1: /* $Id: imach.c,v 1.193 2015/08/04 07:17:42 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.193 2015/08/04 07:17:42 brouard
5: Summary: 0.98q4
6:
7: Revision 1.192 2015/07/16 16:49:02 brouard
8: Summary: Fixing some outputs
9:
10: Revision 1.191 2015/07/14 10:00:33 brouard
11: Summary: Some fixes
12:
13: Revision 1.190 2015/05/05 08:51:13 brouard
14: Summary: Adding digits in output parameters (7 digits instead of 6)
15:
16: Fix 1+age+.
17:
18: Revision 1.189 2015/04/30 14:45:16 brouard
19: Summary: 0.98q2
20:
21: Revision 1.188 2015/04/30 08:27:53 brouard
22: *** empty log message ***
23:
24: Revision 1.187 2015/04/29 09:11:15 brouard
25: *** empty log message ***
26:
27: Revision 1.186 2015/04/23 12:01:52 brouard
28: Summary: V1*age is working now, version 0.98q1
29:
30: Some codes had been disabled in order to simplify and Vn*age was
31: working in the optimization phase, ie, giving correct MLE parameters,
32: but, as usual, outputs were not correct and program core dumped.
33:
34: Revision 1.185 2015/03/11 13:26:42 brouard
35: Summary: Inclusion of compile and links command line for Intel Compiler
36:
37: Revision 1.184 2015/03/11 11:52:39 brouard
38: Summary: Back from Windows 8. Intel Compiler
39:
40: Revision 1.183 2015/03/10 20:34:32 brouard
41: Summary: 0.98q0, trying with directest, mnbrak fixed
42:
43: We use directest instead of original Powell test; probably no
44: incidence on the results, but better justifications;
45: We fixed Numerical Recipes mnbrak routine which was wrong and gave
46: wrong results.
47:
48: Revision 1.182 2015/02/12 08:19:57 brouard
49: Summary: Trying to keep directest which seems simpler and more general
50: Author: Nicolas Brouard
51:
52: Revision 1.181 2015/02/11 23:22:24 brouard
53: Summary: Comments on Powell added
54:
55: Author:
56:
57: Revision 1.180 2015/02/11 17:33:45 brouard
58: Summary: Finishing move from main to function (hpijx and prevalence_limit)
59:
60: Revision 1.179 2015/01/04 09:57:06 brouard
61: Summary: back to OS/X
62:
63: Revision 1.178 2015/01/04 09:35:48 brouard
64: *** empty log message ***
65:
66: Revision 1.177 2015/01/03 18:40:56 brouard
67: Summary: Still testing ilc32 on OSX
68:
69: Revision 1.176 2015/01/03 16:45:04 brouard
70: *** empty log message ***
71:
72: Revision 1.175 2015/01/03 16:33:42 brouard
73: *** empty log message ***
74:
75: Revision 1.174 2015/01/03 16:15:49 brouard
76: Summary: Still in cross-compilation
77:
78: Revision 1.173 2015/01/03 12:06:26 brouard
79: Summary: trying to detect cross-compilation
80:
81: Revision 1.172 2014/12/27 12:07:47 brouard
82: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
83:
84: Revision 1.171 2014/12/23 13:26:59 brouard
85: Summary: Back from Visual C
86:
87: Still problem with utsname.h on Windows
88:
89: Revision 1.170 2014/12/23 11:17:12 brouard
90: Summary: Cleaning some \%% back to %%
91:
92: The escape was mandatory for a specific compiler (which one?), but too many warnings.
93:
94: Revision 1.169 2014/12/22 23:08:31 brouard
95: Summary: 0.98p
96:
97: Outputs some informations on compiler used, OS etc. Testing on different platforms.
98:
99: Revision 1.168 2014/12/22 15:17:42 brouard
100: Summary: update
101:
102: Revision 1.167 2014/12/22 13:50:56 brouard
103: Summary: Testing uname and compiler version and if compiled 32 or 64
104:
105: Testing on Linux 64
106:
107: Revision 1.166 2014/12/22 11:40:47 brouard
108: *** empty log message ***
109:
110: Revision 1.165 2014/12/16 11:20:36 brouard
111: Summary: After compiling on Visual C
112:
113: * imach.c (Module): Merging 1.61 to 1.162
114:
115: Revision 1.164 2014/12/16 10:52:11 brouard
116: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
117:
118: * imach.c (Module): Merging 1.61 to 1.162
119:
120: Revision 1.163 2014/12/16 10:30:11 brouard
121: * imach.c (Module): Merging 1.61 to 1.162
122:
123: Revision 1.162 2014/09/25 11:43:39 brouard
124: Summary: temporary backup 0.99!
125:
126: Revision 1.1 2014/09/16 11:06:58 brouard
127: Summary: With some code (wrong) for nlopt
128:
129: Author:
130:
131: Revision 1.161 2014/09/15 20:41:41 brouard
132: Summary: Problem with macro SQR on Intel compiler
133:
134: Revision 1.160 2014/09/02 09:24:05 brouard
135: *** empty log message ***
136:
137: Revision 1.159 2014/09/01 10:34:10 brouard
138: Summary: WIN32
139: Author: Brouard
140:
141: Revision 1.158 2014/08/27 17:11:51 brouard
142: *** empty log message ***
143:
144: Revision 1.157 2014/08/27 16:26:55 brouard
145: Summary: Preparing windows Visual studio version
146: Author: Brouard
147:
148: In order to compile on Visual studio, time.h is now correct and time_t
149: and tm struct should be used. difftime should be used but sometimes I
150: just make the differences in raw time format (time(&now).
151: Trying to suppress #ifdef LINUX
152: Add xdg-open for __linux in order to open default browser.
153:
154: Revision 1.156 2014/08/25 20:10:10 brouard
155: *** empty log message ***
156:
157: Revision 1.155 2014/08/25 18:32:34 brouard
158: Summary: New compile, minor changes
159: Author: Brouard
160:
161: Revision 1.154 2014/06/20 17:32:08 brouard
162: Summary: Outputs now all graphs of convergence to period prevalence
163:
164: Revision 1.153 2014/06/20 16:45:46 brouard
165: Summary: If 3 live state, convergence to period prevalence on same graph
166: Author: Brouard
167:
168: Revision 1.152 2014/06/18 17:54:09 brouard
169: Summary: open browser, use gnuplot on same dir than imach if not found in the path
170:
171: Revision 1.151 2014/06/18 16:43:30 brouard
172: *** empty log message ***
173:
174: Revision 1.150 2014/06/18 16:42:35 brouard
175: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
176: Author: brouard
177:
178: Revision 1.149 2014/06/18 15:51:14 brouard
179: Summary: Some fixes in parameter files errors
180: Author: Nicolas Brouard
181:
182: Revision 1.148 2014/06/17 17:38:48 brouard
183: Summary: Nothing new
184: Author: Brouard
185:
186: Just a new packaging for OS/X version 0.98nS
187:
188: Revision 1.147 2014/06/16 10:33:11 brouard
189: *** empty log message ***
190:
191: Revision 1.146 2014/06/16 10:20:28 brouard
192: Summary: Merge
193: Author: Brouard
194:
195: Merge, before building revised version.
196:
197: Revision 1.145 2014/06/10 21:23:15 brouard
198: Summary: Debugging with valgrind
199: Author: Nicolas Brouard
200:
201: Lot of changes in order to output the results with some covariates
202: After the Edimburgh REVES conference 2014, it seems mandatory to
203: improve the code.
204: No more memory valgrind error but a lot has to be done in order to
205: continue the work of splitting the code into subroutines.
206: Also, decodemodel has been improved. Tricode is still not
207: optimal. nbcode should be improved. Documentation has been added in
208: the source code.
209:
210: Revision 1.143 2014/01/26 09:45:38 brouard
211: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
212:
213: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
214: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
215:
216: Revision 1.142 2014/01/26 03:57:36 brouard
217: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
218:
219: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
220:
221: Revision 1.141 2014/01/26 02:42:01 brouard
222: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
223:
224: Revision 1.140 2011/09/02 10:37:54 brouard
225: Summary: times.h is ok with mingw32 now.
226:
227: Revision 1.139 2010/06/14 07:50:17 brouard
228: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
229: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
230:
231: Revision 1.138 2010/04/30 18:19:40 brouard
232: *** empty log message ***
233:
234: Revision 1.137 2010/04/29 18:11:38 brouard
235: (Module): Checking covariates for more complex models
236: than V1+V2. A lot of change to be done. Unstable.
237:
238: Revision 1.136 2010/04/26 20:30:53 brouard
239: (Module): merging some libgsl code. Fixing computation
240: of likelione (using inter/intrapolation if mle = 0) in order to
241: get same likelihood as if mle=1.
242: Some cleaning of code and comments added.
243:
244: Revision 1.135 2009/10/29 15:33:14 brouard
245: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
246:
247: Revision 1.134 2009/10/29 13:18:53 brouard
248: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
249:
250: Revision 1.133 2009/07/06 10:21:25 brouard
251: just nforces
252:
253: Revision 1.132 2009/07/06 08:22:05 brouard
254: Many tings
255:
256: Revision 1.131 2009/06/20 16:22:47 brouard
257: Some dimensions resccaled
258:
259: Revision 1.130 2009/05/26 06:44:34 brouard
260: (Module): Max Covariate is now set to 20 instead of 8. A
261: lot of cleaning with variables initialized to 0. Trying to make
262: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
263:
264: Revision 1.129 2007/08/31 13:49:27 lievre
265: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
266:
267: Revision 1.128 2006/06/30 13:02:05 brouard
268: (Module): Clarifications on computing e.j
269:
270: Revision 1.127 2006/04/28 18:11:50 brouard
271: (Module): Yes the sum of survivors was wrong since
272: imach-114 because nhstepm was no more computed in the age
273: loop. Now we define nhstepma in the age loop.
274: (Module): In order to speed up (in case of numerous covariates) we
275: compute health expectancies (without variances) in a first step
276: and then all the health expectancies with variances or standard
277: deviation (needs data from the Hessian matrices) which slows the
278: computation.
279: In the future we should be able to stop the program is only health
280: expectancies and graph are needed without standard deviations.
281:
282: Revision 1.126 2006/04/28 17:23:28 brouard
283: (Module): Yes the sum of survivors was wrong since
284: imach-114 because nhstepm was no more computed in the age
285: loop. Now we define nhstepma in the age loop.
286: Version 0.98h
287:
288: Revision 1.125 2006/04/04 15:20:31 lievre
289: Errors in calculation of health expectancies. Age was not initialized.
290: Forecasting file added.
291:
292: Revision 1.124 2006/03/22 17:13:53 lievre
293: Parameters are printed with %lf instead of %f (more numbers after the comma).
294: The log-likelihood is printed in the log file
295:
296: Revision 1.123 2006/03/20 10:52:43 brouard
297: * imach.c (Module): <title> changed, corresponds to .htm file
298: name. <head> headers where missing.
299:
300: * imach.c (Module): Weights can have a decimal point as for
301: English (a comma might work with a correct LC_NUMERIC environment,
302: otherwise the weight is truncated).
303: Modification of warning when the covariates values are not 0 or
304: 1.
305: Version 0.98g
306:
307: Revision 1.122 2006/03/20 09:45:41 brouard
308: (Module): Weights can have a decimal point as for
309: English (a comma might work with a correct LC_NUMERIC environment,
310: otherwise the weight is truncated).
311: Modification of warning when the covariates values are not 0 or
312: 1.
313: Version 0.98g
314:
315: Revision 1.121 2006/03/16 17:45:01 lievre
316: * imach.c (Module): Comments concerning covariates added
317:
318: * imach.c (Module): refinements in the computation of lli if
319: status=-2 in order to have more reliable computation if stepm is
320: not 1 month. Version 0.98f
321:
322: Revision 1.120 2006/03/16 15:10:38 lievre
323: (Module): refinements in the computation of lli if
324: status=-2 in order to have more reliable computation if stepm is
325: not 1 month. Version 0.98f
326:
327: Revision 1.119 2006/03/15 17:42:26 brouard
328: (Module): Bug if status = -2, the loglikelihood was
329: computed as likelihood omitting the logarithm. Version O.98e
330:
331: Revision 1.118 2006/03/14 18:20:07 brouard
332: (Module): varevsij Comments added explaining the second
333: table of variances if popbased=1 .
334: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
335: (Module): Function pstamp added
336: (Module): Version 0.98d
337:
338: Revision 1.117 2006/03/14 17:16:22 brouard
339: (Module): varevsij Comments added explaining the second
340: table of variances if popbased=1 .
341: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
342: (Module): Function pstamp added
343: (Module): Version 0.98d
344:
345: Revision 1.116 2006/03/06 10:29:27 brouard
346: (Module): Variance-covariance wrong links and
347: varian-covariance of ej. is needed (Saito).
348:
349: Revision 1.115 2006/02/27 12:17:45 brouard
350: (Module): One freematrix added in mlikeli! 0.98c
351:
352: Revision 1.114 2006/02/26 12:57:58 brouard
353: (Module): Some improvements in processing parameter
354: filename with strsep.
355:
356: Revision 1.113 2006/02/24 14:20:24 brouard
357: (Module): Memory leaks checks with valgrind and:
358: datafile was not closed, some imatrix were not freed and on matrix
359: allocation too.
360:
361: Revision 1.112 2006/01/30 09:55:26 brouard
362: (Module): Back to gnuplot.exe instead of wgnuplot.exe
363:
364: Revision 1.111 2006/01/25 20:38:18 brouard
365: (Module): Lots of cleaning and bugs added (Gompertz)
366: (Module): Comments can be added in data file. Missing date values
367: can be a simple dot '.'.
368:
369: Revision 1.110 2006/01/25 00:51:50 brouard
370: (Module): Lots of cleaning and bugs added (Gompertz)
371:
372: Revision 1.109 2006/01/24 19:37:15 brouard
373: (Module): Comments (lines starting with a #) are allowed in data.
374:
375: Revision 1.108 2006/01/19 18:05:42 lievre
376: Gnuplot problem appeared...
377: To be fixed
378:
379: Revision 1.107 2006/01/19 16:20:37 brouard
380: Test existence of gnuplot in imach path
381:
382: Revision 1.106 2006/01/19 13:24:36 brouard
383: Some cleaning and links added in html output
384:
385: Revision 1.105 2006/01/05 20:23:19 lievre
386: *** empty log message ***
387:
388: Revision 1.104 2005/09/30 16:11:43 lievre
389: (Module): sump fixed, loop imx fixed, and simplifications.
390: (Module): If the status is missing at the last wave but we know
391: that the person is alive, then we can code his/her status as -2
392: (instead of missing=-1 in earlier versions) and his/her
393: contributions to the likelihood is 1 - Prob of dying from last
394: health status (= 1-p13= p11+p12 in the easiest case of somebody in
395: the healthy state at last known wave). Version is 0.98
396:
397: Revision 1.103 2005/09/30 15:54:49 lievre
398: (Module): sump fixed, loop imx fixed, and simplifications.
399:
400: Revision 1.102 2004/09/15 17:31:30 brouard
401: Add the possibility to read data file including tab characters.
402:
403: Revision 1.101 2004/09/15 10:38:38 brouard
404: Fix on curr_time
405:
406: Revision 1.100 2004/07/12 18:29:06 brouard
407: Add version for Mac OS X. Just define UNIX in Makefile
408:
409: Revision 1.99 2004/06/05 08:57:40 brouard
410: *** empty log message ***
411:
412: Revision 1.98 2004/05/16 15:05:56 brouard
413: New version 0.97 . First attempt to estimate force of mortality
414: directly from the data i.e. without the need of knowing the health
415: state at each age, but using a Gompertz model: log u =a + b*age .
416: This is the basic analysis of mortality and should be done before any
417: other analysis, in order to test if the mortality estimated from the
418: cross-longitudinal survey is different from the mortality estimated
419: from other sources like vital statistic data.
420:
421: The same imach parameter file can be used but the option for mle should be -3.
422:
423: Agnès, who wrote this part of the code, tried to keep most of the
424: former routines in order to include the new code within the former code.
425:
426: The output is very simple: only an estimate of the intercept and of
427: the slope with 95% confident intervals.
428:
429: Current limitations:
430: A) Even if you enter covariates, i.e. with the
431: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
432: B) There is no computation of Life Expectancy nor Life Table.
433:
434: Revision 1.97 2004/02/20 13:25:42 lievre
435: Version 0.96d. Population forecasting command line is (temporarily)
436: suppressed.
437:
438: Revision 1.96 2003/07/15 15:38:55 brouard
439: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
440: rewritten within the same printf. Workaround: many printfs.
441:
442: Revision 1.95 2003/07/08 07:54:34 brouard
443: * imach.c (Repository):
444: (Repository): Using imachwizard code to output a more meaningful covariance
445: matrix (cov(a12,c31) instead of numbers.
446:
447: Revision 1.94 2003/06/27 13:00:02 brouard
448: Just cleaning
449:
450: Revision 1.93 2003/06/25 16:33:55 brouard
451: (Module): On windows (cygwin) function asctime_r doesn't
452: exist so I changed back to asctime which exists.
453: (Module): Version 0.96b
454:
455: Revision 1.92 2003/06/25 16:30:45 brouard
456: (Module): On windows (cygwin) function asctime_r doesn't
457: exist so I changed back to asctime which exists.
458:
459: Revision 1.91 2003/06/25 15:30:29 brouard
460: * imach.c (Repository): Duplicated warning errors corrected.
461: (Repository): Elapsed time after each iteration is now output. It
462: helps to forecast when convergence will be reached. Elapsed time
463: is stamped in powell. We created a new html file for the graphs
464: concerning matrix of covariance. It has extension -cov.htm.
465:
466: Revision 1.90 2003/06/24 12:34:15 brouard
467: (Module): Some bugs corrected for windows. Also, when
468: mle=-1 a template is output in file "or"mypar.txt with the design
469: of the covariance matrix to be input.
470:
471: Revision 1.89 2003/06/24 12:30:52 brouard
472: (Module): Some bugs corrected for windows. Also, when
473: mle=-1 a template is output in file "or"mypar.txt with the design
474: of the covariance matrix to be input.
475:
476: Revision 1.88 2003/06/23 17:54:56 brouard
477: * 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.
478:
479: Revision 1.87 2003/06/18 12:26:01 brouard
480: Version 0.96
481:
482: Revision 1.86 2003/06/17 20:04:08 brouard
483: (Module): Change position of html and gnuplot routines and added
484: routine fileappend.
485:
486: Revision 1.85 2003/06/17 13:12:43 brouard
487: * imach.c (Repository): Check when date of death was earlier that
488: current date of interview. It may happen when the death was just
489: prior to the death. In this case, dh was negative and likelihood
490: was wrong (infinity). We still send an "Error" but patch by
491: assuming that the date of death was just one stepm after the
492: interview.
493: (Repository): Because some people have very long ID (first column)
494: we changed int to long in num[] and we added a new lvector for
495: memory allocation. But we also truncated to 8 characters (left
496: truncation)
497: (Repository): No more line truncation errors.
498:
499: Revision 1.84 2003/06/13 21:44:43 brouard
500: * imach.c (Repository): Replace "freqsummary" at a correct
501: place. It differs from routine "prevalence" which may be called
502: many times. Probs is memory consuming and must be used with
503: parcimony.
504: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
505:
506: Revision 1.83 2003/06/10 13:39:11 lievre
507: *** empty log message ***
508:
509: Revision 1.82 2003/06/05 15:57:20 brouard
510: Add log in imach.c and fullversion number is now printed.
511:
512: */
513: /*
514: Interpolated Markov Chain
515:
516: Short summary of the programme:
517:
518: This program computes Healthy Life Expectancies from
519: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
520: first survey ("cross") where individuals from different ages are
521: interviewed on their health status or degree of disability (in the
522: case of a health survey which is our main interest) -2- at least a
523: second wave of interviews ("longitudinal") which measure each change
524: (if any) in individual health status. Health expectancies are
525: computed from the time spent in each health state according to a
526: model. More health states you consider, more time is necessary to reach the
527: Maximum Likelihood of the parameters involved in the model. The
528: simplest model is the multinomial logistic model where pij is the
529: probability to be observed in state j at the second wave
530: conditional to be observed in state i at the first wave. Therefore
531: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
532: 'age' is age and 'sex' is a covariate. If you want to have a more
533: complex model than "constant and age", you should modify the program
534: where the markup *Covariates have to be included here again* invites
535: you to do it. More covariates you add, slower the
536: convergence.
537:
538: The advantage of this computer programme, compared to a simple
539: multinomial logistic model, is clear when the delay between waves is not
540: identical for each individual. Also, if a individual missed an
541: intermediate interview, the information is lost, but taken into
542: account using an interpolation or extrapolation.
543:
544: hPijx is the probability to be observed in state i at age x+h
545: conditional to the observed state i at age x. The delay 'h' can be
546: split into an exact number (nh*stepm) of unobserved intermediate
547: states. This elementary transition (by month, quarter,
548: semester or year) is modelled as a multinomial logistic. The hPx
549: matrix is simply the matrix product of nh*stepm elementary matrices
550: and the contribution of each individual to the likelihood is simply
551: hPijx.
552:
553: Also this programme outputs the covariance matrix of the parameters but also
554: of the life expectancies. It also computes the period (stable) prevalence.
555:
556: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
557: Institut national d'études démographiques, Paris.
558: This software have been partly granted by Euro-REVES, a concerted action
559: from the European Union.
560: It is copyrighted identically to a GNU software product, ie programme and
561: software can be distributed freely for non commercial use. Latest version
562: can be accessed at http://euroreves.ined.fr/imach .
563:
564: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
565: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
566:
567: **********************************************************************/
568: /*
569: main
570: read parameterfile
571: read datafile
572: concatwav
573: freqsummary
574: if (mle >= 1)
575: mlikeli
576: print results files
577: if mle==1
578: computes hessian
579: read end of parameter file: agemin, agemax, bage, fage, estepm
580: begin-prev-date,...
581: open gnuplot file
582: open html file
583: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
584: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
585: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
586: freexexit2 possible for memory heap.
587:
588: h Pij x | pij_nom ficrestpij
589: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
590: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
591: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
592:
593: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
594: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
595: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
596: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
597: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
598:
599: forecasting if prevfcast==1 prevforecast call prevalence()
600: health expectancies
601: Variance-covariance of DFLE
602: prevalence()
603: movingaverage()
604: varevsij()
605: if popbased==1 varevsij(,popbased)
606: total life expectancies
607: Variance of period (stable) prevalence
608: end
609: */
610:
611: /* #define DEBUG */
612: /* #define DEBUGBRENT */
613: #define POWELL /* Instead of NLOPT */
614: #define POWELLF1F3 /* Skip test */
615: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
616: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
617:
618: #include <math.h>
619: #include <stdio.h>
620: #include <stdlib.h>
621: #include <string.h>
622:
623: #ifdef _WIN32
624: #include <io.h>
625: #include <windows.h>
626: #include <tchar.h>
627: #else
628: #include <unistd.h>
629: #endif
630:
631: #include <limits.h>
632: #include <sys/types.h>
633:
634: #if defined(__GNUC__)
635: #include <sys/utsname.h> /* Doesn't work on Windows */
636: #endif
637:
638: #include <sys/stat.h>
639: #include <errno.h>
640: /* extern int errno; */
641:
642: /* #ifdef LINUX */
643: /* #include <time.h> */
644: /* #include "timeval.h" */
645: /* #else */
646: /* #include <sys/time.h> */
647: /* #endif */
648:
649: #include <time.h>
650:
651: #ifdef GSL
652: #include <gsl/gsl_errno.h>
653: #include <gsl/gsl_multimin.h>
654: #endif
655:
656:
657: #ifdef NLOPT
658: #include <nlopt.h>
659: typedef struct {
660: double (* function)(double [] );
661: } myfunc_data ;
662: #endif
663:
664: /* #include <libintl.h> */
665: /* #define _(String) gettext (String) */
666:
667: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
668:
669: #define GNUPLOTPROGRAM "gnuplot"
670: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
671: #define FILENAMELENGTH 132
672:
673: #define GLOCK_ERROR_NOPATH -1 /* empty path */
674: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
675:
676: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
677: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
678:
679: #define NINTERVMAX 8
680: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
681: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
682: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
683: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
684: #define MAXN 20000
685: #define YEARM 12. /**< Number of months per year */
686: #define AGESUP 130
687: #define AGEBASE 40
688: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
689: #ifdef _WIN32
690: #define DIRSEPARATOR '\\'
691: #define CHARSEPARATOR "\\"
692: #define ODIRSEPARATOR '/'
693: #else
694: #define DIRSEPARATOR '/'
695: #define CHARSEPARATOR "/"
696: #define ODIRSEPARATOR '\\'
697: #endif
698:
699: /* $Id: imach.c,v 1.193 2015/08/04 07:17:42 brouard Exp $ */
700: /* $State: Exp $ */
701:
702: char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
703: char fullversion[]="$Revision: 1.193 $ $Date: 2015/08/04 07:17:42 $";
704: char strstart[80];
705: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
706: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
707: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
708: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
709: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
710: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
711: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
712: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
713: int cptcovprodnoage=0; /**< Number of covariate products without age */
714: int cptcoveff=0; /* Total number of covariates to vary for printing results */
715: int cptcov=0; /* Working variable */
716: int npar=NPARMAX;
717: int nlstate=2; /* Number of live states */
718: int ndeath=1; /* Number of dead states */
719: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
720: int popbased=0;
721:
722: int *wav; /* Number of waves for this individuual 0 is possible */
723: int maxwav=0; /* Maxim number of waves */
724: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
725: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
726: int gipmx=0, gsw=0; /* Global variables on the number of contributions
727: to the likelihood and the sum of weights (done by funcone)*/
728: int mle=1, weightopt=0;
729: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
730: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
731: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
732: * wave mi and wave mi+1 is not an exact multiple of stepm. */
733: int countcallfunc=0; /* Count the number of calls to func */
734: double jmean=1; /* Mean space between 2 waves */
735: double **matprod2(); /* test */
736: double **oldm, **newm, **savm; /* Working pointers to matrices */
737: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
738: /*FILE *fic ; */ /* Used in readdata only */
739: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
740: FILE *ficlog, *ficrespow;
741: int globpr=0; /* Global variable for printing or not */
742: double fretone; /* Only one call to likelihood */
743: long ipmx=0; /* Number of contributions */
744: double sw; /* Sum of weights */
745: char filerespow[FILENAMELENGTH];
746: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
747: FILE *ficresilk;
748: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
749: FILE *ficresprobmorprev;
750: FILE *fichtm, *fichtmcov; /* Html File */
751: FILE *ficreseij;
752: char filerese[FILENAMELENGTH];
753: FILE *ficresstdeij;
754: char fileresstde[FILENAMELENGTH];
755: FILE *ficrescveij;
756: char filerescve[FILENAMELENGTH];
757: FILE *ficresvij;
758: char fileresv[FILENAMELENGTH];
759: FILE *ficresvpl;
760: char fileresvpl[FILENAMELENGTH];
761: char title[MAXLINE];
762: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
763: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
764: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
765: char command[FILENAMELENGTH];
766: int outcmd=0;
767:
768: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
769:
770: char filelog[FILENAMELENGTH]; /* Log file */
771: char filerest[FILENAMELENGTH];
772: char fileregp[FILENAMELENGTH];
773: char popfile[FILENAMELENGTH];
774:
775: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
776:
777: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
778: /* struct timezone tzp; */
779: /* extern int gettimeofday(); */
780: struct tm tml, *gmtime(), *localtime();
781:
782: extern time_t time();
783:
784: struct tm start_time, end_time, curr_time, last_time, forecast_time;
785: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
786: struct tm tm;
787:
788: char strcurr[80], strfor[80];
789:
790: char *endptr;
791: long lval;
792: double dval;
793:
794: #define NR_END 1
795: #define FREE_ARG char*
796: #define FTOL 1.0e-10
797:
798: #define NRANSI
799: #define ITMAX 200
800:
801: #define TOL 2.0e-4
802:
803: #define CGOLD 0.3819660
804: #define ZEPS 1.0e-10
805: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
806:
807: #define GOLD 1.618034
808: #define GLIMIT 100.0
809: #define TINY 1.0e-20
810:
811: static double maxarg1,maxarg2;
812: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
813: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
814:
815: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
816: #define rint(a) floor(a+0.5)
817: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
818: #define mytinydouble 1.0e-16
819: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
820: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
821: /* static double dsqrarg; */
822: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
823: static double sqrarg;
824: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
825: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
826: int agegomp= AGEGOMP;
827:
828: int imx;
829: int stepm=1;
830: /* Stepm, step in month: minimum step interpolation*/
831:
832: int estepm;
833: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
834:
835: int m,nb;
836: long *num;
837: int firstpass=0, lastpass=4,*cod, *Tage,*cens;
838: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
839: covariate for which somebody answered excluding
840: undefined. Usually 2: 0 and 1. */
841: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
842: covariate for which somebody answered including
843: undefined. Usually 3: -1, 0 and 1. */
844: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
845: double **pmmij, ***probs;
846: double *ageexmed,*agecens;
847: double dateintmean=0;
848:
849: double *weight;
850: int **s; /* Status */
851: double *agedc;
852: double **covar; /**< covar[j,i], value of jth covariate for individual i,
853: * covar=matrix(0,NCOVMAX,1,n);
854: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
855: double idx;
856: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
857: int *Ndum; /** Freq of modality (tricode */
858: int **codtab; /**< codtab=imatrix(1,100,1,10); */
859: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
860: double *lsurv, *lpop, *tpop;
861:
862: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
863: double ftolhess; /**< Tolerance for computing hessian */
864:
865: /**************** split *************************/
866: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
867: {
868: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
869: the name of the file (name), its extension only (ext) and its first part of the name (finame)
870: */
871: char *ss; /* pointer */
872: int l1=0, l2=0; /* length counters */
873:
874: l1 = strlen(path ); /* length of path */
875: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
876: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
877: if ( ss == NULL ) { /* no directory, so determine current directory */
878: strcpy( name, path ); /* we got the fullname name because no directory */
879: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
880: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
881: /* get current working directory */
882: /* extern char* getcwd ( char *buf , int len);*/
883: #ifdef WIN32
884: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
885: #else
886: if (getcwd(dirc, FILENAME_MAX) == NULL) {
887: #endif
888: return( GLOCK_ERROR_GETCWD );
889: }
890: /* got dirc from getcwd*/
891: printf(" DIRC = %s \n",dirc);
892: } else { /* strip direcotry from path */
893: ss++; /* after this, the filename */
894: l2 = strlen( ss ); /* length of filename */
895: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
896: strcpy( name, ss ); /* save file name */
897: strncpy( dirc, path, l1 - l2 ); /* now the directory */
898: dirc[l1-l2] = '\0'; /* add zero */
899: printf(" DIRC2 = %s \n",dirc);
900: }
901: /* We add a separator at the end of dirc if not exists */
902: l1 = strlen( dirc ); /* length of directory */
903: if( dirc[l1-1] != DIRSEPARATOR ){
904: dirc[l1] = DIRSEPARATOR;
905: dirc[l1+1] = 0;
906: printf(" DIRC3 = %s \n",dirc);
907: }
908: ss = strrchr( name, '.' ); /* find last / */
909: if (ss >0){
910: ss++;
911: strcpy(ext,ss); /* save extension */
912: l1= strlen( name);
913: l2= strlen(ss)+1;
914: strncpy( finame, name, l1-l2);
915: finame[l1-l2]= 0;
916: }
917:
918: return( 0 ); /* we're done */
919: }
920:
921:
922: /******************************************/
923:
924: void replace_back_to_slash(char *s, char*t)
925: {
926: int i;
927: int lg=0;
928: i=0;
929: lg=strlen(t);
930: for(i=0; i<= lg; i++) {
931: (s[i] = t[i]);
932: if (t[i]== '\\') s[i]='/';
933: }
934: }
935:
936: char *trimbb(char *out, char *in)
937: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
938: char *s;
939: s=out;
940: while (*in != '\0'){
941: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
942: in++;
943: }
944: *out++ = *in++;
945: }
946: *out='\0';
947: return s;
948: }
949:
950: /* char *substrchaine(char *out, char *in, char *chain) */
951: /* { */
952: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
953: /* char *s, *t; */
954: /* t=in;s=out; */
955: /* while ((*in != *chain) && (*in != '\0')){ */
956: /* *out++ = *in++; */
957: /* } */
958:
959: /* /\* *in matches *chain *\/ */
960: /* while ((*in++ == *chain++) && (*in != '\0')){ */
961: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
962: /* } */
963: /* in--; chain--; */
964: /* while ( (*in != '\0')){ */
965: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
966: /* *out++ = *in++; */
967: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
968: /* } */
969: /* *out='\0'; */
970: /* out=s; */
971: /* return out; */
972: /* } */
973: char *substrchaine(char *out, char *in, char *chain)
974: {
975: /* Substract chain 'chain' from 'in', return and output 'out' */
976: /* in="V1+V1*age+age*age+V2", chain="age*age" */
977:
978: char *strloc;
979:
980: strcpy (out, in);
981: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
982: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
983: if(strloc != NULL){
984: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
985: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
986: /* strcpy (strloc, strloc +strlen(chain));*/
987: }
988: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
989: return out;
990: }
991:
992:
993: char *cutl(char *blocc, char *alocc, char *in, char occ)
994: {
995: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
996: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
997: gives blocc="abcdef" and alocc="ghi2j".
998: If occ is not found blocc is null and alocc is equal to in. Returns blocc
999: */
1000: char *s, *t;
1001: t=in;s=in;
1002: while ((*in != occ) && (*in != '\0')){
1003: *alocc++ = *in++;
1004: }
1005: if( *in == occ){
1006: *(alocc)='\0';
1007: s=++in;
1008: }
1009:
1010: if (s == t) {/* occ not found */
1011: *(alocc-(in-s))='\0';
1012: in=s;
1013: }
1014: while ( *in != '\0'){
1015: *blocc++ = *in++;
1016: }
1017:
1018: *blocc='\0';
1019: return t;
1020: }
1021: char *cutv(char *blocc, char *alocc, char *in, char occ)
1022: {
1023: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1024: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1025: gives blocc="abcdef2ghi" and alocc="j".
1026: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1027: */
1028: char *s, *t;
1029: t=in;s=in;
1030: while (*in != '\0'){
1031: while( *in == occ){
1032: *blocc++ = *in++;
1033: s=in;
1034: }
1035: *blocc++ = *in++;
1036: }
1037: if (s == t) /* occ not found */
1038: *(blocc-(in-s))='\0';
1039: else
1040: *(blocc-(in-s)-1)='\0';
1041: in=s;
1042: while ( *in != '\0'){
1043: *alocc++ = *in++;
1044: }
1045:
1046: *alocc='\0';
1047: return s;
1048: }
1049:
1050: int nbocc(char *s, char occ)
1051: {
1052: int i,j=0;
1053: int lg=20;
1054: i=0;
1055: lg=strlen(s);
1056: for(i=0; i<= lg; i++) {
1057: if (s[i] == occ ) j++;
1058: }
1059: return j;
1060: }
1061:
1062: /* void cutv(char *u,char *v, char*t, char occ) */
1063: /* { */
1064: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1065: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1066: /* gives u="abcdef2ghi" and v="j" *\/ */
1067: /* int i,lg,j,p=0; */
1068: /* i=0; */
1069: /* lg=strlen(t); */
1070: /* for(j=0; j<=lg-1; j++) { */
1071: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1072: /* } */
1073:
1074: /* for(j=0; j<p; j++) { */
1075: /* (u[j] = t[j]); */
1076: /* } */
1077: /* u[p]='\0'; */
1078:
1079: /* for(j=0; j<= lg; j++) { */
1080: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1081: /* } */
1082: /* } */
1083:
1084: #ifdef _WIN32
1085: char * strsep(char **pp, const char *delim)
1086: {
1087: char *p, *q;
1088:
1089: if ((p = *pp) == NULL)
1090: return 0;
1091: if ((q = strpbrk (p, delim)) != NULL)
1092: {
1093: *pp = q + 1;
1094: *q = '\0';
1095: }
1096: else
1097: *pp = 0;
1098: return p;
1099: }
1100: #endif
1101:
1102: /********************** nrerror ********************/
1103:
1104: void nrerror(char error_text[])
1105: {
1106: fprintf(stderr,"ERREUR ...\n");
1107: fprintf(stderr,"%s\n",error_text);
1108: exit(EXIT_FAILURE);
1109: }
1110: /*********************** vector *******************/
1111: double *vector(int nl, int nh)
1112: {
1113: double *v;
1114: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1115: if (!v) nrerror("allocation failure in vector");
1116: return v-nl+NR_END;
1117: }
1118:
1119: /************************ free vector ******************/
1120: void free_vector(double*v, int nl, int nh)
1121: {
1122: free((FREE_ARG)(v+nl-NR_END));
1123: }
1124:
1125: /************************ivector *******************************/
1126: int *ivector(long nl,long nh)
1127: {
1128: int *v;
1129: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1130: if (!v) nrerror("allocation failure in ivector");
1131: return v-nl+NR_END;
1132: }
1133:
1134: /******************free ivector **************************/
1135: void free_ivector(int *v, long nl, long nh)
1136: {
1137: free((FREE_ARG)(v+nl-NR_END));
1138: }
1139:
1140: /************************lvector *******************************/
1141: long *lvector(long nl,long nh)
1142: {
1143: long *v;
1144: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1145: if (!v) nrerror("allocation failure in ivector");
1146: return v-nl+NR_END;
1147: }
1148:
1149: /******************free lvector **************************/
1150: void free_lvector(long *v, long nl, long nh)
1151: {
1152: free((FREE_ARG)(v+nl-NR_END));
1153: }
1154:
1155: /******************* imatrix *******************************/
1156: int **imatrix(long nrl, long nrh, long ncl, long nch)
1157: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1158: {
1159: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1160: int **m;
1161:
1162: /* allocate pointers to rows */
1163: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1164: if (!m) nrerror("allocation failure 1 in matrix()");
1165: m += NR_END;
1166: m -= nrl;
1167:
1168:
1169: /* allocate rows and set pointers to them */
1170: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1171: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1172: m[nrl] += NR_END;
1173: m[nrl] -= ncl;
1174:
1175: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1176:
1177: /* return pointer to array of pointers to rows */
1178: return m;
1179: }
1180:
1181: /****************** free_imatrix *************************/
1182: void free_imatrix(m,nrl,nrh,ncl,nch)
1183: int **m;
1184: long nch,ncl,nrh,nrl;
1185: /* free an int matrix allocated by imatrix() */
1186: {
1187: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1188: free((FREE_ARG) (m+nrl-NR_END));
1189: }
1190:
1191: /******************* matrix *******************************/
1192: double **matrix(long nrl, long nrh, long ncl, long nch)
1193: {
1194: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1195: double **m;
1196:
1197: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1198: if (!m) nrerror("allocation failure 1 in matrix()");
1199: m += NR_END;
1200: m -= nrl;
1201:
1202: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1203: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1204: m[nrl] += NR_END;
1205: m[nrl] -= ncl;
1206:
1207: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1208: return m;
1209: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1210: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1211: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1212: */
1213: }
1214:
1215: /*************************free matrix ************************/
1216: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1217: {
1218: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1219: free((FREE_ARG)(m+nrl-NR_END));
1220: }
1221:
1222: /******************* ma3x *******************************/
1223: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1224: {
1225: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1226: double ***m;
1227:
1228: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1229: if (!m) nrerror("allocation failure 1 in matrix()");
1230: m += NR_END;
1231: m -= nrl;
1232:
1233: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1234: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1235: m[nrl] += NR_END;
1236: m[nrl] -= ncl;
1237:
1238: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1239:
1240: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1241: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1242: m[nrl][ncl] += NR_END;
1243: m[nrl][ncl] -= nll;
1244: for (j=ncl+1; j<=nch; j++)
1245: m[nrl][j]=m[nrl][j-1]+nlay;
1246:
1247: for (i=nrl+1; i<=nrh; i++) {
1248: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1249: for (j=ncl+1; j<=nch; j++)
1250: m[i][j]=m[i][j-1]+nlay;
1251: }
1252: return m;
1253: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1254: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1255: */
1256: }
1257:
1258: /*************************free ma3x ************************/
1259: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1260: {
1261: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1262: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1263: free((FREE_ARG)(m+nrl-NR_END));
1264: }
1265:
1266: /*************** function subdirf ***********/
1267: char *subdirf(char fileres[])
1268: {
1269: /* Caution optionfilefiname is hidden */
1270: strcpy(tmpout,optionfilefiname);
1271: strcat(tmpout,"/"); /* Add to the right */
1272: strcat(tmpout,fileres);
1273: return tmpout;
1274: }
1275:
1276: /*************** function subdirf2 ***********/
1277: char *subdirf2(char fileres[], char *preop)
1278: {
1279:
1280: /* Caution optionfilefiname is hidden */
1281: strcpy(tmpout,optionfilefiname);
1282: strcat(tmpout,"/");
1283: strcat(tmpout,preop);
1284: strcat(tmpout,fileres);
1285: return tmpout;
1286: }
1287:
1288: /*************** function subdirf3 ***********/
1289: char *subdirf3(char fileres[], char *preop, char *preop2)
1290: {
1291:
1292: /* Caution optionfilefiname is hidden */
1293: strcpy(tmpout,optionfilefiname);
1294: strcat(tmpout,"/");
1295: strcat(tmpout,preop);
1296: strcat(tmpout,preop2);
1297: strcat(tmpout,fileres);
1298: return tmpout;
1299: }
1300:
1301: char *asc_diff_time(long time_sec, char ascdiff[])
1302: {
1303: long sec_left, days, hours, minutes;
1304: days = (time_sec) / (60*60*24);
1305: sec_left = (time_sec) % (60*60*24);
1306: hours = (sec_left) / (60*60) ;
1307: sec_left = (sec_left) %(60*60);
1308: minutes = (sec_left) /60;
1309: sec_left = (sec_left) % (60);
1310: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1311: return ascdiff;
1312: }
1313:
1314: /***************** f1dim *************************/
1315: extern int ncom;
1316: extern double *pcom,*xicom;
1317: extern double (*nrfunc)(double []);
1318:
1319: double f1dim(double x)
1320: {
1321: int j;
1322: double f;
1323: double *xt;
1324:
1325: xt=vector(1,ncom);
1326: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1327: f=(*nrfunc)(xt);
1328: free_vector(xt,1,ncom);
1329: return f;
1330: }
1331:
1332: /*****************brent *************************/
1333: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1334: {
1335: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1336: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1337: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1338: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1339: * returned function value.
1340: */
1341: int iter;
1342: double a,b,d,etemp;
1343: double fu=0,fv,fw,fx;
1344: double ftemp=0.;
1345: double p,q,r,tol1,tol2,u,v,w,x,xm;
1346: double e=0.0;
1347:
1348: a=(ax < cx ? ax : cx);
1349: b=(ax > cx ? ax : cx);
1350: x=w=v=bx;
1351: fw=fv=fx=(*f)(x);
1352: for (iter=1;iter<=ITMAX;iter++) {
1353: xm=0.5*(a+b);
1354: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1355: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1356: printf(".");fflush(stdout);
1357: fprintf(ficlog,".");fflush(ficlog);
1358: #ifdef DEBUGBRENT
1359: 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);
1360: 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);
1361: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1362: #endif
1363: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1364: *xmin=x;
1365: return fx;
1366: }
1367: ftemp=fu;
1368: if (fabs(e) > tol1) {
1369: r=(x-w)*(fx-fv);
1370: q=(x-v)*(fx-fw);
1371: p=(x-v)*q-(x-w)*r;
1372: q=2.0*(q-r);
1373: if (q > 0.0) p = -p;
1374: q=fabs(q);
1375: etemp=e;
1376: e=d;
1377: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1378: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1379: else {
1380: d=p/q;
1381: u=x+d;
1382: if (u-a < tol2 || b-u < tol2)
1383: d=SIGN(tol1,xm-x);
1384: }
1385: } else {
1386: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1387: }
1388: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1389: fu=(*f)(u);
1390: if (fu <= fx) {
1391: if (u >= x) a=x; else b=x;
1392: SHFT(v,w,x,u)
1393: SHFT(fv,fw,fx,fu)
1394: } else {
1395: if (u < x) a=u; else b=u;
1396: if (fu <= fw || w == x) {
1397: v=w;
1398: w=u;
1399: fv=fw;
1400: fw=fu;
1401: } else if (fu <= fv || v == x || v == w) {
1402: v=u;
1403: fv=fu;
1404: }
1405: }
1406: }
1407: nrerror("Too many iterations in brent");
1408: *xmin=x;
1409: return fx;
1410: }
1411:
1412: /****************** mnbrak ***********************/
1413:
1414: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1415: double (*func)(double))
1416: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1417: the downhill direction (defined by the function as evaluated at the initial points) and returns
1418: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1419: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1420: */
1421: double ulim,u,r,q, dum;
1422: double fu;
1423:
1424: double scale=10.;
1425: int iterscale=0;
1426:
1427: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1428: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1429:
1430:
1431: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1432: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1433: /* *bx = *ax - (*ax - *bx)/scale; */
1434: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1435: /* } */
1436:
1437: if (*fb > *fa) {
1438: SHFT(dum,*ax,*bx,dum)
1439: SHFT(dum,*fb,*fa,dum)
1440: }
1441: *cx=(*bx)+GOLD*(*bx-*ax);
1442: *fc=(*func)(*cx);
1443: #ifdef DEBUG
1444: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1445: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1446: #endif
1447: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1448: r=(*bx-*ax)*(*fb-*fc);
1449: q=(*bx-*cx)*(*fb-*fa);
1450: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1451: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1452: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1453: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1454: fu=(*func)(u);
1455: #ifdef DEBUG
1456: /* f(x)=A(x-u)**2+f(u) */
1457: double A, fparabu;
1458: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1459: fparabu= *fa - A*(*ax-u)*(*ax-u);
1460: 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);
1461: 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);
1462: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1463: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1464: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1465: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1466: #endif
1467: #ifdef MNBRAKORIGINAL
1468: #else
1469: /* if (fu > *fc) { */
1470: /* #ifdef DEBUG */
1471: /* printf("mnbrak4 fu > fc \n"); */
1472: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1473: /* #endif */
1474: /* /\* 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 *\\/ *\/ */
1475: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1476: /* dum=u; /\* Shifting c and u *\/ */
1477: /* u = *cx; */
1478: /* *cx = dum; */
1479: /* dum = fu; */
1480: /* fu = *fc; */
1481: /* *fc =dum; */
1482: /* } else { /\* end *\/ */
1483: /* #ifdef DEBUG */
1484: /* printf("mnbrak3 fu < fc \n"); */
1485: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1486: /* #endif */
1487: /* dum=u; /\* Shifting c and u *\/ */
1488: /* u = *cx; */
1489: /* *cx = dum; */
1490: /* dum = fu; */
1491: /* fu = *fc; */
1492: /* *fc =dum; */
1493: /* } */
1494: #ifdef DEBUG
1495: printf("mnbrak34 fu < or >= fc \n");
1496: fprintf(ficlog, "mnbrak34 fu < fc\n");
1497: #endif
1498: dum=u; /* Shifting c and u */
1499: u = *cx;
1500: *cx = dum;
1501: dum = fu;
1502: fu = *fc;
1503: *fc =dum;
1504: #endif
1505: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1506: #ifdef DEBUG
1507: printf("mnbrak2 u after c but before ulim\n");
1508: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1509: #endif
1510: fu=(*func)(u);
1511: if (fu < *fc) {
1512: #ifdef DEBUG
1513: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1514: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1515: #endif
1516: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1517: SHFT(*fb,*fc,fu,(*func)(u))
1518: }
1519: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1520: #ifdef DEBUG
1521: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1522: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1523: #endif
1524: u=ulim;
1525: fu=(*func)(u);
1526: } else { /* u could be left to b (if r > q parabola has a maximum) */
1527: #ifdef DEBUG
1528: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1529: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1530: #endif
1531: u=(*cx)+GOLD*(*cx-*bx);
1532: fu=(*func)(u);
1533: } /* end tests */
1534: SHFT(*ax,*bx,*cx,u)
1535: SHFT(*fa,*fb,*fc,fu)
1536: #ifdef DEBUG
1537: 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);
1538: 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);
1539: #endif
1540: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1541: }
1542:
1543: /*************** linmin ************************/
1544: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1545: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1546: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1547: the value of func at the returned location p . This is actually all accomplished by calling the
1548: routines mnbrak and brent .*/
1549: int ncom;
1550: double *pcom,*xicom;
1551: double (*nrfunc)(double []);
1552:
1553: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1554: {
1555: double brent(double ax, double bx, double cx,
1556: double (*f)(double), double tol, double *xmin);
1557: double f1dim(double x);
1558: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1559: double *fc, double (*func)(double));
1560: int j;
1561: double xx,xmin,bx,ax;
1562: double fx,fb,fa;
1563:
1564: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1565:
1566: ncom=n;
1567: pcom=vector(1,n);
1568: xicom=vector(1,n);
1569: nrfunc=func;
1570: for (j=1;j<=n;j++) {
1571: pcom[j]=p[j];
1572: xicom[j]=xi[j];
1573: }
1574:
1575: /* axs=0.0; */
1576: /* xxss=1; /\* 1 and using scale *\/ */
1577: xxs=1;
1578: /* do{ */
1579: ax=0.;
1580: xx= xxs;
1581: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1582: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1583: /* 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)) */
1584: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1585: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1586: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1587: /* 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]]*/
1588: /* if (fx != fx){ */
1589: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1590: /* 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); */
1591: /* } */
1592: /* }while(fx != fx); */
1593:
1594: #ifdef DEBUGLINMIN
1595: printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1596: #endif
1597: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1598: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1599: /* fmin = f(p[j] + xmin * xi[j]) */
1600: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1601: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1602: #ifdef DEBUG
1603: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1604: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1605: #endif
1606: #ifdef DEBUGLINMIN
1607: printf("linmin end ");
1608: #endif
1609: for (j=1;j<=n;j++) {
1610: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1611: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1612: /* if(xxs <1.0) */
1613: /* 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 ); */
1614: p[j] += xi[j]; /* Parameters values are updated accordingly */
1615: }
1616: /* printf("\n"); */
1617: #ifdef DEBUGLINMIN
1618: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1619: for (j=1;j<=n;j++) {
1620: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1621: if(j % ncovmodel == 0)
1622: printf("\n");
1623: }
1624: #endif
1625: free_vector(xicom,1,n);
1626: free_vector(pcom,1,n);
1627: }
1628:
1629:
1630: /*************** powell ************************/
1631: /*
1632: Minimization of a function func of n variables. Input consists of an initial starting point
1633: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1634: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1635: such that failure to decrease by more than this amount on one iteration signals doneness. On
1636: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1637: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1638: */
1639: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1640: double (*func)(double []))
1641: {
1642: void linmin(double p[], double xi[], int n, double *fret,
1643: double (*func)(double []));
1644: int i,ibig,j;
1645: double del,t,*pt,*ptt,*xit;
1646: double directest;
1647: double fp,fptt;
1648: double *xits;
1649: int niterf, itmp;
1650:
1651: pt=vector(1,n);
1652: ptt=vector(1,n);
1653: xit=vector(1,n);
1654: xits=vector(1,n);
1655: *fret=(*func)(p);
1656: for (j=1;j<=n;j++) pt[j]=p[j];
1657: rcurr_time = time(NULL);
1658: for (*iter=1;;++(*iter)) {
1659: fp=(*fret); /* From former iteration or initial value */
1660: ibig=0;
1661: del=0.0;
1662: rlast_time=rcurr_time;
1663: /* (void) gettimeofday(&curr_time,&tzp); */
1664: rcurr_time = time(NULL);
1665: curr_time = *localtime(&rcurr_time);
1666: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1667: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1668: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1669: for (i=1;i<=n;i++) {
1670: printf(" %d %.12f",i, p[i]);
1671: fprintf(ficlog," %d %.12lf",i, p[i]);
1672: fprintf(ficrespow," %.12lf", p[i]);
1673: }
1674: printf("\n");
1675: fprintf(ficlog,"\n");
1676: fprintf(ficrespow,"\n");fflush(ficrespow);
1677: if(*iter <=3){
1678: tml = *localtime(&rcurr_time);
1679: strcpy(strcurr,asctime(&tml));
1680: rforecast_time=rcurr_time;
1681: itmp = strlen(strcurr);
1682: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1683: strcurr[itmp-1]='\0';
1684: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1685: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1686: for(niterf=10;niterf<=30;niterf+=10){
1687: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1688: forecast_time = *localtime(&rforecast_time);
1689: strcpy(strfor,asctime(&forecast_time));
1690: itmp = strlen(strfor);
1691: if(strfor[itmp-1]=='\n')
1692: strfor[itmp-1]='\0';
1693: 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);
1694: 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);
1695: }
1696: }
1697: for (i=1;i<=n;i++) { /* For each direction i */
1698: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1699: fptt=(*fret);
1700: #ifdef DEBUG
1701: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1702: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1703: #endif
1704: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1705: fprintf(ficlog,"%d",i);fflush(ficlog);
1706: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1707: /* Outputs are fret(new point p) p is updated and xit rescaled */
1708: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1709: /* because that direction will be replaced unless the gain del is small */
1710: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1711: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1712: /* with the new direction. */
1713: del=fabs(fptt-(*fret));
1714: ibig=i;
1715: }
1716: #ifdef DEBUG
1717: printf("%d %.12e",i,(*fret));
1718: fprintf(ficlog,"%d %.12e",i,(*fret));
1719: for (j=1;j<=n;j++) {
1720: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1721: printf(" x(%d)=%.12e",j,xit[j]);
1722: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1723: }
1724: for(j=1;j<=n;j++) {
1725: printf(" p(%d)=%.12e",j,p[j]);
1726: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1727: }
1728: printf("\n");
1729: fprintf(ficlog,"\n");
1730: #endif
1731: } /* end loop on each direction i */
1732: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1733: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1734: /* New value of last point Pn is not computed, P(n-1) */
1735: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1736: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1737: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1738: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1739: /* decreased of more than 3.84 */
1740: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1741: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1742: /* By adding 10 parameters more the gain should be 18.31 */
1743:
1744: /* Starting the program with initial values given by a former maximization will simply change */
1745: /* the scales of the directions and the directions, because the are reset to canonical directions */
1746: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1747: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1748: #ifdef DEBUG
1749: int k[2],l;
1750: k[0]=1;
1751: k[1]=-1;
1752: printf("Max: %.12e",(*func)(p));
1753: fprintf(ficlog,"Max: %.12e",(*func)(p));
1754: for (j=1;j<=n;j++) {
1755: printf(" %.12e",p[j]);
1756: fprintf(ficlog," %.12e",p[j]);
1757: }
1758: printf("\n");
1759: fprintf(ficlog,"\n");
1760: for(l=0;l<=1;l++) {
1761: for (j=1;j<=n;j++) {
1762: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1763: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1764: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1765: }
1766: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1767: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1768: }
1769: #endif
1770:
1771:
1772: free_vector(xit,1,n);
1773: free_vector(xits,1,n);
1774: free_vector(ptt,1,n);
1775: free_vector(pt,1,n);
1776: return;
1777: } /* enough precision */
1778: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1779: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1780: ptt[j]=2.0*p[j]-pt[j];
1781: xit[j]=p[j]-pt[j];
1782: pt[j]=p[j];
1783: }
1784: fptt=(*func)(ptt); /* f_3 */
1785: #ifdef POWELLF1F3
1786: #else
1787: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1788: #endif
1789: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1790: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1791: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1792: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1793: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1794: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1795: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1796: #ifdef NRCORIGINAL
1797: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1798: #else
1799: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1800: t= t- del*SQR(fp-fptt);
1801: #endif
1802: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1803: #ifdef DEBUG
1804: 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);
1805: 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);
1806: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1807: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1808: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1809: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1810: 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);
1811: 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);
1812: #endif
1813: #ifdef POWELLORIGINAL
1814: if (t < 0.0) { /* Then we use it for new direction */
1815: #else
1816: if (directest*t < 0.0) { /* Contradiction between both tests */
1817: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1818: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1819: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1820: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1821: }
1822: if (directest < 0.0) { /* Then we use it for new direction */
1823: #endif
1824: #ifdef DEBUGLINMIN
1825: printf("Before linmin in direction P%d-P0\n",n);
1826: for (j=1;j<=n;j++) {
1827: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1828: if(j % ncovmodel == 0)
1829: printf("\n");
1830: }
1831: #endif
1832: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1833: #ifdef DEBUGLINMIN
1834: for (j=1;j<=n;j++) {
1835: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1836: if(j % ncovmodel == 0)
1837: printf("\n");
1838: }
1839: #endif
1840: for (j=1;j<=n;j++) {
1841: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1842: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1843: }
1844: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1845: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1846:
1847: #ifdef DEBUG
1848: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1849: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1850: for(j=1;j<=n;j++){
1851: printf(" %.12e",xit[j]);
1852: fprintf(ficlog," %.12e",xit[j]);
1853: }
1854: printf("\n");
1855: fprintf(ficlog,"\n");
1856: #endif
1857: } /* end of t or directest negative */
1858: #ifdef POWELLF1F3
1859: #else
1860: } /* end if (fptt < fp) */
1861: #endif
1862: } /* loop iteration */
1863: }
1864:
1865: /**** Prevalence limit (stable or period prevalence) ****************/
1866:
1867: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1868: {
1869: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1870: matrix by transitions matrix until convergence is reached */
1871:
1872: int i, ii,j,k;
1873: double min, max, maxmin, maxmax,sumnew=0.;
1874: /* double **matprod2(); */ /* test */
1875: double **out, cov[NCOVMAX+1], **pmij();
1876: double **newm;
1877: double agefin, delaymax=50 ; /* Max number of years to converge */
1878:
1879: for (ii=1;ii<=nlstate+ndeath;ii++)
1880: for (j=1;j<=nlstate+ndeath;j++){
1881: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1882: }
1883:
1884: cov[1]=1.;
1885:
1886: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1887: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1888: newm=savm;
1889: /* Covariates have to be included here again */
1890: cov[2]=agefin;
1891: if(nagesqr==1)
1892: cov[3]= agefin*agefin;;
1893: for (k=1; k<=cptcovn;k++) {
1894: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1895: /*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]]);*/
1896: }
1897: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1898: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1899: for (k=1; k<=cptcovprod;k++) /* Useless */
1900: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1901:
1902: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1903: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1904: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1905: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1906: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1907: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1908:
1909: savm=oldm;
1910: oldm=newm;
1911: maxmax=0.;
1912: for(j=1;j<=nlstate;j++){
1913: min=1.;
1914: max=0.;
1915: for(i=1; i<=nlstate; i++) {
1916: sumnew=0;
1917: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1918: prlim[i][j]= newm[i][j]/(1-sumnew);
1919: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1920: max=FMAX(max,prlim[i][j]);
1921: min=FMIN(min,prlim[i][j]);
1922: }
1923: maxmin=max-min;
1924: maxmax=FMAX(maxmax,maxmin);
1925: } /* j loop */
1926: if(maxmax < ftolpl){
1927: return prlim;
1928: }
1929: } /* age loop */
1930: return prlim; /* should not reach here */
1931: }
1932:
1933: /*************** transition probabilities ***************/
1934:
1935: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1936: {
1937: /* According to parameters values stored in x and the covariate's values stored in cov,
1938: computes the probability to be observed in state j being in state i by appying the
1939: model to the ncovmodel covariates (including constant and age).
1940: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1941: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1942: ncth covariate in the global vector x is given by the formula:
1943: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1944: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1945: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1946: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1947: Outputs ps[i][j] the probability to be observed in j being in j according to
1948: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1949: */
1950: double s1, lnpijopii;
1951: /*double t34;*/
1952: int i,j, nc, ii, jj;
1953:
1954: for(i=1; i<= nlstate; i++){
1955: for(j=1; j<i;j++){
1956: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1957: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1958: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1959: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1960: }
1961: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1962: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1963: }
1964: for(j=i+1; j<=nlstate+ndeath;j++){
1965: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1966: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1967: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1968: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1969: }
1970: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1971: }
1972: }
1973:
1974: for(i=1; i<= nlstate; i++){
1975: s1=0;
1976: for(j=1; j<i; j++){
1977: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1978: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1979: }
1980: for(j=i+1; j<=nlstate+ndeath; j++){
1981: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1982: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1983: }
1984: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1985: ps[i][i]=1./(s1+1.);
1986: /* Computing other pijs */
1987: for(j=1; j<i; j++)
1988: ps[i][j]= exp(ps[i][j])*ps[i][i];
1989: for(j=i+1; j<=nlstate+ndeath; j++)
1990: ps[i][j]= exp(ps[i][j])*ps[i][i];
1991: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1992: } /* end i */
1993:
1994: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1995: for(jj=1; jj<= nlstate+ndeath; jj++){
1996: ps[ii][jj]=0;
1997: ps[ii][ii]=1;
1998: }
1999: }
2000:
2001:
2002: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2003: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2004: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2005: /* } */
2006: /* printf("\n "); */
2007: /* } */
2008: /* printf("\n ");printf("%lf ",cov[2]);*/
2009: /*
2010: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2011: goto end;*/
2012: return ps;
2013: }
2014:
2015: /**************** Product of 2 matrices ******************/
2016:
2017: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
2018: {
2019: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2020: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2021: /* in, b, out are matrice of pointers which should have been initialized
2022: before: only the contents of out is modified. The function returns
2023: a pointer to pointers identical to out */
2024: int i, j, k;
2025: for(i=nrl; i<= nrh; i++)
2026: for(k=ncolol; k<=ncoloh; k++){
2027: out[i][k]=0.;
2028: for(j=ncl; j<=nch; j++)
2029: out[i][k] +=in[i][j]*b[j][k];
2030: }
2031: return out;
2032: }
2033:
2034:
2035: /************* Higher Matrix Product ***************/
2036:
2037: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2038: {
2039: /* Computes the transition matrix starting at age 'age' over
2040: 'nhstepm*hstepm*stepm' months (i.e. until
2041: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2042: nhstepm*hstepm matrices.
2043: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2044: (typically every 2 years instead of every month which is too big
2045: for the memory).
2046: Model is determined by parameters x and covariates have to be
2047: included manually here.
2048:
2049: */
2050:
2051: int i, j, d, h, k;
2052: double **out, cov[NCOVMAX+1];
2053: double **newm;
2054: double agexact;
2055:
2056: /* Hstepm could be zero and should return the unit matrix */
2057: for (i=1;i<=nlstate+ndeath;i++)
2058: for (j=1;j<=nlstate+ndeath;j++){
2059: oldm[i][j]=(i==j ? 1.0 : 0.0);
2060: po[i][j][0]=(i==j ? 1.0 : 0.0);
2061: }
2062: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2063: for(h=1; h <=nhstepm; h++){
2064: for(d=1; d <=hstepm; d++){
2065: newm=savm;
2066: /* Covariates have to be included here again */
2067: cov[1]=1.;
2068: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2069: cov[2]=agexact;
2070: if(nagesqr==1)
2071: cov[3]= agexact*agexact;
2072: for (k=1; k<=cptcovn;k++)
2073: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
2074: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2075: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2076: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
2077: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
2078: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2079:
2080:
2081: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2082: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2083: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2084: pmij(pmmij,cov,ncovmodel,x,nlstate));
2085: savm=oldm;
2086: oldm=newm;
2087: }
2088: for(i=1; i<=nlstate+ndeath; i++)
2089: for(j=1;j<=nlstate+ndeath;j++) {
2090: po[i][j][h]=newm[i][j];
2091: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
2092: }
2093: /*printf("h=%d ",h);*/
2094: } /* end h */
2095: /* printf("\n H=%d \n",h); */
2096: return po;
2097: }
2098:
2099: #ifdef NLOPT
2100: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2101: double fret;
2102: double *xt;
2103: int j;
2104: myfunc_data *d2 = (myfunc_data *) pd;
2105: /* xt = (p1-1); */
2106: xt=vector(1,n);
2107: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2108:
2109: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2110: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2111: printf("Function = %.12lf ",fret);
2112: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2113: printf("\n");
2114: free_vector(xt,1,n);
2115: return fret;
2116: }
2117: #endif
2118:
2119: /*************** log-likelihood *************/
2120: double func( double *x)
2121: {
2122: int i, ii, j, k, mi, d, kk;
2123: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2124: double **out;
2125: double sw; /* Sum of weights */
2126: double lli; /* Individual log likelihood */
2127: int s1, s2;
2128: double bbh, survp;
2129: long ipmx;
2130: double agexact;
2131: /*extern weight */
2132: /* We are differentiating ll according to initial status */
2133: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2134: /*for(i=1;i<imx;i++)
2135: printf(" %d\n",s[4][i]);
2136: */
2137:
2138: ++countcallfunc;
2139:
2140: cov[1]=1.;
2141:
2142: for(k=1; k<=nlstate; k++) ll[k]=0.;
2143:
2144: if(mle==1){
2145: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2146: /* Computes the values of the ncovmodel covariates of the model
2147: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2148: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2149: to be observed in j being in i according to the model.
2150: */
2151: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
2152: cov[2+nagesqr+k]=covar[Tvar[k]][i];
2153: }
2154: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2155: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2156: has been calculated etc */
2157: for(mi=1; mi<= wav[i]-1; mi++){
2158: for (ii=1;ii<=nlstate+ndeath;ii++)
2159: for (j=1;j<=nlstate+ndeath;j++){
2160: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2161: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2162: }
2163: for(d=0; d<dh[mi][i]; d++){
2164: newm=savm;
2165: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2166: cov[2]=agexact;
2167: if(nagesqr==1)
2168: cov[3]= agexact*agexact;
2169: for (kk=1; kk<=cptcovage;kk++) {
2170: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
2171: }
2172: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2173: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2174: savm=oldm;
2175: oldm=newm;
2176: } /* end mult */
2177:
2178: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2179: /* But now since version 0.9 we anticipate for bias at large stepm.
2180: * If stepm is larger than one month (smallest stepm) and if the exact delay
2181: * (in months) between two waves is not a multiple of stepm, we rounded to
2182: * the nearest (and in case of equal distance, to the lowest) interval but now
2183: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2184: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2185: * probability in order to take into account the bias as a fraction of the way
2186: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2187: * -stepm/2 to stepm/2 .
2188: * For stepm=1 the results are the same as for previous versions of Imach.
2189: * For stepm > 1 the results are less biased than in previous versions.
2190: */
2191: s1=s[mw[mi][i]][i];
2192: s2=s[mw[mi+1][i]][i];
2193: bbh=(double)bh[mi][i]/(double)stepm;
2194: /* bias bh is positive if real duration
2195: * is higher than the multiple of stepm and negative otherwise.
2196: */
2197: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2198: if( s2 > nlstate){
2199: /* i.e. if s2 is a death state and if the date of death is known
2200: then the contribution to the likelihood is the probability to
2201: die between last step unit time and current step unit time,
2202: which is also equal to probability to die before dh
2203: minus probability to die before dh-stepm .
2204: In version up to 0.92 likelihood was computed
2205: as if date of death was unknown. Death was treated as any other
2206: health state: the date of the interview describes the actual state
2207: and not the date of a change in health state. The former idea was
2208: to consider that at each interview the state was recorded
2209: (healthy, disable or death) and IMaCh was corrected; but when we
2210: introduced the exact date of death then we should have modified
2211: the contribution of an exact death to the likelihood. This new
2212: contribution is smaller and very dependent of the step unit
2213: stepm. It is no more the probability to die between last interview
2214: and month of death but the probability to survive from last
2215: interview up to one month before death multiplied by the
2216: probability to die within a month. Thanks to Chris
2217: Jackson for correcting this bug. Former versions increased
2218: mortality artificially. The bad side is that we add another loop
2219: which slows down the processing. The difference can be up to 10%
2220: lower mortality.
2221: */
2222: /* If, at the beginning of the maximization mostly, the
2223: cumulative probability or probability to be dead is
2224: constant (ie = 1) over time d, the difference is equal to
2225: 0. out[s1][3] = savm[s1][3]: probability, being at state
2226: s1 at precedent wave, to be dead a month before current
2227: wave is equal to probability, being at state s1 at
2228: precedent wave, to be dead at mont of the current
2229: wave. Then the observed probability (that this person died)
2230: is null according to current estimated parameter. In fact,
2231: it should be very low but not zero otherwise the log go to
2232: infinity.
2233: */
2234: /* #ifdef INFINITYORIGINAL */
2235: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2236: /* #else */
2237: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2238: /* lli=log(mytinydouble); */
2239: /* else */
2240: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2241: /* #endif */
2242: lli=log(out[s1][s2] - savm[s1][s2]);
2243:
2244: } else if (s2==-2) {
2245: for (j=1,survp=0. ; j<=nlstate; j++)
2246: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2247: /*survp += out[s1][j]; */
2248: lli= log(survp);
2249: }
2250:
2251: else if (s2==-4) {
2252: for (j=3,survp=0. ; j<=nlstate; j++)
2253: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2254: lli= log(survp);
2255: }
2256:
2257: else if (s2==-5) {
2258: for (j=1,survp=0. ; j<=2; j++)
2259: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2260: lli= log(survp);
2261: }
2262:
2263: else{
2264: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2265: /* 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 */
2266: }
2267: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2268: /*if(lli ==000.0)*/
2269: /*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); */
2270: ipmx +=1;
2271: sw += weight[i];
2272: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2273: /* if (lli < log(mytinydouble)){ */
2274: /* 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); */
2275: /* 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]); */
2276: /* } */
2277: } /* end of wave */
2278: } /* end of individual */
2279: } else if(mle==2){
2280: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2281: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2282: for(mi=1; mi<= wav[i]-1; mi++){
2283: for (ii=1;ii<=nlstate+ndeath;ii++)
2284: for (j=1;j<=nlstate+ndeath;j++){
2285: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2286: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2287: }
2288: for(d=0; d<=dh[mi][i]; d++){
2289: newm=savm;
2290: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2291: cov[2]=agexact;
2292: if(nagesqr==1)
2293: cov[3]= agexact*agexact;
2294: for (kk=1; kk<=cptcovage;kk++) {
2295: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2296: }
2297: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2298: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2299: savm=oldm;
2300: oldm=newm;
2301: } /* end mult */
2302:
2303: s1=s[mw[mi][i]][i];
2304: s2=s[mw[mi+1][i]][i];
2305: bbh=(double)bh[mi][i]/(double)stepm;
2306: 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 */
2307: ipmx +=1;
2308: sw += weight[i];
2309: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2310: } /* end of wave */
2311: } /* end of individual */
2312: } else if(mle==3){ /* exponential inter-extrapolation */
2313: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2314: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2315: for(mi=1; mi<= wav[i]-1; mi++){
2316: for (ii=1;ii<=nlstate+ndeath;ii++)
2317: for (j=1;j<=nlstate+ndeath;j++){
2318: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2319: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2320: }
2321: for(d=0; d<dh[mi][i]; d++){
2322: newm=savm;
2323: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2324: cov[2]=agexact;
2325: if(nagesqr==1)
2326: cov[3]= agexact*agexact;
2327: for (kk=1; kk<=cptcovage;kk++) {
2328: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2329: }
2330: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2331: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2332: savm=oldm;
2333: oldm=newm;
2334: } /* end mult */
2335:
2336: s1=s[mw[mi][i]][i];
2337: s2=s[mw[mi+1][i]][i];
2338: bbh=(double)bh[mi][i]/(double)stepm;
2339: 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 */
2340: ipmx +=1;
2341: sw += weight[i];
2342: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2343: } /* end of wave */
2344: } /* end of individual */
2345: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2346: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2347: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2348: for(mi=1; mi<= wav[i]-1; mi++){
2349: for (ii=1;ii<=nlstate+ndeath;ii++)
2350: for (j=1;j<=nlstate+ndeath;j++){
2351: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2352: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2353: }
2354: for(d=0; d<dh[mi][i]; d++){
2355: newm=savm;
2356: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2357: cov[2]=agexact;
2358: if(nagesqr==1)
2359: cov[3]= agexact*agexact;
2360: for (kk=1; kk<=cptcovage;kk++) {
2361: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2362: }
2363:
2364: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2365: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2366: savm=oldm;
2367: oldm=newm;
2368: } /* end mult */
2369:
2370: s1=s[mw[mi][i]][i];
2371: s2=s[mw[mi+1][i]][i];
2372: if( s2 > nlstate){
2373: lli=log(out[s1][s2] - savm[s1][s2]);
2374: }else{
2375: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2376: }
2377: ipmx +=1;
2378: sw += weight[i];
2379: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2380: /* 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]); */
2381: } /* end of wave */
2382: } /* end of individual */
2383: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2384: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2385: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2386: for(mi=1; mi<= wav[i]-1; mi++){
2387: for (ii=1;ii<=nlstate+ndeath;ii++)
2388: for (j=1;j<=nlstate+ndeath;j++){
2389: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2390: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2391: }
2392: for(d=0; d<dh[mi][i]; d++){
2393: newm=savm;
2394: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2395: cov[2]=agexact;
2396: if(nagesqr==1)
2397: cov[3]= agexact*agexact;
2398: for (kk=1; kk<=cptcovage;kk++) {
2399: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2400: }
2401:
2402: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2403: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2404: savm=oldm;
2405: oldm=newm;
2406: } /* end mult */
2407:
2408: s1=s[mw[mi][i]][i];
2409: s2=s[mw[mi+1][i]][i];
2410: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2411: ipmx +=1;
2412: sw += weight[i];
2413: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2414: /*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]);*/
2415: } /* end of wave */
2416: } /* end of individual */
2417: } /* End of if */
2418: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2419: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2420: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2421: return -l;
2422: }
2423:
2424: /*************** log-likelihood *************/
2425: double funcone( double *x)
2426: {
2427: /* Same as likeli but slower because of a lot of printf and if */
2428: int i, ii, j, k, mi, d, kk;
2429: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2430: double **out;
2431: double lli; /* Individual log likelihood */
2432: double llt;
2433: int s1, s2;
2434: double bbh, survp;
2435: double agexact;
2436: /*extern weight */
2437: /* We are differentiating ll according to initial status */
2438: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2439: /*for(i=1;i<imx;i++)
2440: printf(" %d\n",s[4][i]);
2441: */
2442: cov[1]=1.;
2443:
2444: for(k=1; k<=nlstate; k++) ll[k]=0.;
2445:
2446: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2447: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2448: for(mi=1; mi<= wav[i]-1; mi++){
2449: for (ii=1;ii<=nlstate+ndeath;ii++)
2450: for (j=1;j<=nlstate+ndeath;j++){
2451: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2452: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2453: }
2454: for(d=0; d<dh[mi][i]; d++){
2455: newm=savm;
2456: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2457: cov[2]=agexact;
2458: if(nagesqr==1)
2459: cov[3]= agexact*agexact;
2460: for (kk=1; kk<=cptcovage;kk++) {
2461: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2462: }
2463:
2464: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2465: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2466: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2467: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2468: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2469: savm=oldm;
2470: oldm=newm;
2471: } /* end mult */
2472:
2473: s1=s[mw[mi][i]][i];
2474: s2=s[mw[mi+1][i]][i];
2475: bbh=(double)bh[mi][i]/(double)stepm;
2476: /* bias is positive if real duration
2477: * is higher than the multiple of stepm and negative otherwise.
2478: */
2479: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2480: lli=log(out[s1][s2] - savm[s1][s2]);
2481: } else if (s2==-2) {
2482: for (j=1,survp=0. ; j<=nlstate; j++)
2483: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2484: lli= log(survp);
2485: }else if (mle==1){
2486: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2487: } else if(mle==2){
2488: 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 */
2489: } else if(mle==3){ /* exponential inter-extrapolation */
2490: 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 */
2491: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2492: lli=log(out[s1][s2]); /* Original formula */
2493: } else{ /* mle=0 back to 1 */
2494: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2495: /*lli=log(out[s1][s2]); */ /* Original formula */
2496: } /* End of if */
2497: ipmx +=1;
2498: sw += weight[i];
2499: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2500: /*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]); */
2501: if(globpr){
2502: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2503: %11.6f %11.6f %11.6f ", \
2504: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2505: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2506: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2507: llt +=ll[k]*gipmx/gsw;
2508: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2509: }
2510: fprintf(ficresilk," %10.6f\n", -llt);
2511: }
2512: } /* end of wave */
2513: } /* end of individual */
2514: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2515: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2516: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2517: if(globpr==0){ /* First time we count the contributions and weights */
2518: gipmx=ipmx;
2519: gsw=sw;
2520: }
2521: return -l;
2522: }
2523:
2524:
2525: /*************** function likelione ***********/
2526: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2527: {
2528: /* This routine should help understanding what is done with
2529: the selection of individuals/waves and
2530: to check the exact contribution to the likelihood.
2531: Plotting could be done.
2532: */
2533: int k;
2534:
2535: if(*globpri !=0){ /* Just counts and sums, no printings */
2536: strcpy(fileresilk,"ilk");
2537: strcat(fileresilk,fileres);
2538: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2539: printf("Problem with resultfile: %s\n", fileresilk);
2540: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2541: }
2542: 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");
2543: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2544: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2545: for(k=1; k<=nlstate; k++)
2546: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2547: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2548: }
2549:
2550: *fretone=(*funcone)(p);
2551: if(*globpri !=0){
2552: fclose(ficresilk);
2553: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2554: fflush(fichtm);
2555: }
2556: return;
2557: }
2558:
2559:
2560: /*********** Maximum Likelihood Estimation ***************/
2561:
2562: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2563: {
2564: int i,j, iter=0;
2565: double **xi;
2566: double fret;
2567: double fretone; /* Only one call to likelihood */
2568: /* char filerespow[FILENAMELENGTH];*/
2569:
2570: #ifdef NLOPT
2571: int creturn;
2572: nlopt_opt opt;
2573: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2574: double *lb;
2575: double minf; /* the minimum objective value, upon return */
2576: double * p1; /* Shifted parameters from 0 instead of 1 */
2577: myfunc_data dinst, *d = &dinst;
2578: #endif
2579:
2580:
2581: xi=matrix(1,npar,1,npar);
2582: for (i=1;i<=npar;i++)
2583: for (j=1;j<=npar;j++)
2584: xi[i][j]=(i==j ? 1.0 : 0.0);
2585: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2586: strcpy(filerespow,"pow");
2587: strcat(filerespow,fileres);
2588: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2589: printf("Problem with resultfile: %s\n", filerespow);
2590: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2591: }
2592: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2593: for (i=1;i<=nlstate;i++)
2594: for(j=1;j<=nlstate+ndeath;j++)
2595: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2596: fprintf(ficrespow,"\n");
2597: #ifdef POWELL
2598: powell(p,xi,npar,ftol,&iter,&fret,func);
2599: #endif
2600:
2601: #ifdef NLOPT
2602: #ifdef NEWUOA
2603: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2604: #else
2605: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2606: #endif
2607: lb=vector(0,npar-1);
2608: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2609: nlopt_set_lower_bounds(opt, lb);
2610: nlopt_set_initial_step1(opt, 0.1);
2611:
2612: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2613: d->function = func;
2614: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2615: nlopt_set_min_objective(opt, myfunc, d);
2616: nlopt_set_xtol_rel(opt, ftol);
2617: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2618: printf("nlopt failed! %d\n",creturn);
2619: }
2620: else {
2621: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2622: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2623: iter=1; /* not equal */
2624: }
2625: nlopt_destroy(opt);
2626: #endif
2627: free_matrix(xi,1,npar,1,npar);
2628: fclose(ficrespow);
2629: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2630: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2631: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2632:
2633: }
2634:
2635: /**** Computes Hessian and covariance matrix ***/
2636: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2637: {
2638: double **a,**y,*x,pd;
2639: double **hess;
2640: int i, j;
2641: int *indx;
2642:
2643: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2644: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2645: void lubksb(double **a, int npar, int *indx, double b[]) ;
2646: void ludcmp(double **a, int npar, int *indx, double *d) ;
2647: double gompertz(double p[]);
2648: hess=matrix(1,npar,1,npar);
2649:
2650: printf("\nCalculation of the hessian matrix. Wait...\n");
2651: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2652: for (i=1;i<=npar;i++){
2653: printf("%d",i);fflush(stdout);
2654: fprintf(ficlog,"%d",i);fflush(ficlog);
2655:
2656: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2657:
2658: /* printf(" %f ",p[i]);
2659: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2660: }
2661:
2662: for (i=1;i<=npar;i++) {
2663: for (j=1;j<=npar;j++) {
2664: if (j>i) {
2665: printf(".%d%d",i,j);fflush(stdout);
2666: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2667: hess[i][j]=hessij(p,delti,i,j,func,npar);
2668:
2669: hess[j][i]=hess[i][j];
2670: /*printf(" %lf ",hess[i][j]);*/
2671: }
2672: }
2673: }
2674: printf("\n");
2675: fprintf(ficlog,"\n");
2676:
2677: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2678: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2679:
2680: a=matrix(1,npar,1,npar);
2681: y=matrix(1,npar,1,npar);
2682: x=vector(1,npar);
2683: indx=ivector(1,npar);
2684: for (i=1;i<=npar;i++)
2685: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2686: ludcmp(a,npar,indx,&pd);
2687:
2688: for (j=1;j<=npar;j++) {
2689: for (i=1;i<=npar;i++) x[i]=0;
2690: x[j]=1;
2691: lubksb(a,npar,indx,x);
2692: for (i=1;i<=npar;i++){
2693: matcov[i][j]=x[i];
2694: }
2695: }
2696:
2697: printf("\n#Hessian matrix#\n");
2698: fprintf(ficlog,"\n#Hessian matrix#\n");
2699: for (i=1;i<=npar;i++) {
2700: for (j=1;j<=npar;j++) {
2701: printf("%.3e ",hess[i][j]);
2702: fprintf(ficlog,"%.3e ",hess[i][j]);
2703: }
2704: printf("\n");
2705: fprintf(ficlog,"\n");
2706: }
2707:
2708: /* Recompute Inverse */
2709: for (i=1;i<=npar;i++)
2710: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2711: ludcmp(a,npar,indx,&pd);
2712:
2713: /* printf("\n#Hessian matrix recomputed#\n");
2714:
2715: for (j=1;j<=npar;j++) {
2716: for (i=1;i<=npar;i++) x[i]=0;
2717: x[j]=1;
2718: lubksb(a,npar,indx,x);
2719: for (i=1;i<=npar;i++){
2720: y[i][j]=x[i];
2721: printf("%.3e ",y[i][j]);
2722: fprintf(ficlog,"%.3e ",y[i][j]);
2723: }
2724: printf("\n");
2725: fprintf(ficlog,"\n");
2726: }
2727: */
2728:
2729: free_matrix(a,1,npar,1,npar);
2730: free_matrix(y,1,npar,1,npar);
2731: free_vector(x,1,npar);
2732: free_ivector(indx,1,npar);
2733: free_matrix(hess,1,npar,1,npar);
2734:
2735:
2736: }
2737:
2738: /*************** hessian matrix ****************/
2739: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2740: {
2741: int i;
2742: int l=1, lmax=20;
2743: double k1,k2;
2744: double p2[MAXPARM+1]; /* identical to x */
2745: double res;
2746: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2747: double fx;
2748: int k=0,kmax=10;
2749: double l1;
2750:
2751: fx=func(x);
2752: for (i=1;i<=npar;i++) p2[i]=x[i];
2753: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2754: l1=pow(10,l);
2755: delts=delt;
2756: for(k=1 ; k <kmax; k=k+1){
2757: delt = delta*(l1*k);
2758: p2[theta]=x[theta] +delt;
2759: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2760: p2[theta]=x[theta]-delt;
2761: k2=func(p2)-fx;
2762: /*res= (k1-2.0*fx+k2)/delt/delt; */
2763: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2764:
2765: #ifdef DEBUGHESS
2766: 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);
2767: 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);
2768: #endif
2769: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2770: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2771: k=kmax;
2772: }
2773: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2774: k=kmax; l=lmax*10;
2775: }
2776: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2777: delts=delt;
2778: }
2779: }
2780: }
2781: delti[theta]=delts;
2782: return res;
2783:
2784: }
2785:
2786: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2787: {
2788: int i;
2789: int l=1, lmax=20;
2790: double k1,k2,k3,k4,res,fx;
2791: double p2[MAXPARM+1];
2792: int k;
2793:
2794: fx=func(x);
2795: for (k=1; k<=2; k++) {
2796: for (i=1;i<=npar;i++) p2[i]=x[i];
2797: p2[thetai]=x[thetai]+delti[thetai]/k;
2798: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2799: k1=func(p2)-fx;
2800:
2801: p2[thetai]=x[thetai]+delti[thetai]/k;
2802: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2803: k2=func(p2)-fx;
2804:
2805: p2[thetai]=x[thetai]-delti[thetai]/k;
2806: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2807: k3=func(p2)-fx;
2808:
2809: p2[thetai]=x[thetai]-delti[thetai]/k;
2810: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2811: k4=func(p2)-fx;
2812: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2813: #ifdef DEBUG
2814: 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);
2815: 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);
2816: #endif
2817: }
2818: return res;
2819: }
2820:
2821: /************** Inverse of matrix **************/
2822: void ludcmp(double **a, int n, int *indx, double *d)
2823: {
2824: int i,imax,j,k;
2825: double big,dum,sum,temp;
2826: double *vv;
2827:
2828: vv=vector(1,n);
2829: *d=1.0;
2830: for (i=1;i<=n;i++) {
2831: big=0.0;
2832: for (j=1;j<=n;j++)
2833: if ((temp=fabs(a[i][j])) > big) big=temp;
2834: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2835: vv[i]=1.0/big;
2836: }
2837: for (j=1;j<=n;j++) {
2838: for (i=1;i<j;i++) {
2839: sum=a[i][j];
2840: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2841: a[i][j]=sum;
2842: }
2843: big=0.0;
2844: for (i=j;i<=n;i++) {
2845: sum=a[i][j];
2846: for (k=1;k<j;k++)
2847: sum -= a[i][k]*a[k][j];
2848: a[i][j]=sum;
2849: if ( (dum=vv[i]*fabs(sum)) >= big) {
2850: big=dum;
2851: imax=i;
2852: }
2853: }
2854: if (j != imax) {
2855: for (k=1;k<=n;k++) {
2856: dum=a[imax][k];
2857: a[imax][k]=a[j][k];
2858: a[j][k]=dum;
2859: }
2860: *d = -(*d);
2861: vv[imax]=vv[j];
2862: }
2863: indx[j]=imax;
2864: if (a[j][j] == 0.0) a[j][j]=TINY;
2865: if (j != n) {
2866: dum=1.0/(a[j][j]);
2867: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2868: }
2869: }
2870: free_vector(vv,1,n); /* Doesn't work */
2871: ;
2872: }
2873:
2874: void lubksb(double **a, int n, int *indx, double b[])
2875: {
2876: int i,ii=0,ip,j;
2877: double sum;
2878:
2879: for (i=1;i<=n;i++) {
2880: ip=indx[i];
2881: sum=b[ip];
2882: b[ip]=b[i];
2883: if (ii)
2884: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2885: else if (sum) ii=i;
2886: b[i]=sum;
2887: }
2888: for (i=n;i>=1;i--) {
2889: sum=b[i];
2890: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2891: b[i]=sum/a[i][i];
2892: }
2893: }
2894:
2895: void pstamp(FILE *fichier)
2896: {
2897: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2898: }
2899:
2900: /************ Frequencies ********************/
2901: 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[])
2902: { /* Some frequencies */
2903:
2904: int i, m, jk, j1, bool, z1,j;
2905: int first;
2906: double ***freq; /* Frequencies */
2907: double *pp, **prop;
2908: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2909: char fileresp[FILENAMELENGTH];
2910:
2911: pp=vector(1,nlstate);
2912: prop=matrix(1,nlstate,iagemin,iagemax+3);
2913: strcpy(fileresp,"p");
2914: strcat(fileresp,fileres);
2915: if((ficresp=fopen(fileresp,"w"))==NULL) {
2916: printf("Problem with prevalence resultfile: %s\n", fileresp);
2917: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2918: exit(0);
2919: }
2920: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2921: j1=0;
2922:
2923: j=cptcoveff;
2924: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2925:
2926: first=1;
2927:
2928: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2929: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2930: /* j1++; */
2931: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2932: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2933: scanf("%d", i);*/
2934: for (i=-5; i<=nlstate+ndeath; i++)
2935: for (jk=-5; jk<=nlstate+ndeath; jk++)
2936: for(m=iagemin; m <= iagemax+3; m++)
2937: freq[i][jk][m]=0;
2938:
2939: for (i=1; i<=nlstate; i++)
2940: for(m=iagemin; m <= iagemax+3; m++)
2941: prop[i][m]=0;
2942:
2943: dateintsum=0;
2944: k2cpt=0;
2945: for (i=1; i<=imx; i++) {
2946: bool=1;
2947: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2948: for (z1=1; z1<=cptcoveff; z1++)
2949: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2950: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2951: bool=0;
2952: /* 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",
2953: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2954: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2955: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2956: }
2957: }
2958:
2959: if (bool==1){
2960: for(m=firstpass; m<=lastpass; m++){
2961: k2=anint[m][i]+(mint[m][i]/12.);
2962: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2963: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2964: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2965: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2966: if (m<lastpass) {
2967: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2968: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2969: }
2970:
2971: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2972: dateintsum=dateintsum+k2;
2973: k2cpt++;
2974: }
2975: /*}*/
2976: }
2977: }
2978: } /* end i */
2979:
2980: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2981: pstamp(ficresp);
2982: if (cptcovn>0) {
2983: fprintf(ficresp, "\n#********** Variable ");
2984: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2985: fprintf(ficresp, "**********\n#");
2986: fprintf(ficlog, "\n#********** Variable ");
2987: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2988: fprintf(ficlog, "**********\n#");
2989: }
2990: for(i=1; i<=nlstate;i++)
2991: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2992: fprintf(ficresp, "\n");
2993:
2994: for(i=iagemin; i <= iagemax+3; i++){
2995: if(i==iagemax+3){
2996: fprintf(ficlog,"Total");
2997: }else{
2998: if(first==1){
2999: first=0;
3000: printf("See log file for details...\n");
3001: }
3002: fprintf(ficlog,"Age %d", i);
3003: }
3004: for(jk=1; jk <=nlstate ; jk++){
3005: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3006: pp[jk] += freq[jk][m][i];
3007: }
3008: for(jk=1; jk <=nlstate ; jk++){
3009: for(m=-1, pos=0; m <=0 ; m++)
3010: pos += freq[jk][m][i];
3011: if(pp[jk]>=1.e-10){
3012: if(first==1){
3013: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3014: }
3015: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3016: }else{
3017: if(first==1)
3018: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3019: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3020: }
3021: }
3022:
3023: for(jk=1; jk <=nlstate ; jk++){
3024: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3025: pp[jk] += freq[jk][m][i];
3026: }
3027: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3028: pos += pp[jk];
3029: posprop += prop[jk][i];
3030: }
3031: for(jk=1; jk <=nlstate ; jk++){
3032: if(pos>=1.e-5){
3033: if(first==1)
3034: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3035: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3036: }else{
3037: if(first==1)
3038: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3039: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3040: }
3041: if( i <= iagemax){
3042: if(pos>=1.e-5){
3043: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3044: /*probs[i][jk][j1]= pp[jk]/pos;*/
3045: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3046: }
3047: else
3048: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3049: }
3050: }
3051:
3052: for(jk=-1; jk <=nlstate+ndeath; jk++)
3053: for(m=-1; m <=nlstate+ndeath; m++)
3054: if(freq[jk][m][i] !=0 ) {
3055: if(first==1)
3056: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3057: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3058: }
3059: if(i <= iagemax)
3060: fprintf(ficresp,"\n");
3061: if(first==1)
3062: printf("Others in log...\n");
3063: fprintf(ficlog,"\n");
3064: }
3065: /*}*/
3066: }
3067: dateintmean=dateintsum/k2cpt;
3068:
3069: fclose(ficresp);
3070: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3071: free_vector(pp,1,nlstate);
3072: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3073: /* End of Freq */
3074: }
3075:
3076: /************ Prevalence ********************/
3077: 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)
3078: {
3079: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3080: in each health status at the date of interview (if between dateprev1 and dateprev2).
3081: We still use firstpass and lastpass as another selection.
3082: */
3083:
3084: int i, m, jk, j1, bool, z1,j;
3085:
3086: double **prop;
3087: double posprop;
3088: double y2; /* in fractional years */
3089: int iagemin, iagemax;
3090: int first; /** to stop verbosity which is redirected to log file */
3091:
3092: iagemin= (int) agemin;
3093: iagemax= (int) agemax;
3094: /*pp=vector(1,nlstate);*/
3095: prop=matrix(1,nlstate,iagemin,iagemax+3);
3096: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3097: j1=0;
3098:
3099: /*j=cptcoveff;*/
3100: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3101:
3102: first=1;
3103: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3104: /*for(i1=1; i1<=ncodemax[k1];i1++){
3105: j1++;*/
3106:
3107: for (i=1; i<=nlstate; i++)
3108: for(m=iagemin; m <= iagemax+3; m++)
3109: prop[i][m]=0.0;
3110:
3111: for (i=1; i<=imx; i++) { /* Each individual */
3112: bool=1;
3113: if (cptcovn>0) {
3114: for (z1=1; z1<=cptcoveff; z1++)
3115: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3116: bool=0;
3117: }
3118: if (bool==1) {
3119: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3120: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3121: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3122: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3123: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3124: 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);
3125: if (s[m][i]>0 && s[m][i]<=nlstate) {
3126: /*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]]);*/
3127: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3128: prop[s[m][i]][iagemax+3] += weight[i];
3129: }
3130: }
3131: } /* end selection of waves */
3132: }
3133: }
3134: for(i=iagemin; i <= iagemax+3; i++){
3135: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3136: posprop += prop[jk][i];
3137: }
3138:
3139: for(jk=1; jk <=nlstate ; jk++){
3140: if( i <= iagemax){
3141: if(posprop>=1.e-5){
3142: probs[i][jk][j1]= prop[jk][i]/posprop;
3143: } else{
3144: if(first==1){
3145: first=0;
3146: 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]);
3147: }
3148: }
3149: }
3150: }/* end jk */
3151: }/* end i */
3152: /*} *//* end i1 */
3153: } /* end j1 */
3154:
3155: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3156: /*free_vector(pp,1,nlstate);*/
3157: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3158: } /* End of prevalence */
3159:
3160: /************* Waves Concatenation ***************/
3161:
3162: 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)
3163: {
3164: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3165: Death is a valid wave (if date is known).
3166: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3167: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3168: and mw[mi+1][i]. dh depends on stepm.
3169: */
3170:
3171: int i, mi, m;
3172: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3173: double sum=0., jmean=0.;*/
3174: int first;
3175: int j, k=0,jk, ju, jl;
3176: double sum=0.;
3177: first=0;
3178: jmin=100000;
3179: jmax=-1;
3180: jmean=0.;
3181: for(i=1; i<=imx; i++){
3182: mi=0;
3183: m=firstpass;
3184: while(s[m][i] <= nlstate){
3185: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3186: mw[++mi][i]=m;
3187: if(m >=lastpass)
3188: break;
3189: else
3190: m++;
3191: }/* end while */
3192: if (s[m][i] > nlstate){
3193: mi++; /* Death is another wave */
3194: /* if(mi==0) never been interviewed correctly before death */
3195: /* Only death is a correct wave */
3196: mw[mi][i]=m;
3197: }
3198:
3199: wav[i]=mi;
3200: if(mi==0){
3201: nbwarn++;
3202: if(first==0){
3203: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3204: first=1;
3205: }
3206: if(first==1){
3207: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3208: }
3209: } /* end mi==0 */
3210: } /* End individuals */
3211:
3212: for(i=1; i<=imx; i++){
3213: for(mi=1; mi<wav[i];mi++){
3214: if (stepm <=0)
3215: dh[mi][i]=1;
3216: else{
3217: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3218: if (agedc[i] < 2*AGESUP) {
3219: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3220: if(j==0) j=1; /* Survives at least one month after exam */
3221: else if(j<0){
3222: nberr++;
3223: 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]);
3224: j=1; /* Temporary Dangerous patch */
3225: 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);
3226: 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]);
3227: 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);
3228: }
3229: k=k+1;
3230: if (j >= jmax){
3231: jmax=j;
3232: ijmax=i;
3233: }
3234: if (j <= jmin){
3235: jmin=j;
3236: ijmin=i;
3237: }
3238: sum=sum+j;
3239: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3240: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3241: }
3242: }
3243: else{
3244: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3245: /* 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]); */
3246:
3247: k=k+1;
3248: if (j >= jmax) {
3249: jmax=j;
3250: ijmax=i;
3251: }
3252: else if (j <= jmin){
3253: jmin=j;
3254: ijmin=i;
3255: }
3256: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3257: /*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]);*/
3258: if(j<0){
3259: nberr++;
3260: 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]);
3261: 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]);
3262: }
3263: sum=sum+j;
3264: }
3265: jk= j/stepm;
3266: jl= j -jk*stepm;
3267: ju= j -(jk+1)*stepm;
3268: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3269: if(jl==0){
3270: dh[mi][i]=jk;
3271: bh[mi][i]=0;
3272: }else{ /* We want a negative bias in order to only have interpolation ie
3273: * to avoid the price of an extra matrix product in likelihood */
3274: dh[mi][i]=jk+1;
3275: bh[mi][i]=ju;
3276: }
3277: }else{
3278: if(jl <= -ju){
3279: dh[mi][i]=jk;
3280: bh[mi][i]=jl; /* bias is positive if real duration
3281: * is higher than the multiple of stepm and negative otherwise.
3282: */
3283: }
3284: else{
3285: dh[mi][i]=jk+1;
3286: bh[mi][i]=ju;
3287: }
3288: if(dh[mi][i]==0){
3289: dh[mi][i]=1; /* At least one step */
3290: bh[mi][i]=ju; /* At least one step */
3291: /* 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);*/
3292: }
3293: } /* end if mle */
3294: }
3295: } /* end wave */
3296: }
3297: jmean=sum/k;
3298: 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);
3299: 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);
3300: }
3301:
3302: /*********** Tricode ****************************/
3303: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
3304: {
3305: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3306: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
3307: * Boring subroutine which should only output nbcode[Tvar[j]][k]
3308: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
3309: * nbcode[Tvar[j]][1]=
3310: */
3311:
3312: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
3313: int modmaxcovj=0; /* Modality max of covariates j */
3314: int cptcode=0; /* Modality max of covariates j */
3315: int modmincovj=0; /* Modality min of covariates j */
3316:
3317:
3318: cptcoveff=0;
3319:
3320: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
3321:
3322: /* Loop on covariates without age and products */
3323: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3324: for (k=-1; k < maxncov; k++) Ndum[k]=0;
3325: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
3326: modality of this covariate Vj*/
3327: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3328: * If product of Vn*Vm, still boolean *:
3329: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3330: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3331: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
3332: modality of the nth covariate of individual i. */
3333: if (ij > modmaxcovj)
3334: modmaxcovj=ij;
3335: else if (ij < modmincovj)
3336: modmincovj=ij;
3337: if ((ij < -1) && (ij > NCOVMAX)){
3338: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3339: exit(1);
3340: }else
3341: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
3342: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
3343: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
3344: /* getting the maximum value of the modality of the covariate
3345: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3346: female is 1, then modmaxcovj=1.*/
3347: } /* end for loop on individuals i */
3348: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3349: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3350: cptcode=modmaxcovj;
3351: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3352: /*for (i=0; i<=cptcode; i++) {*/
3353: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3354: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3355: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3356: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3357: if( k != -1){
3358: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3359: covariate for which somebody answered excluding
3360: undefined. Usually 2: 0 and 1. */
3361: }
3362: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3363: covariate for which somebody answered including
3364: undefined. Usually 3: -1, 0 and 1. */
3365: }
3366: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3367: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3368: } /* Ndum[-1] number of undefined modalities */
3369:
3370: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3371: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3372: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
3373: modmincovj=3; modmaxcovj = 7;
3374: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3375: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3376: defining two dummy variables: variables V1_1 and V1_2.
3377: nbcode[Tvar[j]][ij]=k;
3378: nbcode[Tvar[j]][1]=0;
3379: nbcode[Tvar[j]][2]=1;
3380: nbcode[Tvar[j]][3]=2;
3381: */
3382: ij=0; /* ij is similar to i but can jumps over null modalities */
3383: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
3384: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
3385: break;
3386: }
3387: ij++;
3388: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
3389: cptcode = ij; /* New max modality for covar j */
3390: } /* end of loop on modality i=-1 to 1 or more */
3391:
3392: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3393: /* /\*recode from 0 *\/ */
3394: /* k is a modality. If we have model=V1+V1*sex */
3395: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3396: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3397: /* } */
3398: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3399: /* if (ij > ncodemax[j]) { */
3400: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3401: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3402: /* break; */
3403: /* } */
3404: /* } /\* end of loop on modality k *\/ */
3405: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3406:
3407: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3408:
3409: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
3410: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3411: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3412: Ndum[ij]++; /* Might be supersed V1 + V1*age */
3413: }
3414:
3415: ij=0;
3416: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3417: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3418: if((Ndum[i]!=0) && (i<=ncovcol)){
3419: ij++;
3420: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3421: Tvaraff[ij]=i; /*For printing (unclear) */
3422: }else{
3423: /* Tvaraff[ij]=0; */
3424: }
3425: }
3426: /* ij--; */
3427: cptcoveff=ij; /*Number of total covariates*/
3428:
3429: }
3430:
3431:
3432: /*********** Health Expectancies ****************/
3433:
3434: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3435:
3436: {
3437: /* Health expectancies, no variances */
3438: int i, j, nhstepm, hstepm, h, nstepm;
3439: int nhstepma, nstepma; /* Decreasing with age */
3440: double age, agelim, hf;
3441: double ***p3mat;
3442: double eip;
3443:
3444: pstamp(ficreseij);
3445: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3446: fprintf(ficreseij,"# Age");
3447: for(i=1; i<=nlstate;i++){
3448: for(j=1; j<=nlstate;j++){
3449: fprintf(ficreseij," e%1d%1d ",i,j);
3450: }
3451: fprintf(ficreseij," e%1d. ",i);
3452: }
3453: fprintf(ficreseij,"\n");
3454:
3455:
3456: if(estepm < stepm){
3457: printf ("Problem %d lower than %d\n",estepm, stepm);
3458: }
3459: else hstepm=estepm;
3460: /* We compute the life expectancy from trapezoids spaced every estepm months
3461: * This is mainly to measure the difference between two models: for example
3462: * if stepm=24 months pijx are given only every 2 years and by summing them
3463: * we are calculating an estimate of the Life Expectancy assuming a linear
3464: * progression in between and thus overestimating or underestimating according
3465: * to the curvature of the survival function. If, for the same date, we
3466: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3467: * to compare the new estimate of Life expectancy with the same linear
3468: * hypothesis. A more precise result, taking into account a more precise
3469: * curvature will be obtained if estepm is as small as stepm. */
3470:
3471: /* For example we decided to compute the life expectancy with the smallest unit */
3472: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3473: nhstepm is the number of hstepm from age to agelim
3474: nstepm is the number of stepm from age to agelin.
3475: Look at hpijx to understand the reason of that which relies in memory size
3476: and note for a fixed period like estepm months */
3477: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3478: survival function given by stepm (the optimization length). Unfortunately it
3479: means that if the survival funtion is printed only each two years of age and if
3480: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3481: results. So we changed our mind and took the option of the best precision.
3482: */
3483: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3484:
3485: agelim=AGESUP;
3486: /* If stepm=6 months */
3487: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3488: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3489:
3490: /* nhstepm age range expressed in number of stepm */
3491: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3492: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3493: /* if (stepm >= YEARM) hstepm=1;*/
3494: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3495: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3496:
3497: for (age=bage; age<=fage; age ++){
3498: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3499: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3500: /* if (stepm >= YEARM) hstepm=1;*/
3501: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3502:
3503: /* If stepm=6 months */
3504: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3505: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3506:
3507: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3508:
3509: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3510:
3511: printf("%d|",(int)age);fflush(stdout);
3512: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3513:
3514: /* Computing expectancies */
3515: for(i=1; i<=nlstate;i++)
3516: for(j=1; j<=nlstate;j++)
3517: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3518: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3519:
3520: /* 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]);*/
3521:
3522: }
3523:
3524: fprintf(ficreseij,"%3.0f",age );
3525: for(i=1; i<=nlstate;i++){
3526: eip=0;
3527: for(j=1; j<=nlstate;j++){
3528: eip +=eij[i][j][(int)age];
3529: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3530: }
3531: fprintf(ficreseij,"%9.4f", eip );
3532: }
3533: fprintf(ficreseij,"\n");
3534:
3535: }
3536: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3537: printf("\n");
3538: fprintf(ficlog,"\n");
3539:
3540: }
3541:
3542: 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[] )
3543:
3544: {
3545: /* Covariances of health expectancies eij and of total life expectancies according
3546: to initial status i, ei. .
3547: */
3548: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3549: int nhstepma, nstepma; /* Decreasing with age */
3550: double age, agelim, hf;
3551: double ***p3matp, ***p3matm, ***varhe;
3552: double **dnewm,**doldm;
3553: double *xp, *xm;
3554: double **gp, **gm;
3555: double ***gradg, ***trgradg;
3556: int theta;
3557:
3558: double eip, vip;
3559:
3560: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3561: xp=vector(1,npar);
3562: xm=vector(1,npar);
3563: dnewm=matrix(1,nlstate*nlstate,1,npar);
3564: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3565:
3566: pstamp(ficresstdeij);
3567: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3568: fprintf(ficresstdeij,"# Age");
3569: for(i=1; i<=nlstate;i++){
3570: for(j=1; j<=nlstate;j++)
3571: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3572: fprintf(ficresstdeij," e%1d. ",i);
3573: }
3574: fprintf(ficresstdeij,"\n");
3575:
3576: pstamp(ficrescveij);
3577: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3578: fprintf(ficrescveij,"# Age");
3579: for(i=1; i<=nlstate;i++)
3580: for(j=1; j<=nlstate;j++){
3581: cptj= (j-1)*nlstate+i;
3582: for(i2=1; i2<=nlstate;i2++)
3583: for(j2=1; j2<=nlstate;j2++){
3584: cptj2= (j2-1)*nlstate+i2;
3585: if(cptj2 <= cptj)
3586: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3587: }
3588: }
3589: fprintf(ficrescveij,"\n");
3590:
3591: if(estepm < stepm){
3592: printf ("Problem %d lower than %d\n",estepm, stepm);
3593: }
3594: else hstepm=estepm;
3595: /* We compute the life expectancy from trapezoids spaced every estepm months
3596: * This is mainly to measure the difference between two models: for example
3597: * if stepm=24 months pijx are given only every 2 years and by summing them
3598: * we are calculating an estimate of the Life Expectancy assuming a linear
3599: * progression in between and thus overestimating or underestimating according
3600: * to the curvature of the survival function. If, for the same date, we
3601: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3602: * to compare the new estimate of Life expectancy with the same linear
3603: * hypothesis. A more precise result, taking into account a more precise
3604: * curvature will be obtained if estepm is as small as stepm. */
3605:
3606: /* For example we decided to compute the life expectancy with the smallest unit */
3607: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3608: nhstepm is the number of hstepm from age to agelim
3609: nstepm is the number of stepm from age to agelin.
3610: Look at hpijx to understand the reason of that which relies in memory size
3611: and note for a fixed period like estepm months */
3612: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3613: survival function given by stepm (the optimization length). Unfortunately it
3614: means that if the survival funtion is printed only each two years of age and if
3615: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3616: results. So we changed our mind and took the option of the best precision.
3617: */
3618: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3619:
3620: /* If stepm=6 months */
3621: /* nhstepm age range expressed in number of stepm */
3622: agelim=AGESUP;
3623: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3624: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3625: /* if (stepm >= YEARM) hstepm=1;*/
3626: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3627:
3628: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3629: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3630: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3631: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3632: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3633: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3634:
3635: for (age=bage; age<=fage; age ++){
3636: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3637: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3638: /* if (stepm >= YEARM) hstepm=1;*/
3639: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3640:
3641: /* If stepm=6 months */
3642: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3643: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3644:
3645: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3646:
3647: /* Computing Variances of health expectancies */
3648: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3649: decrease memory allocation */
3650: for(theta=1; theta <=npar; theta++){
3651: for(i=1; i<=npar; i++){
3652: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3653: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3654: }
3655: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3656: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3657:
3658: for(j=1; j<= nlstate; j++){
3659: for(i=1; i<=nlstate; i++){
3660: for(h=0; h<=nhstepm-1; h++){
3661: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3662: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3663: }
3664: }
3665: }
3666:
3667: for(ij=1; ij<= nlstate*nlstate; ij++)
3668: for(h=0; h<=nhstepm-1; h++){
3669: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3670: }
3671: }/* End theta */
3672:
3673:
3674: for(h=0; h<=nhstepm-1; h++)
3675: for(j=1; j<=nlstate*nlstate;j++)
3676: for(theta=1; theta <=npar; theta++)
3677: trgradg[h][j][theta]=gradg[h][theta][j];
3678:
3679:
3680: for(ij=1;ij<=nlstate*nlstate;ij++)
3681: for(ji=1;ji<=nlstate*nlstate;ji++)
3682: varhe[ij][ji][(int)age] =0.;
3683:
3684: printf("%d|",(int)age);fflush(stdout);
3685: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3686: for(h=0;h<=nhstepm-1;h++){
3687: for(k=0;k<=nhstepm-1;k++){
3688: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3689: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3690: for(ij=1;ij<=nlstate*nlstate;ij++)
3691: for(ji=1;ji<=nlstate*nlstate;ji++)
3692: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3693: }
3694: }
3695:
3696: /* Computing expectancies */
3697: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3698: for(i=1; i<=nlstate;i++)
3699: for(j=1; j<=nlstate;j++)
3700: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3701: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3702:
3703: /* 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]);*/
3704:
3705: }
3706:
3707: fprintf(ficresstdeij,"%3.0f",age );
3708: for(i=1; i<=nlstate;i++){
3709: eip=0.;
3710: vip=0.;
3711: for(j=1; j<=nlstate;j++){
3712: eip += eij[i][j][(int)age];
3713: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3714: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3715: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3716: }
3717: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3718: }
3719: fprintf(ficresstdeij,"\n");
3720:
3721: fprintf(ficrescveij,"%3.0f",age );
3722: for(i=1; i<=nlstate;i++)
3723: for(j=1; j<=nlstate;j++){
3724: cptj= (j-1)*nlstate+i;
3725: for(i2=1; i2<=nlstate;i2++)
3726: for(j2=1; j2<=nlstate;j2++){
3727: cptj2= (j2-1)*nlstate+i2;
3728: if(cptj2 <= cptj)
3729: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3730: }
3731: }
3732: fprintf(ficrescveij,"\n");
3733:
3734: }
3735: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3736: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3737: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3738: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3739: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3740: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3741: printf("\n");
3742: fprintf(ficlog,"\n");
3743:
3744: free_vector(xm,1,npar);
3745: free_vector(xp,1,npar);
3746: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3747: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3748: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3749: }
3750:
3751: /************ Variance ******************/
3752: 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[])
3753: {
3754: /* Variance of health expectancies */
3755: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3756: /* double **newm;*/
3757: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3758:
3759: int movingaverage();
3760: double **dnewm,**doldm;
3761: double **dnewmp,**doldmp;
3762: int i, j, nhstepm, hstepm, h, nstepm ;
3763: int k;
3764: double *xp;
3765: double **gp, **gm; /* for var eij */
3766: double ***gradg, ***trgradg; /*for var eij */
3767: double **gradgp, **trgradgp; /* for var p point j */
3768: double *gpp, *gmp; /* for var p point j */
3769: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3770: double ***p3mat;
3771: double age,agelim, hf;
3772: double ***mobaverage;
3773: int theta;
3774: char digit[4];
3775: char digitp[25];
3776:
3777: char fileresprobmorprev[FILENAMELENGTH];
3778:
3779: if(popbased==1){
3780: if(mobilav!=0)
3781: strcpy(digitp,"-populbased-mobilav-");
3782: else strcpy(digitp,"-populbased-nomobil-");
3783: }
3784: else
3785: strcpy(digitp,"-stablbased-");
3786:
3787: if (mobilav!=0) {
3788: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3789: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3790: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3791: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3792: }
3793: }
3794:
3795: strcpy(fileresprobmorprev,"prmorprev");
3796: sprintf(digit,"%-d",ij);
3797: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3798: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3799: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3800: strcat(fileresprobmorprev,fileres);
3801: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3802: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3803: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3804: }
3805: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3806:
3807: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3808: pstamp(ficresprobmorprev);
3809: 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);
3810: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3811: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3812: fprintf(ficresprobmorprev," p.%-d SE",j);
3813: for(i=1; i<=nlstate;i++)
3814: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3815: }
3816: fprintf(ficresprobmorprev,"\n");
3817: fprintf(ficgp,"\n# Routine varevsij");
3818: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3819: 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");
3820: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3821: /* } */
3822: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3823: pstamp(ficresvij);
3824: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3825: if(popbased==1)
3826: 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);
3827: else
3828: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3829: fprintf(ficresvij,"# Age");
3830: for(i=1; i<=nlstate;i++)
3831: for(j=1; j<=nlstate;j++)
3832: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3833: fprintf(ficresvij,"\n");
3834:
3835: xp=vector(1,npar);
3836: dnewm=matrix(1,nlstate,1,npar);
3837: doldm=matrix(1,nlstate,1,nlstate);
3838: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3839: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3840:
3841: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3842: gpp=vector(nlstate+1,nlstate+ndeath);
3843: gmp=vector(nlstate+1,nlstate+ndeath);
3844: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3845:
3846: if(estepm < stepm){
3847: printf ("Problem %d lower than %d\n",estepm, stepm);
3848: }
3849: else hstepm=estepm;
3850: /* For example we decided to compute the life expectancy with the smallest unit */
3851: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3852: nhstepm is the number of hstepm from age to agelim
3853: nstepm is the number of stepm from age to agelin.
3854: Look at function hpijx to understand why (it is linked to memory size questions) */
3855: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3856: survival function given by stepm (the optimization length). Unfortunately it
3857: means that if the survival funtion is printed every two years of age and if
3858: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3859: results. So we changed our mind and took the option of the best precision.
3860: */
3861: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3862: agelim = AGESUP;
3863: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3864: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3865: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3866: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3867: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3868: gp=matrix(0,nhstepm,1,nlstate);
3869: gm=matrix(0,nhstepm,1,nlstate);
3870:
3871:
3872: for(theta=1; theta <=npar; theta++){
3873: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3874: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3875: }
3876: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3877: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3878:
3879: if (popbased==1) {
3880: if(mobilav ==0){
3881: for(i=1; i<=nlstate;i++)
3882: prlim[i][i]=probs[(int)age][i][ij];
3883: }else{ /* mobilav */
3884: for(i=1; i<=nlstate;i++)
3885: prlim[i][i]=mobaverage[(int)age][i][ij];
3886: }
3887: }
3888:
3889: for(j=1; j<= nlstate; j++){
3890: for(h=0; h<=nhstepm; h++){
3891: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3892: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3893: }
3894: }
3895: /* This for computing probability of death (h=1 means
3896: computed over hstepm matrices product = hstepm*stepm months)
3897: as a weighted average of prlim.
3898: */
3899: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3900: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3901: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3902: }
3903: /* end probability of death */
3904:
3905: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3906: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3907: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3908: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3909:
3910: if (popbased==1) {
3911: if(mobilav ==0){
3912: for(i=1; i<=nlstate;i++)
3913: prlim[i][i]=probs[(int)age][i][ij];
3914: }else{ /* mobilav */
3915: for(i=1; i<=nlstate;i++)
3916: prlim[i][i]=mobaverage[(int)age][i][ij];
3917: }
3918: }
3919:
3920: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3921: for(h=0; h<=nhstepm; h++){
3922: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3923: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3924: }
3925: }
3926: /* This for computing probability of death (h=1 means
3927: computed over hstepm matrices product = hstepm*stepm months)
3928: as a weighted average of prlim.
3929: */
3930: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3931: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3932: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3933: }
3934: /* end probability of death */
3935:
3936: for(j=1; j<= nlstate; j++) /* vareij */
3937: for(h=0; h<=nhstepm; h++){
3938: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3939: }
3940:
3941: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3942: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3943: }
3944:
3945: } /* End theta */
3946:
3947: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3948:
3949: for(h=0; h<=nhstepm; h++) /* veij */
3950: for(j=1; j<=nlstate;j++)
3951: for(theta=1; theta <=npar; theta++)
3952: trgradg[h][j][theta]=gradg[h][theta][j];
3953:
3954: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3955: for(theta=1; theta <=npar; theta++)
3956: trgradgp[j][theta]=gradgp[theta][j];
3957:
3958:
3959: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3960: for(i=1;i<=nlstate;i++)
3961: for(j=1;j<=nlstate;j++)
3962: vareij[i][j][(int)age] =0.;
3963:
3964: for(h=0;h<=nhstepm;h++){
3965: for(k=0;k<=nhstepm;k++){
3966: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3967: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3968: for(i=1;i<=nlstate;i++)
3969: for(j=1;j<=nlstate;j++)
3970: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3971: }
3972: }
3973:
3974: /* pptj */
3975: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3976: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3977: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3978: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3979: varppt[j][i]=doldmp[j][i];
3980: /* end ppptj */
3981: /* x centered again */
3982: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3983: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3984:
3985: if (popbased==1) {
3986: if(mobilav ==0){
3987: for(i=1; i<=nlstate;i++)
3988: prlim[i][i]=probs[(int)age][i][ij];
3989: }else{ /* mobilav */
3990: for(i=1; i<=nlstate;i++)
3991: prlim[i][i]=mobaverage[(int)age][i][ij];
3992: }
3993: }
3994:
3995: /* This for computing probability of death (h=1 means
3996: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3997: as a weighted average of prlim.
3998: */
3999: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4000: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4001: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4002: }
4003: /* end probability of death */
4004:
4005: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4006: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4007: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4008: for(i=1; i<=nlstate;i++){
4009: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4010: }
4011: }
4012: fprintf(ficresprobmorprev,"\n");
4013:
4014: fprintf(ficresvij,"%.0f ",age );
4015: for(i=1; i<=nlstate;i++)
4016: for(j=1; j<=nlstate;j++){
4017: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4018: }
4019: fprintf(ficresvij,"\n");
4020: free_matrix(gp,0,nhstepm,1,nlstate);
4021: free_matrix(gm,0,nhstepm,1,nlstate);
4022: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4023: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4024: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4025: } /* End age */
4026: free_vector(gpp,nlstate+1,nlstate+ndeath);
4027: free_vector(gmp,nlstate+1,nlstate+ndeath);
4028: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4029: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4030: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
4031: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
4032: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
4033: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4034: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4035: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
4036: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
4037: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
4038: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
4039: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4040: 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);
4041: /* 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);
4042: */
4043: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4044: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4045:
4046: free_vector(xp,1,npar);
4047: free_matrix(doldm,1,nlstate,1,nlstate);
4048: free_matrix(dnewm,1,nlstate,1,npar);
4049: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4050: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4051: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4052: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4053: fclose(ficresprobmorprev);
4054: fflush(ficgp);
4055: fflush(fichtm);
4056: } /* end varevsij */
4057:
4058: /************ Variance of prevlim ******************/
4059: 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[])
4060: {
4061: /* Variance of prevalence limit */
4062: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
4063:
4064: double **dnewm,**doldm;
4065: int i, j, nhstepm, hstepm;
4066: double *xp;
4067: double *gp, *gm;
4068: double **gradg, **trgradg;
4069: double age,agelim;
4070: int theta;
4071:
4072: pstamp(ficresvpl);
4073: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4074: fprintf(ficresvpl,"# Age");
4075: for(i=1; i<=nlstate;i++)
4076: fprintf(ficresvpl," %1d-%1d",i,i);
4077: fprintf(ficresvpl,"\n");
4078:
4079: xp=vector(1,npar);
4080: dnewm=matrix(1,nlstate,1,npar);
4081: doldm=matrix(1,nlstate,1,nlstate);
4082:
4083: hstepm=1*YEARM; /* Every year of age */
4084: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4085: agelim = AGESUP;
4086: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4087: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4088: if (stepm >= YEARM) hstepm=1;
4089: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4090: gradg=matrix(1,npar,1,nlstate);
4091: gp=vector(1,nlstate);
4092: gm=vector(1,nlstate);
4093:
4094: for(theta=1; theta <=npar; theta++){
4095: for(i=1; i<=npar; i++){ /* Computes gradient */
4096: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4097: }
4098: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4099: for(i=1;i<=nlstate;i++)
4100: gp[i] = prlim[i][i];
4101:
4102: for(i=1; i<=npar; i++) /* Computes gradient */
4103: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4104: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4105: for(i=1;i<=nlstate;i++)
4106: gm[i] = prlim[i][i];
4107:
4108: for(i=1;i<=nlstate;i++)
4109: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4110: } /* End theta */
4111:
4112: trgradg =matrix(1,nlstate,1,npar);
4113:
4114: for(j=1; j<=nlstate;j++)
4115: for(theta=1; theta <=npar; theta++)
4116: trgradg[j][theta]=gradg[theta][j];
4117:
4118: for(i=1;i<=nlstate;i++)
4119: varpl[i][(int)age] =0.;
4120: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4121: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4122: for(i=1;i<=nlstate;i++)
4123: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4124:
4125: fprintf(ficresvpl,"%.0f ",age );
4126: for(i=1; i<=nlstate;i++)
4127: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4128: fprintf(ficresvpl,"\n");
4129: free_vector(gp,1,nlstate);
4130: free_vector(gm,1,nlstate);
4131: free_matrix(gradg,1,npar,1,nlstate);
4132: free_matrix(trgradg,1,nlstate,1,npar);
4133: } /* End age */
4134:
4135: free_vector(xp,1,npar);
4136: free_matrix(doldm,1,nlstate,1,npar);
4137: free_matrix(dnewm,1,nlstate,1,nlstate);
4138:
4139: }
4140:
4141: /************ Variance of one-step probabilities ******************/
4142: 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[])
4143: {
4144: int i, j=0, k1, l1, tj;
4145: int k2, l2, j1, z1;
4146: int k=0, l;
4147: int first=1, first1, first2;
4148: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4149: double **dnewm,**doldm;
4150: double *xp;
4151: double *gp, *gm;
4152: double **gradg, **trgradg;
4153: double **mu;
4154: double age, cov[NCOVMAX+1];
4155: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4156: int theta;
4157: char fileresprob[FILENAMELENGTH];
4158: char fileresprobcov[FILENAMELENGTH];
4159: char fileresprobcor[FILENAMELENGTH];
4160: double ***varpij;
4161:
4162: strcpy(fileresprob,"prob");
4163: strcat(fileresprob,fileres);
4164: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4165: printf("Problem with resultfile: %s\n", fileresprob);
4166: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4167: }
4168: strcpy(fileresprobcov,"probcov");
4169: strcat(fileresprobcov,fileres);
4170: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4171: printf("Problem with resultfile: %s\n", fileresprobcov);
4172: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4173: }
4174: strcpy(fileresprobcor,"probcor");
4175: strcat(fileresprobcor,fileres);
4176: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4177: printf("Problem with resultfile: %s\n", fileresprobcor);
4178: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4179: }
4180: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4181: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4182: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4183: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4184: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4185: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4186: pstamp(ficresprob);
4187: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4188: fprintf(ficresprob,"# Age");
4189: pstamp(ficresprobcov);
4190: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4191: fprintf(ficresprobcov,"# Age");
4192: pstamp(ficresprobcor);
4193: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4194: fprintf(ficresprobcor,"# Age");
4195:
4196:
4197: for(i=1; i<=nlstate;i++)
4198: for(j=1; j<=(nlstate+ndeath);j++){
4199: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4200: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4201: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4202: }
4203: /* fprintf(ficresprob,"\n");
4204: fprintf(ficresprobcov,"\n");
4205: fprintf(ficresprobcor,"\n");
4206: */
4207: xp=vector(1,npar);
4208: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4209: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4210: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4211: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4212: first=1;
4213: fprintf(ficgp,"\n# Routine varprob");
4214: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4215: fprintf(fichtm,"\n");
4216:
4217: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4218: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4219: file %s<br>\n",optionfilehtmcov);
4220: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4221: and drawn. It helps understanding how is the covariance between two incidences.\
4222: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4223: 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. \
4224: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4225: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4226: standard deviations wide on each axis. <br>\
4227: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4228: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4229: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4230:
4231: cov[1]=1;
4232: /* tj=cptcoveff; */
4233: tj = (int) pow(2,cptcoveff);
4234: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4235: j1=0;
4236: for(j1=1; j1<=tj;j1++){
4237: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4238: /*j1++;*/
4239: if (cptcovn>0) {
4240: fprintf(ficresprob, "\n#********** Variable ");
4241: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4242: fprintf(ficresprob, "**********\n#\n");
4243: fprintf(ficresprobcov, "\n#********** Variable ");
4244: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4245: fprintf(ficresprobcov, "**********\n#\n");
4246:
4247: fprintf(ficgp, "\n#********** Variable ");
4248: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4249: fprintf(ficgp, "**********\n#\n");
4250:
4251:
4252: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4253: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4254: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4255:
4256: fprintf(ficresprobcor, "\n#********** Variable ");
4257: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4258: fprintf(ficresprobcor, "**********\n#");
4259: }
4260:
4261: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4262: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4263: gp=vector(1,(nlstate)*(nlstate+ndeath));
4264: gm=vector(1,(nlstate)*(nlstate+ndeath));
4265: for (age=bage; age<=fage; age ++){
4266: cov[2]=age;
4267: if(nagesqr==1)
4268: cov[3]= age*age;
4269: for (k=1; k<=cptcovn;k++) {
4270: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4271: * 1 1 1 1 1
4272: * 2 2 1 1 1
4273: * 3 1 2 1 1
4274: */
4275: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
4276: }
4277: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4278: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
4279: for (k=1; k<=cptcovprod;k++)
4280: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4281:
4282:
4283: for(theta=1; theta <=npar; theta++){
4284: for(i=1; i<=npar; i++)
4285: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4286:
4287: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4288:
4289: k=0;
4290: for(i=1; i<= (nlstate); i++){
4291: for(j=1; j<=(nlstate+ndeath);j++){
4292: k=k+1;
4293: gp[k]=pmmij[i][j];
4294: }
4295: }
4296:
4297: for(i=1; i<=npar; i++)
4298: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4299:
4300: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4301: k=0;
4302: for(i=1; i<=(nlstate); i++){
4303: for(j=1; j<=(nlstate+ndeath);j++){
4304: k=k+1;
4305: gm[k]=pmmij[i][j];
4306: }
4307: }
4308:
4309: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4310: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4311: }
4312:
4313: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4314: for(theta=1; theta <=npar; theta++)
4315: trgradg[j][theta]=gradg[theta][j];
4316:
4317: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4318: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4319:
4320: pmij(pmmij,cov,ncovmodel,x,nlstate);
4321:
4322: k=0;
4323: for(i=1; i<=(nlstate); i++){
4324: for(j=1; j<=(nlstate+ndeath);j++){
4325: k=k+1;
4326: mu[k][(int) age]=pmmij[i][j];
4327: }
4328: }
4329: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4330: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4331: varpij[i][j][(int)age] = doldm[i][j];
4332:
4333: /*printf("\n%d ",(int)age);
4334: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4335: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4336: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4337: }*/
4338:
4339: fprintf(ficresprob,"\n%d ",(int)age);
4340: fprintf(ficresprobcov,"\n%d ",(int)age);
4341: fprintf(ficresprobcor,"\n%d ",(int)age);
4342:
4343: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4344: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4345: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4346: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4347: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4348: }
4349: i=0;
4350: for (k=1; k<=(nlstate);k++){
4351: for (l=1; l<=(nlstate+ndeath);l++){
4352: i++;
4353: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4354: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4355: for (j=1; j<=i;j++){
4356: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
4357: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4358: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4359: }
4360: }
4361: }/* end of loop for state */
4362: } /* end of loop for age */
4363: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4364: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4365: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4366: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4367:
4368: /* Confidence intervalle of pij */
4369: /*
4370: fprintf(ficgp,"\nunset parametric;unset label");
4371: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4372: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4373: 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);
4374: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4375: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4376: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4377: */
4378:
4379: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4380: first1=1;first2=2;
4381: for (k2=1; k2<=(nlstate);k2++){
4382: for (l2=1; l2<=(nlstate+ndeath);l2++){
4383: if(l2==k2) continue;
4384: j=(k2-1)*(nlstate+ndeath)+l2;
4385: for (k1=1; k1<=(nlstate);k1++){
4386: for (l1=1; l1<=(nlstate+ndeath);l1++){
4387: if(l1==k1) continue;
4388: i=(k1-1)*(nlstate+ndeath)+l1;
4389: if(i<=j) continue;
4390: for (age=bage; age<=fage; age ++){
4391: if ((int)age %5==0){
4392: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4393: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4394: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4395: mu1=mu[i][(int) age]/stepm*YEARM ;
4396: mu2=mu[j][(int) age]/stepm*YEARM;
4397: c12=cv12/sqrt(v1*v2);
4398: /* Computing eigen value of matrix of covariance */
4399: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4400: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4401: if ((lc2 <0) || (lc1 <0) ){
4402: if(first2==1){
4403: first1=0;
4404: 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);
4405: }
4406: 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);
4407: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4408: /* lc2=fabs(lc2); */
4409: }
4410:
4411: /* Eigen vectors */
4412: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4413: /*v21=sqrt(1.-v11*v11); *//* error */
4414: v21=(lc1-v1)/cv12*v11;
4415: v12=-v21;
4416: v22=v11;
4417: tnalp=v21/v11;
4418: if(first1==1){
4419: first1=0;
4420: 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);
4421: }
4422: 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);
4423: /*printf(fignu*/
4424: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4425: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4426: if(first==1){
4427: first=0;
4428: fprintf(ficgp,"\nset parametric;unset label");
4429: 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);
4430: fprintf(ficgp,"\nset ter png small size 320, 240");
4431: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4432: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4433: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4434: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4435: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4436: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4437: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4438: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4439: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4440: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4441: 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",\
4442: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4443: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4444: }else{
4445: first=0;
4446: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4447: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4448: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4449: 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",\
4450: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4451: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4452: }/* if first */
4453: } /* age mod 5 */
4454: } /* end loop age */
4455: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4456: first=1;
4457: } /*l12 */
4458: } /* k12 */
4459: } /*l1 */
4460: }/* k1 */
4461: /* } */ /* loop covariates */
4462: }
4463: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4464: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4465: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4466: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4467: free_vector(xp,1,npar);
4468: fclose(ficresprob);
4469: fclose(ficresprobcov);
4470: fclose(ficresprobcor);
4471: fflush(ficgp);
4472: fflush(fichtmcov);
4473: }
4474:
4475:
4476: /******************* Printing html file ***********/
4477: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4478: int lastpass, int stepm, int weightopt, char model[],\
4479: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4480: int popforecast, int estepm ,\
4481: double jprev1, double mprev1,double anprev1, \
4482: double jprev2, double mprev2,double anprev2){
4483: int jj1, k1, i1, cpt;
4484:
4485: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4486: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4487: </ul>");
4488: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4489: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4490: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4491: fprintf(fichtm,"\
4492: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4493: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4494: fprintf(fichtm,"\
4495: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4496: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4497: fprintf(fichtm,"\
4498: - (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): \
4499: <a href=\"%s\">%s</a> <br>\n",
4500: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4501: fprintf(fichtm,"\
4502: - Population projections by age and states: \
4503: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4504:
4505: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4506:
4507: m=pow(2,cptcoveff);
4508: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4509:
4510: jj1=0;
4511: for(k1=1; k1<=m;k1++){
4512: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
4513: jj1++;
4514: if (cptcovn > 0) {
4515: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4516: for (cpt=1; cpt<=cptcoveff;cpt++){
4517: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4518: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
4519: }
4520: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4521: }
4522: /* Pij */
4523: 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> \
4524: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4525: /* Quasi-incidences */
4526: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4527: 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> \
4528: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4529: /* Period (stable) prevalence in each health state */
4530: for(cpt=1; cpt<=nlstate;cpt++){
4531: 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> \
4532: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4533: }
4534: for(cpt=1; cpt<=nlstate;cpt++) {
4535: 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> \
4536: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4537: }
4538: /* } /\* end i1 *\/ */
4539: }/* End k1 */
4540: fprintf(fichtm,"</ul>");
4541:
4542: fprintf(fichtm,"\
4543: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4544: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
4545: - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
4546:
4547: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4548: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4549: fprintf(fichtm,"\
4550: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4551: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4552:
4553: fprintf(fichtm,"\
4554: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4555: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4556: fprintf(fichtm,"\
4557: - 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): \
4558: <a href=\"%s\">%s</a> <br>\n</li>",
4559: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4560: fprintf(fichtm,"\
4561: - (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): \
4562: <a href=\"%s\">%s</a> <br>\n</li>",
4563: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4564: fprintf(fichtm,"\
4565: - 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",
4566: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4567: fprintf(fichtm,"\
4568: - 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",
4569: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4570: fprintf(fichtm,"\
4571: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4572: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4573:
4574: /* if(popforecast==1) fprintf(fichtm,"\n */
4575: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4576: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4577: /* <br>",fileres,fileres,fileres,fileres); */
4578: /* else */
4579: /* 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); */
4580: fflush(fichtm);
4581: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4582:
4583: m=pow(2,cptcoveff);
4584: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4585:
4586: jj1=0;
4587: for(k1=1; k1<=m;k1++){
4588: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
4589: jj1++;
4590: if (cptcovn > 0) {
4591: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4592: for (cpt=1; cpt<=cptcoveff;cpt++)
4593: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4594: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4595: }
4596: for(cpt=1; cpt<=nlstate;cpt++) {
4597: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4598: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4599: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4600: }
4601: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4602: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4603: true period expectancies (those weighted with period prevalences are also\
4604: drawn in addition to the population based expectancies computed using\
4605: observed and cahotic prevalences: %s%d.png<br>\
4606: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4607: /* } /\* end i1 *\/ */
4608: }/* End k1 */
4609: fprintf(fichtm,"</ul>");
4610: fflush(fichtm);
4611: }
4612:
4613: /******************* Gnuplot file **************/
4614: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4615:
4616: char dirfileres[132],optfileres[132];
4617: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4618: int ng=0;
4619: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4620: /* printf("Problem with file %s",optionfilegnuplot); */
4621: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4622: /* } */
4623:
4624: /*#ifdef windows */
4625: fprintf(ficgp,"cd \"%s\" \n",pathc);
4626: /*#endif */
4627: m=pow(2,cptcoveff);
4628:
4629: strcpy(dirfileres,optionfilefiname);
4630: strcpy(optfileres,"vpl");
4631: /* 1eme*/
4632: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4633: for (cpt=1; cpt<= nlstate ; cpt ++) {
4634: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4635: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4636: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4637: fprintf(ficgp,"set xlabel \"Age\" \n\
4638: set ylabel \"Probability\" \n\
4639: set ter png small size 320, 240\n\
4640: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4641:
4642: for (i=1; i<= nlstate ; i ++) {
4643: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4644: else fprintf(ficgp," %%*lf (%%*lf)");
4645: }
4646: 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);
4647: for (i=1; i<= nlstate ; i ++) {
4648: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4649: else fprintf(ficgp," %%*lf (%%*lf)");
4650: }
4651: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4652: for (i=1; i<= nlstate ; i ++) {
4653: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4654: else fprintf(ficgp," %%*lf (%%*lf)");
4655: }
4656: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4657: }
4658: }
4659: /*2 eme*/
4660: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4661: for (k1=1; k1<= m ; k1 ++) {
4662: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4663: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4664:
4665: for (i=1; i<= nlstate+1 ; i ++) {
4666: k=2*i;
4667: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4668: for (j=1; j<= nlstate+1 ; j ++) {
4669: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4670: else fprintf(ficgp," %%*lf (%%*lf)");
4671: }
4672: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4673: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4674: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4675: for (j=1; j<= nlstate+1 ; j ++) {
4676: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4677: else fprintf(ficgp," %%*lf (%%*lf)");
4678: }
4679: fprintf(ficgp,"\" t\"\" w l lt 0,");
4680: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4681: for (j=1; j<= nlstate+1 ; j ++) {
4682: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4683: else fprintf(ficgp," %%*lf (%%*lf)");
4684: }
4685: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4686: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4687: }
4688: }
4689:
4690: /*3eme*/
4691:
4692: for (k1=1; k1<= m ; k1 ++) {
4693: for (cpt=1; cpt<= nlstate ; cpt ++) {
4694: /* k=2+nlstate*(2*cpt-2); */
4695: k=2+(nlstate+1)*(cpt-1);
4696: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4697: fprintf(ficgp,"set ter png small size 320, 240\n\
4698: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4699: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4700: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4701: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4702: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4703: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4704: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4705:
4706: */
4707: for (i=1; i< nlstate ; i ++) {
4708: 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);
4709: /* 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);*/
4710:
4711: }
4712: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4713: }
4714: }
4715:
4716: /* CV preval stable (period) */
4717: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4718: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4719: k=3;
4720: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4721: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4722: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4723: set ter png small size 320, 240\n\
4724: unset log y\n\
4725: plot [%.f:%.f] ", ageminpar, agemaxpar);
4726: for (i=1; i<= nlstate ; i ++){
4727: if(i==1)
4728: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4729: else
4730: fprintf(ficgp,", '' ");
4731: l=(nlstate+ndeath)*(i-1)+1;
4732: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4733: for (j=1; j<= (nlstate-1) ; j ++)
4734: fprintf(ficgp,"+$%d",k+l+j);
4735: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4736: } /* nlstate */
4737: fprintf(ficgp,"\n");
4738: } /* end cpt state*/
4739: } /* end covariate */
4740:
4741: /* proba elementaires */
4742: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
4743: for(i=1,jk=1; i <=nlstate; i++){
4744: fprintf(ficgp,"# initial state %d\n",i);
4745: for(k=1; k <=(nlstate+ndeath); k++){
4746: if (k != i) {
4747: fprintf(ficgp,"# current state %d\n",k);
4748: for(j=1; j <=ncovmodel; j++){
4749: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
4750: jk++;
4751: }
4752: fprintf(ficgp,"\n");
4753: }
4754: }
4755: }
4756: fprintf(ficgp,"##############\n#\n");
4757:
4758: /*goto avoid;*/
4759: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4760: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4761: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4762: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4763: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4764: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4765: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4766: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4767: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4768: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4769: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4770: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4771: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4772: fprintf(ficgp,"#\n");
4773: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4774: fprintf(ficgp,"# ng=%d\n",ng);
4775: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
4776: for(jk=1; jk <=m; jk++) {
4777: fprintf(ficgp,"# jk=%d\n",jk);
4778: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4779: if (ng==2)
4780: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4781: else
4782: fprintf(ficgp,"\nset title \"Probability\"\n");
4783: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4784: i=1;
4785: for(k2=1; k2<=nlstate; k2++) {
4786: k3=i;
4787: for(k=1; k<=(nlstate+ndeath); k++) {
4788: if (k != k2){
4789: if(ng==2)
4790: if(nagesqr==0)
4791: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4792: else /* nagesqr =1 */
4793: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
4794: else
4795: if(nagesqr==0)
4796: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4797: else /* nagesqr =1 */
4798: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
4799: ij=1;/* To be checked else nbcode[0][0] wrong */
4800: for(j=3; j <=ncovmodel-nagesqr; j++) {
4801: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
4802: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4803: ij++;
4804: }
4805: else
4806: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4807: }
4808: fprintf(ficgp,")/(1");
4809:
4810: for(k1=1; k1 <=nlstate; k1++){
4811: if(nagesqr==0)
4812: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4813: else /* nagesqr =1 */
4814: 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);
4815:
4816: ij=1;
4817: for(j=3; j <=ncovmodel-nagesqr; j++){
4818: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
4819: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4820: ij++;
4821: }
4822: else
4823: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4824: }
4825: fprintf(ficgp,")");
4826: }
4827: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4828: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4829: i=i+ncovmodel;
4830: }
4831: } /* end k */
4832: } /* end k2 */
4833: } /* end jk */
4834: } /* end ng */
4835: /* avoid: */
4836: fflush(ficgp);
4837: } /* end gnuplot */
4838:
4839:
4840: /*************** Moving average **************/
4841: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4842:
4843: int i, cpt, cptcod;
4844: int modcovmax =1;
4845: int mobilavrange, mob;
4846: double age;
4847:
4848: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4849: a covariate has 2 modalities */
4850: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4851:
4852: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4853: if(mobilav==1) mobilavrange=5; /* default */
4854: else mobilavrange=mobilav;
4855: for (age=bage; age<=fage; age++)
4856: for (i=1; i<=nlstate;i++)
4857: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4858: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4859: /* We keep the original values on the extreme ages bage, fage and for
4860: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4861: we use a 5 terms etc. until the borders are no more concerned.
4862: */
4863: for (mob=3;mob <=mobilavrange;mob=mob+2){
4864: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4865: for (i=1; i<=nlstate;i++){
4866: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4867: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4868: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4869: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4870: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4871: }
4872: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4873: }
4874: }
4875: }/* end age */
4876: }/* end mob */
4877: }else return -1;
4878: return 0;
4879: }/* End movingaverage */
4880:
4881:
4882: /************** Forecasting ******************/
4883: 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){
4884: /* proj1, year, month, day of starting projection
4885: agemin, agemax range of age
4886: dateprev1 dateprev2 range of dates during which prevalence is computed
4887: anproj2 year of en of projection (same day and month as proj1).
4888: */
4889: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4890: double agec; /* generic age */
4891: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4892: double *popeffectif,*popcount;
4893: double ***p3mat;
4894: double ***mobaverage;
4895: char fileresf[FILENAMELENGTH];
4896:
4897: agelim=AGESUP;
4898: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4899:
4900: strcpy(fileresf,"f");
4901: strcat(fileresf,fileres);
4902: if((ficresf=fopen(fileresf,"w"))==NULL) {
4903: printf("Problem with forecast resultfile: %s\n", fileresf);
4904: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4905: }
4906: printf("Computing forecasting: result on file '%s' \n", fileresf);
4907: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4908:
4909: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4910:
4911: if (mobilav!=0) {
4912: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4913: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4914: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4915: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4916: }
4917: }
4918:
4919: stepsize=(int) (stepm+YEARM-1)/YEARM;
4920: if (stepm<=12) stepsize=1;
4921: if(estepm < stepm){
4922: printf ("Problem %d lower than %d\n",estepm, stepm);
4923: }
4924: else hstepm=estepm;
4925:
4926: hstepm=hstepm/stepm;
4927: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4928: fractional in yp1 */
4929: anprojmean=yp;
4930: yp2=modf((yp1*12),&yp);
4931: mprojmean=yp;
4932: yp1=modf((yp2*30.5),&yp);
4933: jprojmean=yp;
4934: if(jprojmean==0) jprojmean=1;
4935: if(mprojmean==0) jprojmean=1;
4936:
4937: i1=cptcoveff;
4938: if (cptcovn < 1){i1=1;}
4939:
4940: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4941:
4942: fprintf(ficresf,"#****** Routine prevforecast **\n");
4943:
4944: /* if (h==(int)(YEARM*yearp)){ */
4945: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4946: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4947: k=k+1;
4948: fprintf(ficresf,"\n#******");
4949: for(j=1;j<=cptcoveff;j++) {
4950: 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]]);
4951: }
4952: fprintf(ficresf,"******\n");
4953: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4954: for(j=1; j<=nlstate+ndeath;j++){
4955: for(i=1; i<=nlstate;i++)
4956: fprintf(ficresf," p%d%d",i,j);
4957: fprintf(ficresf," p.%d",j);
4958: }
4959: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4960: fprintf(ficresf,"\n");
4961: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4962:
4963: for (agec=fage; agec>=(ageminpar-1); agec--){
4964: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4965: nhstepm = nhstepm/hstepm;
4966: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4967: oldm=oldms;savm=savms;
4968: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4969:
4970: for (h=0; h<=nhstepm; h++){
4971: if (h*hstepm/YEARM*stepm ==yearp) {
4972: fprintf(ficresf,"\n");
4973: for(j=1;j<=cptcoveff;j++)
4974: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4975: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4976: }
4977: for(j=1; j<=nlstate+ndeath;j++) {
4978: ppij=0.;
4979: for(i=1; i<=nlstate;i++) {
4980: if (mobilav==1)
4981: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4982: else {
4983: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4984: }
4985: if (h*hstepm/YEARM*stepm== yearp) {
4986: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4987: }
4988: } /* end i */
4989: if (h*hstepm/YEARM*stepm==yearp) {
4990: fprintf(ficresf," %.3f", ppij);
4991: }
4992: }/* end j */
4993: } /* end h */
4994: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4995: } /* end agec */
4996: } /* end yearp */
4997: } /* end cptcod */
4998: } /* end cptcov */
4999:
5000: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5001:
5002: fclose(ficresf);
5003: }
5004:
5005: /************** Forecasting *****not tested NB*************/
5006: 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){
5007:
5008: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5009: int *popage;
5010: double calagedatem, agelim, kk1, kk2;
5011: double *popeffectif,*popcount;
5012: double ***p3mat,***tabpop,***tabpopprev;
5013: double ***mobaverage;
5014: char filerespop[FILENAMELENGTH];
5015:
5016: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5017: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5018: agelim=AGESUP;
5019: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5020:
5021: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5022:
5023:
5024: strcpy(filerespop,"pop");
5025: strcat(filerespop,fileres);
5026: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5027: printf("Problem with forecast resultfile: %s\n", filerespop);
5028: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5029: }
5030: printf("Computing forecasting: result on file '%s' \n", filerespop);
5031: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5032:
5033: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5034:
5035: if (mobilav!=0) {
5036: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5037: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5038: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5039: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5040: }
5041: }
5042:
5043: stepsize=(int) (stepm+YEARM-1)/YEARM;
5044: if (stepm<=12) stepsize=1;
5045:
5046: agelim=AGESUP;
5047:
5048: hstepm=1;
5049: hstepm=hstepm/stepm;
5050:
5051: if (popforecast==1) {
5052: if((ficpop=fopen(popfile,"r"))==NULL) {
5053: printf("Problem with population file : %s\n",popfile);exit(0);
5054: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5055: }
5056: popage=ivector(0,AGESUP);
5057: popeffectif=vector(0,AGESUP);
5058: popcount=vector(0,AGESUP);
5059:
5060: i=1;
5061: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5062:
5063: imx=i;
5064: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5065: }
5066:
5067: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5068: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5069: k=k+1;
5070: fprintf(ficrespop,"\n#******");
5071: for(j=1;j<=cptcoveff;j++) {
5072: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5073: }
5074: fprintf(ficrespop,"******\n");
5075: fprintf(ficrespop,"# Age");
5076: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5077: if (popforecast==1) fprintf(ficrespop," [Population]");
5078:
5079: for (cpt=0; cpt<=0;cpt++) {
5080: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5081:
5082: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5083: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5084: nhstepm = nhstepm/hstepm;
5085:
5086: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5087: oldm=oldms;savm=savms;
5088: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5089:
5090: for (h=0; h<=nhstepm; h++){
5091: if (h==(int) (calagedatem+YEARM*cpt)) {
5092: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5093: }
5094: for(j=1; j<=nlstate+ndeath;j++) {
5095: kk1=0.;kk2=0;
5096: for(i=1; i<=nlstate;i++) {
5097: if (mobilav==1)
5098: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5099: else {
5100: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5101: }
5102: }
5103: if (h==(int)(calagedatem+12*cpt)){
5104: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5105: /*fprintf(ficrespop," %.3f", kk1);
5106: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5107: }
5108: }
5109: for(i=1; i<=nlstate;i++){
5110: kk1=0.;
5111: for(j=1; j<=nlstate;j++){
5112: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5113: }
5114: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5115: }
5116:
5117: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5118: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5119: }
5120: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5121: }
5122: }
5123:
5124: /******/
5125:
5126: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5127: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5128: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5129: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5130: nhstepm = nhstepm/hstepm;
5131:
5132: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5133: oldm=oldms;savm=savms;
5134: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5135: for (h=0; h<=nhstepm; h++){
5136: if (h==(int) (calagedatem+YEARM*cpt)) {
5137: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5138: }
5139: for(j=1; j<=nlstate+ndeath;j++) {
5140: kk1=0.;kk2=0;
5141: for(i=1; i<=nlstate;i++) {
5142: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5143: }
5144: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5145: }
5146: }
5147: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5148: }
5149: }
5150: }
5151: }
5152:
5153: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5154:
5155: if (popforecast==1) {
5156: free_ivector(popage,0,AGESUP);
5157: free_vector(popeffectif,0,AGESUP);
5158: free_vector(popcount,0,AGESUP);
5159: }
5160: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5161: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5162: fclose(ficrespop);
5163: } /* End of popforecast */
5164:
5165: int fileappend(FILE *fichier, char *optionfich)
5166: {
5167: if((fichier=fopen(optionfich,"a"))==NULL) {
5168: printf("Problem with file: %s\n", optionfich);
5169: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5170: return (0);
5171: }
5172: fflush(fichier);
5173: return (1);
5174: }
5175:
5176:
5177: /**************** function prwizard **********************/
5178: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5179: {
5180:
5181: /* Wizard to print covariance matrix template */
5182:
5183: char ca[32], cb[32];
5184: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
5185: int numlinepar;
5186:
5187: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5188: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5189: for(i=1; i <=nlstate; i++){
5190: jj=0;
5191: for(j=1; j <=nlstate+ndeath; j++){
5192: if(j==i) continue;
5193: jj++;
5194: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5195: printf("%1d%1d",i,j);
5196: fprintf(ficparo,"%1d%1d",i,j);
5197: for(k=1; k<=ncovmodel;k++){
5198: /* printf(" %lf",param[i][j][k]); */
5199: /* fprintf(ficparo," %lf",param[i][j][k]); */
5200: printf(" 0.");
5201: fprintf(ficparo," 0.");
5202: }
5203: printf("\n");
5204: fprintf(ficparo,"\n");
5205: }
5206: }
5207: printf("# Scales (for hessian or gradient estimation)\n");
5208: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5209: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5210: for(i=1; i <=nlstate; i++){
5211: jj=0;
5212: for(j=1; j <=nlstate+ndeath; j++){
5213: if(j==i) continue;
5214: jj++;
5215: fprintf(ficparo,"%1d%1d",i,j);
5216: printf("%1d%1d",i,j);
5217: fflush(stdout);
5218: for(k=1; k<=ncovmodel;k++){
5219: /* printf(" %le",delti3[i][j][k]); */
5220: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5221: printf(" 0.");
5222: fprintf(ficparo," 0.");
5223: }
5224: numlinepar++;
5225: printf("\n");
5226: fprintf(ficparo,"\n");
5227: }
5228: }
5229: printf("# Covariance matrix\n");
5230: /* # 121 Var(a12)\n\ */
5231: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5232: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5233: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5234: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5235: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5236: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5237: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5238: fflush(stdout);
5239: fprintf(ficparo,"# Covariance matrix\n");
5240: /* # 121 Var(a12)\n\ */
5241: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5242: /* # ...\n\ */
5243: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5244:
5245: for(itimes=1;itimes<=2;itimes++){
5246: jj=0;
5247: for(i=1; i <=nlstate; i++){
5248: for(j=1; j <=nlstate+ndeath; j++){
5249: if(j==i) continue;
5250: for(k=1; k<=ncovmodel;k++){
5251: jj++;
5252: ca[0]= k+'a'-1;ca[1]='\0';
5253: if(itimes==1){
5254: printf("#%1d%1d%d",i,j,k);
5255: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5256: }else{
5257: printf("%1d%1d%d",i,j,k);
5258: fprintf(ficparo,"%1d%1d%d",i,j,k);
5259: /* printf(" %.5le",matcov[i][j]); */
5260: }
5261: ll=0;
5262: for(li=1;li <=nlstate; li++){
5263: for(lj=1;lj <=nlstate+ndeath; lj++){
5264: if(lj==li) continue;
5265: for(lk=1;lk<=ncovmodel;lk++){
5266: ll++;
5267: if(ll<=jj){
5268: cb[0]= lk +'a'-1;cb[1]='\0';
5269: if(ll<jj){
5270: if(itimes==1){
5271: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5272: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5273: }else{
5274: printf(" 0.");
5275: fprintf(ficparo," 0.");
5276: }
5277: }else{
5278: if(itimes==1){
5279: printf(" Var(%s%1d%1d)",ca,i,j);
5280: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5281: }else{
5282: printf(" 0.");
5283: fprintf(ficparo," 0.");
5284: }
5285: }
5286: }
5287: } /* end lk */
5288: } /* end lj */
5289: } /* end li */
5290: printf("\n");
5291: fprintf(ficparo,"\n");
5292: numlinepar++;
5293: } /* end k*/
5294: } /*end j */
5295: } /* end i */
5296: } /* end itimes */
5297:
5298: } /* end of prwizard */
5299: /******************* Gompertz Likelihood ******************************/
5300: double gompertz(double x[])
5301: {
5302: double A,B,L=0.0,sump=0.,num=0.;
5303: int i,n=0; /* n is the size of the sample */
5304:
5305: for (i=0;i<=imx-1 ; i++) {
5306: sump=sump+weight[i];
5307: /* sump=sump+1;*/
5308: num=num+1;
5309: }
5310:
5311:
5312: /* for (i=0; i<=imx; i++)
5313: 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]);*/
5314:
5315: for (i=1;i<=imx ; i++)
5316: {
5317: if (cens[i] == 1 && wav[i]>1)
5318: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5319:
5320: if (cens[i] == 0 && wav[i]>1)
5321: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5322: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5323:
5324: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5325: if (wav[i] > 1 ) { /* ??? */
5326: L=L+A*weight[i];
5327: /* 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]);*/
5328: }
5329: }
5330:
5331: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5332:
5333: return -2*L*num/sump;
5334: }
5335:
5336: #ifdef GSL
5337: /******************* Gompertz_f Likelihood ******************************/
5338: double gompertz_f(const gsl_vector *v, void *params)
5339: {
5340: double A,B,LL=0.0,sump=0.,num=0.;
5341: double *x= (double *) v->data;
5342: int i,n=0; /* n is the size of the sample */
5343:
5344: for (i=0;i<=imx-1 ; i++) {
5345: sump=sump+weight[i];
5346: /* sump=sump+1;*/
5347: num=num+1;
5348: }
5349:
5350:
5351: /* for (i=0; i<=imx; i++)
5352: 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]);*/
5353: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5354: for (i=1;i<=imx ; i++)
5355: {
5356: if (cens[i] == 1 && wav[i]>1)
5357: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5358:
5359: if (cens[i] == 0 && wav[i]>1)
5360: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5361: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5362:
5363: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5364: if (wav[i] > 1 ) { /* ??? */
5365: LL=LL+A*weight[i];
5366: /* 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]);*/
5367: }
5368: }
5369:
5370: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5371: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5372:
5373: return -2*LL*num/sump;
5374: }
5375: #endif
5376:
5377: /******************* Printing html file ***********/
5378: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5379: int lastpass, int stepm, int weightopt, char model[],\
5380: int imx, double p[],double **matcov,double agemortsup){
5381: int i,k;
5382:
5383: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5384: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5385: for (i=1;i<=2;i++)
5386: 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]));
5387: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5388: fprintf(fichtm,"</ul>");
5389:
5390: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5391:
5392: 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>");
5393:
5394: for (k=agegomp;k<(agemortsup-2);k++)
5395: 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]);
5396:
5397:
5398: fflush(fichtm);
5399: }
5400:
5401: /******************* Gnuplot file **************/
5402: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5403:
5404: char dirfileres[132],optfileres[132];
5405:
5406: int ng;
5407:
5408:
5409: /*#ifdef windows */
5410: fprintf(ficgp,"cd \"%s\" \n",pathc);
5411: /*#endif */
5412:
5413:
5414: strcpy(dirfileres,optionfilefiname);
5415: strcpy(optfileres,"vpl");
5416: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5417: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5418: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5419: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5420: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5421:
5422: }
5423:
5424: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5425: {
5426:
5427: /*-------- data file ----------*/
5428: FILE *fic;
5429: char dummy[]=" ";
5430: int i=0, j=0, n=0;
5431: int linei, month, year,iout;
5432: char line[MAXLINE], linetmp[MAXLINE];
5433: char stra[MAXLINE], strb[MAXLINE];
5434: char *stratrunc;
5435: int lstra;
5436:
5437:
5438: if((fic=fopen(datafile,"r"))==NULL) {
5439: printf("Problem while opening datafile: %s\n", datafile);return 1;
5440: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5441: }
5442:
5443: i=1;
5444: linei=0;
5445: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5446: linei=linei+1;
5447: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5448: if(line[j] == '\t')
5449: line[j] = ' ';
5450: }
5451: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5452: ;
5453: };
5454: line[j+1]=0; /* Trims blanks at end of line */
5455: if(line[0]=='#'){
5456: fprintf(ficlog,"Comment line\n%s\n",line);
5457: printf("Comment line\n%s\n",line);
5458: continue;
5459: }
5460: trimbb(linetmp,line); /* Trims multiple blanks in line */
5461: strcpy(line, linetmp);
5462:
5463:
5464: for (j=maxwav;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 (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5472: if( strb[0]=='\0' || (*endptr != '\0')){
5473: 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);
5474: 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);
5475: return 1;
5476: }
5477: }
5478: s[j][i]=lval;
5479:
5480: strcpy(line,stra);
5481: cutv(stra, strb,line,' ');
5482: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5483: }
5484: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5485: month=99;
5486: year=9999;
5487: }else{
5488: 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);
5489: 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);
5490: return 1;
5491: }
5492: anint[j][i]= (double) year;
5493: mint[j][i]= (double)month;
5494: strcpy(line,stra);
5495: } /* ENd Waves */
5496:
5497: cutv(stra, strb,line,' ');
5498: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5499: }
5500: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5501: month=99;
5502: year=9999;
5503: }else{
5504: 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);
5505: 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);
5506: return 1;
5507: }
5508: andc[i]=(double) year;
5509: moisdc[i]=(double) month;
5510: strcpy(line,stra);
5511:
5512: cutv(stra, strb,line,' ');
5513: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5514: }
5515: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5516: month=99;
5517: year=9999;
5518: }else{
5519: 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);
5520: 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);
5521: return 1;
5522: }
5523: if (year==9999) {
5524: 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);
5525: 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);
5526: return 1;
5527:
5528: }
5529: annais[i]=(double)(year);
5530: moisnais[i]=(double)(month);
5531: strcpy(line,stra);
5532:
5533: cutv(stra, strb,line,' ');
5534: errno=0;
5535: dval=strtod(strb,&endptr);
5536: if( strb[0]=='\0' || (*endptr != '\0')){
5537: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5538: 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);
5539: fflush(ficlog);
5540: return 1;
5541: }
5542: weight[i]=dval;
5543: strcpy(line,stra);
5544:
5545: for (j=ncovcol;j>=1;j--){
5546: cutv(stra, strb,line,' ');
5547: if(strb[0]=='.') { /* Missing status */
5548: lval=-1;
5549: }else{
5550: errno=0;
5551: lval=strtol(strb,&endptr,10);
5552: if( strb[0]=='\0' || (*endptr != '\0')){
5553: 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);
5554: 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);
5555: return 1;
5556: }
5557: }
5558: if(lval <-1 || lval >1){
5559: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5560: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5561: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5562: For example, for multinomial values like 1, 2 and 3,\n \
5563: build V1=0 V2=0 for the reference value (1),\n \
5564: V1=1 V2=0 for (2) \n \
5565: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5566: output of IMaCh is often meaningless.\n \
5567: Exiting.\n",lval,linei, i,line,j);
5568: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5569: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5570: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5571: For example, for multinomial values like 1, 2 and 3,\n \
5572: build V1=0 V2=0 for the reference value (1),\n \
5573: V1=1 V2=0 for (2) \n \
5574: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5575: output of IMaCh is often meaningless.\n \
5576: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5577: return 1;
5578: }
5579: covar[j][i]=(double)(lval);
5580: strcpy(line,stra);
5581: }
5582: lstra=strlen(stra);
5583:
5584: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5585: stratrunc = &(stra[lstra-9]);
5586: num[i]=atol(stratrunc);
5587: }
5588: else
5589: num[i]=atol(stra);
5590: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5591: 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;}*/
5592:
5593: i=i+1;
5594: } /* End loop reading data */
5595:
5596: *imax=i-1; /* Number of individuals */
5597: fclose(fic);
5598:
5599: return (0);
5600: /* endread: */
5601: printf("Exiting readdata: ");
5602: fclose(fic);
5603: return (1);
5604:
5605:
5606:
5607: }
5608: void removespace(char *str) {
5609: char *p1 = str, *p2 = str;
5610: do
5611: while (*p2 == ' ')
5612: p2++;
5613: while (*p1++ == *p2++);
5614: }
5615:
5616: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5617: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5618: * - nagesqr = 1 if age*age in the model, otherwise 0.
5619: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5620: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
5621: * - cptcovage number of covariates with age*products =2
5622: * - cptcovs number of simple covariates
5623: * - 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
5624: * which is a new column after the 9 (ncovcol) variables.
5625: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5626: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5627: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5628: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5629: */
5630: {
5631: int i, j, k, ks;
5632: int j1, k1, k2;
5633: char modelsav[80];
5634: char stra[80], strb[80], strc[80], strd[80],stre[80];
5635: char *strpt;
5636:
5637: /*removespace(model);*/
5638: if (strlen(model) >1){ /* If there is at least 1 covariate */
5639: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5640: if (strstr(model,"AGE") !=0){
5641: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5642: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
5643: return 1;
5644: }
5645: if (strstr(model,"v") !=0){
5646: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5647: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5648: return 1;
5649: }
5650: strcpy(modelsav,model);
5651: if ((strpt=strstr(model,"age*age")) !=0){
5652: printf(" strpt=%s, model=%s\n",strpt, model);
5653: if(strpt != model){
5654: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5655: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
5656: corresponding column of parameters.\n",model);
5657: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5658: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
5659: corresponding column of parameters.\n",model); fflush(ficlog);
5660: return 1;
5661: }
5662:
5663: nagesqr=1;
5664: if (strstr(model,"+age*age") !=0)
5665: substrchaine(modelsav, model, "+age*age");
5666: else if (strstr(model,"age*age+") !=0)
5667: substrchaine(modelsav, model, "age*age+");
5668: else
5669: substrchaine(modelsav, model, "age*age");
5670: }else
5671: nagesqr=0;
5672: if (strlen(modelsav) >1){
5673: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5674: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5675: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5676: cptcovt= j+1; /* Number of total covariates in the model, not including
5677: * cst, age and age*age
5678: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5679: /* including age products which are counted in cptcovage.
5680: * but the covariates which are products must be treated
5681: * separately: ncovn=4- 2=2 (V1+V3). */
5682: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5683: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5684:
5685:
5686: /* Design
5687: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5688: * < ncovcol=8 >
5689: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5690: * k= 1 2 3 4 5 6 7 8
5691: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5692: * covar[k,i], value of kth covariate if not including age for individual i:
5693: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5694: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5695: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5696: * Tage[++cptcovage]=k
5697: * if products, new covar are created after ncovcol with k1
5698: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5699: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5700: * 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
5701: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5702: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5703: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5704: * < ncovcol=8 >
5705: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5706: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5707: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5708: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5709: * p Tprod[1]@2={ 6, 5}
5710: *p Tvard[1][1]@4= {7, 8, 5, 6}
5711: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5712: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5713: *How to reorganize?
5714: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5715: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5716: * {2, 1, 4, 8, 5, 6, 3, 7}
5717: * Struct []
5718: */
5719:
5720: /* This loop fills the array Tvar from the string 'model'.*/
5721: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5722: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5723: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5724: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5725: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5726: /* k=1 Tvar[1]=2 (from V2) */
5727: /* k=5 Tvar[5] */
5728: /* for (k=1; k<=cptcovn;k++) { */
5729: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5730: /* } */
5731: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5732: /*
5733: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5734: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5735: Tvar[k]=0;
5736: cptcovage=0;
5737: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5738: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5739: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5740: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5741: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5742: /*scanf("%d",i);*/
5743: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5744: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5745: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5746: /* covar is not filled and then is empty */
5747: cptcovprod--;
5748: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5749: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5750: cptcovage++; /* Sums the number of covariates which include age as a product */
5751: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5752: /*printf("stre=%s ", stre);*/
5753: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5754: cptcovprod--;
5755: cutl(stre,strb,strc,'V');
5756: Tvar[k]=atoi(stre);
5757: cptcovage++;
5758: Tage[cptcovage]=k;
5759: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5760: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5761: cptcovn++;
5762: cptcovprodnoage++;k1++;
5763: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5764: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5765: because this model-covariate is a construction we invent a new column
5766: ncovcol + k1
5767: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5768: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5769: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5770: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5771: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5772: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5773: k2=k2+2;
5774: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5775: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5776: for (i=1; i<=lastobs;i++){
5777: /* Computes the new covariate which is a product of
5778: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5779: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5780: }
5781: } /* End age is not in the model */
5782: } /* End if model includes a product */
5783: else { /* no more sum */
5784: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5785: /* scanf("%d",i);*/
5786: cutl(strd,strc,strb,'V');
5787: ks++; /**< Number of simple covariates */
5788: cptcovn++;
5789: Tvar[k]=atoi(strd);
5790: }
5791: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5792: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5793: scanf("%d",i);*/
5794: } /* end of loop + on total covariates */
5795: } /* end if strlen(modelsave == 0) age*age might exist */
5796: } /* end if strlen(model == 0) */
5797:
5798: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5799: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5800:
5801: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5802: printf("cptcovprod=%d ", cptcovprod);
5803: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5804:
5805: scanf("%d ",i);*/
5806:
5807:
5808: return (0); /* with covar[new additional covariate if product] and Tage if age */
5809: /*endread:*/
5810: printf("Exiting decodemodel: ");
5811: return (1);
5812: }
5813:
5814: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5815: {
5816: int i, m;
5817:
5818: for (i=1; i<=imx; i++) {
5819: for(m=2; (m<= maxwav); m++) {
5820: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5821: anint[m][i]=9999;
5822: s[m][i]=-1;
5823: }
5824: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5825: *nberr = *nberr + 1;
5826: 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);
5827: 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);
5828: s[m][i]=-1;
5829: }
5830: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5831: (*nberr)++;
5832: 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]);
5833: 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]);
5834: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5835: }
5836: }
5837: }
5838:
5839: for (i=1; i<=imx; i++) {
5840: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5841: for(m=firstpass; (m<= lastpass); m++){
5842: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5843: if (s[m][i] >= nlstate+1) {
5844: if(agedc[i]>0){
5845: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5846: agev[m][i]=agedc[i];
5847: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5848: }else {
5849: if ((int)andc[i]!=9999){
5850: nbwarn++;
5851: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5852: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5853: agev[m][i]=-1;
5854: }
5855: }
5856: } /* agedc > 0 */
5857: }
5858: else if(s[m][i] !=9){ /* Standard case, age in fractional
5859: years but with the precision of a month */
5860: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5861: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5862: agev[m][i]=1;
5863: else if(agev[m][i] < *agemin){
5864: *agemin=agev[m][i];
5865: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5866: }
5867: else if(agev[m][i] >*agemax){
5868: *agemax=agev[m][i];
5869: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5870: }
5871: /*agev[m][i]=anint[m][i]-annais[i];*/
5872: /* agev[m][i] = age[i]+2*m;*/
5873: }
5874: else { /* =9 */
5875: agev[m][i]=1;
5876: s[m][i]=-1;
5877: }
5878: }
5879: else /*= 0 Unknown */
5880: agev[m][i]=1;
5881: }
5882:
5883: }
5884: for (i=1; i<=imx; i++) {
5885: for(m=firstpass; (m<=lastpass); m++){
5886: if (s[m][i] > (nlstate+ndeath)) {
5887: (*nberr)++;
5888: 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);
5889: 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);
5890: return 1;
5891: }
5892: }
5893: }
5894:
5895: /*for (i=1; i<=imx; i++){
5896: for (m=firstpass; (m<lastpass); m++){
5897: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5898: }
5899:
5900: }*/
5901:
5902:
5903: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5904: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5905:
5906: return (0);
5907: /* endread:*/
5908: printf("Exiting calandcheckages: ");
5909: return (1);
5910: }
5911:
5912: #if defined(_MSC_VER)
5913: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5914: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5915: //#include "stdafx.h"
5916: //#include <stdio.h>
5917: //#include <tchar.h>
5918: //#include <windows.h>
5919: //#include <iostream>
5920: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5921:
5922: LPFN_ISWOW64PROCESS fnIsWow64Process;
5923:
5924: BOOL IsWow64()
5925: {
5926: BOOL bIsWow64 = FALSE;
5927:
5928: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5929: // (HANDLE, PBOOL);
5930:
5931: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5932:
5933: HMODULE module = GetModuleHandle(_T("kernel32"));
5934: const char funcName[] = "IsWow64Process";
5935: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5936: GetProcAddress(module, funcName);
5937:
5938: if (NULL != fnIsWow64Process)
5939: {
5940: if (!fnIsWow64Process(GetCurrentProcess(),
5941: &bIsWow64))
5942: //throw std::exception("Unknown error");
5943: printf("Unknown error\n");
5944: }
5945: return bIsWow64 != FALSE;
5946: }
5947: #endif
5948:
5949: void syscompilerinfo(int logged)
5950: {
5951: /* #include "syscompilerinfo.h"*/
5952: /* command line Intel compiler 32bit windows, XP compatible:*/
5953: /* /GS /W3 /Gy
5954: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5955: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5956: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
5957: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5958: */
5959: /* 64 bits */
5960: /*
5961: /GS /W3 /Gy
5962: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5963: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5964: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5965: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5966: /* Optimization are useless and O3 is slower than O2 */
5967: /*
5968: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5969: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5970: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5971: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5972: */
5973: /* Link is */ /* /OUT:"visual studio
5974: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5975: /PDB:"visual studio
5976: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5977: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5978: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5979: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5980: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5981: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5982: uiAccess='false'"
5983: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5984: /NOLOGO /TLBID:1
5985: */
5986: #if defined __INTEL_COMPILER
5987: #if defined(__GNUC__)
5988: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5989: #endif
5990: #elif defined(__GNUC__)
5991: #ifndef __APPLE__
5992: #include <gnu/libc-version.h> /* Only on gnu */
5993: #endif
5994: struct utsname sysInfo;
5995: int cross = CROSS;
5996: if (cross){
5997: printf("Cross-");
5998: if(logged) fprintf(ficlog, "Cross-");
5999: }
6000: #endif
6001:
6002: #include <stdint.h>
6003:
6004: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
6005: #if defined(__clang__)
6006: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
6007: #endif
6008: #if defined(__ICC) || defined(__INTEL_COMPILER)
6009: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
6010: #endif
6011: #if defined(__GNUC__) || defined(__GNUG__)
6012: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
6013: #endif
6014: #if defined(__HP_cc) || defined(__HP_aCC)
6015: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
6016: #endif
6017: #if defined(__IBMC__) || defined(__IBMCPP__)
6018: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
6019: #endif
6020: #if defined(_MSC_VER)
6021: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
6022: #endif
6023: #if defined(__PGI)
6024: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
6025: #endif
6026: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
6027: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
6028: #endif
6029: printf(" for "); if (logged) fprintf(ficlog, " for ");
6030:
6031: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6032: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6033: // Windows (x64 and x86)
6034: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
6035: #elif __unix__ // all unices, not all compilers
6036: // Unix
6037: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
6038: #elif __linux__
6039: // linux
6040: printf("linux ");if(logged) fprintf(ficlog,"linux ");
6041: #elif __APPLE__
6042: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
6043: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
6044: #endif
6045:
6046: /* __MINGW32__ */
6047: /* __CYGWIN__ */
6048: /* __MINGW64__ */
6049: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6050: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6051: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6052: /* _WIN64 // Defined for applications for Win64. */
6053: /* _M_X64 // Defined for compilations that target x64 processors. */
6054: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
6055:
6056: #if UINTPTR_MAX == 0xffffffff
6057: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
6058: #elif UINTPTR_MAX == 0xffffffffffffffff
6059: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
6060: #else
6061: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
6062: #endif
6063:
6064: #if defined(__GNUC__)
6065: # if defined(__GNUC_PATCHLEVEL__)
6066: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6067: + __GNUC_MINOR__ * 100 \
6068: + __GNUC_PATCHLEVEL__)
6069: # else
6070: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6071: + __GNUC_MINOR__ * 100)
6072: # endif
6073: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
6074: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
6075:
6076: if (uname(&sysInfo) != -1) {
6077: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
6078: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
6079: }
6080: else
6081: perror("uname() error");
6082: //#ifndef __INTEL_COMPILER
6083: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
6084: printf("GNU libc version: %s\n", gnu_get_libc_version());
6085: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
6086: #endif
6087: #endif
6088:
6089: // void main()
6090: // {
6091: #if defined(_MSC_VER)
6092: if (IsWow64()){
6093: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6094: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6095: }
6096: else{
6097: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6098: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6099: }
6100: // printf("\nPress Enter to continue...");
6101: // getchar();
6102: // }
6103:
6104: #endif
6105:
6106:
6107: }
6108:
6109: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6110: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6111: int i, j, k, i1 ;
6112: double ftolpl = 1.e-10;
6113: double age, agebase, agelim;
6114:
6115: strcpy(filerespl,"pl");
6116: strcat(filerespl,fileres);
6117: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6118: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6119: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6120: }
6121: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6122: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6123: pstamp(ficrespl);
6124: fprintf(ficrespl,"# Period (stable) prevalence \n");
6125: fprintf(ficrespl,"#Age ");
6126: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6127: fprintf(ficrespl,"\n");
6128:
6129: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6130:
6131: agebase=ageminpar;
6132: agelim=agemaxpar;
6133:
6134: i1=pow(2,cptcoveff);
6135: if (cptcovn < 1){i1=1;}
6136:
6137: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6138: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6139: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6140: k=k+1;
6141: /* to clean */
6142: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6143: fprintf(ficrespl,"\n#******");
6144: printf("\n#******");
6145: fprintf(ficlog,"\n#******");
6146: for(j=1;j<=cptcoveff;j++) {
6147: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6148: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6149: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6150: }
6151: fprintf(ficrespl,"******\n");
6152: printf("******\n");
6153: fprintf(ficlog,"******\n");
6154:
6155: fprintf(ficrespl,"#Age ");
6156: for(j=1;j<=cptcoveff;j++) {
6157: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6158: }
6159: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6160: fprintf(ficrespl,"\n");
6161:
6162: for (age=agebase; age<=agelim; age++){
6163: /* for (age=agebase; age<=agebase; age++){ */
6164: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6165: fprintf(ficrespl,"%.0f ",age );
6166: for(j=1;j<=cptcoveff;j++)
6167: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6168: for(i=1; i<=nlstate;i++)
6169: fprintf(ficrespl," %.5f", prlim[i][i]);
6170: fprintf(ficrespl,"\n");
6171: } /* Age */
6172: /* was end of cptcod */
6173: } /* cptcov */
6174: return 0;
6175: }
6176:
6177: int hPijx(double *p, int bage, int fage){
6178: /*------------- h Pij x at various ages ------------*/
6179:
6180: int stepsize;
6181: int agelim;
6182: int hstepm;
6183: int nhstepm;
6184: int h, i, i1, j, k;
6185:
6186: double agedeb;
6187: double ***p3mat;
6188:
6189: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6190: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6191: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6192: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6193: }
6194: printf("Computing pij: result on file '%s' \n", filerespij);
6195: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6196:
6197: stepsize=(int) (stepm+YEARM-1)/YEARM;
6198: /*if (stepm<=24) stepsize=2;*/
6199:
6200: agelim=AGESUP;
6201: hstepm=stepsize*YEARM; /* Every year of age */
6202: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6203:
6204: /* hstepm=1; aff par mois*/
6205: pstamp(ficrespij);
6206: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6207: i1= pow(2,cptcoveff);
6208: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6209: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6210: /* k=k+1; */
6211: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6212: fprintf(ficrespij,"\n#****** ");
6213: for(j=1;j<=cptcoveff;j++)
6214: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6215: fprintf(ficrespij,"******\n");
6216:
6217: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6218: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6219: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6220:
6221: /* nhstepm=nhstepm*YEARM; aff par mois*/
6222:
6223: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6224: oldm=oldms;savm=savms;
6225: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6226: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6227: for(i=1; i<=nlstate;i++)
6228: for(j=1; j<=nlstate+ndeath;j++)
6229: fprintf(ficrespij," %1d-%1d",i,j);
6230: fprintf(ficrespij,"\n");
6231: for (h=0; h<=nhstepm; h++){
6232: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6233: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
6234: for(i=1; i<=nlstate;i++)
6235: for(j=1; j<=nlstate+ndeath;j++)
6236: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6237: fprintf(ficrespij,"\n");
6238: }
6239: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6240: fprintf(ficrespij,"\n");
6241: }
6242: /*}*/
6243: }
6244: return 0;
6245: }
6246:
6247:
6248: /***********************************************/
6249: /**************** Main Program *****************/
6250: /***********************************************/
6251:
6252: int main(int argc, char *argv[])
6253: {
6254: #ifdef GSL
6255: const gsl_multimin_fminimizer_type *T;
6256: size_t iteri = 0, it;
6257: int rval = GSL_CONTINUE;
6258: int status = GSL_SUCCESS;
6259: double ssval;
6260: #endif
6261: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
6262: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6263:
6264: int jj, ll, li, lj, lk;
6265: int numlinepar=0; /* Current linenumber of parameter file */
6266: int itimes;
6267: int NDIM=2;
6268: int vpopbased=0;
6269:
6270: char ca[32], cb[32];
6271: /* FILE *fichtm; *//* Html File */
6272: /* FILE *ficgp;*/ /*Gnuplot File */
6273: struct stat info;
6274: double agedeb=0.;
6275: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6276:
6277: double fret;
6278: double dum=0.; /* Dummy variable */
6279: double ***p3mat;
6280: double ***mobaverage;
6281:
6282: char line[MAXLINE];
6283: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6284: char pathr[MAXLINE], pathimach[MAXLINE];
6285: char *tok, *val; /* pathtot */
6286: int firstobs=1, lastobs=10;
6287: int c, h , cpt;
6288: int jl=0;
6289: int i1, j1, jk, stepsize=0;
6290: int *tab;
6291: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6292: int mobilav=0,popforecast=0;
6293: int hstepm=0, nhstepm=0;
6294: int agemortsup;
6295: float sumlpop=0.;
6296: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6297: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6298:
6299: double bage=0, fage=110., age, agelim=0., agebase=0.;
6300: double ftolpl=FTOL;
6301: double **prlim;
6302: double ***param; /* Matrix of parameters */
6303: double *p;
6304: double **matcov; /* Matrix of covariance */
6305: double ***delti3; /* Scale */
6306: double *delti; /* Scale */
6307: double ***eij, ***vareij;
6308: double **varpl; /* Variances of prevalence limits by age */
6309: double *epj, vepp;
6310:
6311: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6312: double **ximort;
6313: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
6314: int *dcwave;
6315:
6316: char z[1]="c";
6317:
6318: /*char *strt;*/
6319: char strtend[80];
6320:
6321:
6322: /* setlocale (LC_ALL, ""); */
6323: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6324: /* textdomain (PACKAGE); */
6325: /* setlocale (LC_CTYPE, ""); */
6326: /* setlocale (LC_MESSAGES, ""); */
6327:
6328: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
6329: rstart_time = time(NULL);
6330: /* (void) gettimeofday(&start_time,&tzp);*/
6331: start_time = *localtime(&rstart_time);
6332: curr_time=start_time;
6333: /*tml = *localtime(&start_time.tm_sec);*/
6334: /* strcpy(strstart,asctime(&tml)); */
6335: strcpy(strstart,asctime(&start_time));
6336:
6337: /* printf("Localtime (at start)=%s",strstart); */
6338: /* tp.tm_sec = tp.tm_sec +86400; */
6339: /* tm = *localtime(&start_time.tm_sec); */
6340: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6341: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6342: /* tmg.tm_hour=tmg.tm_hour + 1; */
6343: /* tp.tm_sec = mktime(&tmg); */
6344: /* strt=asctime(&tmg); */
6345: /* printf("Time(after) =%s",strstart); */
6346: /* (void) time (&time_value);
6347: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6348: * tm = *localtime(&time_value);
6349: * strstart=asctime(&tm);
6350: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6351: */
6352:
6353: nberr=0; /* Number of errors and warnings */
6354: nbwarn=0;
6355: #ifdef WIN32
6356: _getcwd(pathcd, size);
6357: #else
6358: getcwd(pathcd, size);
6359: #endif
6360: syscompilerinfo(0);
6361: printf("\n%s\n%s",version,fullversion);
6362: if(argc <=1){
6363: printf("\nEnter the parameter file name: ");
6364: fgets(pathr,FILENAMELENGTH,stdin);
6365: i=strlen(pathr);
6366: if(pathr[i-1]=='\n')
6367: pathr[i-1]='\0';
6368: i=strlen(pathr);
6369: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6370: pathr[i-1]='\0';
6371: for (tok = pathr; tok != NULL; ){
6372: printf("Pathr |%s|\n",pathr);
6373: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6374: printf("val= |%s| pathr=%s\n",val,pathr);
6375: strcpy (pathtot, val);
6376: if(pathr[0] == '\0') break; /* Dirty */
6377: }
6378: }
6379: else{
6380: strcpy(pathtot,argv[1]);
6381: }
6382: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6383: /*cygwin_split_path(pathtot,path,optionfile);
6384: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6385: /* cutv(path,optionfile,pathtot,'\\');*/
6386:
6387: /* Split argv[0], imach program to get pathimach */
6388: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6389: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6390: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6391: /* strcpy(pathimach,argv[0]); */
6392: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6393: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6394: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
6395: #ifdef WIN32
6396: _chdir(path); /* Can be a relative path */
6397: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6398: #else
6399: chdir(path); /* Can be a relative path */
6400: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6401: #endif
6402: printf("Current directory %s!\n",pathcd);
6403: strcpy(command,"mkdir ");
6404: strcat(command,optionfilefiname);
6405: if((outcmd=system(command)) != 0){
6406: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
6407: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6408: /* fclose(ficlog); */
6409: /* exit(1); */
6410: }
6411: /* if((imk=mkdir(optionfilefiname))<0){ */
6412: /* perror("mkdir"); */
6413: /* } */
6414:
6415: /*-------- arguments in the command line --------*/
6416:
6417: /* Main Log file */
6418: strcat(filelog, optionfilefiname);
6419: strcat(filelog,".log"); /* */
6420: if((ficlog=fopen(filelog,"w"))==NULL) {
6421: printf("Problem with logfile %s\n",filelog);
6422: goto end;
6423: }
6424: fprintf(ficlog,"Log filename:%s\n",filelog);
6425: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6426: fprintf(ficlog,"\nEnter the parameter file name: \n");
6427: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6428: path=%s \n\
6429: optionfile=%s\n\
6430: optionfilext=%s\n\
6431: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
6432:
6433: syscompilerinfo(0);
6434:
6435: printf("Local time (at start):%s",strstart);
6436: fprintf(ficlog,"Local time (at start): %s",strstart);
6437: fflush(ficlog);
6438: /* (void) gettimeofday(&curr_time,&tzp); */
6439: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
6440:
6441: /* */
6442: strcpy(fileres,"r");
6443: strcat(fileres, optionfilefiname);
6444: strcat(fileres,".txt"); /* Other files have txt extension */
6445:
6446: /* Main ---------arguments file --------*/
6447:
6448: if((ficpar=fopen(optionfile,"r"))==NULL) {
6449: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6450: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6451: fflush(ficlog);
6452: /* goto end; */
6453: exit(70);
6454: }
6455:
6456:
6457:
6458: strcpy(filereso,"o");
6459: strcat(filereso,fileres);
6460: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6461: printf("Problem with Output resultfile: %s\n", filereso);
6462: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6463: fflush(ficlog);
6464: goto end;
6465: }
6466:
6467: /* Reads comments: lines beginning with '#' */
6468: numlinepar=0;
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: 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);
6480: numlinepar++;
6481: 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);
6482: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6483: model[strlen(model)-1]='\0';
6484: 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);
6485: 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);
6486: fflush(ficlog);
6487: /* if(model[0]=='#'|| model[0]== '\0'){ */
6488: if(model[0]=='#'){
6489: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6490: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6491: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6492: if(mle != -1){
6493: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6494: exit(1);
6495: }
6496: }
6497: while((c=getc(ficpar))=='#' && c!= EOF){
6498: ungetc(c,ficpar);
6499: fgets(line, MAXLINE, ficpar);
6500: numlinepar++;
6501: fputs(line, stdout);
6502: //puts(line);
6503: fputs(line,ficparo);
6504: fputs(line,ficlog);
6505: }
6506: ungetc(c,ficpar);
6507:
6508:
6509: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
6510: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6511: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6512: v1+v2*age+v2*v3 makes cptcovn = 3
6513: */
6514: if (strlen(model)>1)
6515: 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*/
6516: else
6517: ncovmodel=2; /* Constant and age */
6518: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6519: npar= nforce*ncovmodel; /* Number of parameters like aij*/
6520: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6521: 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);
6522: 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);
6523: fflush(stdout);
6524: fclose (ficlog);
6525: goto end;
6526: }
6527: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6528: delti=delti3[1][1];
6529: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6530: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6531: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6532: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6533: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6534: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6535: fclose (ficparo);
6536: fclose (ficlog);
6537: goto end;
6538: exit(0);
6539: }
6540: else if(mle==-3) { /* Main Wizard */
6541: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6542: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6543: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6544: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6545: matcov=matrix(1,npar,1,npar);
6546: }
6547: else{
6548: /* Read guessed parameters */
6549: /* Reads comments: lines beginning with '#' */
6550: while((c=getc(ficpar))=='#' && c!= EOF){
6551: ungetc(c,ficpar);
6552: fgets(line, MAXLINE, ficpar);
6553: numlinepar++;
6554: fputs(line,stdout);
6555: fputs(line,ficparo);
6556: fputs(line,ficlog);
6557: }
6558: ungetc(c,ficpar);
6559:
6560: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6561: for(i=1; i <=nlstate; i++){
6562: j=0;
6563: for(jj=1; jj <=nlstate+ndeath; jj++){
6564: if(jj==i) continue;
6565: j++;
6566: fscanf(ficpar,"%1d%1d",&i1,&j1);
6567: if ((i1 != i) || (j1 != jj)){
6568: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6569: It might be a problem of design; if ncovcol and the model are correct\n \
6570: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6571: exit(1);
6572: }
6573: fprintf(ficparo,"%1d%1d",i1,j1);
6574: if(mle==1)
6575: printf("%1d%1d",i,jj);
6576: fprintf(ficlog,"%1d%1d",i,jj);
6577: for(k=1; k<=ncovmodel;k++){
6578: fscanf(ficpar," %lf",¶m[i][j][k]);
6579: if(mle==1){
6580: printf(" %lf",param[i][j][k]);
6581: fprintf(ficlog," %lf",param[i][j][k]);
6582: }
6583: else
6584: fprintf(ficlog," %lf",param[i][j][k]);
6585: fprintf(ficparo," %lf",param[i][j][k]);
6586: }
6587: fscanf(ficpar,"\n");
6588: numlinepar++;
6589: if(mle==1)
6590: printf("\n");
6591: fprintf(ficlog,"\n");
6592: fprintf(ficparo,"\n");
6593: }
6594: }
6595: fflush(ficlog);
6596:
6597: /* Reads scales values */
6598: p=param[1][1];
6599:
6600: /* Reads comments: lines beginning with '#' */
6601: while((c=getc(ficpar))=='#' && c!= EOF){
6602: ungetc(c,ficpar);
6603: fgets(line, MAXLINE, ficpar);
6604: numlinepar++;
6605: fputs(line,stdout);
6606: fputs(line,ficparo);
6607: fputs(line,ficlog);
6608: }
6609: ungetc(c,ficpar);
6610:
6611: for(i=1; i <=nlstate; i++){
6612: for(j=1; j <=nlstate+ndeath-1; j++){
6613: fscanf(ficpar,"%1d%1d",&i1,&j1);
6614: if ( (i1-i) * (j1-j) != 0){
6615: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6616: exit(1);
6617: }
6618: printf("%1d%1d",i,j);
6619: fprintf(ficparo,"%1d%1d",i1,j1);
6620: fprintf(ficlog,"%1d%1d",i1,j1);
6621: for(k=1; k<=ncovmodel;k++){
6622: fscanf(ficpar,"%le",&delti3[i][j][k]);
6623: printf(" %le",delti3[i][j][k]);
6624: fprintf(ficparo," %le",delti3[i][j][k]);
6625: fprintf(ficlog," %le",delti3[i][j][k]);
6626: }
6627: fscanf(ficpar,"\n");
6628: numlinepar++;
6629: printf("\n");
6630: fprintf(ficparo,"\n");
6631: fprintf(ficlog,"\n");
6632: }
6633: }
6634: fflush(ficlog);
6635:
6636: /* Reads covariance matrix */
6637: delti=delti3[1][1];
6638:
6639:
6640: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6641:
6642: /* Reads comments: lines beginning with '#' */
6643: while((c=getc(ficpar))=='#' && c!= EOF){
6644: ungetc(c,ficpar);
6645: fgets(line, MAXLINE, ficpar);
6646: numlinepar++;
6647: fputs(line,stdout);
6648: fputs(line,ficparo);
6649: fputs(line,ficlog);
6650: }
6651: ungetc(c,ficpar);
6652:
6653: matcov=matrix(1,npar,1,npar);
6654: for(i=1; i <=npar; i++)
6655: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6656:
6657: for(i=1; i <=npar; i++){
6658: fscanf(ficpar,"%s",str);
6659: if(mle==1)
6660: printf("%s",str);
6661: fprintf(ficlog,"%s",str);
6662: fprintf(ficparo,"%s",str);
6663: for(j=1; j <=i; j++){
6664: fscanf(ficpar," %le",&matcov[i][j]);
6665: if(mle==1){
6666: printf(" %.5le",matcov[i][j]);
6667: }
6668: fprintf(ficlog," %.5le",matcov[i][j]);
6669: fprintf(ficparo," %.5le",matcov[i][j]);
6670: }
6671: fscanf(ficpar,"\n");
6672: numlinepar++;
6673: if(mle==1)
6674: printf("\n");
6675: fprintf(ficlog,"\n");
6676: fprintf(ficparo,"\n");
6677: }
6678: for(i=1; i <=npar; i++)
6679: for(j=i+1;j<=npar;j++)
6680: matcov[i][j]=matcov[j][i];
6681:
6682: if(mle==1)
6683: printf("\n");
6684: fprintf(ficlog,"\n");
6685:
6686: fflush(ficlog);
6687:
6688: /*-------- Rewriting parameter file ----------*/
6689: strcpy(rfileres,"r"); /* "Rparameterfile */
6690: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6691: strcat(rfileres,"."); /* */
6692: strcat(rfileres,optionfilext); /* Other files have txt extension */
6693: if((ficres =fopen(rfileres,"w"))==NULL) {
6694: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6695: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6696: }
6697: fprintf(ficres,"#%s\n",version);
6698: } /* End of mle != -3 */
6699:
6700: /* Main data
6701: */
6702: n= lastobs;
6703: num=lvector(1,n);
6704: moisnais=vector(1,n);
6705: annais=vector(1,n);
6706: moisdc=vector(1,n);
6707: andc=vector(1,n);
6708: agedc=vector(1,n);
6709: cod=ivector(1,n);
6710: weight=vector(1,n);
6711: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6712: mint=matrix(1,maxwav,1,n);
6713: anint=matrix(1,maxwav,1,n);
6714: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6715: tab=ivector(1,NCOVMAX);
6716: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6717: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6718:
6719: /* Reads data from file datafile */
6720: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6721: goto end;
6722:
6723: /* Calculation of the number of parameters from char model */
6724: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6725: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6726: k=3 V4 Tvar[k=3]= 4 (from V4)
6727: k=2 V1 Tvar[k=2]= 1 (from V1)
6728: k=1 Tvar[1]=2 (from V2)
6729: */
6730: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6731: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6732: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6733: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6734: */
6735: /* For model-covariate k tells which data-covariate to use but
6736: because this model-covariate is a construction we invent a new column
6737: ncovcol + k1
6738: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6739: Tvar[3=V1*V4]=4+1 etc */
6740: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6741: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6742: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6743: */
6744: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6745: 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
6746: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6747: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6748: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6749: 4 covariates (3 plus signs)
6750: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6751: */
6752:
6753: /* Main decodemodel */
6754:
6755:
6756: if(decodemodel(model, lastobs) == 1)
6757: goto end;
6758:
6759: if((double)(lastobs-imx)/(double)imx > 1.10){
6760: nbwarn++;
6761: 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);
6762: 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);
6763: }
6764: /* if(mle==1){*/
6765: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6766: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6767: }
6768:
6769: /*-calculation of age at interview from date of interview and age at death -*/
6770: agev=matrix(1,maxwav,1,imx);
6771:
6772: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6773: goto end;
6774:
6775:
6776: agegomp=(int)agemin;
6777: free_vector(moisnais,1,n);
6778: free_vector(annais,1,n);
6779: /* free_matrix(mint,1,maxwav,1,n);
6780: free_matrix(anint,1,maxwav,1,n);*/
6781: free_vector(moisdc,1,n);
6782: free_vector(andc,1,n);
6783: /* */
6784:
6785: wav=ivector(1,imx);
6786: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6787: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6788: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6789:
6790: /* Concatenates waves */
6791: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6792: /* */
6793:
6794: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6795:
6796: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6797: ncodemax[1]=1;
6798: Ndum =ivector(-1,NCOVMAX);
6799: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
6800: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6801: /* Nbcode gives the value of the lth modality of jth covariate, in
6802: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6803: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
6804:
6805: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6806: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6807: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
6808: h=0;
6809:
6810:
6811: /*if (cptcovn > 0) */
6812:
6813:
6814: m=pow(2,cptcoveff);
6815:
6816: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6817: 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 */
6818: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6819: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6820: h++;
6821: if (h>m)
6822: h=1;
6823: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6824: * For k=4 covariates, h goes from 1 to 2**k
6825: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6826: * h\k 1 2 3 4
6827: *______________________________
6828: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6829: * 2 2 1 1 1
6830: * 3 i=2 1 2 1 1
6831: * 4 2 2 1 1
6832: * 5 i=3 1 i=2 1 2 1
6833: * 6 2 1 2 1
6834: * 7 i=4 1 2 2 1
6835: * 8 2 2 2 1
6836: * 9 i=5 1 i=3 1 i=2 1 1
6837: * 10 2 1 1 1
6838: * 11 i=6 1 2 1 1
6839: * 12 2 2 1 1
6840: * 13 i=7 1 i=4 1 2 1
6841: * 14 2 1 2 1
6842: * 15 i=8 1 2 2 1
6843: * 16 2 2 2 1
6844: */
6845: codtab[h][k]=j;
6846: /* codtab[12][3]=1; */
6847: /*codtab[h][Tvar[k]]=j;*/
6848: 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]]);
6849: }
6850: }
6851: }
6852: }
6853: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6854: codtab[1][2]=1;codtab[2][2]=2; */
6855: /* for(i=1; i <=m ;i++){
6856: for(k=1; k <=cptcovn; k++){
6857: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6858: }
6859: printf("\n");
6860: }
6861: scanf("%d",i);*/
6862:
6863: free_ivector(Ndum,-1,NCOVMAX);
6864:
6865:
6866:
6867: /* Initialisation of ----------- gnuplot -------------*/
6868: strcpy(optionfilegnuplot,optionfilefiname);
6869: if(mle==-3)
6870: strcat(optionfilegnuplot,"-mort");
6871: strcat(optionfilegnuplot,".gp");
6872:
6873: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6874: printf("Problem with file %s",optionfilegnuplot);
6875: }
6876: else{
6877: fprintf(ficgp,"\n# %s\n", version);
6878: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6879: //fprintf(ficgp,"set missing 'NaNq'\n");
6880: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6881: }
6882: /* fclose(ficgp);*/
6883:
6884:
6885: /* Initialisation of --------- index.htm --------*/
6886:
6887: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6888: if(mle==-3)
6889: strcat(optionfilehtm,"-mort");
6890: strcat(optionfilehtm,".htm");
6891: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6892: printf("Problem with %s \n",optionfilehtm);
6893: exit(0);
6894: }
6895:
6896: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6897: strcat(optionfilehtmcov,"-cov.htm");
6898: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6899: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6900: }
6901: else{
6902: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6903: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6904: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6905: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6906: }
6907:
6908: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6909: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6910: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6911: \n\
6912: <hr size=\"2\" color=\"#EC5E5E\">\
6913: <ul><li><h4>Parameter files</h4>\n\
6914: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6915: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6916: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6917: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6918: - Date and time at start: %s</ul>\n",\
6919: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6920: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6921: fileres,fileres,\
6922: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6923: fflush(fichtm);
6924:
6925: strcpy(pathr,path);
6926: strcat(pathr,optionfilefiname);
6927: #ifdef WIN32
6928: _chdir(optionfilefiname); /* Move to directory named optionfile */
6929: #else
6930: chdir(optionfilefiname); /* Move to directory named optionfile */
6931: #endif
6932:
6933:
6934: /* Calculates basic frequencies. Computes observed prevalence at single age
6935: and prints on file fileres'p'. */
6936: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6937:
6938: fprintf(fichtm,"\n");
6939: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6940: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6941: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6942: imx,agemin,agemax,jmin,jmax,jmean);
6943: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6944: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6945: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6946: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6947: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6948:
6949:
6950: /* For Powell, parameters are in a vector p[] starting at p[1]
6951: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6952: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6953:
6954: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6955: /* For mortality only */
6956: if (mle==-3){
6957: ximort=matrix(1,NDIM,1,NDIM);
6958: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6959: cens=ivector(1,n);
6960: ageexmed=vector(1,n);
6961: agecens=vector(1,n);
6962: dcwave=ivector(1,n);
6963:
6964: for (i=1; i<=imx; i++){
6965: dcwave[i]=-1;
6966: for (m=firstpass; m<=lastpass; m++)
6967: if (s[m][i]>nlstate) {
6968: dcwave[i]=m;
6969: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6970: break;
6971: }
6972: }
6973:
6974: for (i=1; i<=imx; i++) {
6975: if (wav[i]>0){
6976: ageexmed[i]=agev[mw[1][i]][i];
6977: j=wav[i];
6978: agecens[i]=1.;
6979:
6980: if (ageexmed[i]> 1 && wav[i] > 0){
6981: agecens[i]=agev[mw[j][i]][i];
6982: cens[i]= 1;
6983: }else if (ageexmed[i]< 1)
6984: cens[i]= -1;
6985: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6986: cens[i]=0 ;
6987: }
6988: else cens[i]=-1;
6989: }
6990:
6991: for (i=1;i<=NDIM;i++) {
6992: for (j=1;j<=NDIM;j++)
6993: ximort[i][j]=(i == j ? 1.0 : 0.0);
6994: }
6995:
6996: /*p[1]=0.0268; p[NDIM]=0.083;*/
6997: /*printf("%lf %lf", p[1], p[2]);*/
6998:
6999:
7000: #ifdef GSL
7001: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
7002: #else
7003: printf("Powell\n"); fprintf(ficlog,"Powell\n");
7004: #endif
7005: strcpy(filerespow,"pow-mort");
7006: strcat(filerespow,fileres);
7007: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7008: printf("Problem with resultfile: %s\n", filerespow);
7009: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7010: }
7011: #ifdef GSL
7012: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
7013: #else
7014: fprintf(ficrespow,"# Powell\n# iter -2*LL");
7015: #endif
7016: /* for (i=1;i<=nlstate;i++)
7017: for(j=1;j<=nlstate+ndeath;j++)
7018: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7019: */
7020: fprintf(ficrespow,"\n");
7021: #ifdef GSL
7022: /* gsl starts here */
7023: T = gsl_multimin_fminimizer_nmsimplex;
7024: gsl_multimin_fminimizer *sfm = NULL;
7025: gsl_vector *ss, *x;
7026: gsl_multimin_function minex_func;
7027:
7028: /* Initial vertex size vector */
7029: ss = gsl_vector_alloc (NDIM);
7030:
7031: if (ss == NULL){
7032: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7033: }
7034: /* Set all step sizes to 1 */
7035: gsl_vector_set_all (ss, 0.001);
7036:
7037: /* Starting point */
7038:
7039: x = gsl_vector_alloc (NDIM);
7040:
7041: if (x == NULL){
7042: gsl_vector_free(ss);
7043: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7044: }
7045:
7046: /* Initialize method and iterate */
7047: /* p[1]=0.0268; p[NDIM]=0.083; */
7048: /* gsl_vector_set(x, 0, 0.0268); */
7049: /* gsl_vector_set(x, 1, 0.083); */
7050: gsl_vector_set(x, 0, p[1]);
7051: gsl_vector_set(x, 1, p[2]);
7052:
7053: minex_func.f = &gompertz_f;
7054: minex_func.n = NDIM;
7055: minex_func.params = (void *)&p; /* ??? */
7056:
7057: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7058: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7059:
7060: printf("Iterations beginning .....\n\n");
7061: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7062:
7063: iteri=0;
7064: while (rval == GSL_CONTINUE){
7065: iteri++;
7066: status = gsl_multimin_fminimizer_iterate(sfm);
7067:
7068: if (status) printf("error: %s\n", gsl_strerror (status));
7069: fflush(0);
7070:
7071: if (status)
7072: break;
7073:
7074: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7075: ssval = gsl_multimin_fminimizer_size (sfm);
7076:
7077: if (rval == GSL_SUCCESS)
7078: printf ("converged to a local maximum at\n");
7079:
7080: printf("%5d ", iteri);
7081: for (it = 0; it < NDIM; it++){
7082: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7083: }
7084: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7085: }
7086:
7087: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7088:
7089: gsl_vector_free(x); /* initial values */
7090: gsl_vector_free(ss); /* inital step size */
7091: for (it=0; it<NDIM; it++){
7092: p[it+1]=gsl_vector_get(sfm->x,it);
7093: fprintf(ficrespow," %.12lf", p[it]);
7094: }
7095: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7096: #endif
7097: #ifdef POWELL
7098: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7099: #endif
7100: fclose(ficrespow);
7101:
7102: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7103:
7104: for(i=1; i <=NDIM; i++)
7105: for(j=i+1;j<=NDIM;j++)
7106: matcov[i][j]=matcov[j][i];
7107:
7108: printf("\nCovariance matrix\n ");
7109: for(i=1; i <=NDIM; i++) {
7110: for(j=1;j<=NDIM;j++){
7111: printf("%f ",matcov[i][j]);
7112: }
7113: printf("\n ");
7114: }
7115:
7116: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7117: for (i=1;i<=NDIM;i++) {
7118: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7119: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7120: }
7121: lsurv=vector(1,AGESUP);
7122: lpop=vector(1,AGESUP);
7123: tpop=vector(1,AGESUP);
7124: lsurv[agegomp]=100000;
7125:
7126: for (k=agegomp;k<=AGESUP;k++) {
7127: agemortsup=k;
7128: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7129: }
7130:
7131: for (k=agegomp;k<agemortsup;k++)
7132: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7133:
7134: for (k=agegomp;k<agemortsup;k++){
7135: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7136: sumlpop=sumlpop+lpop[k];
7137: }
7138:
7139: tpop[agegomp]=sumlpop;
7140: for (k=agegomp;k<(agemortsup-3);k++){
7141: /* tpop[k+1]=2;*/
7142: tpop[k+1]=tpop[k]-lpop[k];
7143: }
7144:
7145:
7146: printf("\nAge lx qx dx Lx Tx e(x)\n");
7147: for (k=agegomp;k<(agemortsup-2);k++)
7148: 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]);
7149:
7150:
7151: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7152: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7153:
7154: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7155: stepm, weightopt,\
7156: model,imx,p,matcov,agemortsup);
7157:
7158: free_vector(lsurv,1,AGESUP);
7159: free_vector(lpop,1,AGESUP);
7160: free_vector(tpop,1,AGESUP);
7161: #ifdef GSL
7162: free_ivector(cens,1,n);
7163: free_vector(agecens,1,n);
7164: free_ivector(dcwave,1,n);
7165: free_matrix(ximort,1,NDIM,1,NDIM);
7166: #endif
7167: } /* Endof if mle==-3 mortality only */
7168: /* Standard maximisation */
7169: else{ /* For mle >=1 */
7170: globpr=0;/* debug */
7171: /* Computes likelihood for initial parameters */
7172: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7173: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7174: for (k=1; k<=npar;k++)
7175: printf(" %d %8.5f",k,p[k]);
7176: printf("\n");
7177: globpr=1; /* again, to print the contributions */
7178: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7179: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7180: for (k=1; k<=npar;k++)
7181: printf(" %d %8.5f",k,p[k]);
7182: printf("\n");
7183: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
7184: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7185: }
7186:
7187: /*--------- results files --------------*/
7188: 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);
7189:
7190:
7191: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7192: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7193: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7194: for(i=1,jk=1; i <=nlstate; i++){
7195: for(k=1; k <=(nlstate+ndeath); k++){
7196: if (k != i) {
7197: printf("%d%d ",i,k);
7198: fprintf(ficlog,"%d%d ",i,k);
7199: fprintf(ficres,"%1d%1d ",i,k);
7200: for(j=1; j <=ncovmodel; j++){
7201: printf("%12.7f ",p[jk]);
7202: fprintf(ficlog,"%12.7f ",p[jk]);
7203: fprintf(ficres,"%12.7f ",p[jk]);
7204: jk++;
7205: }
7206: printf("\n");
7207: fprintf(ficlog,"\n");
7208: fprintf(ficres,"\n");
7209: }
7210: }
7211: }
7212: if(mle!=0){
7213: /* Computing hessian and covariance matrix */
7214: ftolhess=ftol; /* Usually correct */
7215: hesscov(matcov, p, npar, delti, ftolhess, func);
7216: }
7217: printf("Parameters and 95%% confidence intervals\n");
7218: fprintf(ficlog, "Parameters, T and confidence intervals\n");
7219: for(i=1,jk=1; i <=nlstate; i++){
7220: for(k=1; k <=(nlstate+ndeath); k++){
7221: if (k != i) {
7222: printf("%d%d ",i,k);
7223: fprintf(ficlog,"%d%d ",i,k);
7224: for(j=1; j <=ncovmodel; j++){
7225: printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7226: fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7227: jk++;
7228: }
7229: printf("\n");
7230: fprintf(ficlog,"\n");
7231: }
7232: }
7233: }
7234:
7235: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7236: printf("# Scales (for hessian or gradient estimation)\n");
7237: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7238: for(i=1,jk=1; i <=nlstate; i++){
7239: for(j=1; j <=nlstate+ndeath; j++){
7240: if (j!=i) {
7241: fprintf(ficres,"%1d%1d",i,j);
7242: printf("%1d%1d",i,j);
7243: fprintf(ficlog,"%1d%1d",i,j);
7244: for(k=1; k<=ncovmodel;k++){
7245: printf(" %.5e",delti[jk]);
7246: fprintf(ficlog," %.5e",delti[jk]);
7247: fprintf(ficres," %.5e",delti[jk]);
7248: jk++;
7249: }
7250: printf("\n");
7251: fprintf(ficlog,"\n");
7252: fprintf(ficres,"\n");
7253: }
7254: }
7255: }
7256:
7257: 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");
7258: if(mle>=1)
7259: 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");
7260: 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");
7261: /* # 121 Var(a12)\n\ */
7262: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7263: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7264: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7265: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7266: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7267: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7268: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7269:
7270:
7271: /* Just to have a covariance matrix which will be more understandable
7272: even is we still don't want to manage dictionary of variables
7273: */
7274: for(itimes=1;itimes<=2;itimes++){
7275: jj=0;
7276: for(i=1; i <=nlstate; i++){
7277: for(j=1; j <=nlstate+ndeath; j++){
7278: if(j==i) continue;
7279: for(k=1; k<=ncovmodel;k++){
7280: jj++;
7281: ca[0]= k+'a'-1;ca[1]='\0';
7282: if(itimes==1){
7283: if(mle>=1)
7284: printf("#%1d%1d%d",i,j,k);
7285: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7286: fprintf(ficres,"#%1d%1d%d",i,j,k);
7287: }else{
7288: if(mle>=1)
7289: printf("%1d%1d%d",i,j,k);
7290: fprintf(ficlog,"%1d%1d%d",i,j,k);
7291: fprintf(ficres,"%1d%1d%d",i,j,k);
7292: }
7293: ll=0;
7294: for(li=1;li <=nlstate; li++){
7295: for(lj=1;lj <=nlstate+ndeath; lj++){
7296: if(lj==li) continue;
7297: for(lk=1;lk<=ncovmodel;lk++){
7298: ll++;
7299: if(ll<=jj){
7300: cb[0]= lk +'a'-1;cb[1]='\0';
7301: if(ll<jj){
7302: if(itimes==1){
7303: if(mle>=1)
7304: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7305: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7306: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7307: }else{
7308: if(mle>=1)
7309: printf(" %.5e",matcov[jj][ll]);
7310: fprintf(ficlog," %.5e",matcov[jj][ll]);
7311: fprintf(ficres," %.5e",matcov[jj][ll]);
7312: }
7313: }else{
7314: if(itimes==1){
7315: if(mle>=1)
7316: printf(" Var(%s%1d%1d)",ca,i,j);
7317: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7318: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7319: }else{
7320: if(mle>=1)
7321: printf(" %.5e",matcov[jj][ll]);
7322: fprintf(ficlog," %.5e",matcov[jj][ll]);
7323: fprintf(ficres," %.5e",matcov[jj][ll]);
7324: }
7325: }
7326: }
7327: } /* end lk */
7328: } /* end lj */
7329: } /* end li */
7330: if(mle>=1)
7331: printf("\n");
7332: fprintf(ficlog,"\n");
7333: fprintf(ficres,"\n");
7334: numlinepar++;
7335: } /* end k*/
7336: } /*end j */
7337: } /* end i */
7338: } /* end itimes */
7339:
7340: fflush(ficlog);
7341: fflush(ficres);
7342:
7343: while((c=getc(ficpar))=='#' && c!= EOF){
7344: ungetc(c,ficpar);
7345: fgets(line, MAXLINE, ficpar);
7346: fputs(line,stdout);
7347: fputs(line,ficparo);
7348: }
7349: ungetc(c,ficpar);
7350:
7351: estepm=0;
7352: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7353: if (estepm==0 || estepm < stepm) estepm=stepm;
7354: if (fage <= 2) {
7355: bage = ageminpar;
7356: fage = agemaxpar;
7357: }
7358:
7359: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7360: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7361: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7362:
7363: /* Other stuffs, more or less useful */
7364: while((c=getc(ficpar))=='#' && c!= EOF){
7365: ungetc(c,ficpar);
7366: fgets(line, MAXLINE, ficpar);
7367: fputs(line,stdout);
7368: fputs(line,ficparo);
7369: }
7370: ungetc(c,ficpar);
7371:
7372: 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);
7373: 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);
7374: 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);
7375: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7376: 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);
7377:
7378: while((c=getc(ficpar))=='#' && c!= EOF){
7379: ungetc(c,ficpar);
7380: fgets(line, MAXLINE, ficpar);
7381: fputs(line,stdout);
7382: fputs(line,ficparo);
7383: }
7384: ungetc(c,ficpar);
7385:
7386:
7387: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7388: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7389:
7390: fscanf(ficpar,"pop_based=%d\n",&popbased);
7391: fprintf(ficlog,"pop_based=%d\n",popbased);
7392: fprintf(ficparo,"pop_based=%d\n",popbased);
7393: fprintf(ficres,"pop_based=%d\n",popbased);
7394:
7395: while((c=getc(ficpar))=='#' && c!= EOF){
7396: ungetc(c,ficpar);
7397: fgets(line, MAXLINE, ficpar);
7398: fputs(line,stdout);
7399: fputs(line,ficparo);
7400: }
7401: ungetc(c,ficpar);
7402:
7403: 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);
7404: 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);
7405: 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);
7406: 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);
7407: 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);
7408: /* day and month of proj2 are not used but only year anproj2.*/
7409:
7410:
7411:
7412: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7413: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
7414:
7415: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7416: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7417:
7418: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7419: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7420: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7421:
7422: /*------------ free_vector -------------*/
7423: /* chdir(path); */
7424:
7425: free_ivector(wav,1,imx);
7426: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7427: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7428: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7429: free_lvector(num,1,n);
7430: free_vector(agedc,1,n);
7431: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7432: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7433: fclose(ficparo);
7434: fclose(ficres);
7435:
7436:
7437: /* Other results (useful)*/
7438:
7439:
7440: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7441: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7442: prlim=matrix(1,nlstate,1,nlstate);
7443: prevalence_limit(p, prlim, ageminpar, agemaxpar);
7444: fclose(ficrespl);
7445:
7446: #ifdef FREEEXIT2
7447: #include "freeexit2.h"
7448: #endif
7449:
7450: /*------------- h Pij x at various ages ------------*/
7451: /*#include "hpijx.h"*/
7452: hPijx(p, bage, fage);
7453: fclose(ficrespij);
7454:
7455: /*-------------- Variance of one-step probabilities---*/
7456: k=1;
7457: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7458:
7459:
7460: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7461: for(i=1;i<=AGESUP;i++)
7462: for(j=1;j<=NCOVMAX;j++)
7463: for(k=1;k<=NCOVMAX;k++)
7464: probs[i][j][k]=0.;
7465:
7466: /*---------- Forecasting ------------------*/
7467: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7468: if(prevfcast==1){
7469: /* if(stepm ==1){*/
7470: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7471: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7472: /* } */
7473: /* else{ */
7474: /* erreur=108; */
7475: /* 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); */
7476: /* 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); */
7477: /* } */
7478: }
7479:
7480: /* ------ Other prevalence ratios------------ */
7481:
7482: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7483:
7484: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7485: /* 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",\
7486: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7487: */
7488:
7489: if (mobilav!=0) {
7490: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7491: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7492: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7493: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7494: }
7495: }
7496:
7497:
7498: /*---------- Health expectancies, no variances ------------*/
7499:
7500: strcpy(filerese,"e");
7501: strcat(filerese,fileres);
7502: if((ficreseij=fopen(filerese,"w"))==NULL) {
7503: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7504: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7505: }
7506: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7507: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
7508: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7509: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7510:
7511: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7512: fprintf(ficreseij,"\n#****** ");
7513: for(j=1;j<=cptcoveff;j++) {
7514: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7515: }
7516: fprintf(ficreseij,"******\n");
7517:
7518: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7519: oldm=oldms;savm=savms;
7520: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7521:
7522: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7523: /*}*/
7524: }
7525: fclose(ficreseij);
7526:
7527:
7528: /*---------- Health expectancies and variances ------------*/
7529:
7530:
7531: strcpy(filerest,"t");
7532: strcat(filerest,fileres);
7533: if((ficrest=fopen(filerest,"w"))==NULL) {
7534: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7535: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7536: }
7537: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7538: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7539:
7540:
7541: strcpy(fileresstde,"stde");
7542: strcat(fileresstde,fileres);
7543: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7544: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7545: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7546: }
7547: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7548: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7549:
7550: strcpy(filerescve,"cve");
7551: strcat(filerescve,fileres);
7552: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7553: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7554: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7555: }
7556: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7557: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7558:
7559: strcpy(fileresv,"v");
7560: strcat(fileresv,fileres);
7561: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7562: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7563: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7564: }
7565: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7566: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7567:
7568: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7569: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7570:
7571: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7572: fprintf(ficrest,"\n#****** ");
7573: for(j=1;j<=cptcoveff;j++)
7574: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7575: fprintf(ficrest,"******\n");
7576:
7577: fprintf(ficresstdeij,"\n#****** ");
7578: fprintf(ficrescveij,"\n#****** ");
7579: for(j=1;j<=cptcoveff;j++) {
7580: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7581: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7582: }
7583: fprintf(ficresstdeij,"******\n");
7584: fprintf(ficrescveij,"******\n");
7585:
7586: fprintf(ficresvij,"\n#****** ");
7587: for(j=1;j<=cptcoveff;j++)
7588: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7589: fprintf(ficresvij,"******\n");
7590:
7591: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7592: oldm=oldms;savm=savms;
7593: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
7594: /*
7595: */
7596: /* goto endfree; */
7597:
7598: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7599: pstamp(ficrest);
7600:
7601:
7602: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
7603: oldm=oldms;savm=savms; /* Segmentation fault */
7604: cptcod= 0; /* To be deleted */
7605: 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 */
7606: 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 ");
7607: if(vpopbased==1)
7608: 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);
7609: else
7610: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7611: fprintf(ficrest,"# Age e.. (std) ");
7612: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7613: fprintf(ficrest,"\n");
7614:
7615: epj=vector(1,nlstate+1);
7616: for(age=bage; age <=fage ;age++){
7617: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7618: if (vpopbased==1) {
7619: if(mobilav ==0){
7620: for(i=1; i<=nlstate;i++)
7621: prlim[i][i]=probs[(int)age][i][k];
7622: }else{ /* mobilav */
7623: for(i=1; i<=nlstate;i++)
7624: prlim[i][i]=mobaverage[(int)age][i][k];
7625: }
7626: }
7627:
7628: fprintf(ficrest," %4.0f",age);
7629: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7630: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7631: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7632: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7633: }
7634: epj[nlstate+1] +=epj[j];
7635: }
7636:
7637: for(i=1, vepp=0.;i <=nlstate;i++)
7638: for(j=1;j <=nlstate;j++)
7639: vepp += vareij[i][j][(int)age];
7640: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7641: for(j=1;j <=nlstate;j++){
7642: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7643: }
7644: fprintf(ficrest,"\n");
7645: }
7646: }
7647: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7648: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7649: free_vector(epj,1,nlstate+1);
7650: /*}*/
7651: }
7652: free_vector(weight,1,n);
7653: free_imatrix(Tvard,1,NCOVMAX,1,2);
7654: free_imatrix(s,1,maxwav+1,1,n);
7655: free_matrix(anint,1,maxwav,1,n);
7656: free_matrix(mint,1,maxwav,1,n);
7657: free_ivector(cod,1,n);
7658: free_ivector(tab,1,NCOVMAX);
7659: fclose(ficresstdeij);
7660: fclose(ficrescveij);
7661: fclose(ficresvij);
7662: fclose(ficrest);
7663: fclose(ficpar);
7664:
7665: /*------- Variance of period (stable) prevalence------*/
7666:
7667: strcpy(fileresvpl,"vpl");
7668: strcat(fileresvpl,fileres);
7669: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7670: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7671: exit(0);
7672: }
7673: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7674:
7675: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7676: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7677:
7678: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7679: fprintf(ficresvpl,"\n#****** ");
7680: for(j=1;j<=cptcoveff;j++)
7681: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7682: fprintf(ficresvpl,"******\n");
7683:
7684: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7685: oldm=oldms;savm=savms;
7686: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7687: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7688: /*}*/
7689: }
7690:
7691: fclose(ficresvpl);
7692:
7693: /*---------- End : free ----------------*/
7694: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7695: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7696: } /* mle==-3 arrives here for freeing */
7697: /* endfree:*/
7698: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7699: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7700: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7701: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7702: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7703: free_matrix(covar,0,NCOVMAX,1,n);
7704: free_matrix(matcov,1,npar,1,npar);
7705: /*free_vector(delti,1,npar);*/
7706: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7707: free_matrix(agev,1,maxwav,1,imx);
7708: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7709:
7710: free_ivector(ncodemax,1,NCOVMAX);
7711: free_ivector(ncodemaxwundef,1,NCOVMAX);
7712: free_ivector(Tvar,1,NCOVMAX);
7713: free_ivector(Tprod,1,NCOVMAX);
7714: free_ivector(Tvaraff,1,NCOVMAX);
7715: free_ivector(Tage,1,NCOVMAX);
7716:
7717: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7718: free_imatrix(codtab,1,100,1,10);
7719: fflush(fichtm);
7720: fflush(ficgp);
7721:
7722:
7723: if((nberr >0) || (nbwarn>0)){
7724: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7725: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7726: }else{
7727: printf("End of Imach\n");
7728: fprintf(ficlog,"End of Imach\n");
7729: }
7730: printf("See log file on %s\n",filelog);
7731: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7732: /*(void) gettimeofday(&end_time,&tzp);*/
7733: rend_time = time(NULL);
7734: end_time = *localtime(&rend_time);
7735: /* tml = *localtime(&end_time.tm_sec); */
7736: strcpy(strtend,asctime(&end_time));
7737: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7738: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7739: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7740:
7741: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7742: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7743: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7744: /* printf("Total time was %d uSec.\n", total_usecs);*/
7745: /* if(fileappend(fichtm,optionfilehtm)){ */
7746: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7747: fclose(fichtm);
7748: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7749: fclose(fichtmcov);
7750: fclose(ficgp);
7751: fclose(ficlog);
7752: /*------ End -----------*/
7753:
7754:
7755: printf("Before Current directory %s!\n",pathcd);
7756: #ifdef WIN32
7757: if (_chdir(pathcd) != 0)
7758: printf("Can't move to directory %s!\n",path);
7759: if(_getcwd(pathcd,MAXLINE) > 0)
7760: #else
7761: if(chdir(pathcd) != 0)
7762: printf("Can't move to directory %s!\n", path);
7763: if (getcwd(pathcd, MAXLINE) > 0)
7764: #endif
7765: printf("Current directory %s!\n",pathcd);
7766: /*strcat(plotcmd,CHARSEPARATOR);*/
7767: sprintf(plotcmd,"gnuplot");
7768: #ifdef _WIN32
7769: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7770: #endif
7771: if(!stat(plotcmd,&info)){
7772: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7773: if(!stat(getenv("GNUPLOTBIN"),&info)){
7774: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7775: }else
7776: strcpy(pplotcmd,plotcmd);
7777: #ifdef __unix
7778: strcpy(plotcmd,GNUPLOTPROGRAM);
7779: if(!stat(plotcmd,&info)){
7780: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7781: }else
7782: strcpy(pplotcmd,plotcmd);
7783: #endif
7784: }else
7785: strcpy(pplotcmd,plotcmd);
7786:
7787: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7788: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7789:
7790: if((outcmd=system(plotcmd)) != 0){
7791: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7792: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7793: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7794: if((outcmd=system(plotcmd)) != 0)
7795: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7796: }
7797: printf(" Successful, please wait...");
7798: while (z[0] != 'q') {
7799: /* chdir(path); */
7800: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7801: scanf("%s",z);
7802: /* if (z[0] == 'c') system("./imach"); */
7803: if (z[0] == 'e') {
7804: #ifdef __APPLE__
7805: sprintf(pplotcmd, "open %s", optionfilehtm);
7806: #elif __linux
7807: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7808: #else
7809: sprintf(pplotcmd, "%s", optionfilehtm);
7810: #endif
7811: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7812: system(pplotcmd);
7813: }
7814: else if (z[0] == 'g') system(plotcmd);
7815: else if (z[0] == 'q') exit(0);
7816: }
7817: end:
7818: while (z[0] != 'q') {
7819: printf("\nType q for exiting: ");
7820: scanf("%s",z);
7821: }
7822: }
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