struct tm tm;
777:
778: char strcurr[80], strfor[80];
779:
780: char *endptr;
781: long lval;
782: double dval;
783:
784: #define NR_END 1
785: #define FREE_ARG char*
786: #define FTOL 1.0e-10
787:
788: #define NRANSI
789: #define ITMAX 200
790:
791: #define TOL 2.0e-4
792:
793: #define CGOLD 0.3819660
794: #define ZEPS 1.0e-10
795: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
796:
797: #define GOLD 1.618034
798: #define GLIMIT 100.0
799: #define TINY 1.0e-20
800:
801: static double maxarg1,maxarg2;
802: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
803: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
804:
805: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
806: #define rint(a) floor(a+0.5)
807: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
808: #define mytinydouble 1.0e-16
809: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
810: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
811: /* static double dsqrarg; */
812: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
813: static double sqrarg;
814: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
815: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
816: int agegomp= AGEGOMP;
817:
818: int imx;
819: int stepm=1;
820: /* Stepm, step in month: minimum step interpolation*/
821:
822: int estepm;
823: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
824:
825: int m,nb;
826: long *num;
827: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
828: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
829: double **pmmij, ***probs;
830: double *ageexmed,*agecens;
831: double dateintmean=0;
832:
833: double *weight;
834: int **s; /* Status */
835: double *agedc;
836: double **covar; /**< covar[j,i], value of jth covariate for individual i,
837: * covar=matrix(0,NCOVMAX,1,n);
838: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
839: double idx;
840: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
841: int *Ndum; /** Freq of modality (tricode */
842: int **codtab; /**< codtab=imatrix(1,100,1,10); */
843: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
844: double *lsurv, *lpop, *tpop;
845:
846: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
847: double ftolhess; /**< Tolerance for computing hessian */
848:
849: /**************** split *************************/
850: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
851: {
852: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
853: the name of the file (name), its extension only (ext) and its first part of the name (finame)
854: */
855: char *ss; /* pointer */
856: int l1=0, l2=0; /* length counters */
857:
858: l1 = strlen(path ); /* length of path */
859: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
860: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
861: if ( ss == NULL ) { /* no directory, so determine current directory */
862: strcpy( name, path ); /* we got the fullname name because no directory */
863: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
864: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
865: /* get current working directory */
866: /* extern char* getcwd ( char *buf , int len);*/
867: #ifdef WIN32
868: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
869: #else
870: if (getcwd(dirc, FILENAME_MAX) == NULL) {
871: #endif
872: return( GLOCK_ERROR_GETCWD );
873: }
874: /* got dirc from getcwd*/
875: printf(" DIRC = %s \n",dirc);
876: } else { /* strip direcotry from path */
877: ss++; /* after this, the filename */
878: l2 = strlen( ss ); /* length of filename */
879: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
880: strcpy( name, ss ); /* save file name */
881: strncpy( dirc, path, l1 - l2 ); /* now the directory */
882: dirc[l1-l2] = '\0'; /* add zero */
883: printf(" DIRC2 = %s \n",dirc);
884: }
885: /* We add a separator at the end of dirc if not exists */
886: l1 = strlen( dirc ); /* length of directory */
887: if( dirc[l1-1] != DIRSEPARATOR ){
888: dirc[l1] = DIRSEPARATOR;
889: dirc[l1+1] = 0;
890: printf(" DIRC3 = %s \n",dirc);
891: }
892: ss = strrchr( name, '.' ); /* find last / */
893: if (ss >0){
894: ss++;
895: strcpy(ext,ss); /* save extension */
896: l1= strlen( name);
897: l2= strlen(ss)+1;
898: strncpy( finame, name, l1-l2);
899: finame[l1-l2]= 0;
900: }
901:
902: return( 0 ); /* we're done */
903: }
904:
905:
906: /******************************************/
907:
908: void replace_back_to_slash(char *s, char*t)
909: {
910: int i;
911: int lg=0;
912: i=0;
913: lg=strlen(t);
914: for(i=0; i<= lg; i++) {
915: (s[i] = t[i]);
916: if (t[i]== '\\') s[i]='/';
917: }
918: }
919:
920: char *trimbb(char *out, char *in)
921: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
922: char *s;
923: s=out;
924: while (*in != '\0'){
925: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
926: in++;
927: }
928: *out++ = *in++;
929: }
930: *out='\0';
931: return s;
932: }
933:
934: /* char *substrchaine(char *out, char *in, char *chain) */
935: /* { */
936: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
937: /* char *s, *t; */
938: /* t=in;s=out; */
939: /* while ((*in != *chain) && (*in != '\0')){ */
940: /* *out++ = *in++; */
941: /* } */
942:
943: /* /\* *in matches *chain *\/ */
944: /* while ((*in++ == *chain++) && (*in != '\0')){ */
945: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
946: /* } */
947: /* in--; chain--; */
948: /* while ( (*in != '\0')){ */
949: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
950: /* *out++ = *in++; */
951: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
952: /* } */
953: /* *out='\0'; */
954: /* out=s; */
955: /* return out; */
956: /* } */
957: char *substrchaine(char *out, char *in, char *chain)
958: {
959: /* Substract chain 'chain' from 'in', return and output 'out' */
960: /* in="V1+V1*age+age*age+V2", chain="age*age" */
961:
962: char *strloc;
963:
964: strcpy (out, in);
965: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
966: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
967: if(strloc != NULL){
968: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
969: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
970: /* strcpy (strloc, strloc +strlen(chain));*/
971: }
972: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
973: return out;
974: }
975:
976:
977: char *cutl(char *blocc, char *alocc, char *in, char occ)
978: {
979: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
980: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
981: gives blocc="abcdef" and alocc="ghi2j".
982: If occ is not found blocc is null and alocc is equal to in. Returns blocc
983: */
984: char *s, *t;
985: t=in;s=in;
986: while ((*in != occ) && (*in != '\0')){
987: *alocc++ = *in++;
988: }
989: if( *in == occ){
990: *(alocc)='\0';
991: s=++in;
992: }
993:
994: if (s == t) {/* occ not found */
995: *(alocc-(in-s))='\0';
996: in=s;
997: }
998: while ( *in != '\0'){
999: *blocc++ = *in++;
1000: }
1001:
1002: *blocc='\0';
1003: return t;
1004: }
1005: char *cutv(char *blocc, char *alocc, char *in, char occ)
1006: {
1007: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1008: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1009: gives blocc="abcdef2ghi" and alocc="j".
1010: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1011: */
1012: char *s, *t;
1013: t=in;s=in;
1014: while (*in != '\0'){
1015: while( *in == occ){
1016: *blocc++ = *in++;
1017: s=in;
1018: }
1019: *blocc++ = *in++;
1020: }
1021: if (s == t) /* occ not found */
1022: *(blocc-(in-s))='\0';
1023: else
1024: *(blocc-(in-s)-1)='\0';
1025: in=s;
1026: while ( *in != '\0'){
1027: *alocc++ = *in++;
1028: }
1029:
1030: *alocc='\0';
1031: return s;
1032: }
1033:
1034: int nbocc(char *s, char occ)
1035: {
1036: int i,j=0;
1037: int lg=20;
1038: i=0;
1039: lg=strlen(s);
1040: for(i=0; i<= lg; i++) {
1041: if (s[i] == occ ) j++;
1042: }
1043: return j;
1044: }
1045:
1046: /* void cutv(char *u,char *v, char*t, char occ) */
1047: /* { */
1048: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1049: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1050: /* gives u="abcdef2ghi" and v="j" *\/ */
1051: /* int i,lg,j,p=0; */
1052: /* i=0; */
1053: /* lg=strlen(t); */
1054: /* for(j=0; j<=lg-1; j++) { */
1055: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1056: /* } */
1057:
1058: /* for(j=0; j<p; j++) { */
1059: /* (u[j] = t[j]); */
1060: /* } */
1061: /* u[p]='\0'; */
1062:
1063: /* for(j=0; j<= lg; j++) { */
1064: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1065: /* } */
1066: /* } */
1067:
1068: #ifdef _WIN32
1069: char * strsep(char **pp, const char *delim)
1070: {
1071: char *p, *q;
1072:
1073: if ((p = *pp) == NULL)
1074: return 0;
1075: if ((q = strpbrk (p, delim)) != NULL)
1076: {
1077: *pp = q + 1;
1078: *q = '\0';
1079: }
1080: else
1081: *pp = 0;
1082: return p;
1083: }
1084: #endif
1085:
1086: /********************** nrerror ********************/
1087:
1088: void nrerror(char error_text[])
1089: {
1090: fprintf(stderr,"ERREUR ...\n");
1091: fprintf(stderr,"%s\n",error_text);
1092: exit(EXIT_FAILURE);
1093: }
1094: /*********************** vector *******************/
1095: double *vector(int nl, int nh)
1096: {
1097: double *v;
1098: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1099: if (!v) nrerror("allocation failure in vector");
1100: return v-nl+NR_END;
1101: }
1102:
1103: /************************ free vector ******************/
1104: void free_vector(double*v, int nl, int nh)
1105: {
1106: free((FREE_ARG)(v+nl-NR_END));
1107: }
1108:
1109: /************************ivector *******************************/
1110: int *ivector(long nl,long nh)
1111: {
1112: int *v;
1113: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1114: if (!v) nrerror("allocation failure in ivector");
1115: return v-nl+NR_END;
1116: }
1117:
1118: /******************free ivector **************************/
1119: void free_ivector(int *v, long nl, long nh)
1120: {
1121: free((FREE_ARG)(v+nl-NR_END));
1122: }
1123:
1124: /************************lvector *******************************/
1125: long *lvector(long nl,long nh)
1126: {
1127: long *v;
1128: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1129: if (!v) nrerror("allocation failure in ivector");
1130: return v-nl+NR_END;
1131: }
1132:
1133: /******************free lvector **************************/
1134: void free_lvector(long *v, long nl, long nh)
1135: {
1136: free((FREE_ARG)(v+nl-NR_END));
1137: }
1138:
1139: /******************* imatrix *******************************/
1140: int **imatrix(long nrl, long nrh, long ncl, long nch)
1141: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1142: {
1143: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1144: int **m;
1145:
1146: /* allocate pointers to rows */
1147: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1148: if (!m) nrerror("allocation failure 1 in matrix()");
1149: m += NR_END;
1150: m -= nrl;
1151:
1152:
1153: /* allocate rows and set pointers to them */
1154: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1155: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1156: m[nrl] += NR_END;
1157: m[nrl] -= ncl;
1158:
1159: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1160:
1161: /* return pointer to array of pointers to rows */
1162: return m;
1163: }
1164:
1165: /****************** free_imatrix *************************/
1166: void free_imatrix(m,nrl,nrh,ncl,nch)
1167: int **m;
1168: long nch,ncl,nrh,nrl;
1169: /* free an int matrix allocated by imatrix() */
1170: {
1171: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1172: free((FREE_ARG) (m+nrl-NR_END));
1173: }
1174:
1175: /******************* matrix *******************************/
1176: double **matrix(long nrl, long nrh, long ncl, long nch)
1177: {
1178: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1179: double **m;
1180:
1181: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1182: if (!m) nrerror("allocation failure 1 in matrix()");
1183: m += NR_END;
1184: m -= nrl;
1185:
1186: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1187: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1188: m[nrl] += NR_END;
1189: m[nrl] -= ncl;
1190:
1191: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1192: return m;
1193: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1194: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1195: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1196: */
1197: }
1198:
1199: /*************************free matrix ************************/
1200: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1201: {
1202: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1203: free((FREE_ARG)(m+nrl-NR_END));
1204: }
1205:
1206: /******************* ma3x *******************************/
1207: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1208: {
1209: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1210: double ***m;
1211:
1212: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1213: if (!m) nrerror("allocation failure 1 in matrix()");
1214: m += NR_END;
1215: m -= nrl;
1216:
1217: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1218: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1219: m[nrl] += NR_END;
1220: m[nrl] -= ncl;
1221:
1222: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1223:
1224: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1225: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1226: m[nrl][ncl] += NR_END;
1227: m[nrl][ncl] -= nll;
1228: for (j=ncl+1; j<=nch; j++)
1229: m[nrl][j]=m[nrl][j-1]+nlay;
1230:
1231: for (i=nrl+1; i<=nrh; i++) {
1232: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1233: for (j=ncl+1; j<=nch; j++)
1234: m[i][j]=m[i][j-1]+nlay;
1235: }
1236: return m;
1237: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1238: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1239: */
1240: }
1241:
1242: /*************************free ma3x ************************/
1243: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1244: {
1245: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1246: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1247: free((FREE_ARG)(m+nrl-NR_END));
1248: }
1249:
1250: /*************** function subdirf ***********/
1251: char *subdirf(char fileres[])
1252: {
1253: /* Caution optionfilefiname is hidden */
1254: strcpy(tmpout,optionfilefiname);
1255: strcat(tmpout,"/"); /* Add to the right */
1256: strcat(tmpout,fileres);
1257: return tmpout;
1258: }
1259:
1260: /*************** function subdirf2 ***********/
1261: char *subdirf2(char fileres[], char *preop)
1262: {
1263:
1264: /* Caution optionfilefiname is hidden */
1265: strcpy(tmpout,optionfilefiname);
1266: strcat(tmpout,"/");
1267: strcat(tmpout,preop);
1268: strcat(tmpout,fileres);
1269: return tmpout;
1270: }
1271:
1272: /*************** function subdirf3 ***********/
1273: char *subdirf3(char fileres[], char *preop, char *preop2)
1274: {
1275:
1276: /* Caution optionfilefiname is hidden */
1277: strcpy(tmpout,optionfilefiname);
1278: strcat(tmpout,"/");
1279: strcat(tmpout,preop);
1280: strcat(tmpout,preop2);
1281: strcat(tmpout,fileres);
1282: return tmpout;
1283: }
1284:
1285: char *asc_diff_time(long time_sec, char ascdiff[])
1286: {
1287: long sec_left, days, hours, minutes;
1288: days = (time_sec) / (60*60*24);
1289: sec_left = (time_sec) % (60*60*24);
1290: hours = (sec_left) / (60*60) ;
1291: sec_left = (sec_left) %(60*60);
1292: minutes = (sec_left) /60;
1293: sec_left = (sec_left) % (60);
1294: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1295: return ascdiff;
1296: }
1297:
1298: /***************** f1dim *************************/
1299: extern int ncom;
1300: extern double *pcom,*xicom;
1301: extern double (*nrfunc)(double []);
1302:
1303: double f1dim(double x)
1304: {
1305: int j;
1306: double f;
1307: double *xt;
1308:
1309: xt=vector(1,ncom);
1310: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1311: f=(*nrfunc)(xt);
1312: free_vector(xt,1,ncom);
1313: return f;
1314: }
1315:
1316: /*****************brent *************************/
1317: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1318: {
1319: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1320: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1321: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1322: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1323: * returned function value.
1324: */
1325: int iter;
1326: double a,b,d,etemp;
1327: double fu=0,fv,fw,fx;
1328: double ftemp=0.;
1329: double p,q,r,tol1,tol2,u,v,w,x,xm;
1330: double e=0.0;
1331:
1332: a=(ax < cx ? ax : cx);
1333: b=(ax > cx ? ax : cx);
1334: x=w=v=bx;
1335: fw=fv=fx=(*f)(x);
1336: for (iter=1;iter<=ITMAX;iter++) {
1337: xm=0.5*(a+b);
1338: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1339: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1340: printf(".");fflush(stdout);
1341: fprintf(ficlog,".");fflush(ficlog);
1342: #ifdef DEBUGBRENT
1343: 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);
1344: 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);
1345: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1346: #endif
1347: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1348: *xmin=x;
1349: return fx;
1350: }
1351: ftemp=fu;
1352: if (fabs(e) > tol1) {
1353: r=(x-w)*(fx-fv);
1354: q=(x-v)*(fx-fw);
1355: p=(x-v)*q-(x-w)*r;
1356: q=2.0*(q-r);
1357: if (q > 0.0) p = -p;
1358: q=fabs(q);
1359: etemp=e;
1360: e=d;
1361: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1362: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1363: else {
1364: d=p/q;
1365: u=x+d;
1366: if (u-a < tol2 || b-u < tol2)
1367: d=SIGN(tol1,xm-x);
1368: }
1369: } else {
1370: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1371: }
1372: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1373: fu=(*f)(u);
1374: if (fu <= fx) {
1375: if (u >= x) a=x; else b=x;
1376: SHFT(v,w,x,u)
1377: SHFT(fv,fw,fx,fu)
1378: } else {
1379: if (u < x) a=u; else b=u;
1380: if (fu <= fw || w == x) {
1381: v=w;
1382: w=u;
1383: fv=fw;
1384: fw=fu;
1385: } else if (fu <= fv || v == x || v == w) {
1386: v=u;
1387: fv=fu;
1388: }
1389: }
1390: }
1391: nrerror("Too many iterations in brent");
1392: *xmin=x;
1393: return fx;
1394: }
1395:
1396: /****************** mnbrak ***********************/
1397:
1398: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1399: double (*func)(double))
1400: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1401: the downhill direction (defined by the function as evaluated at the initial points) and returns
1402: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1403: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1404: */
1405: double ulim,u,r,q, dum;
1406: double fu;
1407:
1408: double scale=10.;
1409: int iterscale=0;
1410:
1411: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1412: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1413:
1414:
1415: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1416: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1417: /* *bx = *ax - (*ax - *bx)/scale; */
1418: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1419: /* } */
1420:
1421: if (*fb > *fa) {
1422: SHFT(dum,*ax,*bx,dum)
1423: SHFT(dum,*fb,*fa,dum)
1424: }
1425: *cx=(*bx)+GOLD*(*bx-*ax);
1426: *fc=(*func)(*cx);
1427: #ifdef DEBUG
1428: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1429: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1430: #endif
1431: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1432: r=(*bx-*ax)*(*fb-*fc);
1433: q=(*bx-*cx)*(*fb-*fa);
1434: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1435: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1436: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1437: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1438: fu=(*func)(u);
1439: #ifdef DEBUG
1440: /* f(x)=A(x-u)**2+f(u) */
1441: double A, fparabu;
1442: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1443: fparabu= *fa - A*(*ax-u)*(*ax-u);
1444: 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);
1445: 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);
1446: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1447: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1448: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1449: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1450: #endif
1451: #ifdef MNBRAKORIGINAL
1452: #else
1453: if (fu > *fc) {
1454: #ifdef DEBUG
1455: printf("mnbrak4 fu > fc \n");
1456: fprintf(ficlog, "mnbrak4 fu > fc\n");
1457: #endif
1458: /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/ */
1459: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1460: dum=u; /* Shifting c and u */
1461: u = *cx;
1462: *cx = dum;
1463: dum = fu;
1464: fu = *fc;
1465: *fc =dum;
1466: } else { /* end */
1467: #ifdef DEBUG
1468: printf("mnbrak3 fu < fc \n");
1469: fprintf(ficlog, "mnbrak3 fu < fc\n");
1470: #endif
1471: dum=u; /* Shifting c and u */
1472: u = *cx;
1473: *cx = dum;
1474: dum = fu;
1475: fu = *fc;
1476: *fc =dum;
1477: }
1478: #endif
1479: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1480: #ifdef DEBUG
1481: printf("mnbrak2 u after c but before ulim\n");
1482: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1483: #endif
1484: fu=(*func)(u);
1485: if (fu < *fc) {
1486: #ifdef DEBUG
1487: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1488: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1489: #endif
1490: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1491: SHFT(*fb,*fc,fu,(*func)(u))
1492: }
1493: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1494: #ifdef DEBUG
1495: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1496: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1497: #endif
1498: u=ulim;
1499: fu=(*func)(u);
1500: } else { /* u could be left to b (if r > q parabola has a maximum) */
1501: #ifdef DEBUG
1502: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1503: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1504: #endif
1505: u=(*cx)+GOLD*(*cx-*bx);
1506: fu=(*func)(u);
1507: } /* end tests */
1508: SHFT(*ax,*bx,*cx,u)
1509: SHFT(*fa,*fb,*fc,fu)
1510: #ifdef DEBUG
1511: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1512: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1513: #endif
1514: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1515: }
1516:
1517: /*************** linmin ************************/
1518: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1519: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1520: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1521: the value of func at the returned location p . This is actually all accomplished by calling the
1522: routines mnbrak and brent .*/
1523: int ncom;
1524: double *pcom,*xicom;
1525: double (*nrfunc)(double []);
1526:
1527: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1528: {
1529: double brent(double ax, double bx, double cx,
1530: double (*f)(double), double tol, double *xmin);
1531: double f1dim(double x);
1532: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1533: double *fc, double (*func)(double));
1534: int j;
1535: double xx,xmin,bx,ax;
1536: double fx,fb,fa;
1537:
1538: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1539:
1540: ncom=n;
1541: pcom=vector(1,n);
1542: xicom=vector(1,n);
1543: nrfunc=func;
1544: for (j=1;j<=n;j++) {
1545: pcom[j]=p[j];
1546: xicom[j]=xi[j];
1547: }
1548:
1549: axs=0.0;
1550: xxss=1; /* 1 and using scale */
1551: xxs=1;
1552: do{
1553: ax=0.;
1554: xx= xxs;
1555: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1556: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1557: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
1558: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1559: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1560: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1561: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/
1562: if (fx != fx){
1563: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1564: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
1565: }
1566: }while(fx != fx);
1567:
1568: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1569: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1570: /* fmin = f(p[j] + xmin * xi[j]) */
1571: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1572: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1573: #ifdef DEBUG
1574: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1575: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1576: #endif
1577: /* printf("linmin end "); */
1578: for (j=1;j<=n;j++) {
1579: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1580: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1581: /* if(xxs <1.0) */
1582: /* printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */
1583: p[j] += xi[j]; /* Parameters values are updated accordingly */
1584: }
1585: /* printf("\n"); */
1586: /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */
1587: free_vector(xicom,1,n);
1588: free_vector(pcom,1,n);
1589: }
1590:
1591:
1592: /*************** powell ************************/
1593: /*
1594: Minimization of a function func of n variables. Input consists of an initial starting point
1595: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1596: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1597: such that failure to decrease by more than this amount on one iteration signals doneness. On
1598: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1599: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1600: */
1601: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1602: double (*func)(double []))
1603: {
1604: void linmin(double p[], double xi[], int n, double *fret,
1605: double (*func)(double []));
1606: int i,ibig,j;
1607: double del,t,*pt,*ptt,*xit;
1608: double directest;
1609: double fp,fptt;
1610: double *xits;
1611: int niterf, itmp;
1612:
1613: pt=vector(1,n);
1614: ptt=vector(1,n);
1615: xit=vector(1,n);
1616: xits=vector(1,n);
1617: *fret=(*func)(p);
1618: for (j=1;j<=n;j++) pt[j]=p[j];
1619: rcurr_time = time(NULL);
1620: for (*iter=1;;++(*iter)) {
1621: fp=(*fret); /* From former iteration or initial value */
1622: ibig=0;
1623: del=0.0;
1624: rlast_time=rcurr_time;
1625: /* (void) gettimeofday(&curr_time,&tzp); */
1626: rcurr_time = time(NULL);
1627: curr_time = *localtime(&rcurr_time);
1628: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1629: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1630: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1631: for (i=1;i<=n;i++) {
1632: printf(" %d %.12f",i, p[i]);
1633: fprintf(ficlog," %d %.12lf",i, p[i]);
1634: fprintf(ficrespow," %.12lf", p[i]);
1635: }
1636: printf("\n");
1637: fprintf(ficlog,"\n");
1638: fprintf(ficrespow,"\n");fflush(ficrespow);
1639: if(*iter <=3){
1640: tml = *localtime(&rcurr_time);
1641: strcpy(strcurr,asctime(&tml));
1642: rforecast_time=rcurr_time;
1643: itmp = strlen(strcurr);
1644: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1645: strcurr[itmp-1]='\0';
1646: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1647: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1648: for(niterf=10;niterf<=30;niterf+=10){
1649: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1650: forecast_time = *localtime(&rforecast_time);
1651: strcpy(strfor,asctime(&forecast_time));
1652: itmp = strlen(strfor);
1653: if(strfor[itmp-1]=='\n')
1654: strfor[itmp-1]='\0';
1655: 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);
1656: 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);
1657: }
1658: }
1659: for (i=1;i<=n;i++) { /* For each direction i */
1660: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1661: fptt=(*fret);
1662: #ifdef DEBUG
1663: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1664: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1665: #endif
1666: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1667: fprintf(ficlog,"%d",i);fflush(ficlog);
1668: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1669: /* Outputs are fret(new point p) p is updated and xit rescaled */
1670: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1671: /* because that direction will be replaced unless the gain del is small */
1672: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1673: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1674: /* with the new direction. */
1675: del=fabs(fptt-(*fret));
1676: ibig=i;
1677: }
1678: #ifdef DEBUG
1679: printf("%d %.12e",i,(*fret));
1680: fprintf(ficlog,"%d %.12e",i,(*fret));
1681: for (j=1;j<=n;j++) {
1682: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1683: printf(" x(%d)=%.12e",j,xit[j]);
1684: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1685: }
1686: for(j=1;j<=n;j++) {
1687: printf(" p(%d)=%.12e",j,p[j]);
1688: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1689: }
1690: printf("\n");
1691: fprintf(ficlog,"\n");
1692: #endif
1693: } /* end loop on each direction i */
1694: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1695: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1696: /* New value of last point Pn is not computed, P(n-1) */
1697: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1698: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1699: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1700: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1701: /* decreased of more than 3.84 */
1702: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1703: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1704: /* By adding 10 parameters more the gain should be 18.31 */
1705:
1706: /* Starting the program with initial values given by a former maximization will simply change */
1707: /* the scales of the directions and the directions, because the are reset to canonical directions */
1708: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1709: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1710: #ifdef DEBUG
1711: int k[2],l;
1712: k[0]=1;
1713: k[1]=-1;
1714: printf("Max: %.12e",(*func)(p));
1715: fprintf(ficlog,"Max: %.12e",(*func)(p));
1716: for (j=1;j<=n;j++) {
1717: printf(" %.12e",p[j]);
1718: fprintf(ficlog," %.12e",p[j]);
1719: }
1720: printf("\n");
1721: fprintf(ficlog,"\n");
1722: for(l=0;l<=1;l++) {
1723: for (j=1;j<=n;j++) {
1724: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1725: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1726: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1727: }
1728: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1729: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1730: }
1731: #endif
1732:
1733:
1734: free_vector(xit,1,n);
1735: free_vector(xits,1,n);
1736: free_vector(ptt,1,n);
1737: free_vector(pt,1,n);
1738: return;
1739: }
1740: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1741: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1742: ptt[j]=2.0*p[j]-pt[j];
1743: xit[j]=p[j]-pt[j];
1744: pt[j]=p[j];
1745: }
1746: fptt=(*func)(ptt); /* f_3 */
1747: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1748: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1749: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1750: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1751: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1752: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1753: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1754: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1755: #ifdef NRCORIGINAL
1756: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1757: #else
1758: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1759: t= t- del*SQR(fp-fptt);
1760: #endif
1761: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1762: #ifdef DEBUG
1763: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1764: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1765: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1766: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1767: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1768: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1769: 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);
1770: 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);
1771: #endif
1772: #ifdef POWELLORIGINAL
1773: if (t < 0.0) { /* Then we use it for new direction */
1774: #else
1775: if (directest*t < 0.0) { /* Contradiction between both tests */
1776: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1777: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1778: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1779: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1780: }
1781: if (directest < 0.0) { /* Then we use it for new direction */
1782: #endif
1783: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1784: for (j=1;j<=n;j++) {
1785: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1786: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1787: }
1788: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1789: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1790:
1791: #ifdef DEBUG
1792: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1793: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1794: for(j=1;j<=n;j++){
1795: printf(" %.12e",xit[j]);
1796: fprintf(ficlog," %.12e",xit[j]);
1797: }
1798: printf("\n");
1799: fprintf(ficlog,"\n");
1800: #endif
1801: } /* end of t negative */
1802: } /* end if (fptt < fp) */
1803: }
1804: }
1805:
1806: /**** Prevalence limit (stable or period prevalence) ****************/
1807:
1808: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1809: {
1810: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1811: matrix by transitions matrix until convergence is reached */
1812:
1813: int i, ii,j,k;
1814: double min, max, maxmin, maxmax,sumnew=0.;
1815: /* double **matprod2(); */ /* test */
1816: double **out, cov[NCOVMAX+1], **pmij();
1817: double **newm;
1818: double agefin, delaymax=50 ; /* Max number of years to converge */
1819:
1820: for (ii=1;ii<=nlstate+ndeath;ii++)
1821: for (j=1;j<=nlstate+ndeath;j++){
1822: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1823: }
1824:
1825: cov[1]=1.;
1826:
1827: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1828: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1829: newm=savm;
1830: /* Covariates have to be included here again */
1831: cov[2]=agefin;
1832: if(nagesqr==1)
1833: cov[3]= agefin*agefin;;
1834: for (k=1; k<=cptcovn;k++) {
1835: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1836: /*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]]);*/
1837: }
1838: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1839: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1840: for (k=1; k<=cptcovprod;k++) /* Useless */
1841: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1842:
1843: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1844: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1845: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1846: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1847: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1848: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1849:
1850: savm=oldm;
1851: oldm=newm;
1852: maxmax=0.;
1853: for(j=1;j<=nlstate;j++){
1854: min=1.;
1855: max=0.;
1856: for(i=1; i<=nlstate; i++) {
1857: sumnew=0;
1858: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1859: prlim[i][j]= newm[i][j]/(1-sumnew);
1860: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1861: max=FMAX(max,prlim[i][j]);
1862: min=FMIN(min,prlim[i][j]);
1863: }
1864: maxmin=max-min;
1865: maxmax=FMAX(maxmax,maxmin);
1866: } /* j loop */
1867: if(maxmax < ftolpl){
1868: return prlim;
1869: }
1870: } /* age loop */
1871: return prlim; /* should not reach here */
1872: }
1873:
1874: /*************** transition probabilities ***************/
1875:
1876: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1877: {
1878: /* According to parameters values stored in x and the covariate's values stored in cov,
1879: computes the probability to be observed in state j being in state i by appying the
1880: model to the ncovmodel covariates (including constant and age).
1881: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1882: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1883: ncth covariate in the global vector x is given by the formula:
1884: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1885: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1886: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1887: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1888: Outputs ps[i][j] the probability to be observed in j being in j according to
1889: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1890: */
1891: double s1, lnpijopii;
1892: /*double t34;*/
1893: int i,j, nc, ii, jj;
1894:
1895: for(i=1; i<= nlstate; i++){
1896: for(j=1; j<i;j++){
1897: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1898: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1899: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1900: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1901: }
1902: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1903: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1904: }
1905: for(j=i+1; j<=nlstate+ndeath;j++){
1906: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1907: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1908: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1909: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1910: }
1911: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1912: }
1913: }
1914:
1915: for(i=1; i<= nlstate; i++){
1916: s1=0;
1917: for(j=1; j<i; j++){
1918: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1919: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1920: }
1921: for(j=i+1; j<=nlstate+ndeath; j++){
1922: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1923: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1924: }
1925: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1926: ps[i][i]=1./(s1+1.);
1927: /* Computing other pijs */
1928: for(j=1; j<i; j++)
1929: ps[i][j]= exp(ps[i][j])*ps[i][i];
1930: for(j=i+1; j<=nlstate+ndeath; j++)
1931: ps[i][j]= exp(ps[i][j])*ps[i][i];
1932: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1933: } /* end i */
1934:
1935: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1936: for(jj=1; jj<= nlstate+ndeath; jj++){
1937: ps[ii][jj]=0;
1938: ps[ii][ii]=1;
1939: }
1940: }
1941:
1942:
1943: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1944: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1945: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1946: /* } */
1947: /* printf("\n "); */
1948: /* } */
1949: /* printf("\n ");printf("%lf ",cov[2]);*/
1950: /*
1951: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1952: goto end;*/
1953: return ps;
1954: }
1955:
1956: /**************** Product of 2 matrices ******************/
1957:
1958: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1959: {
1960: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1961: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1962: /* in, b, out are matrice of pointers which should have been initialized
1963: before: only the contents of out is modified. The function returns
1964: a pointer to pointers identical to out */
1965: int i, j, k;
1966: for(i=nrl; i<= nrh; i++)
1967: for(k=ncolol; k<=ncoloh; k++){
1968: out[i][k]=0.;
1969: for(j=ncl; j<=nch; j++)
1970: out[i][k] +=in[i][j]*b[j][k];
1971: }
1972: return out;
1973: }
1974:
1975:
1976: /************* Higher Matrix Product ***************/
1977:
1978: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1979: {
1980: /* Computes the transition matrix starting at age 'age' over
1981: 'nhstepm*hstepm*stepm' months (i.e. until
1982: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1983: nhstepm*hstepm matrices.
1984: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1985: (typically every 2 years instead of every month which is too big
1986: for the memory).
1987: Model is determined by parameters x and covariates have to be
1988: included manually here.
1989:
1990: */
1991:
1992: int i, j, d, h, k;
1993: double **out, cov[NCOVMAX+1];
1994: double **newm;
1995: double agexact;
1996:
1997: /* Hstepm could be zero and should return the unit matrix */
1998: for (i=1;i<=nlstate+ndeath;i++)
1999: for (j=1;j<=nlstate+ndeath;j++){
2000: oldm[i][j]=(i==j ? 1.0 : 0.0);
2001: po[i][j][0]=(i==j ? 1.0 : 0.0);
2002: }
2003: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2004: for(h=1; h <=nhstepm; h++){
2005: for(d=1; d <=hstepm; d++){
2006: newm=savm;
2007: /* Covariates have to be included here again */
2008: cov[1]=1.;
2009: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2010: cov[2]=agexact;
2011: if(nagesqr==1)
2012: cov[3]= agexact*agexact;
2013: for (k=1; k<=cptcovn;k++)
2014: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
2015: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2016: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2017: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
2018: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
2019: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2020:
2021:
2022: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2023: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2024: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2025: pmij(pmmij,cov,ncovmodel,x,nlstate));
2026: savm=oldm;
2027: oldm=newm;
2028: }
2029: for(i=1; i<=nlstate+ndeath; i++)
2030: for(j=1;j<=nlstate+ndeath;j++) {
2031: po[i][j][h]=newm[i][j];
2032: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
2033: }
2034: /*printf("h=%d ",h);*/
2035: } /* end h */
2036: /* printf("\n H=%d \n",h); */
2037: return po;
2038: }
2039:
2040: #ifdef NLOPT
2041: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2042: double fret;
2043: double *xt;
2044: int j;
2045: myfunc_data *d2 = (myfunc_data *) pd;
2046: /* xt = (p1-1); */
2047: xt=vector(1,n);
2048: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2049:
2050: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2051: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2052: printf("Function = %.12lf ",fret);
2053: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2054: printf("\n");
2055: free_vector(xt,1,n);
2056: return fret;
2057: }
2058: #endif
2059:
2060: /*************** log-likelihood *************/
2061: double func( double *x)
2062: {
2063: int i, ii, j, k, mi, d, kk;
2064: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2065: double **out;
2066: double sw; /* Sum of weights */
2067: double lli; /* Individual log likelihood */
2068: int s1, s2;
2069: double bbh, survp;
2070: long ipmx;
2071: double agexact;
2072: /*extern weight */
2073: /* We are differentiating ll according to initial status */
2074: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2075: /*for(i=1;i<imx;i++)
2076: printf(" %d\n",s[4][i]);
2077: */
2078:
2079: ++countcallfunc;
2080:
2081: cov[1]=1.;
2082:
2083: for(k=1; k<=nlstate; k++) ll[k]=0.;
2084:
2085: if(mle==1){
2086: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2087: /* Computes the values of the ncovmodel covariates of the model
2088: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2089: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2090: to be observed in j being in i according to the model.
2091: */
2092: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
2093: cov[2+nagesqr+k]=covar[Tvar[k]][i];
2094: }
2095: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2096: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2097: has been calculated etc */
2098: for(mi=1; mi<= wav[i]-1; mi++){
2099: for (ii=1;ii<=nlstate+ndeath;ii++)
2100: for (j=1;j<=nlstate+ndeath;j++){
2101: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2102: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2103: }
2104: for(d=0; d<dh[mi][i]; d++){
2105: newm=savm;
2106: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2107: cov[2]=agexact;
2108: if(nagesqr==1)
2109: cov[3]= agexact*agexact;
2110: for (kk=1; kk<=cptcovage;kk++) {
2111: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
2112: }
2113: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2114: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2115: savm=oldm;
2116: oldm=newm;
2117: } /* end mult */
2118:
2119: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2120: /* But now since version 0.9 we anticipate for bias at large stepm.
2121: * If stepm is larger than one month (smallest stepm) and if the exact delay
2122: * (in months) between two waves is not a multiple of stepm, we rounded to
2123: * the nearest (and in case of equal distance, to the lowest) interval but now
2124: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2125: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2126: * probability in order to take into account the bias as a fraction of the way
2127: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2128: * -stepm/2 to stepm/2 .
2129: * For stepm=1 the results are the same as for previous versions of Imach.
2130: * For stepm > 1 the results are less biased than in previous versions.
2131: */
2132: s1=s[mw[mi][i]][i];
2133: s2=s[mw[mi+1][i]][i];
2134: bbh=(double)bh[mi][i]/(double)stepm;
2135: /* bias bh is positive if real duration
2136: * is higher than the multiple of stepm and negative otherwise.
2137: */
2138: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2139: if( s2 > nlstate){
2140: /* i.e. if s2 is a death state and if the date of death is known
2141: then the contribution to the likelihood is the probability to
2142: die between last step unit time and current step unit time,
2143: which is also equal to probability to die before dh
2144: minus probability to die before dh-stepm .
2145: In version up to 0.92 likelihood was computed
2146: as if date of death was unknown. Death was treated as any other
2147: health state: the date of the interview describes the actual state
2148: and not the date of a change in health state. The former idea was
2149: to consider that at each interview the state was recorded
2150: (healthy, disable or death) and IMaCh was corrected; but when we
2151: introduced the exact date of death then we should have modified
2152: the contribution of an exact death to the likelihood. This new
2153: contribution is smaller and very dependent of the step unit
2154: stepm. It is no more the probability to die between last interview
2155: and month of death but the probability to survive from last
2156: interview up to one month before death multiplied by the
2157: probability to die within a month. Thanks to Chris
2158: Jackson for correcting this bug. Former versions increased
2159: mortality artificially. The bad side is that we add another loop
2160: which slows down the processing. The difference can be up to 10%
2161: lower mortality.
2162: */
2163: /* If, at the beginning of the maximization mostly, the
2164: cumulative probability or probability to be dead is
2165: constant (ie = 1) over time d, the difference is equal to
2166: 0. out[s1][3] = savm[s1][3]: probability, being at state
2167: s1 at precedent wave, to be dead a month before current
2168: wave is equal to probability, being at state s1 at
2169: precedent wave, to be dead at mont of the current
2170: wave. Then the observed probability (that this person died)
2171: is null according to current estimated parameter. In fact,
2172: it should be very low but not zero otherwise the log go to
2173: infinity.
2174: */
2175: /* #ifdef INFINITYORIGINAL */
2176: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2177: /* #else */
2178: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2179: /* lli=log(mytinydouble); */
2180: /* else */
2181: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2182: /* #endif */
2183: lli=log(out[s1][s2] - savm[s1][s2]);
2184:
2185: } else if (s2==-2) {
2186: for (j=1,survp=0. ; j<=nlstate; j++)
2187: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2188: /*survp += out[s1][j]; */
2189: lli= log(survp);
2190: }
2191:
2192: else if (s2==-4) {
2193: for (j=3,survp=0. ; j<=nlstate; j++)
2194: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2195: lli= log(survp);
2196: }
2197:
2198: else if (s2==-5) {
2199: for (j=1,survp=0. ; j<=2; j++)
2200: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2201: lli= log(survp);
2202: }
2203:
2204: else{
2205: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2206: /* 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 */
2207: }
2208: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2209: /*if(lli ==000.0)*/
2210: /*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); */
2211: ipmx +=1;
2212: sw += weight[i];
2213: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2214: /* if (lli < log(mytinydouble)){ */
2215: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
2216: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
2217: /* } */
2218: } /* end of wave */
2219: } /* end of individual */
2220: } else if(mle==2){
2221: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2222: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2223: for(mi=1; mi<= wav[i]-1; mi++){
2224: for (ii=1;ii<=nlstate+ndeath;ii++)
2225: for (j=1;j<=nlstate+ndeath;j++){
2226: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2227: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2228: }
2229: for(d=0; d<=dh[mi][i]; d++){
2230: newm=savm;
2231: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2232: cov[2]=agexact;
2233: if(nagesqr==1)
2234: cov[3]= agexact*agexact;
2235: for (kk=1; kk<=cptcovage;kk++) {
2236: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2237: }
2238: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2239: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2240: savm=oldm;
2241: oldm=newm;
2242: } /* end mult */
2243:
2244: s1=s[mw[mi][i]][i];
2245: s2=s[mw[mi+1][i]][i];
2246: bbh=(double)bh[mi][i]/(double)stepm;
2247: 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 */
2248: ipmx +=1;
2249: sw += weight[i];
2250: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2251: } /* end of wave */
2252: } /* end of individual */
2253: } else if(mle==3){ /* exponential inter-extrapolation */
2254: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2255: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2256: for(mi=1; mi<= wav[i]-1; mi++){
2257: for (ii=1;ii<=nlstate+ndeath;ii++)
2258: for (j=1;j<=nlstate+ndeath;j++){
2259: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2260: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2261: }
2262: for(d=0; d<dh[mi][i]; d++){
2263: newm=savm;
2264: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2265: cov[2]=agexact;
2266: if(nagesqr==1)
2267: cov[3]= agexact*agexact;
2268: for (kk=1; kk<=cptcovage;kk++) {
2269: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2270: }
2271: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2272: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2273: savm=oldm;
2274: oldm=newm;
2275: } /* end mult */
2276:
2277: s1=s[mw[mi][i]][i];
2278: s2=s[mw[mi+1][i]][i];
2279: bbh=(double)bh[mi][i]/(double)stepm;
2280: 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 */
2281: ipmx +=1;
2282: sw += weight[i];
2283: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2284: } /* end of wave */
2285: } /* end of individual */
2286: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2287: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2288: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2289: for(mi=1; mi<= wav[i]-1; mi++){
2290: for (ii=1;ii<=nlstate+ndeath;ii++)
2291: for (j=1;j<=nlstate+ndeath;j++){
2292: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2293: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2294: }
2295: for(d=0; d<dh[mi][i]; d++){
2296: newm=savm;
2297: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2298: cov[2]=agexact;
2299: if(nagesqr==1)
2300: cov[3]= agexact*agexact;
2301: for (kk=1; kk<=cptcovage;kk++) {
2302: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2303: }
2304:
2305: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2306: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2307: savm=oldm;
2308: oldm=newm;
2309: } /* end mult */
2310:
2311: s1=s[mw[mi][i]][i];
2312: s2=s[mw[mi+1][i]][i];
2313: if( s2 > nlstate){
2314: lli=log(out[s1][s2] - savm[s1][s2]);
2315: }else{
2316: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2317: }
2318: ipmx +=1;
2319: sw += weight[i];
2320: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2321: /* 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]); */
2322: } /* end of wave */
2323: } /* end of individual */
2324: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2325: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2326: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2327: for(mi=1; mi<= wav[i]-1; mi++){
2328: for (ii=1;ii<=nlstate+ndeath;ii++)
2329: for (j=1;j<=nlstate+ndeath;j++){
2330: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2331: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2332: }
2333: for(d=0; d<dh[mi][i]; d++){
2334: newm=savm;
2335: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2336: cov[2]=agexact;
2337: if(nagesqr==1)
2338: cov[3]= agexact*agexact;
2339: for (kk=1; kk<=cptcovage;kk++) {
2340: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2341: }
2342:
2343: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2344: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2345: savm=oldm;
2346: oldm=newm;
2347: } /* end mult */
2348:
2349: s1=s[mw[mi][i]][i];
2350: s2=s[mw[mi+1][i]][i];
2351: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2352: ipmx +=1;
2353: sw += weight[i];
2354: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2355: /*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]);*/
2356: } /* end of wave */
2357: } /* end of individual */
2358: } /* End of if */
2359: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2360: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2361: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2362: return -l;
2363: }
2364:
2365: /*************** log-likelihood *************/
2366: double funcone( double *x)
2367: {
2368: /* Same as likeli but slower because of a lot of printf and if */
2369: int i, ii, j, k, mi, d, kk;
2370: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2371: double **out;
2372: double lli; /* Individual log likelihood */
2373: double llt;
2374: int s1, s2;
2375: double bbh, survp;
2376: double agexact;
2377: /*extern weight */
2378: /* We are differentiating ll according to initial status */
2379: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2380: /*for(i=1;i<imx;i++)
2381: printf(" %d\n",s[4][i]);
2382: */
2383: cov[1]=1.;
2384:
2385: for(k=1; k<=nlstate; k++) ll[k]=0.;
2386:
2387: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2388: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2389: for(mi=1; mi<= wav[i]-1; mi++){
2390: for (ii=1;ii<=nlstate+ndeath;ii++)
2391: for (j=1;j<=nlstate+ndeath;j++){
2392: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2393: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2394: }
2395: for(d=0; d<dh[mi][i]; d++){
2396: newm=savm;
2397: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2398: cov[2]=agexact;
2399: if(nagesqr==1)
2400: cov[3]= agexact*agexact;
2401: for (kk=1; kk<=cptcovage;kk++) {
2402: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2403: }
2404:
2405: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2406: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2407: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2408: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2409: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2410: savm=oldm;
2411: oldm=newm;
2412: } /* end mult */
2413:
2414: s1=s[mw[mi][i]][i];
2415: s2=s[mw[mi+1][i]][i];
2416: bbh=(double)bh[mi][i]/(double)stepm;
2417: /* bias is positive if real duration
2418: * is higher than the multiple of stepm and negative otherwise.
2419: */
2420: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2421: lli=log(out[s1][s2] - savm[s1][s2]);
2422: } else if (s2==-2) {
2423: for (j=1,survp=0. ; j<=nlstate; j++)
2424: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2425: lli= log(survp);
2426: }else if (mle==1){
2427: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2428: } else if(mle==2){
2429: 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 */
2430: } else if(mle==3){ /* exponential inter-extrapolation */
2431: 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 */
2432: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2433: lli=log(out[s1][s2]); /* Original formula */
2434: } else{ /* mle=0 back to 1 */
2435: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2436: /*lli=log(out[s1][s2]); */ /* Original formula */
2437: } /* End of if */
2438: ipmx +=1;
2439: sw += weight[i];
2440: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2441: /*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]); */
2442: if(globpr){
2443: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2444: %11.6f %11.6f %11.6f ", \
2445: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2446: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2447: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2448: llt +=ll[k]*gipmx/gsw;
2449: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2450: }
2451: fprintf(ficresilk," %10.6f\n", -llt);
2452: }
2453: } /* end of wave */
2454: } /* end of individual */
2455: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2456: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2457: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2458: if(globpr==0){ /* First time we count the contributions and weights */
2459: gipmx=ipmx;
2460: gsw=sw;
2461: }
2462: return -l;
2463: }
2464:
2465:
2466: /*************** function likelione ***********/
2467: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2468: {
2469: /* This routine should help understanding what is done with
2470: the selection of individuals/waves and
2471: to check the exact contribution to the likelihood.
2472: Plotting could be done.
2473: */
2474: int k;
2475:
2476: if(*globpri !=0){ /* Just counts and sums, no printings */
2477: strcpy(fileresilk,"ilk");
2478: strcat(fileresilk,fileres);
2479: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2480: printf("Problem with resultfile: %s\n", fileresilk);
2481: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2482: }
2483: 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");
2484: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2485: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2486: for(k=1; k<=nlstate; k++)
2487: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2488: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2489: }
2490:
2491: *fretone=(*funcone)(p);
2492: if(*globpri !=0){
2493: fclose(ficresilk);
2494: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2495: fflush(fichtm);
2496: }
2497: return;
2498: }
2499:
2500:
2501: /*********** Maximum Likelihood Estimation ***************/
2502:
2503: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2504: {
2505: int i,j, iter=0;
2506: double **xi;
2507: double fret;
2508: double fretone; /* Only one call to likelihood */
2509: /* char filerespow[FILENAMELENGTH];*/
2510:
2511: #ifdef NLOPT
2512: int creturn;
2513: nlopt_opt opt;
2514: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2515: double *lb;
2516: double minf; /* the minimum objective value, upon return */
2517: double * p1; /* Shifted parameters from 0 instead of 1 */
2518: myfunc_data dinst, *d = &dinst;
2519: #endif
2520:
2521:
2522: xi=matrix(1,npar,1,npar);
2523: for (i=1;i<=npar;i++)
2524: for (j=1;j<=npar;j++)
2525: xi[i][j]=(i==j ? 1.0 : 0.0);
2526: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2527: strcpy(filerespow,"pow");
2528: strcat(filerespow,fileres);
2529: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2530: printf("Problem with resultfile: %s\n", filerespow);
2531: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2532: }
2533: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2534: for (i=1;i<=nlstate;i++)
2535: for(j=1;j<=nlstate+ndeath;j++)
2536: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2537: fprintf(ficrespow,"\n");
2538: #ifdef POWELL
2539: powell(p,xi,npar,ftol,&iter,&fret,func);
2540: #endif
2541:
2542: #ifdef NLOPT
2543: #ifdef NEWUOA
2544: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2545: #else
2546: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2547: #endif
2548: lb=vector(0,npar-1);
2549: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2550: nlopt_set_lower_bounds(opt, lb);
2551: nlopt_set_initial_step1(opt, 0.1);
2552:
2553: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2554: d->function = func;
2555: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2556: nlopt_set_min_objective(opt, myfunc, d);
2557: nlopt_set_xtol_rel(opt, ftol);
2558: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2559: printf("nlopt failed! %d\n",creturn);
2560: }
2561: else {
2562: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2563: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2564: iter=1; /* not equal */
2565: }
2566: nlopt_destroy(opt);
2567: #endif
2568: free_matrix(xi,1,npar,1,npar);
2569: fclose(ficrespow);
2570: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2571: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2572: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2573:
2574: }
2575:
2576: /**** Computes Hessian and covariance matrix ***/
2577: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2578: {
2579: double **a,**y,*x,pd;
2580: double **hess;
2581: int i, j;
2582: int *indx;
2583:
2584: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2585: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2586: void lubksb(double **a, int npar, int *indx, double b[]) ;
2587: void ludcmp(double **a, int npar, int *indx, double *d) ;
2588: double gompertz(double p[]);
2589: hess=matrix(1,npar,1,npar);
2590:
2591: printf("\nCalculation of the hessian matrix. Wait...\n");
2592: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2593: for (i=1;i<=npar;i++){
2594: printf("%d",i);fflush(stdout);
2595: fprintf(ficlog,"%d",i);fflush(ficlog);
2596:
2597: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2598:
2599: /* printf(" %f ",p[i]);
2600: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2601: }
2602:
2603: for (i=1;i<=npar;i++) {
2604: for (j=1;j<=npar;j++) {
2605: if (j>i) {
2606: printf(".%d%d",i,j);fflush(stdout);
2607: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2608: hess[i][j]=hessij(p,delti,i,j,func,npar);
2609:
2610: hess[j][i]=hess[i][j];
2611: /*printf(" %lf ",hess[i][j]);*/
2612: }
2613: }
2614: }
2615: printf("\n");
2616: fprintf(ficlog,"\n");
2617:
2618: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2619: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2620:
2621: a=matrix(1,npar,1,npar);
2622: y=matrix(1,npar,1,npar);
2623: x=vector(1,npar);
2624: indx=ivector(1,npar);
2625: for (i=1;i<=npar;i++)
2626: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2627: ludcmp(a,npar,indx,&pd);
2628:
2629: for (j=1;j<=npar;j++) {
2630: for (i=1;i<=npar;i++) x[i]=0;
2631: x[j]=1;
2632: lubksb(a,npar,indx,x);
2633: for (i=1;i<=npar;i++){
2634: matcov[i][j]=x[i];
2635: }
2636: }
2637:
2638: printf("\n#Hessian matrix#\n");
2639: fprintf(ficlog,"\n#Hessian matrix#\n");
2640: for (i=1;i<=npar;i++) {
2641: for (j=1;j<=npar;j++) {
2642: printf("%.3e ",hess[i][j]);
2643: fprintf(ficlog,"%.3e ",hess[i][j]);
2644: }
2645: printf("\n");
2646: fprintf(ficlog,"\n");
2647: }
2648:
2649: /* Recompute Inverse */
2650: for (i=1;i<=npar;i++)
2651: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2652: ludcmp(a,npar,indx,&pd);
2653:
2654: /* printf("\n#Hessian matrix recomputed#\n");
2655:
2656: for (j=1;j<=npar;j++) {
2657: for (i=1;i<=npar;i++) x[i]=0;
2658: x[j]=1;
2659: lubksb(a,npar,indx,x);
2660: for (i=1;i<=npar;i++){
2661: y[i][j]=x[i];
2662: printf("%.3e ",y[i][j]);
2663: fprintf(ficlog,"%.3e ",y[i][j]);
2664: }
2665: printf("\n");
2666: fprintf(ficlog,"\n");
2667: }
2668: */
2669:
2670: free_matrix(a,1,npar,1,npar);
2671: free_matrix(y,1,npar,1,npar);
2672: free_vector(x,1,npar);
2673: free_ivector(indx,1,npar);
2674: free_matrix(hess,1,npar,1,npar);
2675:
2676:
2677: }
2678:
2679: /*************** hessian matrix ****************/
2680: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2681: {
2682: int i;
2683: int l=1, lmax=20;
2684: double k1,k2;
2685: double p2[MAXPARM+1]; /* identical to x */
2686: double res;
2687: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2688: double fx;
2689: int k=0,kmax=10;
2690: double l1;
2691:
2692: fx=func(x);
2693: for (i=1;i<=npar;i++) p2[i]=x[i];
2694: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2695: l1=pow(10,l);
2696: delts=delt;
2697: for(k=1 ; k <kmax; k=k+1){
2698: delt = delta*(l1*k);
2699: p2[theta]=x[theta] +delt;
2700: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2701: p2[theta]=x[theta]-delt;
2702: k2=func(p2)-fx;
2703: /*res= (k1-2.0*fx+k2)/delt/delt; */
2704: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2705:
2706: #ifdef DEBUGHESS
2707: 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);
2708: 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);
2709: #endif
2710: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2711: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2712: k=kmax;
2713: }
2714: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2715: k=kmax; l=lmax*10;
2716: }
2717: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2718: delts=delt;
2719: }
2720: }
2721: }
2722: delti[theta]=delts;
2723: return res;
2724:
2725: }
2726:
2727: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2728: {
2729: int i;
2730: int l=1, lmax=20;
2731: double k1,k2,k3,k4,res,fx;
2732: double p2[MAXPARM+1];
2733: int k;
2734:
2735: fx=func(x);
2736: for (k=1; k<=2; k++) {
2737: for (i=1;i<=npar;i++) p2[i]=x[i];
2738: p2[thetai]=x[thetai]+delti[thetai]/k;
2739: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2740: k1=func(p2)-fx;
2741:
2742: p2[thetai]=x[thetai]+delti[thetai]/k;
2743: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2744: k2=func(p2)-fx;
2745:
2746: p2[thetai]=x[thetai]-delti[thetai]/k;
2747: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2748: k3=func(p2)-fx;
2749:
2750: p2[thetai]=x[thetai]-delti[thetai]/k;
2751: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2752: k4=func(p2)-fx;
2753: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2754: #ifdef DEBUG
2755: 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);
2756: 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);
2757: #endif
2758: }
2759: return res;
2760: }
2761:
2762: /************** Inverse of matrix **************/
2763: void ludcmp(double **a, int n, int *indx, double *d)
2764: {
2765: int i,imax,j,k;
2766: double big,dum,sum,temp;
2767: double *vv;
2768:
2769: vv=vector(1,n);
2770: *d=1.0;
2771: for (i=1;i<=n;i++) {
2772: big=0.0;
2773: for (j=1;j<=n;j++)
2774: if ((temp=fabs(a[i][j])) > big) big=temp;
2775: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2776: vv[i]=1.0/big;
2777: }
2778: for (j=1;j<=n;j++) {
2779: for (i=1;i<j;i++) {
2780: sum=a[i][j];
2781: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2782: a[i][j]=sum;
2783: }
2784: big=0.0;
2785: for (i=j;i<=n;i++) {
2786: sum=a[i][j];
2787: for (k=1;k<j;k++)
2788: sum -= a[i][k]*a[k][j];
2789: a[i][j]=sum;
2790: if ( (dum=vv[i]*fabs(sum)) >= big) {
2791: big=dum;
2792: imax=i;
2793: }
2794: }
2795: if (j != imax) {
2796: for (k=1;k<=n;k++) {
2797: dum=a[imax][k];
2798: a[imax][k]=a[j][k];
2799: a[j][k]=dum;
2800: }
2801: *d = -(*d);
2802: vv[imax]=vv[j];
2803: }
2804: indx[j]=imax;
2805: if (a[j][j] == 0.0) a[j][j]=TINY;
2806: if (j != n) {
2807: dum=1.0/(a[j][j]);
2808: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2809: }
2810: }
2811: free_vector(vv,1,n); /* Doesn't work */
2812: ;
2813: }
2814:
2815: void lubksb(double **a, int n, int *indx, double b[])
2816: {
2817: int i,ii=0,ip,j;
2818: double sum;
2819:
2820: for (i=1;i<=n;i++) {
2821: ip=indx[i];
2822: sum=b[ip];
2823: b[ip]=b[i];
2824: if (ii)
2825: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2826: else if (sum) ii=i;
2827: b[i]=sum;
2828: }
2829: for (i=n;i>=1;i--) {
2830: sum=b[i];
2831: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2832: b[i]=sum/a[i][i];
2833: }
2834: }
2835:
2836: void pstamp(FILE *fichier)
2837: {
2838: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2839: }
2840:
2841: /************ Frequencies ********************/
2842: 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[])
2843: { /* Some frequencies */
2844:
2845: int i, m, jk, j1, bool, z1,j;
2846: int first;
2847: double ***freq; /* Frequencies */
2848: double *pp, **prop;
2849: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2850: char fileresp[FILENAMELENGTH];
2851:
2852: pp=vector(1,nlstate);
2853: prop=matrix(1,nlstate,iagemin,iagemax+3);
2854: strcpy(fileresp,"p");
2855: strcat(fileresp,fileres);
2856: if((ficresp=fopen(fileresp,"w"))==NULL) {
2857: printf("Problem with prevalence resultfile: %s\n", fileresp);
2858: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2859: exit(0);
2860: }
2861: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2862: j1=0;
2863:
2864: j=cptcoveff;
2865: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2866:
2867: first=1;
2868:
2869: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2870: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2871: /* j1++; */
2872: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2873: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2874: scanf("%d", i);*/
2875: for (i=-5; i<=nlstate+ndeath; i++)
2876: for (jk=-5; jk<=nlstate+ndeath; jk++)
2877: for(m=iagemin; m <= iagemax+3; m++)
2878: freq[i][jk][m]=0;
2879:
2880: for (i=1; i<=nlstate; i++)
2881: for(m=iagemin; m <= iagemax+3; m++)
2882: prop[i][m]=0;
2883:
2884: dateintsum=0;
2885: k2cpt=0;
2886: for (i=1; i<=imx; i++) {
2887: bool=1;
2888: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2889: for (z1=1; z1<=cptcoveff; z1++)
2890: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2891: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2892: bool=0;
2893: /* 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",
2894: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2895: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2896: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2897: }
2898: }
2899:
2900: if (bool==1){
2901: for(m=firstpass; m<=lastpass; m++){
2902: k2=anint[m][i]+(mint[m][i]/12.);
2903: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2904: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2905: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2906: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2907: if (m<lastpass) {
2908: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2909: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2910: }
2911:
2912: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2913: dateintsum=dateintsum+k2;
2914: k2cpt++;
2915: }
2916: /*}*/
2917: }
2918: }
2919: } /* end i */
2920:
2921: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2922: pstamp(ficresp);
2923: if (cptcovn>0) {
2924: fprintf(ficresp, "\n#********** Variable ");
2925: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2926: fprintf(ficresp, "**********\n#");
2927: fprintf(ficlog, "\n#********** Variable ");
2928: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2929: fprintf(ficlog, "**********\n#");
2930: }
2931: for(i=1; i<=nlstate;i++)
2932: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2933: fprintf(ficresp, "\n");
2934:
2935: for(i=iagemin; i <= iagemax+3; i++){
2936: if(i==iagemax+3){
2937: fprintf(ficlog,"Total");
2938: }else{
2939: if(first==1){
2940: first=0;
2941: printf("See log file for details...\n");
2942: }
2943: fprintf(ficlog,"Age %d", i);
2944: }
2945: for(jk=1; jk <=nlstate ; jk++){
2946: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2947: pp[jk] += freq[jk][m][i];
2948: }
2949: for(jk=1; jk <=nlstate ; jk++){
2950: for(m=-1, pos=0; m <=0 ; m++)
2951: pos += freq[jk][m][i];
2952: if(pp[jk]>=1.e-10){
2953: if(first==1){
2954: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2955: }
2956: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2957: }else{
2958: if(first==1)
2959: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2960: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2961: }
2962: }
2963:
2964: for(jk=1; jk <=nlstate ; jk++){
2965: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2966: pp[jk] += freq[jk][m][i];
2967: }
2968: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2969: pos += pp[jk];
2970: posprop += prop[jk][i];
2971: }
2972: for(jk=1; jk <=nlstate ; jk++){
2973: if(pos>=1.e-5){
2974: if(first==1)
2975: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2976: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2977: }else{
2978: if(first==1)
2979: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2980: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2981: }
2982: if( i <= iagemax){
2983: if(pos>=1.e-5){
2984: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2985: /*probs[i][jk][j1]= pp[jk]/pos;*/
2986: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2987: }
2988: else
2989: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2990: }
2991: }
2992:
2993: for(jk=-1; jk <=nlstate+ndeath; jk++)
2994: for(m=-1; m <=nlstate+ndeath; m++)
2995: if(freq[jk][m][i] !=0 ) {
2996: if(first==1)
2997: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2998: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2999: }
3000: if(i <= iagemax)
3001: fprintf(ficresp,"\n");
3002: if(first==1)
3003: printf("Others in log...\n");
3004: fprintf(ficlog,"\n");
3005: }
3006: /*}*/
3007: }
3008: dateintmean=dateintsum/k2cpt;
3009:
3010: fclose(ficresp);
3011: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3012: free_vector(pp,1,nlstate);
3013: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3014: /* End of Freq */
3015: }
3016:
3017: /************ Prevalence ********************/
3018: 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)
3019: {
3020: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3021: in each health status at the date of interview (if between dateprev1 and dateprev2).
3022: We still use firstpass and lastpass as another selection.
3023: */
3024:
3025: int i, m, jk, j1, bool, z1,j;
3026:
3027: double **prop;
3028: double posprop;
3029: double y2; /* in fractional years */
3030: int iagemin, iagemax;
3031: int first; /** to stop verbosity which is redirected to log file */
3032:
3033: iagemin= (int) agemin;
3034: iagemax= (int) agemax;
3035: /*pp=vector(1,nlstate);*/
3036: prop=matrix(1,nlstate,iagemin,iagemax+3);
3037: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3038: j1=0;
3039:
3040: /*j=cptcoveff;*/
3041: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3042:
3043: first=1;
3044: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3045: /*for(i1=1; i1<=ncodemax[k1];i1++){
3046: j1++;*/
3047:
3048: for (i=1; i<=nlstate; i++)
3049: for(m=iagemin; m <= iagemax+3; m++)
3050: prop[i][m]=0.0;
3051:
3052: for (i=1; i<=imx; i++) { /* Each individual */
3053: bool=1;
3054: if (cptcovn>0) {
3055: for (z1=1; z1<=cptcoveff; z1++)
3056: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3057: bool=0;
3058: }
3059: if (bool==1) {
3060: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3061: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3062: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3063: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3064: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3065: 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);
3066: if (s[m][i]>0 && s[m][i]<=nlstate) {
3067: /*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]]);*/
3068: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3069: prop[s[m][i]][iagemax+3] += weight[i];
3070: }
3071: }
3072: } /* end selection of waves */
3073: }
3074: }
3075: for(i=iagemin; i <= iagemax+3; i++){
3076: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3077: posprop += prop[jk][i];
3078: }
3079:
3080: for(jk=1; jk <=nlstate ; jk++){
3081: if( i <= iagemax){
3082: if(posprop>=1.e-5){
3083: probs[i][jk][j1]= prop[jk][i]/posprop;
3084: } else{
3085: if(first==1){
3086: first=0;
3087: 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]);
3088: }
3089: }
3090: }
3091: }/* end jk */
3092: }/* end i */
3093: /*} *//* end i1 */
3094: } /* end j1 */
3095:
3096: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3097: /*free_vector(pp,1,nlstate);*/
3098: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3099: } /* End of prevalence */
3100:
3101: /************* Waves Concatenation ***************/
3102:
3103: 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)
3104: {
3105: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3106: Death is a valid wave (if date is known).
3107: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3108: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3109: and mw[mi+1][i]. dh depends on stepm.
3110: */
3111:
3112: int i, mi, m;
3113: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3114: double sum=0., jmean=0.;*/
3115: int first;
3116: int j, k=0,jk, ju, jl;
3117: double sum=0.;
3118: first=0;
3119: jmin=100000;
3120: jmax=-1;
3121: jmean=0.;
3122: for(i=1; i<=imx; i++){
3123: mi=0;
3124: m=firstpass;
3125: while(s[m][i] <= nlstate){
3126: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3127: mw[++mi][i]=m;
3128: if(m >=lastpass)
3129: break;
3130: else
3131: m++;
3132: }/* end while */
3133: if (s[m][i] > nlstate){
3134: mi++; /* Death is another wave */
3135: /* if(mi==0) never been interviewed correctly before death */
3136: /* Only death is a correct wave */
3137: mw[mi][i]=m;
3138: }
3139:
3140: wav[i]=mi;
3141: if(mi==0){
3142: nbwarn++;
3143: if(first==0){
3144: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3145: first=1;
3146: }
3147: if(first==1){
3148: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3149: }
3150: } /* end mi==0 */
3151: } /* End individuals */
3152:
3153: for(i=1; i<=imx; i++){
3154: for(mi=1; mi<wav[i];mi++){
3155: if (stepm <=0)
3156: dh[mi][i]=1;
3157: else{
3158: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3159: if (agedc[i] < 2*AGESUP) {
3160: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3161: if(j==0) j=1; /* Survives at least one month after exam */
3162: else if(j<0){
3163: nberr++;
3164: 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]);
3165: j=1; /* Temporary Dangerous patch */
3166: 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);
3167: 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]);
3168: 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);
3169: }
3170: k=k+1;
3171: if (j >= jmax){
3172: jmax=j;
3173: ijmax=i;
3174: }
3175: if (j <= jmin){
3176: jmin=j;
3177: ijmin=i;
3178: }
3179: sum=sum+j;
3180: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3181: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3182: }
3183: }
3184: else{
3185: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3186: /* 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]); */
3187:
3188: k=k+1;
3189: if (j >= jmax) {
3190: jmax=j;
3191: ijmax=i;
3192: }
3193: else if (j <= jmin){
3194: jmin=j;
3195: ijmin=i;
3196: }
3197: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3198: /*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]);*/
3199: if(j<0){
3200: nberr++;
3201: 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]);
3202: 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]);
3203: }
3204: sum=sum+j;
3205: }
3206: jk= j/stepm;
3207: jl= j -jk*stepm;
3208: ju= j -(jk+1)*stepm;
3209: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3210: if(jl==0){
3211: dh[mi][i]=jk;
3212: bh[mi][i]=0;
3213: }else{ /* We want a negative bias in order to only have interpolation ie
3214: * to avoid the price of an extra matrix product in likelihood */
3215: dh[mi][i]=jk+1;
3216: bh[mi][i]=ju;
3217: }
3218: }else{
3219: if(jl <= -ju){
3220: dh[mi][i]=jk;
3221: bh[mi][i]=jl; /* bias is positive if real duration
3222: * is higher than the multiple of stepm and negative otherwise.
3223: */
3224: }
3225: else{
3226: dh[mi][i]=jk+1;
3227: bh[mi][i]=ju;
3228: }
3229: if(dh[mi][i]==0){
3230: dh[mi][i]=1; /* At least one step */
3231: bh[mi][i]=ju; /* At least one step */
3232: /* 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);*/
3233: }
3234: } /* end if mle */
3235: }
3236: } /* end wave */
3237: }
3238: jmean=sum/k;
3239: 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);
3240: 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);
3241: }
3242:
3243: /*********** Tricode ****************************/
3244: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
3245: {
3246: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3247: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
3248: * Boring subroutine which should only output nbcode[Tvar[j]][k]
3249: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
3250: * nbcode[Tvar[j]][1]=
3251: */
3252:
3253: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
3254: int modmaxcovj=0; /* Modality max of covariates j */
3255: int cptcode=0; /* Modality max of covariates j */
3256: int modmincovj=0; /* Modality min of covariates j */
3257:
3258:
3259: cptcoveff=0;
3260:
3261: for (k=-1; k < maxncov; k++) Ndum[k]=0;
3262: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
3263:
3264: /* Loop on covariates without age and products */
3265: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3266: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
3267: modality of this covariate Vj*/
3268: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3269: * If product of Vn*Vm, still boolean *:
3270: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3271: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3272: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
3273: modality of the nth covariate of individual i. */
3274: if (ij > modmaxcovj)
3275: modmaxcovj=ij;
3276: else if (ij < modmincovj)
3277: modmincovj=ij;
3278: if ((ij < -1) && (ij > NCOVMAX)){
3279: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3280: exit(1);
3281: }else
3282: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
3283: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
3284: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
3285: /* getting the maximum value of the modality of the covariate
3286: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3287: female is 1, then modmaxcovj=1.*/
3288: } /* end for loop on individuals */
3289: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3290: cptcode=modmaxcovj;
3291: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3292: /*for (i=0; i<=cptcode; i++) {*/
3293: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3294: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
3295: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3296: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3297: }
3298: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3299: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3300: } /* Ndum[-1] number of undefined modalities */
3301:
3302: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3303: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3304: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
3305: modmincovj=3; modmaxcovj = 7;
3306: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3307: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3308: defining two dummy variables: variables V1_1 and V1_2.
3309: nbcode[Tvar[j]][ij]=k;
3310: nbcode[Tvar[j]][1]=0;
3311: nbcode[Tvar[j]][2]=1;
3312: nbcode[Tvar[j]][3]=2;
3313: */
3314: ij=1; /* ij is similar to i but can jumps over null modalities */
3315: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3316: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3317: /*recode from 0 */
3318: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3319: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
3320: k is a modality. If we have model=V1+V1*sex
3321: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3322: ij++;
3323: }
3324: if (ij > ncodemax[j]) break;
3325: } /* end of loop on */
3326: } /* end of loop on modality */
3327: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3328:
3329: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3330:
3331: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
3332: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3333: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3334: Ndum[ij]++; /* Might be supersed V1 + V1*age */
3335: }
3336:
3337: ij=1;
3338: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3339: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3340: if((Ndum[i]!=0) && (i<=ncovcol)){
3341: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3342: Tvaraff[ij]=i; /*For printing (unclear) */
3343: ij++;
3344: }else
3345: Tvaraff[ij]=0;
3346: }
3347: ij--;
3348: cptcoveff=ij; /*Number of total covariates*/
3349:
3350: }
3351:
3352:
3353: /*********** Health Expectancies ****************/
3354:
3355: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3356:
3357: {
3358: /* Health expectancies, no variances */
3359: int i, j, nhstepm, hstepm, h, nstepm;
3360: int nhstepma, nstepma; /* Decreasing with age */
3361: double age, agelim, hf;
3362: double ***p3mat;
3363: double eip;
3364:
3365: pstamp(ficreseij);
3366: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3367: fprintf(ficreseij,"# Age");
3368: for(i=1; i<=nlstate;i++){
3369: for(j=1; j<=nlstate;j++){
3370: fprintf(ficreseij," e%1d%1d ",i,j);
3371: }
3372: fprintf(ficreseij," e%1d. ",i);
3373: }
3374: fprintf(ficreseij,"\n");
3375:
3376:
3377: if(estepm < stepm){
3378: printf ("Problem %d lower than %d\n",estepm, stepm);
3379: }
3380: else hstepm=estepm;
3381: /* We compute the life expectancy from trapezoids spaced every estepm months
3382: * This is mainly to measure the difference between two models: for example
3383: * if stepm=24 months pijx are given only every 2 years and by summing them
3384: * we are calculating an estimate of the Life Expectancy assuming a linear
3385: * progression in between and thus overestimating or underestimating according
3386: * to the curvature of the survival function. If, for the same date, we
3387: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3388: * to compare the new estimate of Life expectancy with the same linear
3389: * hypothesis. A more precise result, taking into account a more precise
3390: * curvature will be obtained if estepm is as small as stepm. */
3391:
3392: /* For example we decided to compute the life expectancy with the smallest unit */
3393: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3394: nhstepm is the number of hstepm from age to agelim
3395: nstepm is the number of stepm from age to agelin.
3396: Look at hpijx to understand the reason of that which relies in memory size
3397: and note for a fixed period like estepm months */
3398: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3399: survival function given by stepm (the optimization length). Unfortunately it
3400: means that if the survival funtion is printed only each two years of age and if
3401: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3402: results. So we changed our mind and took the option of the best precision.
3403: */
3404: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3405:
3406: agelim=AGESUP;
3407: /* If stepm=6 months */
3408: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3409: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3410:
3411: /* nhstepm age range expressed in number of stepm */
3412: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3413: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3414: /* if (stepm >= YEARM) hstepm=1;*/
3415: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3416: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3417:
3418: for (age=bage; age<=fage; age ++){
3419: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3420: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3421: /* if (stepm >= YEARM) hstepm=1;*/
3422: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3423:
3424: /* If stepm=6 months */
3425: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3426: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3427:
3428: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3429:
3430: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3431:
3432: printf("%d|",(int)age);fflush(stdout);
3433: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3434:
3435: /* Computing expectancies */
3436: for(i=1; i<=nlstate;i++)
3437: for(j=1; j<=nlstate;j++)
3438: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3439: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3440:
3441: /* 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]);*/
3442:
3443: }
3444:
3445: fprintf(ficreseij,"%3.0f",age );
3446: for(i=1; i<=nlstate;i++){
3447: eip=0;
3448: for(j=1; j<=nlstate;j++){
3449: eip +=eij[i][j][(int)age];
3450: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3451: }
3452: fprintf(ficreseij,"%9.4f", eip );
3453: }
3454: fprintf(ficreseij,"\n");
3455:
3456: }
3457: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3458: printf("\n");
3459: fprintf(ficlog,"\n");
3460:
3461: }
3462:
3463: 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[] )
3464:
3465: {
3466: /* Covariances of health expectancies eij and of total life expectancies according
3467: to initial status i, ei. .
3468: */
3469: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3470: int nhstepma, nstepma; /* Decreasing with age */
3471: double age, agelim, hf;
3472: double ***p3matp, ***p3matm, ***varhe;
3473: double **dnewm,**doldm;
3474: double *xp, *xm;
3475: double **gp, **gm;
3476: double ***gradg, ***trgradg;
3477: int theta;
3478:
3479: double eip, vip;
3480:
3481: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3482: xp=vector(1,npar);
3483: xm=vector(1,npar);
3484: dnewm=matrix(1,nlstate*nlstate,1,npar);
3485: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3486:
3487: pstamp(ficresstdeij);
3488: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3489: fprintf(ficresstdeij,"# Age");
3490: for(i=1; i<=nlstate;i++){
3491: for(j=1; j<=nlstate;j++)
3492: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3493: fprintf(ficresstdeij," e%1d. ",i);
3494: }
3495: fprintf(ficresstdeij,"\n");
3496:
3497: pstamp(ficrescveij);
3498: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3499: fprintf(ficrescveij,"# Age");
3500: for(i=1; i<=nlstate;i++)
3501: for(j=1; j<=nlstate;j++){
3502: cptj= (j-1)*nlstate+i;
3503: for(i2=1; i2<=nlstate;i2++)
3504: for(j2=1; j2<=nlstate;j2++){
3505: cptj2= (j2-1)*nlstate+i2;
3506: if(cptj2 <= cptj)
3507: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3508: }
3509: }
3510: fprintf(ficrescveij,"\n");
3511:
3512: if(estepm < stepm){
3513: printf ("Problem %d lower than %d\n",estepm, stepm);
3514: }
3515: else hstepm=estepm;
3516: /* We compute the life expectancy from trapezoids spaced every estepm months
3517: * This is mainly to measure the difference between two models: for example
3518: * if stepm=24 months pijx are given only every 2 years and by summing them
3519: * we are calculating an estimate of the Life Expectancy assuming a linear
3520: * progression in between and thus overestimating or underestimating according
3521: * to the curvature of the survival function. If, for the same date, we
3522: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3523: * to compare the new estimate of Life expectancy with the same linear
3524: * hypothesis. A more precise result, taking into account a more precise
3525: * curvature will be obtained if estepm is as small as stepm. */
3526:
3527: /* For example we decided to compute the life expectancy with the smallest unit */
3528: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3529: nhstepm is the number of hstepm from age to agelim
3530: nstepm is the number of stepm from age to agelin.
3531: Look at hpijx to understand the reason of that which relies in memory size
3532: and note for a fixed period like estepm months */
3533: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3534: survival function given by stepm (the optimization length). Unfortunately it
3535: means that if the survival funtion is printed only each two years of age and if
3536: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3537: results. So we changed our mind and took the option of the best precision.
3538: */
3539: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3540:
3541: /* If stepm=6 months */
3542: /* nhstepm age range expressed in number of stepm */
3543: agelim=AGESUP;
3544: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3545: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3546: /* if (stepm >= YEARM) hstepm=1;*/
3547: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3548:
3549: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3550: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3551: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3552: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3553: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3554: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3555:
3556: for (age=bage; age<=fage; age ++){
3557: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3558: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3559: /* if (stepm >= YEARM) hstepm=1;*/
3560: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3561:
3562: /* If stepm=6 months */
3563: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3564: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3565:
3566: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3567:
3568: /* Computing Variances of health expectancies */
3569: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3570: decrease memory allocation */
3571: for(theta=1; theta <=npar; theta++){
3572: for(i=1; i<=npar; i++){
3573: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3574: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3575: }
3576: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3577: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3578:
3579: for(j=1; j<= nlstate; j++){
3580: for(i=1; i<=nlstate; i++){
3581: for(h=0; h<=nhstepm-1; h++){
3582: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3583: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3584: }
3585: }
3586: }
3587:
3588: for(ij=1; ij<= nlstate*nlstate; ij++)
3589: for(h=0; h<=nhstepm-1; h++){
3590: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3591: }
3592: }/* End theta */
3593:
3594:
3595: for(h=0; h<=nhstepm-1; h++)
3596: for(j=1; j<=nlstate*nlstate;j++)
3597: for(theta=1; theta <=npar; theta++)
3598: trgradg[h][j][theta]=gradg[h][theta][j];
3599:
3600:
3601: for(ij=1;ij<=nlstate*nlstate;ij++)
3602: for(ji=1;ji<=nlstate*nlstate;ji++)
3603: varhe[ij][ji][(int)age] =0.;
3604:
3605: printf("%d|",(int)age);fflush(stdout);
3606: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3607: for(h=0;h<=nhstepm-1;h++){
3608: for(k=0;k<=nhstepm-1;k++){
3609: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3610: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3611: for(ij=1;ij<=nlstate*nlstate;ij++)
3612: for(ji=1;ji<=nlstate*nlstate;ji++)
3613: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3614: }
3615: }
3616:
3617: /* Computing expectancies */
3618: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3619: for(i=1; i<=nlstate;i++)
3620: for(j=1; j<=nlstate;j++)
3621: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3622: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3623:
3624: /* 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]);*/
3625:
3626: }
3627:
3628: fprintf(ficresstdeij,"%3.0f",age );
3629: for(i=1; i<=nlstate;i++){
3630: eip=0.;
3631: vip=0.;
3632: for(j=1; j<=nlstate;j++){
3633: eip += eij[i][j][(int)age];
3634: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3635: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3636: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3637: }
3638: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3639: }
3640: fprintf(ficresstdeij,"\n");
3641:
3642: fprintf(ficrescveij,"%3.0f",age );
3643: for(i=1; i<=nlstate;i++)
3644: for(j=1; j<=nlstate;j++){
3645: cptj= (j-1)*nlstate+i;
3646: for(i2=1; i2<=nlstate;i2++)
3647: for(j2=1; j2<=nlstate;j2++){
3648: cptj2= (j2-1)*nlstate+i2;
3649: if(cptj2 <= cptj)
3650: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3651: }
3652: }
3653: fprintf(ficrescveij,"\n");
3654:
3655: }
3656: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3657: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3658: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3659: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3660: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3661: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3662: printf("\n");
3663: fprintf(ficlog,"\n");
3664:
3665: free_vector(xm,1,npar);
3666: free_vector(xp,1,npar);
3667: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3668: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3669: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3670: }
3671:
3672: /************ Variance ******************/
3673: 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[])
3674: {
3675: /* Variance of health expectancies */
3676: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3677: /* double **newm;*/
3678: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3679:
3680: int movingaverage();
3681: double **dnewm,**doldm;
3682: double **dnewmp,**doldmp;
3683: int i, j, nhstepm, hstepm, h, nstepm ;
3684: int k;
3685: double *xp;
3686: double **gp, **gm; /* for var eij */
3687: double ***gradg, ***trgradg; /*for var eij */
3688: double **gradgp, **trgradgp; /* for var p point j */
3689: double *gpp, *gmp; /* for var p point j */
3690: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3691: double ***p3mat;
3692: double age,agelim, hf;
3693: double ***mobaverage;
3694: int theta;
3695: char digit[4];
3696: char digitp[25];
3697:
3698: char fileresprobmorprev[FILENAMELENGTH];
3699:
3700: if(popbased==1){
3701: if(mobilav!=0)
3702: strcpy(digitp,"-populbased-mobilav-");
3703: else strcpy(digitp,"-populbased-nomobil-");
3704: }
3705: else
3706: strcpy(digitp,"-stablbased-");
3707:
3708: if (mobilav!=0) {
3709: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3710: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3711: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3712: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3713: }
3714: }
3715:
3716: strcpy(fileresprobmorprev,"prmorprev");
3717: sprintf(digit,"%-d",ij);
3718: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3719: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3720: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3721: strcat(fileresprobmorprev,fileres);
3722: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3723: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3724: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3725: }
3726: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3727:
3728: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3729: pstamp(ficresprobmorprev);
3730: 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);
3731: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3732: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3733: fprintf(ficresprobmorprev," p.%-d SE",j);
3734: for(i=1; i<=nlstate;i++)
3735: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3736: }
3737: fprintf(ficresprobmorprev,"\n");
3738: fprintf(ficgp,"\n# Routine varevsij");
3739: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3740: 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");
3741: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3742: /* } */
3743: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3744: pstamp(ficresvij);
3745: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3746: if(popbased==1)
3747: 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);
3748: else
3749: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3750: fprintf(ficresvij,"# Age");
3751: for(i=1; i<=nlstate;i++)
3752: for(j=1; j<=nlstate;j++)
3753: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3754: fprintf(ficresvij,"\n");
3755:
3756: xp=vector(1,npar);
3757: dnewm=matrix(1,nlstate,1,npar);
3758: doldm=matrix(1,nlstate,1,nlstate);
3759: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3760: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3761:
3762: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3763: gpp=vector(nlstate+1,nlstate+ndeath);
3764: gmp=vector(nlstate+1,nlstate+ndeath);
3765: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3766:
3767: if(estepm < stepm){
3768: printf ("Problem %d lower than %d\n",estepm, stepm);
3769: }
3770: else hstepm=estepm;
3771: /* For example we decided to compute the life expectancy with the smallest unit */
3772: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3773: nhstepm is the number of hstepm from age to agelim
3774: nstepm is the number of stepm from age to agelin.
3775: Look at function hpijx to understand why (it is linked to memory size questions) */
3776: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3777: survival function given by stepm (the optimization length). Unfortunately it
3778: means that if the survival funtion is printed every two years of age and if
3779: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3780: results. So we changed our mind and took the option of the best precision.
3781: */
3782: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3783: agelim = AGESUP;
3784: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3785: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3786: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3787: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3788: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3789: gp=matrix(0,nhstepm,1,nlstate);
3790: gm=matrix(0,nhstepm,1,nlstate);
3791:
3792:
3793: for(theta=1; theta <=npar; theta++){
3794: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3795: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3796: }
3797: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3798: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3799:
3800: if (popbased==1) {
3801: if(mobilav ==0){
3802: for(i=1; i<=nlstate;i++)
3803: prlim[i][i]=probs[(int)age][i][ij];
3804: }else{ /* mobilav */
3805: for(i=1; i<=nlstate;i++)
3806: prlim[i][i]=mobaverage[(int)age][i][ij];
3807: }
3808: }
3809:
3810: for(j=1; j<= nlstate; j++){
3811: for(h=0; h<=nhstepm; h++){
3812: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3813: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3814: }
3815: }
3816: /* This for computing probability of death (h=1 means
3817: computed over hstepm matrices product = hstepm*stepm months)
3818: as a weighted average of prlim.
3819: */
3820: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3821: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3822: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3823: }
3824: /* end probability of death */
3825:
3826: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3827: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3828: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3829: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3830:
3831: if (popbased==1) {
3832: if(mobilav ==0){
3833: for(i=1; i<=nlstate;i++)
3834: prlim[i][i]=probs[(int)age][i][ij];
3835: }else{ /* mobilav */
3836: for(i=1; i<=nlstate;i++)
3837: prlim[i][i]=mobaverage[(int)age][i][ij];
3838: }
3839: }
3840:
3841: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3842: for(h=0; h<=nhstepm; h++){
3843: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3844: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3845: }
3846: }
3847: /* This for computing probability of death (h=1 means
3848: computed over hstepm matrices product = hstepm*stepm months)
3849: as a weighted average of prlim.
3850: */
3851: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3852: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3853: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3854: }
3855: /* end probability of death */
3856:
3857: for(j=1; j<= nlstate; j++) /* vareij */
3858: for(h=0; h<=nhstepm; h++){
3859: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3860: }
3861:
3862: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3863: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3864: }
3865:
3866: } /* End theta */
3867:
3868: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3869:
3870: for(h=0; h<=nhstepm; h++) /* veij */
3871: for(j=1; j<=nlstate;j++)
3872: for(theta=1; theta <=npar; theta++)
3873: trgradg[h][j][theta]=gradg[h][theta][j];
3874:
3875: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3876: for(theta=1; theta <=npar; theta++)
3877: trgradgp[j][theta]=gradgp[theta][j];
3878:
3879:
3880: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3881: for(i=1;i<=nlstate;i++)
3882: for(j=1;j<=nlstate;j++)
3883: vareij[i][j][(int)age] =0.;
3884:
3885: for(h=0;h<=nhstepm;h++){
3886: for(k=0;k<=nhstepm;k++){
3887: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3888: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3889: for(i=1;i<=nlstate;i++)
3890: for(j=1;j<=nlstate;j++)
3891: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3892: }
3893: }
3894:
3895: /* pptj */
3896: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3897: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3898: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3899: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3900: varppt[j][i]=doldmp[j][i];
3901: /* end ppptj */
3902: /* x centered again */
3903: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3904: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3905:
3906: if (popbased==1) {
3907: if(mobilav ==0){
3908: for(i=1; i<=nlstate;i++)
3909: prlim[i][i]=probs[(int)age][i][ij];
3910: }else{ /* mobilav */
3911: for(i=1; i<=nlstate;i++)
3912: prlim[i][i]=mobaverage[(int)age][i][ij];
3913: }
3914: }
3915:
3916: /* This for computing probability of death (h=1 means
3917: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3918: as a weighted average of prlim.
3919: */
3920: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3921: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3922: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3923: }
3924: /* end probability of death */
3925:
3926: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3927: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3928: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3929: for(i=1; i<=nlstate;i++){
3930: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3931: }
3932: }
3933: fprintf(ficresprobmorprev,"\n");
3934:
3935: fprintf(ficresvij,"%.0f ",age );
3936: for(i=1; i<=nlstate;i++)
3937: for(j=1; j<=nlstate;j++){
3938: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3939: }
3940: fprintf(ficresvij,"\n");
3941: free_matrix(gp,0,nhstepm,1,nlstate);
3942: free_matrix(gm,0,nhstepm,1,nlstate);
3943: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3944: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3945: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3946: } /* End age */
3947: free_vector(gpp,nlstate+1,nlstate+ndeath);
3948: free_vector(gmp,nlstate+1,nlstate+ndeath);
3949: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3950: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3951: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3952: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3953: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3954: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3955: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3956: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3957: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3958: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3959: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3960: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3961: 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);
3962: /* 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);
3963: */
3964: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3965: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3966:
3967: free_vector(xp,1,npar);
3968: free_matrix(doldm,1,nlstate,1,nlstate);
3969: free_matrix(dnewm,1,nlstate,1,npar);
3970: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3971: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3972: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3973: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3974: fclose(ficresprobmorprev);
3975: fflush(ficgp);
3976: fflush(fichtm);
3977: } /* end varevsij */
3978:
3979: /************ Variance of prevlim ******************/
3980: 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[])
3981: {
3982: /* Variance of prevalence limit */
3983: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3984:
3985: double **dnewm,**doldm;
3986: int i, j, nhstepm, hstepm;
3987: double *xp;
3988: double *gp, *gm;
3989: double **gradg, **trgradg;
3990: double age,agelim;
3991: int theta;
3992:
3993: pstamp(ficresvpl);
3994: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3995: fprintf(ficresvpl,"# Age");
3996: for(i=1; i<=nlstate;i++)
3997: fprintf(ficresvpl," %1d-%1d",i,i);
3998: fprintf(ficresvpl,"\n");
3999:
4000: xp=vector(1,npar);
4001: dnewm=matrix(1,nlstate,1,npar);
4002: doldm=matrix(1,nlstate,1,nlstate);
4003:
4004: hstepm=1*YEARM; /* Every year of age */
4005: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4006: agelim = AGESUP;
4007: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4008: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4009: if (stepm >= YEARM) hstepm=1;
4010: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4011: gradg=matrix(1,npar,1,nlstate);
4012: gp=vector(1,nlstate);
4013: gm=vector(1,nlstate);
4014:
4015: for(theta=1; theta <=npar; theta++){
4016: for(i=1; i<=npar; i++){ /* Computes gradient */
4017: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4018: }
4019: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4020: for(i=1;i<=nlstate;i++)
4021: gp[i] = prlim[i][i];
4022:
4023: for(i=1; i<=npar; i++) /* Computes gradient */
4024: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4025: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4026: for(i=1;i<=nlstate;i++)
4027: gm[i] = prlim[i][i];
4028:
4029: for(i=1;i<=nlstate;i++)
4030: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4031: } /* End theta */
4032:
4033: trgradg =matrix(1,nlstate,1,npar);
4034:
4035: for(j=1; j<=nlstate;j++)
4036: for(theta=1; theta <=npar; theta++)
4037: trgradg[j][theta]=gradg[theta][j];
4038:
4039: for(i=1;i<=nlstate;i++)
4040: varpl[i][(int)age] =0.;
4041: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4042: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4043: for(i=1;i<=nlstate;i++)
4044: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4045:
4046: fprintf(ficresvpl,"%.0f ",age );
4047: for(i=1; i<=nlstate;i++)
4048: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4049: fprintf(ficresvpl,"\n");
4050: free_vector(gp,1,nlstate);
4051: free_vector(gm,1,nlstate);
4052: free_matrix(gradg,1,npar,1,nlstate);
4053: free_matrix(trgradg,1,nlstate,1,npar);
4054: } /* End age */
4055:
4056: free_vector(xp,1,npar);
4057: free_matrix(doldm,1,nlstate,1,npar);
4058: free_matrix(dnewm,1,nlstate,1,nlstate);
4059:
4060: }
4061:
4062: /************ Variance of one-step probabilities ******************/
4063: 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[])
4064: {
4065: int i, j=0, k1, l1, tj;
4066: int k2, l2, j1, z1;
4067: int k=0, l;
4068: int first=1, first1, first2;
4069: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4070: double **dnewm,**doldm;
4071: double *xp;
4072: double *gp, *gm;
4073: double **gradg, **trgradg;
4074: double **mu;
4075: double age, cov[NCOVMAX+1];
4076: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4077: int theta;
4078: char fileresprob[FILENAMELENGTH];
4079: char fileresprobcov[FILENAMELENGTH];
4080: char fileresprobcor[FILENAMELENGTH];
4081: double ***varpij;
4082:
4083: strcpy(fileresprob,"prob");
4084: strcat(fileresprob,fileres);
4085: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4086: printf("Problem with resultfile: %s\n", fileresprob);
4087: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4088: }
4089: strcpy(fileresprobcov,"probcov");
4090: strcat(fileresprobcov,fileres);
4091: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4092: printf("Problem with resultfile: %s\n", fileresprobcov);
4093: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4094: }
4095: strcpy(fileresprobcor,"probcor");
4096: strcat(fileresprobcor,fileres);
4097: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4098: printf("Problem with resultfile: %s\n", fileresprobcor);
4099: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4100: }
4101: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4102: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4103: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4104: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4105: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4106: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4107: pstamp(ficresprob);
4108: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4109: fprintf(ficresprob,"# Age");
4110: pstamp(ficresprobcov);
4111: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4112: fprintf(ficresprobcov,"# Age");
4113: pstamp(ficresprobcor);
4114: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4115: fprintf(ficresprobcor,"# Age");
4116:
4117:
4118: for(i=1; i<=nlstate;i++)
4119: for(j=1; j<=(nlstate+ndeath);j++){
4120: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4121: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4122: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4123: }
4124: /* fprintf(ficresprob,"\n");
4125: fprintf(ficresprobcov,"\n");
4126: fprintf(ficresprobcor,"\n");
4127: */
4128: xp=vector(1,npar);
4129: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4130: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4131: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4132: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4133: first=1;
4134: fprintf(ficgp,"\n# Routine varprob");
4135: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4136: fprintf(fichtm,"\n");
4137:
4138: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4139: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4140: file %s<br>\n",optionfilehtmcov);
4141: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4142: and drawn. It helps understanding how is the covariance between two incidences.\
4143: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4144: 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. \
4145: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4146: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4147: standard deviations wide on each axis. <br>\
4148: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4149: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4150: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4151:
4152: cov[1]=1;
4153: /* tj=cptcoveff; */
4154: tj = (int) pow(2,cptcoveff);
4155: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4156: j1=0;
4157: for(j1=1; j1<=tj;j1++){
4158: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4159: /*j1++;*/
4160: if (cptcovn>0) {
4161: fprintf(ficresprob, "\n#********** Variable ");
4162: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4163: fprintf(ficresprob, "**********\n#\n");
4164: fprintf(ficresprobcov, "\n#********** Variable ");
4165: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4166: fprintf(ficresprobcov, "**********\n#\n");
4167:
4168: fprintf(ficgp, "\n#********** Variable ");
4169: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4170: fprintf(ficgp, "**********\n#\n");
4171:
4172:
4173: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4174: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4175: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4176:
4177: fprintf(ficresprobcor, "\n#********** Variable ");
4178: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4179: fprintf(ficresprobcor, "**********\n#");
4180: }
4181:
4182: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4183: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4184: gp=vector(1,(nlstate)*(nlstate+ndeath));
4185: gm=vector(1,(nlstate)*(nlstate+ndeath));
4186: for (age=bage; age<=fage; age ++){
4187: cov[2]=age;
4188: if(nagesqr==1)
4189: cov[3]= age*age;
4190: for (k=1; k<=cptcovn;k++) {
4191: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4192: * 1 1 1 1 1
4193: * 2 2 1 1 1
4194: * 3 1 2 1 1
4195: */
4196: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
4197: }
4198: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4199: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
4200: for (k=1; k<=cptcovprod;k++)
4201: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4202:
4203:
4204: for(theta=1; theta <=npar; theta++){
4205: for(i=1; i<=npar; i++)
4206: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4207:
4208: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4209:
4210: k=0;
4211: for(i=1; i<= (nlstate); i++){
4212: for(j=1; j<=(nlstate+ndeath);j++){
4213: k=k+1;
4214: gp[k]=pmmij[i][j];
4215: }
4216: }
4217:
4218: for(i=1; i<=npar; i++)
4219: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4220:
4221: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4222: k=0;
4223: for(i=1; i<=(nlstate); i++){
4224: for(j=1; j<=(nlstate+ndeath);j++){
4225: k=k+1;
4226: gm[k]=pmmij[i][j];
4227: }
4228: }
4229:
4230: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4231: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4232: }
4233:
4234: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4235: for(theta=1; theta <=npar; theta++)
4236: trgradg[j][theta]=gradg[theta][j];
4237:
4238: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4239: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4240:
4241: pmij(pmmij,cov,ncovmodel,x,nlstate);
4242:
4243: k=0;
4244: for(i=1; i<=(nlstate); i++){
4245: for(j=1; j<=(nlstate+ndeath);j++){
4246: k=k+1;
4247: mu[k][(int) age]=pmmij[i][j];
4248: }
4249: }
4250: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4251: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4252: varpij[i][j][(int)age] = doldm[i][j];
4253:
4254: /*printf("\n%d ",(int)age);
4255: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4256: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4257: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4258: }*/
4259:
4260: fprintf(ficresprob,"\n%d ",(int)age);
4261: fprintf(ficresprobcov,"\n%d ",(int)age);
4262: fprintf(ficresprobcor,"\n%d ",(int)age);
4263:
4264: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4265: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4266: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4267: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4268: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4269: }
4270: i=0;
4271: for (k=1; k<=(nlstate);k++){
4272: for (l=1; l<=(nlstate+ndeath);l++){
4273: i++;
4274: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4275: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4276: for (j=1; j<=i;j++){
4277: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
4278: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4279: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4280: }
4281: }
4282: }/* end of loop for state */
4283: } /* end of loop for age */
4284: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4285: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4286: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4287: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4288:
4289: /* Confidence intervalle of pij */
4290: /*
4291: fprintf(ficgp,"\nunset parametric;unset label");
4292: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4293: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4294: 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);
4295: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4296: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4297: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4298: */
4299:
4300: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4301: first1=1;first2=2;
4302: for (k2=1; k2<=(nlstate);k2++){
4303: for (l2=1; l2<=(nlstate+ndeath);l2++){
4304: if(l2==k2) continue;
4305: j=(k2-1)*(nlstate+ndeath)+l2;
4306: for (k1=1; k1<=(nlstate);k1++){
4307: for (l1=1; l1<=(nlstate+ndeath);l1++){
4308: if(l1==k1) continue;
4309: i=(k1-1)*(nlstate+ndeath)+l1;
4310: if(i<=j) continue;
4311: for (age=bage; age<=fage; age ++){
4312: if ((int)age %5==0){
4313: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4314: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4315: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4316: mu1=mu[i][(int) age]/stepm*YEARM ;
4317: mu2=mu[j][(int) age]/stepm*YEARM;
4318: c12=cv12/sqrt(v1*v2);
4319: /* Computing eigen value of matrix of covariance */
4320: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4321: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4322: if ((lc2 <0) || (lc1 <0) ){
4323: if(first2==1){
4324: first1=0;
4325: 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);
4326: }
4327: 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);
4328: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4329: /* lc2=fabs(lc2); */
4330: }
4331:
4332: /* Eigen vectors */
4333: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4334: /*v21=sqrt(1.-v11*v11); *//* error */
4335: v21=(lc1-v1)/cv12*v11;
4336: v12=-v21;
4337: v22=v11;
4338: tnalp=v21/v11;
4339: if(first1==1){
4340: first1=0;
4341: 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);
4342: }
4343: 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);
4344: /*printf(fignu*/
4345: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4346: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4347: if(first==1){
4348: first=0;
4349: fprintf(ficgp,"\nset parametric;unset label");
4350: 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);
4351: fprintf(ficgp,"\nset ter png small size 320, 240");
4352: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4353: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4354: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4355: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4356: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4357: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4358: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4359: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4360: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4361: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4362: 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",\
4363: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4364: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4365: }else{
4366: first=0;
4367: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4368: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4369: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4370: 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",\
4371: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4372: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4373: }/* if first */
4374: } /* age mod 5 */
4375: } /* end loop age */
4376: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4377: first=1;
4378: } /*l12 */
4379: } /* k12 */
4380: } /*l1 */
4381: }/* k1 */
4382: /* } */ /* loop covariates */
4383: }
4384: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4385: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4386: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4387: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4388: free_vector(xp,1,npar);
4389: fclose(ficresprob);
4390: fclose(ficresprobcov);
4391: fclose(ficresprobcor);
4392: fflush(ficgp);
4393: fflush(fichtmcov);
4394: }
4395:
4396:
4397: /******************* Printing html file ***********/
4398: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4399: int lastpass, int stepm, int weightopt, char model[],\
4400: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4401: int popforecast, int estepm ,\
4402: double jprev1, double mprev1,double anprev1, \
4403: double jprev2, double mprev2,double anprev2){
4404: int jj1, k1, i1, cpt;
4405:
4406: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4407: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4408: </ul>");
4409: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4410: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4411: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4412: fprintf(fichtm,"\
4413: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4414: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4415: fprintf(fichtm,"\
4416: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4417: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4418: fprintf(fichtm,"\
4419: - (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): \
4420: <a href=\"%s\">%s</a> <br>\n",
4421: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4422: fprintf(fichtm,"\
4423: - Population projections by age and states: \
4424: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4425:
4426: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4427:
4428: m=pow(2,cptcoveff);
4429: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4430:
4431: jj1=0;
4432: for(k1=1; k1<=m;k1++){
4433: for(i1=1; i1<=ncodemax[k1];i1++){
4434: jj1++;
4435: if (cptcovn > 0) {
4436: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4437: for (cpt=1; cpt<=cptcoveff;cpt++)
4438: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4439: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4440: }
4441: /* Pij */
4442: 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> \
4443: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4444: /* Quasi-incidences */
4445: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4446: 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> \
4447: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4448: /* Period (stable) prevalence in each health state */
4449: for(cpt=1; cpt<=nlstate;cpt++){
4450: 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> \
4451: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4452: }
4453: for(cpt=1; cpt<=nlstate;cpt++) {
4454: 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> \
4455: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4456: }
4457: } /* end i1 */
4458: }/* End k1 */
4459: fprintf(fichtm,"</ul>");
4460:
4461:
4462: fprintf(fichtm,"\
4463: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4464: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4465:
4466: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4467: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4468: fprintf(fichtm,"\
4469: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4470: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4471:
4472: fprintf(fichtm,"\
4473: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4474: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4475: fprintf(fichtm,"\
4476: - 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): \
4477: <a href=\"%s\">%s</a> <br>\n</li>",
4478: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4479: fprintf(fichtm,"\
4480: - (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): \
4481: <a href=\"%s\">%s</a> <br>\n</li>",
4482: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4483: fprintf(fichtm,"\
4484: - 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",
4485: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4486: fprintf(fichtm,"\
4487: - 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",
4488: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4489: fprintf(fichtm,"\
4490: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4491: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4492:
4493: /* if(popforecast==1) fprintf(fichtm,"\n */
4494: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4495: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4496: /* <br>",fileres,fileres,fileres,fileres); */
4497: /* else */
4498: /* 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); */
4499: fflush(fichtm);
4500: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4501:
4502: m=pow(2,cptcoveff);
4503: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4504:
4505: jj1=0;
4506: for(k1=1; k1<=m;k1++){
4507: for(i1=1; i1<=ncodemax[k1];i1++){
4508: jj1++;
4509: if (cptcovn > 0) {
4510: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4511: for (cpt=1; cpt<=cptcoveff;cpt++)
4512: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4513: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4514: }
4515: for(cpt=1; cpt<=nlstate;cpt++) {
4516: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4517: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4518: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4519: }
4520: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4521: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4522: true period expectancies (those weighted with period prevalences are also\
4523: drawn in addition to the population based expectancies computed using\
4524: observed and cahotic prevalences: %s%d.png<br>\
4525: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4526: } /* end i1 */
4527: }/* End k1 */
4528: fprintf(fichtm,"</ul>");
4529: fflush(fichtm);
4530: }
4531:
4532: /******************* Gnuplot file **************/
4533: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4534:
4535: char dirfileres[132],optfileres[132];
4536: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4537: int ng=0;
4538: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4539: /* printf("Problem with file %s",optionfilegnuplot); */
4540: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4541: /* } */
4542:
4543: /*#ifdef windows */
4544: fprintf(ficgp,"cd \"%s\" \n",pathc);
4545: /*#endif */
4546: m=pow(2,cptcoveff);
4547:
4548: strcpy(dirfileres,optionfilefiname);
4549: strcpy(optfileres,"vpl");
4550: /* 1eme*/
4551: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4552: for (cpt=1; cpt<= nlstate ; cpt ++) {
4553: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4554: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4555: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4556: fprintf(ficgp,"set xlabel \"Age\" \n\
4557: set ylabel \"Probability\" \n\
4558: set ter png small size 320, 240\n\
4559: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4560:
4561: for (i=1; i<= nlstate ; i ++) {
4562: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4563: else fprintf(ficgp," %%*lf (%%*lf)");
4564: }
4565: 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);
4566: for (i=1; i<= nlstate ; i ++) {
4567: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4568: else fprintf(ficgp," %%*lf (%%*lf)");
4569: }
4570: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4571: for (i=1; i<= nlstate ; i ++) {
4572: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4573: else fprintf(ficgp," %%*lf (%%*lf)");
4574: }
4575: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4576: }
4577: }
4578: /*2 eme*/
4579: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4580: for (k1=1; k1<= m ; k1 ++) {
4581: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4582: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4583:
4584: for (i=1; i<= nlstate+1 ; i ++) {
4585: k=2*i;
4586: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4587: for (j=1; j<= nlstate+1 ; j ++) {
4588: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4589: else fprintf(ficgp," %%*lf (%%*lf)");
4590: }
4591: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4592: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4593: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4594: for (j=1; j<= nlstate+1 ; j ++) {
4595: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4596: else fprintf(ficgp," %%*lf (%%*lf)");
4597: }
4598: fprintf(ficgp,"\" t\"\" w l lt 0,");
4599: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4600: for (j=1; j<= nlstate+1 ; j ++) {
4601: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4602: else fprintf(ficgp," %%*lf (%%*lf)");
4603: }
4604: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4605: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4606: }
4607: }
4608:
4609: /*3eme*/
4610:
4611: for (k1=1; k1<= m ; k1 ++) {
4612: for (cpt=1; cpt<= nlstate ; cpt ++) {
4613: /* k=2+nlstate*(2*cpt-2); */
4614: k=2+(nlstate+1)*(cpt-1);
4615: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4616: fprintf(ficgp,"set ter png small size 320, 240\n\
4617: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4618: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4619: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4620: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4621: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4622: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4623: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4624:
4625: */
4626: for (i=1; i< nlstate ; i ++) {
4627: 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);
4628: /* 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);*/
4629:
4630: }
4631: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4632: }
4633: }
4634:
4635: /* CV preval stable (period) */
4636: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4637: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4638: k=3;
4639: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4640: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4641: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4642: set ter png small size 320, 240\n\
4643: unset log y\n\
4644: plot [%.f:%.f] ", ageminpar, agemaxpar);
4645: for (i=1; i<= nlstate ; i ++){
4646: if(i==1)
4647: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4648: else
4649: fprintf(ficgp,", '' ");
4650: l=(nlstate+ndeath)*(i-1)+1;
4651: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4652: for (j=1; j<= (nlstate-1) ; j ++)
4653: fprintf(ficgp,"+$%d",k+l+j);
4654: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4655: } /* nlstate */
4656: fprintf(ficgp,"\n");
4657: } /* end cpt state*/
4658: } /* end covariate */
4659:
4660: /* proba elementaires */
4661: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
4662: for(i=1,jk=1; i <=nlstate; i++){
4663: fprintf(ficgp,"# initial state %d\n",i);
4664: for(k=1; k <=(nlstate+ndeath); k++){
4665: if (k != i) {
4666: fprintf(ficgp,"# current state %d\n",k);
4667: for(j=1; j <=ncovmodel; j++){
4668: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
4669: jk++;
4670: }
4671: fprintf(ficgp,"\n");
4672: }
4673: }
4674: }
4675: fprintf(ficgp,"##############\n#\n");
4676:
4677: /*goto avoid;*/
4678: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4679: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4680: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4681: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4682: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4683: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4684: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4685: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4686: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4687: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4688: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4689: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4690: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4691: fprintf(ficgp,"#\n");
4692: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4693: fprintf(ficgp,"# ng=%d\n",ng);
4694: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
4695: for(jk=1; jk <=m; jk++) {
4696: fprintf(ficgp,"# jk=%d\n",jk);
4697: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4698: if (ng==2)
4699: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4700: else
4701: fprintf(ficgp,"\nset title \"Probability\"\n");
4702: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4703: i=1;
4704: for(k2=1; k2<=nlstate; k2++) {
4705: k3=i;
4706: for(k=1; k<=(nlstate+ndeath); k++) {
4707: if (k != k2){
4708: if(ng==2)
4709: if(nagesqr==0)
4710: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4711: else /* nagesqr =1 */
4712: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
4713: else
4714: if(nagesqr==0)
4715: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4716: else /* nagesqr =1 */
4717: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
4718: ij=1;/* To be checked else nbcode[0][0] wrong */
4719: for(j=3; j <=ncovmodel-nagesqr; j++) {
4720: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
4721: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4722: ij++;
4723: }
4724: else
4725: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4726: }
4727: fprintf(ficgp,")/(1");
4728:
4729: for(k1=1; k1 <=nlstate; k1++){
4730: if(nagesqr==0)
4731: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4732: else /* nagesqr =1 */
4733: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
4734:
4735: ij=1;
4736: for(j=3; j <=ncovmodel-nagesqr; j++){
4737: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
4738: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4739: ij++;
4740: }
4741: else
4742: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4743: }
4744: fprintf(ficgp,")");
4745: }
4746: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4747: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4748: i=i+ncovmodel;
4749: }
4750: } /* end k */
4751: } /* end k2 */
4752: } /* end jk */
4753: } /* end ng */
4754: /* avoid: */
4755: fflush(ficgp);
4756: } /* end gnuplot */
4757:
4758:
4759: /*************** Moving average **************/
4760: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4761:
4762: int i, cpt, cptcod;
4763: int modcovmax =1;
4764: int mobilavrange, mob;
4765: double age;
4766:
4767: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4768: a covariate has 2 modalities */
4769: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4770:
4771: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4772: if(mobilav==1) mobilavrange=5; /* default */
4773: else mobilavrange=mobilav;
4774: for (age=bage; age<=fage; age++)
4775: for (i=1; i<=nlstate;i++)
4776: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4777: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4778: /* We keep the original values on the extreme ages bage, fage and for
4779: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4780: we use a 5 terms etc. until the borders are no more concerned.
4781: */
4782: for (mob=3;mob <=mobilavrange;mob=mob+2){
4783: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4784: for (i=1; i<=nlstate;i++){
4785: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4786: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4787: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4788: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4789: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4790: }
4791: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4792: }
4793: }
4794: }/* end age */
4795: }/* end mob */
4796: }else return -1;
4797: return 0;
4798: }/* End movingaverage */
4799:
4800:
4801: /************** Forecasting ******************/
4802: 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){
4803: /* proj1, year, month, day of starting projection
4804: agemin, agemax range of age
4805: dateprev1 dateprev2 range of dates during which prevalence is computed
4806: anproj2 year of en of projection (same day and month as proj1).
4807: */
4808: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4809: double agec; /* generic age */
4810: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4811: double *popeffectif,*popcount;
4812: double ***p3mat;
4813: double ***mobaverage;
4814: char fileresf[FILENAMELENGTH];
4815:
4816: agelim=AGESUP;
4817: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4818:
4819: strcpy(fileresf,"f");
4820: strcat(fileresf,fileres);
4821: if((ficresf=fopen(fileresf,"w"))==NULL) {
4822: printf("Problem with forecast resultfile: %s\n", fileresf);
4823: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4824: }
4825: printf("Computing forecasting: result on file '%s' \n", fileresf);
4826: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4827:
4828: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4829:
4830: if (mobilav!=0) {
4831: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4832: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4833: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4834: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4835: }
4836: }
4837:
4838: stepsize=(int) (stepm+YEARM-1)/YEARM;
4839: if (stepm<=12) stepsize=1;
4840: if(estepm < stepm){
4841: printf ("Problem %d lower than %d\n",estepm, stepm);
4842: }
4843: else hstepm=estepm;
4844:
4845: hstepm=hstepm/stepm;
4846: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4847: fractional in yp1 */
4848: anprojmean=yp;
4849: yp2=modf((yp1*12),&yp);
4850: mprojmean=yp;
4851: yp1=modf((yp2*30.5),&yp);
4852: jprojmean=yp;
4853: if(jprojmean==0) jprojmean=1;
4854: if(mprojmean==0) jprojmean=1;
4855:
4856: i1=cptcoveff;
4857: if (cptcovn < 1){i1=1;}
4858:
4859: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4860:
4861: fprintf(ficresf,"#****** Routine prevforecast **\n");
4862:
4863: /* if (h==(int)(YEARM*yearp)){ */
4864: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4865: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4866: k=k+1;
4867: fprintf(ficresf,"\n#******");
4868: for(j=1;j<=cptcoveff;j++) {
4869: 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]]);
4870: }
4871: fprintf(ficresf,"******\n");
4872: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4873: for(j=1; j<=nlstate+ndeath;j++){
4874: for(i=1; i<=nlstate;i++)
4875: fprintf(ficresf," p%d%d",i,j);
4876: fprintf(ficresf," p.%d",j);
4877: }
4878: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4879: fprintf(ficresf,"\n");
4880: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4881:
4882: for (agec=fage; agec>=(ageminpar-1); agec--){
4883: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4884: nhstepm = nhstepm/hstepm;
4885: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4886: oldm=oldms;savm=savms;
4887: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4888:
4889: for (h=0; h<=nhstepm; h++){
4890: if (h*hstepm/YEARM*stepm ==yearp) {
4891: fprintf(ficresf,"\n");
4892: for(j=1;j<=cptcoveff;j++)
4893: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4894: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4895: }
4896: for(j=1; j<=nlstate+ndeath;j++) {
4897: ppij=0.;
4898: for(i=1; i<=nlstate;i++) {
4899: if (mobilav==1)
4900: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4901: else {
4902: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4903: }
4904: if (h*hstepm/YEARM*stepm== yearp) {
4905: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4906: }
4907: } /* end i */
4908: if (h*hstepm/YEARM*stepm==yearp) {
4909: fprintf(ficresf," %.3f", ppij);
4910: }
4911: }/* end j */
4912: } /* end h */
4913: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4914: } /* end agec */
4915: } /* end yearp */
4916: } /* end cptcod */
4917: } /* end cptcov */
4918:
4919: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4920:
4921: fclose(ficresf);
4922: }
4923:
4924: /************** Forecasting *****not tested NB*************/
4925: 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){
4926:
4927: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4928: int *popage;
4929: double calagedatem, agelim, kk1, kk2;
4930: double *popeffectif,*popcount;
4931: double ***p3mat,***tabpop,***tabpopprev;
4932: double ***mobaverage;
4933: char filerespop[FILENAMELENGTH];
4934:
4935: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4936: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4937: agelim=AGESUP;
4938: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4939:
4940: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4941:
4942:
4943: strcpy(filerespop,"pop");
4944: strcat(filerespop,fileres);
4945: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4946: printf("Problem with forecast resultfile: %s\n", filerespop);
4947: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4948: }
4949: printf("Computing forecasting: result on file '%s' \n", filerespop);
4950: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4951:
4952: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4953:
4954: if (mobilav!=0) {
4955: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4956: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4957: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4958: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4959: }
4960: }
4961:
4962: stepsize=(int) (stepm+YEARM-1)/YEARM;
4963: if (stepm<=12) stepsize=1;
4964:
4965: agelim=AGESUP;
4966:
4967: hstepm=1;
4968: hstepm=hstepm/stepm;
4969:
4970: if (popforecast==1) {
4971: if((ficpop=fopen(popfile,"r"))==NULL) {
4972: printf("Problem with population file : %s\n",popfile);exit(0);
4973: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4974: }
4975: popage=ivector(0,AGESUP);
4976: popeffectif=vector(0,AGESUP);
4977: popcount=vector(0,AGESUP);
4978:
4979: i=1;
4980: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4981:
4982: imx=i;
4983: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4984: }
4985:
4986: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4987: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4988: k=k+1;
4989: fprintf(ficrespop,"\n#******");
4990: for(j=1;j<=cptcoveff;j++) {
4991: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4992: }
4993: fprintf(ficrespop,"******\n");
4994: fprintf(ficrespop,"# Age");
4995: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4996: if (popforecast==1) fprintf(ficrespop," [Population]");
4997:
4998: for (cpt=0; cpt<=0;cpt++) {
4999: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5000:
5001: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5002: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5003: nhstepm = nhstepm/hstepm;
5004:
5005: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5006: oldm=oldms;savm=savms;
5007: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5008:
5009: for (h=0; h<=nhstepm; h++){
5010: if (h==(int) (calagedatem+YEARM*cpt)) {
5011: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5012: }
5013: for(j=1; j<=nlstate+ndeath;j++) {
5014: kk1=0.;kk2=0;
5015: for(i=1; i<=nlstate;i++) {
5016: if (mobilav==1)
5017: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5018: else {
5019: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5020: }
5021: }
5022: if (h==(int)(calagedatem+12*cpt)){
5023: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5024: /*fprintf(ficrespop," %.3f", kk1);
5025: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5026: }
5027: }
5028: for(i=1; i<=nlstate;i++){
5029: kk1=0.;
5030: for(j=1; j<=nlstate;j++){
5031: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5032: }
5033: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5034: }
5035:
5036: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5037: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5038: }
5039: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5040: }
5041: }
5042:
5043: /******/
5044:
5045: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5046: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5047: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5048: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5049: nhstepm = nhstepm/hstepm;
5050:
5051: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5052: oldm=oldms;savm=savms;
5053: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5054: for (h=0; h<=nhstepm; h++){
5055: if (h==(int) (calagedatem+YEARM*cpt)) {
5056: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5057: }
5058: for(j=1; j<=nlstate+ndeath;j++) {
5059: kk1=0.;kk2=0;
5060: for(i=1; i<=nlstate;i++) {
5061: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5062: }
5063: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5064: }
5065: }
5066: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5067: }
5068: }
5069: }
5070: }
5071:
5072: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5073:
5074: if (popforecast==1) {
5075: free_ivector(popage,0,AGESUP);
5076: free_vector(popeffectif,0,AGESUP);
5077: free_vector(popcount,0,AGESUP);
5078: }
5079: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5080: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5081: fclose(ficrespop);
5082: } /* End of popforecast */
5083:
5084: int fileappend(FILE *fichier, char *optionfich)
5085: {
5086: if((fichier=fopen(optionfich,"a"))==NULL) {
5087: printf("Problem with file: %s\n", optionfich);
5088: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5089: return (0);
5090: }
5091: fflush(fichier);
5092: return (1);
5093: }
5094:
5095:
5096: /**************** function prwizard **********************/
5097: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5098: {
5099:
5100: /* Wizard to print covariance matrix template */
5101:
5102: char ca[32], cb[32];
5103: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
5104: int numlinepar;
5105:
5106: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5107: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5108: for(i=1; i <=nlstate; i++){
5109: jj=0;
5110: for(j=1; j <=nlstate+ndeath; j++){
5111: if(j==i) continue;
5112: jj++;
5113: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5114: printf("%1d%1d",i,j);
5115: fprintf(ficparo,"%1d%1d",i,j);
5116: for(k=1; k<=ncovmodel;k++){
5117: /* printf(" %lf",param[i][j][k]); */
5118: /* fprintf(ficparo," %lf",param[i][j][k]); */
5119: printf(" 0.");
5120: fprintf(ficparo," 0.");
5121: }
5122: printf("\n");
5123: fprintf(ficparo,"\n");
5124: }
5125: }
5126: printf("# Scales (for hessian or gradient estimation)\n");
5127: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5128: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5129: for(i=1; i <=nlstate; i++){
5130: jj=0;
5131: for(j=1; j <=nlstate+ndeath; j++){
5132: if(j==i) continue;
5133: jj++;
5134: fprintf(ficparo,"%1d%1d",i,j);
5135: printf("%1d%1d",i,j);
5136: fflush(stdout);
5137: for(k=1; k<=ncovmodel;k++){
5138: /* printf(" %le",delti3[i][j][k]); */
5139: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5140: printf(" 0.");
5141: fprintf(ficparo," 0.");
5142: }
5143: numlinepar++;
5144: printf("\n");
5145: fprintf(ficparo,"\n");
5146: }
5147: }
5148: printf("# Covariance matrix\n");
5149: /* # 121 Var(a12)\n\ */
5150: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5151: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5152: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5153: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5154: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5155: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5156: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5157: fflush(stdout);
5158: fprintf(ficparo,"# Covariance matrix\n");
5159: /* # 121 Var(a12)\n\ */
5160: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5161: /* # ...\n\ */
5162: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5163:
5164: for(itimes=1;itimes<=2;itimes++){
5165: jj=0;
5166: for(i=1; i <=nlstate; i++){
5167: for(j=1; j <=nlstate+ndeath; j++){
5168: if(j==i) continue;
5169: for(k=1; k<=ncovmodel;k++){
5170: jj++;
5171: ca[0]= k+'a'-1;ca[1]='\0';
5172: if(itimes==1){
5173: printf("#%1d%1d%d",i,j,k);
5174: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5175: }else{
5176: printf("%1d%1d%d",i,j,k);
5177: fprintf(ficparo,"%1d%1d%d",i,j,k);
5178: /* printf(" %.5le",matcov[i][j]); */
5179: }
5180: ll=0;
5181: for(li=1;li <=nlstate; li++){
5182: for(lj=1;lj <=nlstate+ndeath; lj++){
5183: if(lj==li) continue;
5184: for(lk=1;lk<=ncovmodel;lk++){
5185: ll++;
5186: if(ll<=jj){
5187: cb[0]= lk +'a'-1;cb[1]='\0';
5188: if(ll<jj){
5189: if(itimes==1){
5190: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5191: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5192: }else{
5193: printf(" 0.");
5194: fprintf(ficparo," 0.");
5195: }
5196: }else{
5197: if(itimes==1){
5198: printf(" Var(%s%1d%1d)",ca,i,j);
5199: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5200: }else{
5201: printf(" 0.");
5202: fprintf(ficparo," 0.");
5203: }
5204: }
5205: }
5206: } /* end lk */
5207: } /* end lj */
5208: } /* end li */
5209: printf("\n");
5210: fprintf(ficparo,"\n");
5211: numlinepar++;
5212: } /* end k*/
5213: } /*end j */
5214: } /* end i */
5215: } /* end itimes */
5216:
5217: } /* end of prwizard */
5218: /******************* Gompertz Likelihood ******************************/
5219: double gompertz(double x[])
5220: {
5221: double A,B,L=0.0,sump=0.,num=0.;
5222: int i,n=0; /* n is the size of the sample */
5223:
5224: for (i=0;i<=imx-1 ; i++) {
5225: sump=sump+weight[i];
5226: /* sump=sump+1;*/
5227: num=num+1;
5228: }
5229:
5230:
5231: /* for (i=0; i<=imx; i++)
5232: 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]);*/
5233:
5234: for (i=1;i<=imx ; i++)
5235: {
5236: if (cens[i] == 1 && wav[i]>1)
5237: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5238:
5239: if (cens[i] == 0 && wav[i]>1)
5240: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5241: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5242:
5243: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5244: if (wav[i] > 1 ) { /* ??? */
5245: L=L+A*weight[i];
5246: /* 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]);*/
5247: }
5248: }
5249:
5250: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5251:
5252: return -2*L*num/sump;
5253: }
5254:
5255: #ifdef GSL
5256: /******************* Gompertz_f Likelihood ******************************/
5257: double gompertz_f(const gsl_vector *v, void *params)
5258: {
5259: double A,B,LL=0.0,sump=0.,num=0.;
5260: double *x= (double *) v->data;
5261: int i,n=0; /* n is the size of the sample */
5262:
5263: for (i=0;i<=imx-1 ; i++) {
5264: sump=sump+weight[i];
5265: /* sump=sump+1;*/
5266: num=num+1;
5267: }
5268:
5269:
5270: /* for (i=0; i<=imx; i++)
5271: 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]);*/
5272: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5273: for (i=1;i<=imx ; i++)
5274: {
5275: if (cens[i] == 1 && wav[i]>1)
5276: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5277:
5278: if (cens[i] == 0 && wav[i]>1)
5279: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5280: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5281:
5282: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5283: if (wav[i] > 1 ) { /* ??? */
5284: LL=LL+A*weight[i];
5285: /* 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]);*/
5286: }
5287: }
5288:
5289: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5290: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5291:
5292: return -2*LL*num/sump;
5293: }
5294: #endif
5295:
5296: /******************* Printing html file ***********/
5297: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5298: int lastpass, int stepm, int weightopt, char model[],\
5299: int imx, double p[],double **matcov,double agemortsup){
5300: int i,k;
5301:
5302: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5303: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5304: for (i=1;i<=2;i++)
5305: 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]));
5306: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5307: fprintf(fichtm,"</ul>");
5308:
5309: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5310:
5311: 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>");
5312:
5313: for (k=agegomp;k<(agemortsup-2);k++)
5314: 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]);
5315:
5316:
5317: fflush(fichtm);
5318: }
5319:
5320: /******************* Gnuplot file **************/
5321: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5322:
5323: char dirfileres[132],optfileres[132];
5324:
5325: int ng;
5326:
5327:
5328: /*#ifdef windows */
5329: fprintf(ficgp,"cd \"%s\" \n",pathc);
5330: /*#endif */
5331:
5332:
5333: strcpy(dirfileres,optionfilefiname);
5334: strcpy(optfileres,"vpl");
5335: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5336: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5337: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5338: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5339: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5340:
5341: }
5342:
5343: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5344: {
5345:
5346: /*-------- data file ----------*/
5347: FILE *fic;
5348: char dummy[]=" ";
5349: int i=0, j=0, n=0;
5350: int linei, month, year,iout;
5351: char line[MAXLINE], linetmp[MAXLINE];
5352: char stra[MAXLINE], strb[MAXLINE];
5353: char *stratrunc;
5354: int lstra;
5355:
5356:
5357: if((fic=fopen(datafile,"r"))==NULL) {
5358: printf("Problem while opening datafile: %s\n", datafile);return 1;
5359: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5360: }
5361:
5362: i=1;
5363: linei=0;
5364: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5365: linei=linei+1;
5366: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5367: if(line[j] == '\t')
5368: line[j] = ' ';
5369: }
5370: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5371: ;
5372: };
5373: line[j+1]=0; /* Trims blanks at end of line */
5374: if(line[0]=='#'){
5375: fprintf(ficlog,"Comment line\n%s\n",line);
5376: printf("Comment line\n%s\n",line);
5377: continue;
5378: }
5379: trimbb(linetmp,line); /* Trims multiple blanks in line */
5380: strcpy(line, linetmp);
5381:
5382:
5383: for (j=maxwav;j>=1;j--){
5384: cutv(stra, strb, line, ' ');
5385: if(strb[0]=='.') { /* Missing status */
5386: lval=-1;
5387: }else{
5388: errno=0;
5389: lval=strtol(strb,&endptr,10);
5390: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5391: if( strb[0]=='\0' || (*endptr != '\0')){
5392: 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);
5393: 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);
5394: return 1;
5395: }
5396: }
5397: s[j][i]=lval;
5398:
5399: strcpy(line,stra);
5400: cutv(stra, strb,line,' ');
5401: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5402: }
5403: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5404: month=99;
5405: year=9999;
5406: }else{
5407: 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);
5408: 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);
5409: return 1;
5410: }
5411: anint[j][i]= (double) year;
5412: mint[j][i]= (double)month;
5413: strcpy(line,stra);
5414: } /* ENd Waves */
5415:
5416: cutv(stra, strb,line,' ');
5417: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5418: }
5419: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5420: month=99;
5421: year=9999;
5422: }else{
5423: 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);
5424: 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);
5425: return 1;
5426: }
5427: andc[i]=(double) year;
5428: moisdc[i]=(double) month;
5429: strcpy(line,stra);
5430:
5431: cutv(stra, strb,line,' ');
5432: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5433: }
5434: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5435: month=99;
5436: year=9999;
5437: }else{
5438: 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);
5439: 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);
5440: return 1;
5441: }
5442: if (year==9999) {
5443: 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);
5444: 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);
5445: return 1;
5446:
5447: }
5448: annais[i]=(double)(year);
5449: moisnais[i]=(double)(month);
5450: strcpy(line,stra);
5451:
5452: cutv(stra, strb,line,' ');
5453: errno=0;
5454: dval=strtod(strb,&endptr);
5455: if( strb[0]=='\0' || (*endptr != '\0')){
5456: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5457: 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);
5458: fflush(ficlog);
5459: return 1;
5460: }
5461: weight[i]=dval;
5462: strcpy(line,stra);
5463:
5464: for (j=ncovcol;j>=1;j--){
5465: cutv(stra, strb,line,' ');
5466: if(strb[0]=='.') { /* Missing status */
5467: lval=-1;
5468: }else{
5469: errno=0;
5470: lval=strtol(strb,&endptr,10);
5471: if( strb[0]=='\0' || (*endptr != '\0')){
5472: 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);
5473: 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);
5474: return 1;
5475: }
5476: }
5477: if(lval <-1 || lval >1){
5478: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5479: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5480: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5481: For example, for multinomial values like 1, 2 and 3,\n \
5482: build V1=0 V2=0 for the reference value (1),\n \
5483: V1=1 V2=0 for (2) \n \
5484: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5485: output of IMaCh is often meaningless.\n \
5486: Exiting.\n",lval,linei, i,line,j);
5487: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5488: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5489: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5490: For example, for multinomial values like 1, 2 and 3,\n \
5491: build V1=0 V2=0 for the reference value (1),\n \
5492: V1=1 V2=0 for (2) \n \
5493: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5494: output of IMaCh is often meaningless.\n \
5495: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5496: return 1;
5497: }
5498: covar[j][i]=(double)(lval);
5499: strcpy(line,stra);
5500: }
5501: lstra=strlen(stra);
5502:
5503: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5504: stratrunc = &(stra[lstra-9]);
5505: num[i]=atol(stratrunc);
5506: }
5507: else
5508: num[i]=atol(stra);
5509: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5510: 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;}*/
5511:
5512: i=i+1;
5513: } /* End loop reading data */
5514:
5515: *imax=i-1; /* Number of individuals */
5516: fclose(fic);
5517:
5518: return (0);
5519: /* endread: */
5520: printf("Exiting readdata: ");
5521: fclose(fic);
5522: return (1);
5523:
5524:
5525:
5526: }
5527: void removespace(char *str) {
5528: char *p1 = str, *p2 = str;
5529: do
5530: while (*p2 == ' ')
5531: p2++;
5532: while (*p1++ == *p2++);
5533: }
5534:
5535: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5536: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5537: * - nagesqr = 1 if age*age in the model, otherwise 0.
5538: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5539: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
5540: * - cptcovage number of covariates with age*products =2
5541: * - cptcovs number of simple covariates
5542: * - 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
5543: * which is a new column after the 9 (ncovcol) variables.
5544: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5545: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5546: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5547: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5548: */
5549: {
5550: int i, j, k, ks;
5551: int j1, k1, k2;
5552: char modelsav[80];
5553: char stra[80], strb[80], strc[80], strd[80],stre[80];
5554: char *strpt;
5555:
5556: /*removespace(model);*/
5557: if (strlen(model) >1){ /* If there is at least 1 covariate */
5558: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5559: if (strstr(model,"AGE") !=0){
5560: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
5561: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
5562: return 1;
5563: }
5564: if (strstr(model,"v") !=0){
5565: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5566: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5567: return 1;
5568: }
5569: strcpy(modelsav,model);
5570: if ((strpt=strstr(model,"age*age")) !=0){
5571: printf(" strpt=%s, model=%s\n",strpt, model);
5572: if(strpt != model){
5573: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5574: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5575: corresponding column of parameters.\n",model);
5576: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5577: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5578: corresponding column of parameters.\n",model); fflush(ficlog);
5579: return 1;
5580: }
5581:
5582: nagesqr=1;
5583: if (strstr(model,"+age*age") !=0)
5584: substrchaine(modelsav, model, "+age*age");
5585: else if (strstr(model,"age*age+") !=0)
5586: substrchaine(modelsav, model, "age*age+");
5587: else
5588: substrchaine(modelsav, model, "age*age");
5589: }else
5590: nagesqr=0;
5591: if (strlen(modelsav) >1){
5592: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5593: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5594: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5595: cptcovt= j+1; /* Number of total covariates in the model, not including
5596: * cst, age and age*age
5597: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5598: /* including age products which are counted in cptcovage.
5599: * but the covariates which are products must be treated
5600: * separately: ncovn=4- 2=2 (V1+V3). */
5601: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5602: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5603:
5604:
5605: /* Design
5606: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5607: * < ncovcol=8 >
5608: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5609: * k= 1 2 3 4 5 6 7 8
5610: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5611: * covar[k,i], value of kth covariate if not including age for individual i:
5612: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5613: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5614: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5615: * Tage[++cptcovage]=k
5616: * if products, new covar are created after ncovcol with k1
5617: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5618: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5619: * 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
5620: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5621: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5622: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5623: * < ncovcol=8 >
5624: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5625: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5626: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5627: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5628: * p Tprod[1]@2={ 6, 5}
5629: *p Tvard[1][1]@4= {7, 8, 5, 6}
5630: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5631: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5632: *How to reorganize?
5633: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5634: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5635: * {2, 1, 4, 8, 5, 6, 3, 7}
5636: * Struct []
5637: */
5638:
5639: /* This loop fills the array Tvar from the string 'model'.*/
5640: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5641: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5642: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5643: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5644: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5645: /* k=1 Tvar[1]=2 (from V2) */
5646: /* k=5 Tvar[5] */
5647: /* for (k=1; k<=cptcovn;k++) { */
5648: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5649: /* } */
5650: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5651: /*
5652: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5653: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5654: Tvar[k]=0;
5655: cptcovage=0;
5656: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5657: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5658: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5659: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5660: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5661: /*scanf("%d",i);*/
5662: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5663: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5664: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5665: /* covar is not filled and then is empty */
5666: cptcovprod--;
5667: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5668: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5669: cptcovage++; /* Sums the number of covariates which include age as a product */
5670: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5671: /*printf("stre=%s ", stre);*/
5672: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5673: cptcovprod--;
5674: cutl(stre,strb,strc,'V');
5675: Tvar[k]=atoi(stre);
5676: cptcovage++;
5677: Tage[cptcovage]=k;
5678: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5679: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5680: cptcovn++;
5681: cptcovprodnoage++;k1++;
5682: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5683: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5684: because this model-covariate is a construction we invent a new column
5685: ncovcol + k1
5686: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5687: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5688: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5689: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5690: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5691: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5692: k2=k2+2;
5693: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5694: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5695: for (i=1; i<=lastobs;i++){
5696: /* Computes the new covariate which is a product of
5697: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5698: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5699: }
5700: } /* End age is not in the model */
5701: } /* End if model includes a product */
5702: else { /* no more sum */
5703: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5704: /* scanf("%d",i);*/
5705: cutl(strd,strc,strb,'V');
5706: ks++; /**< Number of simple covariates */
5707: cptcovn++;
5708: Tvar[k]=atoi(strd);
5709: }
5710: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5711: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5712: scanf("%d",i);*/
5713: } /* end of loop + on total covariates */
5714: } /* end if strlen(modelsave == 0) age*age might exist */
5715: } /* end if strlen(model == 0) */
5716:
5717: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5718: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5719:
5720: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5721: printf("cptcovprod=%d ", cptcovprod);
5722: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5723:
5724: scanf("%d ",i);*/
5725:
5726:
5727: return (0); /* with covar[new additional covariate if product] and Tage if age */
5728: /*endread:*/
5729: printf("Exiting decodemodel: ");
5730: return (1);
5731: }
5732:
5733: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5734: {
5735: int i, m;
5736:
5737: for (i=1; i<=imx; i++) {
5738: for(m=2; (m<= maxwav); m++) {
5739: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5740: anint[m][i]=9999;
5741: s[m][i]=-1;
5742: }
5743: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5744: *nberr = *nberr + 1;
5745: 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);
5746: 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);
5747: s[m][i]=-1;
5748: }
5749: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5750: (*nberr)++;
5751: 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]);
5752: 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]);
5753: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5754: }
5755: }
5756: }
5757:
5758: for (i=1; i<=imx; i++) {
5759: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5760: for(m=firstpass; (m<= lastpass); m++){
5761: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5762: if (s[m][i] >= nlstate+1) {
5763: if(agedc[i]>0){
5764: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5765: agev[m][i]=agedc[i];
5766: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5767: }else {
5768: if ((int)andc[i]!=9999){
5769: nbwarn++;
5770: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5771: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5772: agev[m][i]=-1;
5773: }
5774: }
5775: } /* agedc > 0 */
5776: }
5777: else if(s[m][i] !=9){ /* Standard case, age in fractional
5778: years but with the precision of a month */
5779: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5780: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5781: agev[m][i]=1;
5782: else if(agev[m][i] < *agemin){
5783: *agemin=agev[m][i];
5784: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5785: }
5786: else if(agev[m][i] >*agemax){
5787: *agemax=agev[m][i];
5788: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5789: }
5790: /*agev[m][i]=anint[m][i]-annais[i];*/
5791: /* agev[m][i] = age[i]+2*m;*/
5792: }
5793: else { /* =9 */
5794: agev[m][i]=1;
5795: s[m][i]=-1;
5796: }
5797: }
5798: else /*= 0 Unknown */
5799: agev[m][i]=1;
5800: }
5801:
5802: }
5803: for (i=1; i<=imx; i++) {
5804: for(m=firstpass; (m<=lastpass); m++){
5805: if (s[m][i] > (nlstate+ndeath)) {
5806: (*nberr)++;
5807: 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);
5808: 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);
5809: return 1;
5810: }
5811: }
5812: }
5813:
5814: /*for (i=1; i<=imx; i++){
5815: for (m=firstpass; (m<lastpass); m++){
5816: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5817: }
5818:
5819: }*/
5820:
5821:
5822: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5823: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5824:
5825: return (0);
5826: /* endread:*/
5827: printf("Exiting calandcheckages: ");
5828: return (1);
5829: }
5830:
5831: #if defined(_MSC_VER)
5832: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5833: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5834: //#include "stdafx.h"
5835: //#include <stdio.h>
5836: //#include <tchar.h>
5837: //#include <windows.h>
5838: //#include <iostream>
5839: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5840:
5841: LPFN_ISWOW64PROCESS fnIsWow64Process;
5842:
5843: BOOL IsWow64()
5844: {
5845: BOOL bIsWow64 = FALSE;
5846:
5847: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5848: // (HANDLE, PBOOL);
5849:
5850: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5851:
5852: HMODULE module = GetModuleHandle(_T("kernel32"));
5853: const char funcName[] = "IsWow64Process";
5854: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5855: GetProcAddress(module, funcName);
5856:
5857: if (NULL != fnIsWow64Process)
5858: {
5859: if (!fnIsWow64Process(GetCurrentProcess(),
5860: &bIsWow64))
5861: //throw std::exception("Unknown error");
5862: printf("Unknown error\n");
5863: }
5864: return bIsWow64 != FALSE;
5865: }
5866: #endif
5867:
5868: void syscompilerinfo()
5869: {
5870: /* #include "syscompilerinfo.h"*/
5871: /* command line Intel compiler 32bit windows, XP compatible:*/
5872: /* /GS /W3 /Gy
5873: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5874: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5875: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
5876: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5877: */
5878: /* 64 bits */
5879: /*
5880: /GS /W3 /Gy
5881: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5882: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5883: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5884: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5885: /* Optimization are useless and O3 is slower than O2 */
5886: /*
5887: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5888: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5889: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5890: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5891: */
5892: /* Link is */ /* /OUT:"visual studio
5893: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5894: /PDB:"visual studio
5895: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5896: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5897: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5898: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5899: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5900: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5901: uiAccess='false'"
5902: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5903: /NOLOGO /TLBID:1
5904: */
5905: #if defined __INTEL_COMPILER
5906: #if defined(__GNUC__)
5907: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5908: #endif
5909: #elif defined(__GNUC__)
5910: #ifndef __APPLE__
5911: #include <gnu/libc-version.h> /* Only on gnu */
5912: #endif
5913: struct utsname sysInfo;
5914: int cross = CROSS;
5915: if (cross){
5916: printf("Cross-");
5917: fprintf(ficlog, "Cross-");
5918: }
5919: #endif
5920:
5921: #include <stdint.h>
5922:
5923: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5924: #if defined(__clang__)
5925: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5926: #endif
5927: #if defined(__ICC) || defined(__INTEL_COMPILER)
5928: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5929: #endif
5930: #if defined(__GNUC__) || defined(__GNUG__)
5931: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5932: #endif
5933: #if defined(__HP_cc) || defined(__HP_aCC)
5934: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5935: #endif
5936: #if defined(__IBMC__) || defined(__IBMCPP__)
5937: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5938: #endif
5939: #if defined(_MSC_VER)
5940: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5941: #endif
5942: #if defined(__PGI)
5943: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5944: #endif
5945: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5946: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5947: #endif
5948: printf(" for ");fprintf(ficlog," for ");
5949:
5950: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5951: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5952: // Windows (x64 and x86)
5953: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5954: #elif __unix__ // all unices, not all compilers
5955: // Unix
5956: printf("Unix ");fprintf(ficlog,"Unix ");
5957: #elif __linux__
5958: // linux
5959: printf("linux ");fprintf(ficlog,"linux ");
5960: #elif __APPLE__
5961: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5962: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5963: #endif
5964:
5965: /* __MINGW32__ */
5966: /* __CYGWIN__ */
5967: /* __MINGW64__ */
5968: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5969: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5970: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5971: /* _WIN64 // Defined for applications for Win64. */
5972: /* _M_X64 // Defined for compilations that target x64 processors. */
5973: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5974:
5975: #if UINTPTR_MAX == 0xffffffff
5976: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5977: #elif UINTPTR_MAX == 0xffffffffffffffff
5978: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5979: #else
5980: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5981: #endif
5982:
5983: #if defined(__GNUC__)
5984: # if defined(__GNUC_PATCHLEVEL__)
5985: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5986: + __GNUC_MINOR__ * 100 \
5987: + __GNUC_PATCHLEVEL__)
5988: # else
5989: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5990: + __GNUC_MINOR__ * 100)
5991: # endif
5992: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5993: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5994:
5995: if (uname(&sysInfo) != -1) {
5996: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5997: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5998: }
5999: else
6000: perror("uname() error");
6001: //#ifndef __INTEL_COMPILER
6002: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
6003: printf("GNU libc version: %s\n", gnu_get_libc_version());
6004: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
6005: #endif
6006: #endif
6007:
6008: // void main()
6009: // {
6010: #if defined(_MSC_VER)
6011: if (IsWow64()){
6012: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6013: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6014: }
6015: else{
6016: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6017: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6018: }
6019: // printf("\nPress Enter to continue...");
6020: // getchar();
6021: // }
6022:
6023: #endif
6024:
6025:
6026: }
6027:
6028: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6029: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6030: int i, j, k, i1 ;
6031: double ftolpl = 1.e-10;
6032: double age, agebase, agelim;
6033:
6034: strcpy(filerespl,"pl");
6035: strcat(filerespl,fileres);
6036: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6037: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6038: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6039: }
6040: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6041: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6042: pstamp(ficrespl);
6043: fprintf(ficrespl,"# Period (stable) prevalence \n");
6044: fprintf(ficrespl,"#Age ");
6045: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6046: fprintf(ficrespl,"\n");
6047:
6048: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6049:
6050: agebase=ageminpar;
6051: agelim=agemaxpar;
6052:
6053: i1=pow(2,cptcoveff);
6054: if (cptcovn < 1){i1=1;}
6055:
6056: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6057: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6058: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6059: k=k+1;
6060: /* to clean */
6061: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6062: fprintf(ficrespl,"\n#******");
6063: printf("\n#******");
6064: fprintf(ficlog,"\n#******");
6065: for(j=1;j<=cptcoveff;j++) {
6066: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6067: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6068: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6069: }
6070: fprintf(ficrespl,"******\n");
6071: printf("******\n");
6072: fprintf(ficlog,"******\n");
6073:
6074: fprintf(ficrespl,"#Age ");
6075: for(j=1;j<=cptcoveff;j++) {
6076: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6077: }
6078: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6079: fprintf(ficrespl,"\n");
6080:
6081: for (age=agebase; age<=agelim; age++){
6082: /* for (age=agebase; age<=agebase; age++){ */
6083: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6084: fprintf(ficrespl,"%.0f ",age );
6085: for(j=1;j<=cptcoveff;j++)
6086: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6087: for(i=1; i<=nlstate;i++)
6088: fprintf(ficrespl," %.5f", prlim[i][i]);
6089: fprintf(ficrespl,"\n");
6090: } /* Age */
6091: /* was end of cptcod */
6092: } /* cptcov */
6093: return 0;
6094: }
6095:
6096: int hPijx(double *p, int bage, int fage){
6097: /*------------- h Pij x at various ages ------------*/
6098:
6099: int stepsize;
6100: int agelim;
6101: int hstepm;
6102: int nhstepm;
6103: int h, i, i1, j, k;
6104:
6105: double agedeb;
6106: double ***p3mat;
6107:
6108: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6109: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6110: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6111: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6112: }
6113: printf("Computing pij: result on file '%s' \n", filerespij);
6114: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6115:
6116: stepsize=(int) (stepm+YEARM-1)/YEARM;
6117: /*if (stepm<=24) stepsize=2;*/
6118:
6119: agelim=AGESUP;
6120: hstepm=stepsize*YEARM; /* Every year of age */
6121: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6122:
6123: /* hstepm=1; aff par mois*/
6124: pstamp(ficrespij);
6125: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6126: i1= pow(2,cptcoveff);
6127: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6128: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6129: /* k=k+1; */
6130: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6131: fprintf(ficrespij,"\n#****** ");
6132: for(j=1;j<=cptcoveff;j++)
6133: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6134: fprintf(ficrespij,"******\n");
6135:
6136: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6137: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6138: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6139:
6140: /* nhstepm=nhstepm*YEARM; aff par mois*/
6141:
6142: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6143: oldm=oldms;savm=savms;
6144: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6145: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6146: for(i=1; i<=nlstate;i++)
6147: for(j=1; j<=nlstate+ndeath;j++)
6148: fprintf(ficrespij," %1d-%1d",i,j);
6149: fprintf(ficrespij,"\n");
6150: for (h=0; h<=nhstepm; h++){
6151: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6152: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
6153: for(i=1; i<=nlstate;i++)
6154: for(j=1; j<=nlstate+ndeath;j++)
6155: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6156: fprintf(ficrespij,"\n");
6157: }
6158: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6159: fprintf(ficrespij,"\n");
6160: }
6161: /*}*/
6162: }
6163: return 0;
6164: }
6165:
6166:
6167: /***********************************************/
6168: /**************** Main Program *****************/
6169: /***********************************************/
6170:
6171: int main(int argc, char *argv[])
6172: {
6173: #ifdef GSL
6174: const gsl_multimin_fminimizer_type *T;
6175: size_t iteri = 0, it;
6176: int rval = GSL_CONTINUE;
6177: int status = GSL_SUCCESS;
6178: double ssval;
6179: #endif
6180: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
6181: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6182:
6183: int jj, ll, li, lj, lk;
6184: int numlinepar=0; /* Current linenumber of parameter file */
6185: int itimes;
6186: int NDIM=2;
6187: int vpopbased=0;
6188:
6189: char ca[32], cb[32];
6190: /* FILE *fichtm; *//* Html File */
6191: /* FILE *ficgp;*/ /*Gnuplot File */
6192: struct stat info;
6193: double agedeb;
6194: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6195:
6196: double fret;
6197: double dum; /* Dummy variable */
6198: double ***p3mat;
6199: double ***mobaverage;
6200:
6201: char line[MAXLINE];
6202: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6203: char pathr[MAXLINE], pathimach[MAXLINE];
6204: char *tok, *val; /* pathtot */
6205: int firstobs=1, lastobs=10;
6206: int c, h , cpt;
6207: int jl;
6208: int i1, j1, jk, stepsize;
6209: int *tab;
6210: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6211: int mobilav=0,popforecast=0;
6212: int hstepm, nhstepm;
6213: int agemortsup;
6214: float sumlpop=0.;
6215: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6216: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6217:
6218: double bage=0, fage=110, age, agelim, agebase;
6219: double ftolpl=FTOL;
6220: double **prlim;
6221: double ***param; /* Matrix of parameters */
6222: double *p;
6223: double **matcov; /* Matrix of covariance */
6224: double ***delti3; /* Scale */
6225: double *delti; /* Scale */
6226: double ***eij, ***vareij;
6227: double **varpl; /* Variances of prevalence limits by age */
6228: double *epj, vepp;
6229:
6230: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6231: double **ximort;
6232: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
6233: int *dcwave;
6234:
6235: char z[1]="c";
6236:
6237: /*char *strt;*/
6238: char strtend[80];
6239:
6240:
6241: /* setlocale (LC_ALL, ""); */
6242: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6243: /* textdomain (PACKAGE); */
6244: /* setlocale (LC_CTYPE, ""); */
6245: /* setlocale (LC_MESSAGES, ""); */
6246:
6247: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
6248: rstart_time = time(NULL);
6249: /* (void) gettimeofday(&start_time,&tzp);*/
6250: start_time = *localtime(&rstart_time);
6251: curr_time=start_time;
6252: /*tml = *localtime(&start_time.tm_sec);*/
6253: /* strcpy(strstart,asctime(&tml)); */
6254: strcpy(strstart,asctime(&start_time));
6255:
6256: /* printf("Localtime (at start)=%s",strstart); */
6257: /* tp.tm_sec = tp.tm_sec +86400; */
6258: /* tm = *localtime(&start_time.tm_sec); */
6259: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6260: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6261: /* tmg.tm_hour=tmg.tm_hour + 1; */
6262: /* tp.tm_sec = mktime(&tmg); */
6263: /* strt=asctime(&tmg); */
6264: /* printf("Time(after) =%s",strstart); */
6265: /* (void) time (&time_value);
6266: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6267: * tm = *localtime(&time_value);
6268: * strstart=asctime(&tm);
6269: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6270: */
6271:
6272: nberr=0; /* Number of errors and warnings */
6273: nbwarn=0;
6274: #ifdef WIN32
6275: _getcwd(pathcd, size);
6276: #else
6277: getcwd(pathcd, size);
6278: #endif
6279:
6280: printf("\n%s\n%s",version,fullversion);
6281: if(argc <=1){
6282: printf("\nEnter the parameter file name: ");
6283: fgets(pathr,FILENAMELENGTH,stdin);
6284: i=strlen(pathr);
6285: if(pathr[i-1]=='\n')
6286: pathr[i-1]='\0';
6287: i=strlen(pathr);
6288: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6289: pathr[i-1]='\0';
6290: for (tok = pathr; tok != NULL; ){
6291: printf("Pathr |%s|\n",pathr);
6292: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6293: printf("val= |%s| pathr=%s\n",val,pathr);
6294: strcpy (pathtot, val);
6295: if(pathr[0] == '\0') break; /* Dirty */
6296: }
6297: }
6298: else{
6299: strcpy(pathtot,argv[1]);
6300: }
6301: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6302: /*cygwin_split_path(pathtot,path,optionfile);
6303: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6304: /* cutv(path,optionfile,pathtot,'\\');*/
6305:
6306: /* Split argv[0], imach program to get pathimach */
6307: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6308: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6309: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6310: /* strcpy(pathimach,argv[0]); */
6311: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6312: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6313: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
6314: #ifdef WIN32
6315: _chdir(path); /* Can be a relative path */
6316: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6317: #else
6318: chdir(path); /* Can be a relative path */
6319: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6320: #endif
6321: printf("Current directory %s!\n",pathcd);
6322: strcpy(command,"mkdir ");
6323: strcat(command,optionfilefiname);
6324: if((outcmd=system(command)) != 0){
6325: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
6326: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6327: /* fclose(ficlog); */
6328: /* exit(1); */
6329: }
6330: /* if((imk=mkdir(optionfilefiname))<0){ */
6331: /* perror("mkdir"); */
6332: /* } */
6333:
6334: /*-------- arguments in the command line --------*/
6335:
6336: /* Main Log file */
6337: strcat(filelog, optionfilefiname);
6338: strcat(filelog,".log"); /* */
6339: if((ficlog=fopen(filelog,"w"))==NULL) {
6340: printf("Problem with logfile %s\n",filelog);
6341: goto end;
6342: }
6343: fprintf(ficlog,"Log filename:%s\n",filelog);
6344: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6345: fprintf(ficlog,"\nEnter the parameter file name: \n");
6346: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6347: path=%s \n\
6348: optionfile=%s\n\
6349: optionfilext=%s\n\
6350: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
6351:
6352: syscompilerinfo();
6353:
6354: printf("Local time (at start):%s",strstart);
6355: fprintf(ficlog,"Local time (at start): %s",strstart);
6356: fflush(ficlog);
6357: /* (void) gettimeofday(&curr_time,&tzp); */
6358: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
6359:
6360: /* */
6361: strcpy(fileres,"r");
6362: strcat(fileres, optionfilefiname);
6363: strcat(fileres,".txt"); /* Other files have txt extension */
6364:
6365: /* Main ---------arguments file --------*/
6366:
6367: if((ficpar=fopen(optionfile,"r"))==NULL) {
6368: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6369: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6370: fflush(ficlog);
6371: /* goto end; */
6372: exit(70);
6373: }
6374:
6375:
6376:
6377: strcpy(filereso,"o");
6378: strcat(filereso,fileres);
6379: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6380: printf("Problem with Output resultfile: %s\n", filereso);
6381: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6382: fflush(ficlog);
6383: goto end;
6384: }
6385:
6386: /* Reads comments: lines beginning with '#' */
6387: numlinepar=0;
6388: while((c=getc(ficpar))=='#' && c!= EOF){
6389: ungetc(c,ficpar);
6390: fgets(line, MAXLINE, ficpar);
6391: numlinepar++;
6392: fputs(line,stdout);
6393: fputs(line,ficparo);
6394: fputs(line,ficlog);
6395: }
6396: ungetc(c,ficpar);
6397:
6398: 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6399: numlinepar++;
6400: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6401: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6402: model[strlen(model)-1]='\0';
6403: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6404: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6405: fflush(ficlog);
6406: /* if(model[0]=='#'|| model[0]== '\0'){ */
6407: if(model[0]=='#'){
6408: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6409: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6410: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6411: if(mle != -1){
6412: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6413: exit(1);
6414: }
6415: }
6416: while((c=getc(ficpar))=='#' && c!= EOF){
6417: ungetc(c,ficpar);
6418: fgets(line, MAXLINE, ficpar);
6419: numlinepar++;
6420: fputs(line, stdout);
6421: //puts(line);
6422: fputs(line,ficparo);
6423: fputs(line,ficlog);
6424: }
6425: ungetc(c,ficpar);
6426:
6427:
6428: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
6429: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6430: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6431: v1+v2*age+v2*v3 makes cptcovn = 3
6432: */
6433: if (strlen(model)>1)
6434: 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,age*age makes 3*/
6435: else
6436: ncovmodel=2; /* Constant and age */
6437: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6438: npar= nforce*ncovmodel; /* Number of parameters like aij*/
6439: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6440: 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);
6441: 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);
6442: fflush(stdout);
6443: fclose (ficlog);
6444: goto end;
6445: }
6446: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6447: delti=delti3[1][1];
6448: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6449: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6450: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6451: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6452: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6453: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6454: fclose (ficparo);
6455: fclose (ficlog);
6456: goto end;
6457: exit(0);
6458: }
6459: else if(mle==-3) { /* Main Wizard */
6460: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6461: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6462: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6463: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6464: matcov=matrix(1,npar,1,npar);
6465: }
6466: else{
6467: /* Read guessed parameters */
6468: /* Reads comments: lines beginning with '#' */
6469: while((c=getc(ficpar))=='#' && c!= EOF){
6470: ungetc(c,ficpar);
6471: fgets(line, MAXLINE, ficpar);
6472: numlinepar++;
6473: fputs(line,stdout);
6474: fputs(line,ficparo);
6475: fputs(line,ficlog);
6476: }
6477: ungetc(c,ficpar);
6478:
6479: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6480: for(i=1; i <=nlstate; i++){
6481: j=0;
6482: for(jj=1; jj <=nlstate+ndeath; jj++){
6483: if(jj==i) continue;
6484: j++;
6485: fscanf(ficpar,"%1d%1d",&i1,&j1);
6486: if ((i1 != i) && (j1 != j)){
6487: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6488: It might be a problem of design; if ncovcol and the model are correct\n \
6489: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6490: exit(1);
6491: }
6492: fprintf(ficparo,"%1d%1d",i1,j1);
6493: if(mle==1)
6494: printf("%1d%1d",i,j);
6495: fprintf(ficlog,"%1d%1d",i,j);
6496: for(k=1; k<=ncovmodel;k++){
6497: fscanf(ficpar," %lf",¶m[i][j][k]);
6498: if(mle==1){
6499: printf(" %lf",param[i][j][k]);
6500: fprintf(ficlog," %lf",param[i][j][k]);
6501: }
6502: else
6503: fprintf(ficlog," %lf",param[i][j][k]);
6504: fprintf(ficparo," %lf",param[i][j][k]);
6505: }
6506: fscanf(ficpar,"\n");
6507: numlinepar++;
6508: if(mle==1)
6509: printf("\n");
6510: fprintf(ficlog,"\n");
6511: fprintf(ficparo,"\n");
6512: }
6513: }
6514: fflush(ficlog);
6515:
6516: /* Reads scales values */
6517: p=param[1][1];
6518:
6519: /* Reads comments: lines beginning with '#' */
6520: while((c=getc(ficpar))=='#' && c!= EOF){
6521: ungetc(c,ficpar);
6522: fgets(line, MAXLINE, ficpar);
6523: numlinepar++;
6524: fputs(line,stdout);
6525: fputs(line,ficparo);
6526: fputs(line,ficlog);
6527: }
6528: ungetc(c,ficpar);
6529:
6530: for(i=1; i <=nlstate; i++){
6531: for(j=1; j <=nlstate+ndeath-1; j++){
6532: fscanf(ficpar,"%1d%1d",&i1,&j1);
6533: if ( (i1-i) * (j1-j) != 0){
6534: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6535: exit(1);
6536: }
6537: printf("%1d%1d",i,j);
6538: fprintf(ficparo,"%1d%1d",i1,j1);
6539: fprintf(ficlog,"%1d%1d",i1,j1);
6540: for(k=1; k<=ncovmodel;k++){
6541: fscanf(ficpar,"%le",&delti3[i][j][k]);
6542: printf(" %le",delti3[i][j][k]);
6543: fprintf(ficparo," %le",delti3[i][j][k]);
6544: fprintf(ficlog," %le",delti3[i][j][k]);
6545: }
6546: fscanf(ficpar,"\n");
6547: numlinepar++;
6548: printf("\n");
6549: fprintf(ficparo,"\n");
6550: fprintf(ficlog,"\n");
6551: }
6552: }
6553: fflush(ficlog);
6554:
6555: /* Reads covariance matrix */
6556: delti=delti3[1][1];
6557:
6558:
6559: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6560:
6561: /* Reads comments: lines beginning with '#' */
6562: while((c=getc(ficpar))=='#' && c!= EOF){
6563: ungetc(c,ficpar);
6564: fgets(line, MAXLINE, ficpar);
6565: numlinepar++;
6566: fputs(line,stdout);
6567: fputs(line,ficparo);
6568: fputs(line,ficlog);
6569: }
6570: ungetc(c,ficpar);
6571:
6572: matcov=matrix(1,npar,1,npar);
6573: for(i=1; i <=npar; i++)
6574: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6575:
6576: for(i=1; i <=npar; i++){
6577: fscanf(ficpar,"%s",str);
6578: if(mle==1)
6579: printf("%s",str);
6580: fprintf(ficlog,"%s",str);
6581: fprintf(ficparo,"%s",str);
6582: for(j=1; j <=i; j++){
6583: fscanf(ficpar," %le",&matcov[i][j]);
6584: if(mle==1){
6585: printf(" %.5le",matcov[i][j]);
6586: }
6587: fprintf(ficlog," %.5le",matcov[i][j]);
6588: fprintf(ficparo," %.5le",matcov[i][j]);
6589: }
6590: fscanf(ficpar,"\n");
6591: numlinepar++;
6592: if(mle==1)
6593: printf("\n");
6594: fprintf(ficlog,"\n");
6595: fprintf(ficparo,"\n");
6596: }
6597: for(i=1; i <=npar; i++)
6598: for(j=i+1;j<=npar;j++)
6599: matcov[i][j]=matcov[j][i];
6600:
6601: if(mle==1)
6602: printf("\n");
6603: fprintf(ficlog,"\n");
6604:
6605: fflush(ficlog);
6606:
6607: /*-------- Rewriting parameter file ----------*/
6608: strcpy(rfileres,"r"); /* "Rparameterfile */
6609: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6610: strcat(rfileres,"."); /* */
6611: strcat(rfileres,optionfilext); /* Other files have txt extension */
6612: if((ficres =fopen(rfileres,"w"))==NULL) {
6613: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6614: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6615: }
6616: fprintf(ficres,"#%s\n",version);
6617: } /* End of mle != -3 */
6618:
6619: /* Main data
6620: */
6621: n= lastobs;
6622: num=lvector(1,n);
6623: moisnais=vector(1,n);
6624: annais=vector(1,n);
6625: moisdc=vector(1,n);
6626: andc=vector(1,n);
6627: agedc=vector(1,n);
6628: cod=ivector(1,n);
6629: weight=vector(1,n);
6630: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6631: mint=matrix(1,maxwav,1,n);
6632: anint=matrix(1,maxwav,1,n);
6633: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6634: tab=ivector(1,NCOVMAX);
6635: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6636:
6637: /* Reads data from file datafile */
6638: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6639: goto end;
6640:
6641: /* Calculation of the number of parameters from char model */
6642: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6643: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6644: k=3 V4 Tvar[k=3]= 4 (from V4)
6645: k=2 V1 Tvar[k=2]= 1 (from V1)
6646: k=1 Tvar[1]=2 (from V2)
6647: */
6648: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6649: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6650: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6651: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6652: */
6653: /* For model-covariate k tells which data-covariate to use but
6654: because this model-covariate is a construction we invent a new column
6655: ncovcol + k1
6656: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6657: Tvar[3=V1*V4]=4+1 etc */
6658: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6659: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6660: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6661: */
6662: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6663: 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
6664: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6665: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6666: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6667: 4 covariates (3 plus signs)
6668: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6669: */
6670:
6671: /* Main decodemodel */
6672:
6673:
6674: if(decodemodel(model, lastobs) == 1)
6675: goto end;
6676:
6677: if((double)(lastobs-imx)/(double)imx > 1.10){
6678: nbwarn++;
6679: 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);
6680: 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);
6681: }
6682: /* if(mle==1){*/
6683: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6684: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6685: }
6686:
6687: /*-calculation of age at interview from date of interview and age at death -*/
6688: agev=matrix(1,maxwav,1,imx);
6689:
6690: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6691: goto end;
6692:
6693:
6694: agegomp=(int)agemin;
6695: free_vector(moisnais,1,n);
6696: free_vector(annais,1,n);
6697: /* free_matrix(mint,1,maxwav,1,n);
6698: free_matrix(anint,1,maxwav,1,n);*/
6699: free_vector(moisdc,1,n);
6700: free_vector(andc,1,n);
6701: /* */
6702:
6703: wav=ivector(1,imx);
6704: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6705: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6706: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6707:
6708: /* Concatenates waves */
6709: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6710: /* */
6711:
6712: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6713:
6714: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6715: ncodemax[1]=1;
6716: Ndum =ivector(-1,NCOVMAX);
6717: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
6718: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6719: /* Nbcode gives the value of the lth modality of jth covariate, in
6720: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6721: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
6722:
6723: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6724: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6725: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
6726: h=0;
6727:
6728:
6729: /*if (cptcovn > 0) */
6730:
6731:
6732: m=pow(2,cptcoveff);
6733:
6734: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6735: 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 */
6736: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6737: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6738: h++;
6739: if (h>m)
6740: h=1;
6741: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6742: * For k=4 covariates, h goes from 1 to 2**k
6743: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6744: * h\k 1 2 3 4
6745: *______________________________
6746: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6747: * 2 2 1 1 1
6748: * 3 i=2 1 2 1 1
6749: * 4 2 2 1 1
6750: * 5 i=3 1 i=2 1 2 1
6751: * 6 2 1 2 1
6752: * 7 i=4 1 2 2 1
6753: * 8 2 2 2 1
6754: * 9 i=5 1 i=3 1 i=2 1 1
6755: * 10 2 1 1 1
6756: * 11 i=6 1 2 1 1
6757: * 12 2 2 1 1
6758: * 13 i=7 1 i=4 1 2 1
6759: * 14 2 1 2 1
6760: * 15 i=8 1 2 2 1
6761: * 16 2 2 2 1
6762: */
6763: codtab[h][k]=j;
6764: /* codtab[12][3]=1; */
6765: /*codtab[h][Tvar[k]]=j;*/
6766: 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]]);
6767: }
6768: }
6769: }
6770: }
6771: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6772: codtab[1][2]=1;codtab[2][2]=2; */
6773: /* for(i=1; i <=m ;i++){
6774: for(k=1; k <=cptcovn; k++){
6775: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6776: }
6777: printf("\n");
6778: }
6779: scanf("%d",i);*/
6780:
6781: free_ivector(Ndum,-1,NCOVMAX);
6782:
6783:
6784:
6785: /* Initialisation of ----------- gnuplot -------------*/
6786: strcpy(optionfilegnuplot,optionfilefiname);
6787: if(mle==-3)
6788: strcat(optionfilegnuplot,"-mort");
6789: strcat(optionfilegnuplot,".gp");
6790:
6791: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6792: printf("Problem with file %s",optionfilegnuplot);
6793: }
6794: else{
6795: fprintf(ficgp,"\n# %s\n", version);
6796: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6797: //fprintf(ficgp,"set missing 'NaNq'\n");
6798: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6799: }
6800: /* fclose(ficgp);*/
6801:
6802:
6803: /* Initialisation of --------- index.htm --------*/
6804:
6805: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6806: if(mle==-3)
6807: strcat(optionfilehtm,"-mort");
6808: strcat(optionfilehtm,".htm");
6809: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6810: printf("Problem with %s \n",optionfilehtm);
6811: exit(0);
6812: }
6813:
6814: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6815: strcat(optionfilehtmcov,"-cov.htm");
6816: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6817: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6818: }
6819: else{
6820: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6821: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6822: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6823: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6824: }
6825:
6826: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6827: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6828: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6829: \n\
6830: <hr size=\"2\" color=\"#EC5E5E\">\
6831: <ul><li><h4>Parameter files</h4>\n\
6832: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6833: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6834: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6835: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6836: - Date and time at start: %s</ul>\n",\
6837: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6838: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6839: fileres,fileres,\
6840: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6841: fflush(fichtm);
6842:
6843: strcpy(pathr,path);
6844: strcat(pathr,optionfilefiname);
6845: #ifdef WIN32
6846: _chdir(optionfilefiname); /* Move to directory named optionfile */
6847: #else
6848: chdir(optionfilefiname); /* Move to directory named optionfile */
6849: #endif
6850:
6851:
6852: /* Calculates basic frequencies. Computes observed prevalence at single age
6853: and prints on file fileres'p'. */
6854: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6855:
6856: fprintf(fichtm,"\n");
6857: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6858: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6859: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6860: imx,agemin,agemax,jmin,jmax,jmean);
6861: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6862: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6863: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6864: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6865: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6866:
6867:
6868: /* For Powell, parameters are in a vector p[] starting at p[1]
6869: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6870: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6871:
6872: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6873: /* For mortality only */
6874: if (mle==-3){
6875: ximort=matrix(1,NDIM,1,NDIM);
6876: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6877: cens=ivector(1,n);
6878: ageexmed=vector(1,n);
6879: agecens=vector(1,n);
6880: dcwave=ivector(1,n);
6881:
6882: for (i=1; i<=imx; i++){
6883: dcwave[i]=-1;
6884: for (m=firstpass; m<=lastpass; m++)
6885: if (s[m][i]>nlstate) {
6886: dcwave[i]=m;
6887: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6888: break;
6889: }
6890: }
6891:
6892: for (i=1; i<=imx; i++) {
6893: if (wav[i]>0){
6894: ageexmed[i]=agev[mw[1][i]][i];
6895: j=wav[i];
6896: agecens[i]=1.;
6897:
6898: if (ageexmed[i]> 1 && wav[i] > 0){
6899: agecens[i]=agev[mw[j][i]][i];
6900: cens[i]= 1;
6901: }else if (ageexmed[i]< 1)
6902: cens[i]= -1;
6903: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6904: cens[i]=0 ;
6905: }
6906: else cens[i]=-1;
6907: }
6908:
6909: for (i=1;i<=NDIM;i++) {
6910: for (j=1;j<=NDIM;j++)
6911: ximort[i][j]=(i == j ? 1.0 : 0.0);
6912: }
6913:
6914: /*p[1]=0.0268; p[NDIM]=0.083;*/
6915: /*printf("%lf %lf", p[1], p[2]);*/
6916:
6917:
6918: #ifdef GSL
6919: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6920: #else
6921: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6922: #endif
6923: strcpy(filerespow,"pow-mort");
6924: strcat(filerespow,fileres);
6925: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6926: printf("Problem with resultfile: %s\n", filerespow);
6927: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6928: }
6929: #ifdef GSL
6930: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6931: #else
6932: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6933: #endif
6934: /* for (i=1;i<=nlstate;i++)
6935: for(j=1;j<=nlstate+ndeath;j++)
6936: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6937: */
6938: fprintf(ficrespow,"\n");
6939: #ifdef GSL
6940: /* gsl starts here */
6941: T = gsl_multimin_fminimizer_nmsimplex;
6942: gsl_multimin_fminimizer *sfm = NULL;
6943: gsl_vector *ss, *x;
6944: gsl_multimin_function minex_func;
6945:
6946: /* Initial vertex size vector */
6947: ss = gsl_vector_alloc (NDIM);
6948:
6949: if (ss == NULL){
6950: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6951: }
6952: /* Set all step sizes to 1 */
6953: gsl_vector_set_all (ss, 0.001);
6954:
6955: /* Starting point */
6956:
6957: x = gsl_vector_alloc (NDIM);
6958:
6959: if (x == NULL){
6960: gsl_vector_free(ss);
6961: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6962: }
6963:
6964: /* Initialize method and iterate */
6965: /* p[1]=0.0268; p[NDIM]=0.083; */
6966: /* gsl_vector_set(x, 0, 0.0268); */
6967: /* gsl_vector_set(x, 1, 0.083); */
6968: gsl_vector_set(x, 0, p[1]);
6969: gsl_vector_set(x, 1, p[2]);
6970:
6971: minex_func.f = &gompertz_f;
6972: minex_func.n = NDIM;
6973: minex_func.params = (void *)&p; /* ??? */
6974:
6975: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6976: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6977:
6978: printf("Iterations beginning .....\n\n");
6979: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6980:
6981: iteri=0;
6982: while (rval == GSL_CONTINUE){
6983: iteri++;
6984: status = gsl_multimin_fminimizer_iterate(sfm);
6985:
6986: if (status) printf("error: %s\n", gsl_strerror (status));
6987: fflush(0);
6988:
6989: if (status)
6990: break;
6991:
6992: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6993: ssval = gsl_multimin_fminimizer_size (sfm);
6994:
6995: if (rval == GSL_SUCCESS)
6996: printf ("converged to a local maximum at\n");
6997:
6998: printf("%5d ", iteri);
6999: for (it = 0; it < NDIM; it++){
7000: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7001: }
7002: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7003: }
7004:
7005: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7006:
7007: gsl_vector_free(x); /* initial values */
7008: gsl_vector_free(ss); /* inital step size */
7009: for (it=0; it<NDIM; it++){
7010: p[it+1]=gsl_vector_get(sfm->x,it);
7011: fprintf(ficrespow," %.12lf", p[it]);
7012: }
7013: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7014: #endif
7015: #ifdef POWELL
7016: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7017: #endif
7018: fclose(ficrespow);
7019:
7020: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7021:
7022: for(i=1; i <=NDIM; i++)
7023: for(j=i+1;j<=NDIM;j++)
7024: matcov[i][j]=matcov[j][i];
7025:
7026: printf("\nCovariance matrix\n ");
7027: for(i=1; i <=NDIM; i++) {
7028: for(j=1;j<=NDIM;j++){
7029: printf("%f ",matcov[i][j]);
7030: }
7031: printf("\n ");
7032: }
7033:
7034: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7035: for (i=1;i<=NDIM;i++)
7036: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7037:
7038: lsurv=vector(1,AGESUP);
7039: lpop=vector(1,AGESUP);
7040: tpop=vector(1,AGESUP);
7041: lsurv[agegomp]=100000;
7042:
7043: for (k=agegomp;k<=AGESUP;k++) {
7044: agemortsup=k;
7045: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7046: }
7047:
7048: for (k=agegomp;k<agemortsup;k++)
7049: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7050:
7051: for (k=agegomp;k<agemortsup;k++){
7052: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7053: sumlpop=sumlpop+lpop[k];
7054: }
7055:
7056: tpop[agegomp]=sumlpop;
7057: for (k=agegomp;k<(agemortsup-3);k++){
7058: /* tpop[k+1]=2;*/
7059: tpop[k+1]=tpop[k]-lpop[k];
7060: }
7061:
7062:
7063: printf("\nAge lx qx dx Lx Tx e(x)\n");
7064: for (k=agegomp;k<(agemortsup-2);k++)
7065: 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]);
7066:
7067:
7068: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7069: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7070:
7071: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7072: stepm, weightopt,\
7073: model,imx,p,matcov,agemortsup);
7074:
7075: free_vector(lsurv,1,AGESUP);
7076: free_vector(lpop,1,AGESUP);
7077: free_vector(tpop,1,AGESUP);
7078: #ifdef GSL
7079: free_ivector(cens,1,n);
7080: free_vector(agecens,1,n);
7081: free_ivector(dcwave,1,n);
7082: free_matrix(ximort,1,NDIM,1,NDIM);
7083: #endif
7084: } /* Endof if mle==-3 mortality only */
7085: /* Standard maximisation */
7086: else{ /* For mle >=1 */
7087: globpr=0;/* debug */
7088: /* Computes likelihood for initial parameters */
7089: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7090: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7091: for (k=1; k<=npar;k++)
7092: printf(" %d %8.5f",k,p[k]);
7093: printf("\n");
7094: globpr=1; /* again, to print the contributions */
7095: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7096: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7097: for (k=1; k<=npar;k++)
7098: printf(" %d %8.5f",k,p[k]);
7099: printf("\n");
7100: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
7101: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7102: }
7103:
7104: /*--------- results files --------------*/
7105: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
7106:
7107:
7108: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7109: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7110: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7111: for(i=1,jk=1; i <=nlstate; i++){
7112: for(k=1; k <=(nlstate+ndeath); k++){
7113: if (k != i) {
7114: printf("%d%d ",i,k);
7115: fprintf(ficlog,"%d%d ",i,k);
7116: fprintf(ficres,"%1d%1d ",i,k);
7117: for(j=1; j <=ncovmodel; j++){
7118: printf("%12.7f ",p[jk]);
7119: fprintf(ficlog,"%12.7f ",p[jk]);
7120: fprintf(ficres,"%12.7f ",p[jk]);
7121: jk++;
7122: }
7123: printf("\n");
7124: fprintf(ficlog,"\n");
7125: fprintf(ficres,"\n");
7126: }
7127: }
7128: }
7129: if(mle!=0){
7130: /* Computing hessian and covariance matrix */
7131: ftolhess=ftol; /* Usually correct */
7132: hesscov(matcov, p, npar, delti, ftolhess, func);
7133: }
7134: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7135: printf("# Scales (for hessian or gradient estimation)\n");
7136: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7137: for(i=1,jk=1; i <=nlstate; i++){
7138: for(j=1; j <=nlstate+ndeath; j++){
7139: if (j!=i) {
7140: fprintf(ficres,"%1d%1d",i,j);
7141: printf("%1d%1d",i,j);
7142: fprintf(ficlog,"%1d%1d",i,j);
7143: for(k=1; k<=ncovmodel;k++){
7144: printf(" %.5e",delti[jk]);
7145: fprintf(ficlog," %.5e",delti[jk]);
7146: fprintf(ficres," %.5e",delti[jk]);
7147: jk++;
7148: }
7149: printf("\n");
7150: fprintf(ficlog,"\n");
7151: fprintf(ficres,"\n");
7152: }
7153: }
7154: }
7155:
7156: 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");
7157: if(mle>=1)
7158: 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");
7159: 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");
7160: /* # 121 Var(a12)\n\ */
7161: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7162: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7163: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7164: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7165: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7166: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7167: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7168:
7169:
7170: /* Just to have a covariance matrix which will be more understandable
7171: even is we still don't want to manage dictionary of variables
7172: */
7173: for(itimes=1;itimes<=2;itimes++){
7174: jj=0;
7175: for(i=1; i <=nlstate; i++){
7176: for(j=1; j <=nlstate+ndeath; j++){
7177: if(j==i) continue;
7178: for(k=1; k<=ncovmodel;k++){
7179: jj++;
7180: ca[0]= k+'a'-1;ca[1]='\0';
7181: if(itimes==1){
7182: if(mle>=1)
7183: printf("#%1d%1d%d",i,j,k);
7184: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7185: fprintf(ficres,"#%1d%1d%d",i,j,k);
7186: }else{
7187: if(mle>=1)
7188: printf("%1d%1d%d",i,j,k);
7189: fprintf(ficlog,"%1d%1d%d",i,j,k);
7190: fprintf(ficres,"%1d%1d%d",i,j,k);
7191: }
7192: ll=0;
7193: for(li=1;li <=nlstate; li++){
7194: for(lj=1;lj <=nlstate+ndeath; lj++){
7195: if(lj==li) continue;
7196: for(lk=1;lk<=ncovmodel;lk++){
7197: ll++;
7198: if(ll<=jj){
7199: cb[0]= lk +'a'-1;cb[1]='\0';
7200: if(ll<jj){
7201: if(itimes==1){
7202: if(mle>=1)
7203: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7204: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7205: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7206: }else{
7207: if(mle>=1)
7208: printf(" %.5e",matcov[jj][ll]);
7209: fprintf(ficlog," %.5e",matcov[jj][ll]);
7210: fprintf(ficres," %.5e",matcov[jj][ll]);
7211: }
7212: }else{
7213: if(itimes==1){
7214: if(mle>=1)
7215: printf(" Var(%s%1d%1d)",ca,i,j);
7216: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7217: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7218: }else{
7219: if(mle>=1)
7220: printf(" %.5e",matcov[jj][ll]);
7221: fprintf(ficlog," %.5e",matcov[jj][ll]);
7222: fprintf(ficres," %.5e",matcov[jj][ll]);
7223: }
7224: }
7225: }
7226: } /* end lk */
7227: } /* end lj */
7228: } /* end li */
7229: if(mle>=1)
7230: printf("\n");
7231: fprintf(ficlog,"\n");
7232: fprintf(ficres,"\n");
7233: numlinepar++;
7234: } /* end k*/
7235: } /*end j */
7236: } /* end i */
7237: } /* end itimes */
7238:
7239: fflush(ficlog);
7240: fflush(ficres);
7241:
7242: while((c=getc(ficpar))=='#' && c!= EOF){
7243: ungetc(c,ficpar);
7244: fgets(line, MAXLINE, ficpar);
7245: fputs(line,stdout);
7246: fputs(line,ficparo);
7247: }
7248: ungetc(c,ficpar);
7249:
7250: estepm=0;
7251: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7252: if (estepm==0 || estepm < stepm) estepm=stepm;
7253: if (fage <= 2) {
7254: bage = ageminpar;
7255: fage = agemaxpar;
7256: }
7257:
7258: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7259: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7260: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7261:
7262: /* Other stuffs, more or less useful */
7263: while((c=getc(ficpar))=='#' && c!= EOF){
7264: ungetc(c,ficpar);
7265: fgets(line, MAXLINE, ficpar);
7266: fputs(line,stdout);
7267: fputs(line,ficparo);
7268: }
7269: ungetc(c,ficpar);
7270:
7271: 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);
7272: 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);
7273: 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);
7274: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7275: 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);
7276:
7277: while((c=getc(ficpar))=='#' && c!= EOF){
7278: ungetc(c,ficpar);
7279: fgets(line, MAXLINE, ficpar);
7280: fputs(line,stdout);
7281: fputs(line,ficparo);
7282: }
7283: ungetc(c,ficpar);
7284:
7285:
7286: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7287: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7288:
7289: fscanf(ficpar,"pop_based=%d\n",&popbased);
7290: fprintf(ficparo,"pop_based=%d\n",popbased);
7291: fprintf(ficres,"pop_based=%d\n",popbased);
7292:
7293: while((c=getc(ficpar))=='#' && c!= EOF){
7294: ungetc(c,ficpar);
7295: fgets(line, MAXLINE, ficpar);
7296: fputs(line,stdout);
7297: fputs(line,ficparo);
7298: }
7299: ungetc(c,ficpar);
7300:
7301: 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);
7302: 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);
7303: 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);
7304: 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);
7305: 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);
7306: /* day and month of proj2 are not used but only year anproj2.*/
7307:
7308:
7309:
7310: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7311: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
7312:
7313: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7314: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7315:
7316: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7317: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7318: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7319:
7320: /*------------ free_vector -------------*/
7321: /* chdir(path); */
7322:
7323: free_ivector(wav,1,imx);
7324: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7325: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7326: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7327: free_lvector(num,1,n);
7328: free_vector(agedc,1,n);
7329: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7330: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7331: fclose(ficparo);
7332: fclose(ficres);
7333:
7334:
7335: /* Other results (useful)*/
7336:
7337:
7338: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7339: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7340: prlim=matrix(1,nlstate,1,nlstate);
7341: prevalence_limit(p, prlim, ageminpar, agemaxpar);
7342: fclose(ficrespl);
7343:
7344: #ifdef FREEEXIT2
7345: #include "freeexit2.h"
7346: #endif
7347:
7348: /*------------- h Pij x at various ages ------------*/
7349: /*#include "hpijx.h"*/
7350: hPijx(p, bage, fage);
7351: fclose(ficrespij);
7352:
7353: /*-------------- Variance of one-step probabilities---*/
7354: k=1;
7355: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7356:
7357:
7358: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7359: for(i=1;i<=AGESUP;i++)
7360: for(j=1;j<=NCOVMAX;j++)
7361: for(k=1;k<=NCOVMAX;k++)
7362: probs[i][j][k]=0.;
7363:
7364: /*---------- Forecasting ------------------*/
7365: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7366: if(prevfcast==1){
7367: /* if(stepm ==1){*/
7368: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7369: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7370: /* } */
7371: /* else{ */
7372: /* erreur=108; */
7373: /* 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); */
7374: /* 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); */
7375: /* } */
7376: }
7377:
7378: /* ------ Other prevalence ratios------------ */
7379:
7380: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7381:
7382: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7383: /* 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",\
7384: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7385: */
7386:
7387: if (mobilav!=0) {
7388: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7389: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7390: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7391: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7392: }
7393: }
7394:
7395:
7396: /*---------- Health expectancies, no variances ------------*/
7397:
7398: strcpy(filerese,"e");
7399: strcat(filerese,fileres);
7400: if((ficreseij=fopen(filerese,"w"))==NULL) {
7401: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7402: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7403: }
7404: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7405: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
7406: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7407: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7408:
7409: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7410: fprintf(ficreseij,"\n#****** ");
7411: for(j=1;j<=cptcoveff;j++) {
7412: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7413: }
7414: fprintf(ficreseij,"******\n");
7415:
7416: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7417: oldm=oldms;savm=savms;
7418: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7419:
7420: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7421: /*}*/
7422: }
7423: fclose(ficreseij);
7424:
7425:
7426: /*---------- Health expectancies and variances ------------*/
7427:
7428:
7429: strcpy(filerest,"t");
7430: strcat(filerest,fileres);
7431: if((ficrest=fopen(filerest,"w"))==NULL) {
7432: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7433: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7434: }
7435: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7436: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7437:
7438:
7439: strcpy(fileresstde,"stde");
7440: strcat(fileresstde,fileres);
7441: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7442: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7443: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7444: }
7445: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7446: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7447:
7448: strcpy(filerescve,"cve");
7449: strcat(filerescve,fileres);
7450: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7451: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7452: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7453: }
7454: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7455: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7456:
7457: strcpy(fileresv,"v");
7458: strcat(fileresv,fileres);
7459: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7460: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7461: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7462: }
7463: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7464: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7465:
7466: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7467: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7468:
7469: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7470: fprintf(ficrest,"\n#****** ");
7471: for(j=1;j<=cptcoveff;j++)
7472: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7473: fprintf(ficrest,"******\n");
7474:
7475: fprintf(ficresstdeij,"\n#****** ");
7476: fprintf(ficrescveij,"\n#****** ");
7477: for(j=1;j<=cptcoveff;j++) {
7478: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7479: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7480: }
7481: fprintf(ficresstdeij,"******\n");
7482: fprintf(ficrescveij,"******\n");
7483:
7484: fprintf(ficresvij,"\n#****** ");
7485: for(j=1;j<=cptcoveff;j++)
7486: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7487: fprintf(ficresvij,"******\n");
7488:
7489: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7490: oldm=oldms;savm=savms;
7491: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
7492: /*
7493: */
7494: /* goto endfree; */
7495:
7496: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7497: pstamp(ficrest);
7498:
7499:
7500: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
7501: oldm=oldms;savm=savms; /* Segmentation fault */
7502: cptcod= 0; /* To be deleted */
7503: 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 */
7504: 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 ");
7505: if(vpopbased==1)
7506: 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);
7507: else
7508: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7509: fprintf(ficrest,"# Age e.. (std) ");
7510: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7511: fprintf(ficrest,"\n");
7512:
7513: epj=vector(1,nlstate+1);
7514: for(age=bage; age <=fage ;age++){
7515: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7516: if (vpopbased==1) {
7517: if(mobilav ==0){
7518: for(i=1; i<=nlstate;i++)
7519: prlim[i][i]=probs[(int)age][i][k];
7520: }else{ /* mobilav */
7521: for(i=1; i<=nlstate;i++)
7522: prlim[i][i]=mobaverage[(int)age][i][k];
7523: }
7524: }
7525:
7526: fprintf(ficrest," %4.0f",age);
7527: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7528: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7529: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7530: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7531: }
7532: epj[nlstate+1] +=epj[j];
7533: }
7534:
7535: for(i=1, vepp=0.;i <=nlstate;i++)
7536: for(j=1;j <=nlstate;j++)
7537: vepp += vareij[i][j][(int)age];
7538: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7539: for(j=1;j <=nlstate;j++){
7540: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7541: }
7542: fprintf(ficrest,"\n");
7543: }
7544: }
7545: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7546: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7547: free_vector(epj,1,nlstate+1);
7548: /*}*/
7549: }
7550: free_vector(weight,1,n);
7551: free_imatrix(Tvard,1,NCOVMAX,1,2);
7552: free_imatrix(s,1,maxwav+1,1,n);
7553: free_matrix(anint,1,maxwav,1,n);
7554: free_matrix(mint,1,maxwav,1,n);
7555: free_ivector(cod,1,n);
7556: free_ivector(tab,1,NCOVMAX);
7557: fclose(ficresstdeij);
7558: fclose(ficrescveij);
7559: fclose(ficresvij);
7560: fclose(ficrest);
7561: fclose(ficpar);
7562:
7563: /*------- Variance of period (stable) prevalence------*/
7564:
7565: strcpy(fileresvpl,"vpl");
7566: strcat(fileresvpl,fileres);
7567: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7568: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7569: exit(0);
7570: }
7571: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7572:
7573: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7574: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7575:
7576: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7577: fprintf(ficresvpl,"\n#****** ");
7578: for(j=1;j<=cptcoveff;j++)
7579: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7580: fprintf(ficresvpl,"******\n");
7581:
7582: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7583: oldm=oldms;savm=savms;
7584: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7585: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7586: /*}*/
7587: }
7588:
7589: fclose(ficresvpl);
7590:
7591: /*---------- End : free ----------------*/
7592: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7593: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7594: } /* mle==-3 arrives here for freeing */
7595: /* endfree:*/
7596: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7597: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7598: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7599: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7600: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7601: free_matrix(covar,0,NCOVMAX,1,n);
7602: free_matrix(matcov,1,npar,1,npar);
7603: /*free_vector(delti,1,npar);*/
7604: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7605: free_matrix(agev,1,maxwav,1,imx);
7606: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7607:
7608: free_ivector(ncodemax,1,NCOVMAX);
7609: free_ivector(Tvar,1,NCOVMAX);
7610: free_ivector(Tprod,1,NCOVMAX);
7611: free_ivector(Tvaraff,1,NCOVMAX);
7612: free_ivector(Tage,1,NCOVMAX);
7613:
7614: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7615: free_imatrix(codtab,1,100,1,10);
7616: fflush(fichtm);
7617: fflush(ficgp);
7618:
7619:
7620: if((nberr >0) || (nbwarn>0)){
7621: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7622: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7623: }else{
7624: printf("End of Imach\n");
7625: fprintf(ficlog,"End of Imach\n");
7626: }
7627: printf("See log file on %s\n",filelog);
7628: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7629: /*(void) gettimeofday(&end_time,&tzp);*/
7630: rend_time = time(NULL);
7631: end_time = *localtime(&rend_time);
7632: /* tml = *localtime(&end_time.tm_sec); */
7633: strcpy(strtend,asctime(&end_time));
7634: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7635: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7636: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7637:
7638: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7639: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7640: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7641: /* printf("Total time was %d uSec.\n", total_usecs);*/
7642: /* if(fileappend(fichtm,optionfilehtm)){ */
7643: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7644: fclose(fichtm);
7645: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7646: fclose(fichtmcov);
7647: fclose(ficgp);
7648: fclose(ficlog);
7649: /*------ End -----------*/
7650:
7651:
7652: printf("Before Current directory %s!\n",pathcd);
7653: #ifdef WIN32
7654: if (_chdir(pathcd) != 0)
7655: printf("Can't move to directory %s!\n",path);
7656: if(_getcwd(pathcd,MAXLINE) > 0)
7657: #else
7658: if(chdir(pathcd) != 0)
7659: printf("Can't move to directory %s!\n", path);
7660: if (getcwd(pathcd, MAXLINE) > 0)
7661: #endif
7662: printf("Current directory %s!\n",pathcd);
7663: /*strcat(plotcmd,CHARSEPARATOR);*/
7664: sprintf(plotcmd,"gnuplot");
7665: #ifdef _WIN32
7666: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7667: #endif
7668: if(!stat(plotcmd,&info)){
7669: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7670: if(!stat(getenv("GNUPLOTBIN"),&info)){
7671: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7672: }else
7673: strcpy(pplotcmd,plotcmd);
7674: #ifdef __unix
7675: strcpy(plotcmd,GNUPLOTPROGRAM);
7676: if(!stat(plotcmd,&info)){
7677: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7678: }else
7679: strcpy(pplotcmd,plotcmd);
7680: #endif
7681: }else
7682: strcpy(pplotcmd,plotcmd);
7683:
7684: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7685: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7686:
7687: if((outcmd=system(plotcmd)) != 0){
7688: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7689: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7690: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7691: if((outcmd=system(plotcmd)) != 0)
7692: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7693: }
7694: printf(" Successful, please wait...");
7695: while (z[0] != 'q') {
7696: /* chdir(path); */
7697: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7698: scanf("%s",z);
7699: /* if (z[0] == 'c') system("./imach"); */
7700: if (z[0] == 'e') {
7701: #ifdef __APPLE__
7702: sprintf(pplotcmd, "open %s", optionfilehtm);
7703: #elif __linux
7704: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7705: #else
7706: sprintf(pplotcmd, "%s", optionfilehtm);
7707: #endif
7708: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7709: system(pplotcmd);
7710: }
7711: else if (z[0] == 'g') system(plotcmd);
7712: else if (z[0] == 'q') exit(0);
7713: }
7714: end:
7715: while (z[0] != 'q') {
7716: printf("\nType q for exiting: ");
7717: scanf("%s",z);
7718: }
7719: }
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