Annotation of imach/src/imach.c, revision 1.191
1.191 ! brouard 1: /* $Id: imach.c,v 1.190 2015/05/05 08:51:13 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.191 ! brouard 4: Revision 1.190 2015/05/05 08:51:13 brouard
! 5: Summary: Adding digits in output parameters (7 digits instead of 6)
! 6:
! 7: Fix 1+age+.
! 8:
1.190 brouard 9: Revision 1.189 2015/04/30 14:45:16 brouard
10: Summary: 0.98q2
11:
1.189 brouard 12: Revision 1.188 2015/04/30 08:27:53 brouard
13: *** empty log message ***
14:
1.188 brouard 15: Revision 1.187 2015/04/29 09:11:15 brouard
16: *** empty log message ***
17:
1.187 brouard 18: Revision 1.186 2015/04/23 12:01:52 brouard
19: Summary: V1*age is working now, version 0.98q1
20:
21: Some codes had been disabled in order to simplify and Vn*age was
22: working in the optimization phase, ie, giving correct MLE parameters,
23: but, as usual, outputs were not correct and program core dumped.
24:
1.186 brouard 25: Revision 1.185 2015/03/11 13:26:42 brouard
26: Summary: Inclusion of compile and links command line for Intel Compiler
27:
1.185 brouard 28: Revision 1.184 2015/03/11 11:52:39 brouard
29: Summary: Back from Windows 8. Intel Compiler
30:
1.184 brouard 31: Revision 1.183 2015/03/10 20:34:32 brouard
32: Summary: 0.98q0, trying with directest, mnbrak fixed
33:
34: We use directest instead of original Powell test; probably no
35: incidence on the results, but better justifications;
36: We fixed Numerical Recipes mnbrak routine which was wrong and gave
37: wrong results.
38:
1.183 brouard 39: Revision 1.182 2015/02/12 08:19:57 brouard
40: Summary: Trying to keep directest which seems simpler and more general
41: Author: Nicolas Brouard
42:
1.182 brouard 43: Revision 1.181 2015/02/11 23:22:24 brouard
44: Summary: Comments on Powell added
45:
46: Author:
47:
1.181 brouard 48: Revision 1.180 2015/02/11 17:33:45 brouard
49: Summary: Finishing move from main to function (hpijx and prevalence_limit)
50:
1.180 brouard 51: Revision 1.179 2015/01/04 09:57:06 brouard
52: Summary: back to OS/X
53:
1.179 brouard 54: Revision 1.178 2015/01/04 09:35:48 brouard
55: *** empty log message ***
56:
1.178 brouard 57: Revision 1.177 2015/01/03 18:40:56 brouard
58: Summary: Still testing ilc32 on OSX
59:
1.177 brouard 60: Revision 1.176 2015/01/03 16:45:04 brouard
61: *** empty log message ***
62:
1.176 brouard 63: Revision 1.175 2015/01/03 16:33:42 brouard
64: *** empty log message ***
65:
1.175 brouard 66: Revision 1.174 2015/01/03 16:15:49 brouard
67: Summary: Still in cross-compilation
68:
1.174 brouard 69: Revision 1.173 2015/01/03 12:06:26 brouard
70: Summary: trying to detect cross-compilation
71:
1.173 brouard 72: Revision 1.172 2014/12/27 12:07:47 brouard
73: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
74:
1.172 brouard 75: Revision 1.171 2014/12/23 13:26:59 brouard
76: Summary: Back from Visual C
77:
78: Still problem with utsname.h on Windows
79:
1.171 brouard 80: Revision 1.170 2014/12/23 11:17:12 brouard
81: Summary: Cleaning some \%% back to %%
82:
83: The escape was mandatory for a specific compiler (which one?), but too many warnings.
84:
1.170 brouard 85: Revision 1.169 2014/12/22 23:08:31 brouard
86: Summary: 0.98p
87:
88: Outputs some informations on compiler used, OS etc. Testing on different platforms.
89:
1.169 brouard 90: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 91: Summary: update
1.169 brouard 92:
1.168 brouard 93: Revision 1.167 2014/12/22 13:50:56 brouard
94: Summary: Testing uname and compiler version and if compiled 32 or 64
95:
96: Testing on Linux 64
97:
1.167 brouard 98: Revision 1.166 2014/12/22 11:40:47 brouard
99: *** empty log message ***
100:
1.166 brouard 101: Revision 1.165 2014/12/16 11:20:36 brouard
102: Summary: After compiling on Visual C
103:
104: * imach.c (Module): Merging 1.61 to 1.162
105:
1.165 brouard 106: Revision 1.164 2014/12/16 10:52:11 brouard
107: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
108:
109: * imach.c (Module): Merging 1.61 to 1.162
110:
1.164 brouard 111: Revision 1.163 2014/12/16 10:30:11 brouard
112: * imach.c (Module): Merging 1.61 to 1.162
113:
1.163 brouard 114: Revision 1.162 2014/09/25 11:43:39 brouard
115: Summary: temporary backup 0.99!
116:
1.162 brouard 117: Revision 1.1 2014/09/16 11:06:58 brouard
118: Summary: With some code (wrong) for nlopt
119:
120: Author:
121:
122: Revision 1.161 2014/09/15 20:41:41 brouard
123: Summary: Problem with macro SQR on Intel compiler
124:
1.161 brouard 125: Revision 1.160 2014/09/02 09:24:05 brouard
126: *** empty log message ***
127:
1.160 brouard 128: Revision 1.159 2014/09/01 10:34:10 brouard
129: Summary: WIN32
130: Author: Brouard
131:
1.159 brouard 132: Revision 1.158 2014/08/27 17:11:51 brouard
133: *** empty log message ***
134:
1.158 brouard 135: Revision 1.157 2014/08/27 16:26:55 brouard
136: Summary: Preparing windows Visual studio version
137: Author: Brouard
138:
139: In order to compile on Visual studio, time.h is now correct and time_t
140: and tm struct should be used. difftime should be used but sometimes I
141: just make the differences in raw time format (time(&now).
142: Trying to suppress #ifdef LINUX
143: Add xdg-open for __linux in order to open default browser.
144:
1.157 brouard 145: Revision 1.156 2014/08/25 20:10:10 brouard
146: *** empty log message ***
147:
1.156 brouard 148: Revision 1.155 2014/08/25 18:32:34 brouard
149: Summary: New compile, minor changes
150: Author: Brouard
151:
1.155 brouard 152: Revision 1.154 2014/06/20 17:32:08 brouard
153: Summary: Outputs now all graphs of convergence to period prevalence
154:
1.154 brouard 155: Revision 1.153 2014/06/20 16:45:46 brouard
156: Summary: If 3 live state, convergence to period prevalence on same graph
157: Author: Brouard
158:
1.153 brouard 159: Revision 1.152 2014/06/18 17:54:09 brouard
160: Summary: open browser, use gnuplot on same dir than imach if not found in the path
161:
1.152 brouard 162: Revision 1.151 2014/06/18 16:43:30 brouard
163: *** empty log message ***
164:
1.151 brouard 165: Revision 1.150 2014/06/18 16:42:35 brouard
166: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
167: Author: brouard
168:
1.150 brouard 169: Revision 1.149 2014/06/18 15:51:14 brouard
170: Summary: Some fixes in parameter files errors
171: Author: Nicolas Brouard
172:
1.149 brouard 173: Revision 1.148 2014/06/17 17:38:48 brouard
174: Summary: Nothing new
175: Author: Brouard
176:
177: Just a new packaging for OS/X version 0.98nS
178:
1.148 brouard 179: Revision 1.147 2014/06/16 10:33:11 brouard
180: *** empty log message ***
181:
1.147 brouard 182: Revision 1.146 2014/06/16 10:20:28 brouard
183: Summary: Merge
184: Author: Brouard
185:
186: Merge, before building revised version.
187:
1.146 brouard 188: Revision 1.145 2014/06/10 21:23:15 brouard
189: Summary: Debugging with valgrind
190: Author: Nicolas Brouard
191:
192: Lot of changes in order to output the results with some covariates
193: After the Edimburgh REVES conference 2014, it seems mandatory to
194: improve the code.
195: No more memory valgrind error but a lot has to be done in order to
196: continue the work of splitting the code into subroutines.
197: Also, decodemodel has been improved. Tricode is still not
198: optimal. nbcode should be improved. Documentation has been added in
199: the source code.
200:
1.144 brouard 201: Revision 1.143 2014/01/26 09:45:38 brouard
202: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
203:
204: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
205: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
206:
1.143 brouard 207: Revision 1.142 2014/01/26 03:57:36 brouard
208: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
209:
210: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
211:
1.142 brouard 212: Revision 1.141 2014/01/26 02:42:01 brouard
213: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
214:
1.141 brouard 215: Revision 1.140 2011/09/02 10:37:54 brouard
216: Summary: times.h is ok with mingw32 now.
217:
1.140 brouard 218: Revision 1.139 2010/06/14 07:50:17 brouard
219: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
220: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
221:
1.139 brouard 222: Revision 1.138 2010/04/30 18:19:40 brouard
223: *** empty log message ***
224:
1.138 brouard 225: Revision 1.137 2010/04/29 18:11:38 brouard
226: (Module): Checking covariates for more complex models
227: than V1+V2. A lot of change to be done. Unstable.
228:
1.137 brouard 229: Revision 1.136 2010/04/26 20:30:53 brouard
230: (Module): merging some libgsl code. Fixing computation
231: of likelione (using inter/intrapolation if mle = 0) in order to
232: get same likelihood as if mle=1.
233: Some cleaning of code and comments added.
234:
1.136 brouard 235: Revision 1.135 2009/10/29 15:33:14 brouard
236: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
237:
1.135 brouard 238: Revision 1.134 2009/10/29 13:18:53 brouard
239: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
240:
1.134 brouard 241: Revision 1.133 2009/07/06 10:21:25 brouard
242: just nforces
243:
1.133 brouard 244: Revision 1.132 2009/07/06 08:22:05 brouard
245: Many tings
246:
1.132 brouard 247: Revision 1.131 2009/06/20 16:22:47 brouard
248: Some dimensions resccaled
249:
1.131 brouard 250: Revision 1.130 2009/05/26 06:44:34 brouard
251: (Module): Max Covariate is now set to 20 instead of 8. A
252: lot of cleaning with variables initialized to 0. Trying to make
253: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
254:
1.130 brouard 255: Revision 1.129 2007/08/31 13:49:27 lievre
256: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
257:
1.129 lievre 258: Revision 1.128 2006/06/30 13:02:05 brouard
259: (Module): Clarifications on computing e.j
260:
1.128 brouard 261: Revision 1.127 2006/04/28 18:11:50 brouard
262: (Module): Yes the sum of survivors was wrong since
263: imach-114 because nhstepm was no more computed in the age
264: loop. Now we define nhstepma in the age loop.
265: (Module): In order to speed up (in case of numerous covariates) we
266: compute health expectancies (without variances) in a first step
267: and then all the health expectancies with variances or standard
268: deviation (needs data from the Hessian matrices) which slows the
269: computation.
270: In the future we should be able to stop the program is only health
271: expectancies and graph are needed without standard deviations.
272:
1.127 brouard 273: Revision 1.126 2006/04/28 17:23:28 brouard
274: (Module): Yes the sum of survivors was wrong since
275: imach-114 because nhstepm was no more computed in the age
276: loop. Now we define nhstepma in the age loop.
277: Version 0.98h
278:
1.126 brouard 279: Revision 1.125 2006/04/04 15:20:31 lievre
280: Errors in calculation of health expectancies. Age was not initialized.
281: Forecasting file added.
282:
283: Revision 1.124 2006/03/22 17:13:53 lievre
284: Parameters are printed with %lf instead of %f (more numbers after the comma).
285: The log-likelihood is printed in the log file
286:
287: Revision 1.123 2006/03/20 10:52:43 brouard
288: * imach.c (Module): <title> changed, corresponds to .htm file
289: name. <head> headers where missing.
290:
291: * imach.c (Module): Weights can have a decimal point as for
292: English (a comma might work with a correct LC_NUMERIC environment,
293: otherwise the weight is truncated).
294: Modification of warning when the covariates values are not 0 or
295: 1.
296: Version 0.98g
297:
298: Revision 1.122 2006/03/20 09:45:41 brouard
299: (Module): Weights can have a decimal point as for
300: English (a comma might work with a correct LC_NUMERIC environment,
301: otherwise the weight is truncated).
302: Modification of warning when the covariates values are not 0 or
303: 1.
304: Version 0.98g
305:
306: Revision 1.121 2006/03/16 17:45:01 lievre
307: * imach.c (Module): Comments concerning covariates added
308:
309: * imach.c (Module): refinements in the computation of lli if
310: status=-2 in order to have more reliable computation if stepm is
311: not 1 month. Version 0.98f
312:
313: Revision 1.120 2006/03/16 15:10:38 lievre
314: (Module): refinements in the computation of lli if
315: status=-2 in order to have more reliable computation if stepm is
316: not 1 month. Version 0.98f
317:
318: Revision 1.119 2006/03/15 17:42:26 brouard
319: (Module): Bug if status = -2, the loglikelihood was
320: computed as likelihood omitting the logarithm. Version O.98e
321:
322: Revision 1.118 2006/03/14 18:20:07 brouard
323: (Module): varevsij Comments added explaining the second
324: table of variances if popbased=1 .
325: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
326: (Module): Function pstamp added
327: (Module): Version 0.98d
328:
329: Revision 1.117 2006/03/14 17:16:22 brouard
330: (Module): varevsij Comments added explaining the second
331: table of variances if popbased=1 .
332: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
333: (Module): Function pstamp added
334: (Module): Version 0.98d
335:
336: Revision 1.116 2006/03/06 10:29:27 brouard
337: (Module): Variance-covariance wrong links and
338: varian-covariance of ej. is needed (Saito).
339:
340: Revision 1.115 2006/02/27 12:17:45 brouard
341: (Module): One freematrix added in mlikeli! 0.98c
342:
343: Revision 1.114 2006/02/26 12:57:58 brouard
344: (Module): Some improvements in processing parameter
345: filename with strsep.
346:
347: Revision 1.113 2006/02/24 14:20:24 brouard
348: (Module): Memory leaks checks with valgrind and:
349: datafile was not closed, some imatrix were not freed and on matrix
350: allocation too.
351:
352: Revision 1.112 2006/01/30 09:55:26 brouard
353: (Module): Back to gnuplot.exe instead of wgnuplot.exe
354:
355: Revision 1.111 2006/01/25 20:38:18 brouard
356: (Module): Lots of cleaning and bugs added (Gompertz)
357: (Module): Comments can be added in data file. Missing date values
358: can be a simple dot '.'.
359:
360: Revision 1.110 2006/01/25 00:51:50 brouard
361: (Module): Lots of cleaning and bugs added (Gompertz)
362:
363: Revision 1.109 2006/01/24 19:37:15 brouard
364: (Module): Comments (lines starting with a #) are allowed in data.
365:
366: Revision 1.108 2006/01/19 18:05:42 lievre
367: Gnuplot problem appeared...
368: To be fixed
369:
370: Revision 1.107 2006/01/19 16:20:37 brouard
371: Test existence of gnuplot in imach path
372:
373: Revision 1.106 2006/01/19 13:24:36 brouard
374: Some cleaning and links added in html output
375:
376: Revision 1.105 2006/01/05 20:23:19 lievre
377: *** empty log message ***
378:
379: Revision 1.104 2005/09/30 16:11:43 lievre
380: (Module): sump fixed, loop imx fixed, and simplifications.
381: (Module): If the status is missing at the last wave but we know
382: that the person is alive, then we can code his/her status as -2
383: (instead of missing=-1 in earlier versions) and his/her
384: contributions to the likelihood is 1 - Prob of dying from last
385: health status (= 1-p13= p11+p12 in the easiest case of somebody in
386: the healthy state at last known wave). Version is 0.98
387:
388: Revision 1.103 2005/09/30 15:54:49 lievre
389: (Module): sump fixed, loop imx fixed, and simplifications.
390:
391: Revision 1.102 2004/09/15 17:31:30 brouard
392: Add the possibility to read data file including tab characters.
393:
394: Revision 1.101 2004/09/15 10:38:38 brouard
395: Fix on curr_time
396:
397: Revision 1.100 2004/07/12 18:29:06 brouard
398: Add version for Mac OS X. Just define UNIX in Makefile
399:
400: Revision 1.99 2004/06/05 08:57:40 brouard
401: *** empty log message ***
402:
403: Revision 1.98 2004/05/16 15:05:56 brouard
404: New version 0.97 . First attempt to estimate force of mortality
405: directly from the data i.e. without the need of knowing the health
406: state at each age, but using a Gompertz model: log u =a + b*age .
407: This is the basic analysis of mortality and should be done before any
408: other analysis, in order to test if the mortality estimated from the
409: cross-longitudinal survey is different from the mortality estimated
410: from other sources like vital statistic data.
411:
412: The same imach parameter file can be used but the option for mle should be -3.
413:
1.133 brouard 414: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 415: former routines in order to include the new code within the former code.
416:
417: The output is very simple: only an estimate of the intercept and of
418: the slope with 95% confident intervals.
419:
420: Current limitations:
421: A) Even if you enter covariates, i.e. with the
422: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
423: B) There is no computation of Life Expectancy nor Life Table.
424:
425: Revision 1.97 2004/02/20 13:25:42 lievre
426: Version 0.96d. Population forecasting command line is (temporarily)
427: suppressed.
428:
429: Revision 1.96 2003/07/15 15:38:55 brouard
430: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
431: rewritten within the same printf. Workaround: many printfs.
432:
433: Revision 1.95 2003/07/08 07:54:34 brouard
434: * imach.c (Repository):
435: (Repository): Using imachwizard code to output a more meaningful covariance
436: matrix (cov(a12,c31) instead of numbers.
437:
438: Revision 1.94 2003/06/27 13:00:02 brouard
439: Just cleaning
440:
441: Revision 1.93 2003/06/25 16:33:55 brouard
442: (Module): On windows (cygwin) function asctime_r doesn't
443: exist so I changed back to asctime which exists.
444: (Module): Version 0.96b
445:
446: Revision 1.92 2003/06/25 16:30:45 brouard
447: (Module): On windows (cygwin) function asctime_r doesn't
448: exist so I changed back to asctime which exists.
449:
450: Revision 1.91 2003/06/25 15:30:29 brouard
451: * imach.c (Repository): Duplicated warning errors corrected.
452: (Repository): Elapsed time after each iteration is now output. It
453: helps to forecast when convergence will be reached. Elapsed time
454: is stamped in powell. We created a new html file for the graphs
455: concerning matrix of covariance. It has extension -cov.htm.
456:
457: Revision 1.90 2003/06/24 12:34:15 brouard
458: (Module): Some bugs corrected for windows. Also, when
459: mle=-1 a template is output in file "or"mypar.txt with the design
460: of the covariance matrix to be input.
461:
462: Revision 1.89 2003/06/24 12:30:52 brouard
463: (Module): Some bugs corrected for windows. Also, when
464: mle=-1 a template is output in file "or"mypar.txt with the design
465: of the covariance matrix to be input.
466:
467: Revision 1.88 2003/06/23 17:54:56 brouard
468: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
469:
470: Revision 1.87 2003/06/18 12:26:01 brouard
471: Version 0.96
472:
473: Revision 1.86 2003/06/17 20:04:08 brouard
474: (Module): Change position of html and gnuplot routines and added
475: routine fileappend.
476:
477: Revision 1.85 2003/06/17 13:12:43 brouard
478: * imach.c (Repository): Check when date of death was earlier that
479: current date of interview. It may happen when the death was just
480: prior to the death. In this case, dh was negative and likelihood
481: was wrong (infinity). We still send an "Error" but patch by
482: assuming that the date of death was just one stepm after the
483: interview.
484: (Repository): Because some people have very long ID (first column)
485: we changed int to long in num[] and we added a new lvector for
486: memory allocation. But we also truncated to 8 characters (left
487: truncation)
488: (Repository): No more line truncation errors.
489:
490: Revision 1.84 2003/06/13 21:44:43 brouard
491: * imach.c (Repository): Replace "freqsummary" at a correct
492: place. It differs from routine "prevalence" which may be called
493: many times. Probs is memory consuming and must be used with
494: parcimony.
495: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
496:
497: Revision 1.83 2003/06/10 13:39:11 lievre
498: *** empty log message ***
499:
500: Revision 1.82 2003/06/05 15:57:20 brouard
501: Add log in imach.c and fullversion number is now printed.
502:
503: */
504: /*
505: Interpolated Markov Chain
506:
507: Short summary of the programme:
508:
509: This program computes Healthy Life Expectancies from
510: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
511: first survey ("cross") where individuals from different ages are
512: interviewed on their health status or degree of disability (in the
513: case of a health survey which is our main interest) -2- at least a
514: second wave of interviews ("longitudinal") which measure each change
515: (if any) in individual health status. Health expectancies are
516: computed from the time spent in each health state according to a
517: model. More health states you consider, more time is necessary to reach the
518: Maximum Likelihood of the parameters involved in the model. The
519: simplest model is the multinomial logistic model where pij is the
520: probability to be observed in state j at the second wave
521: conditional to be observed in state i at the first wave. Therefore
522: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
523: 'age' is age and 'sex' is a covariate. If you want to have a more
524: complex model than "constant and age", you should modify the program
525: where the markup *Covariates have to be included here again* invites
526: you to do it. More covariates you add, slower the
527: convergence.
528:
529: The advantage of this computer programme, compared to a simple
530: multinomial logistic model, is clear when the delay between waves is not
531: identical for each individual. Also, if a individual missed an
532: intermediate interview, the information is lost, but taken into
533: account using an interpolation or extrapolation.
534:
535: hPijx is the probability to be observed in state i at age x+h
536: conditional to the observed state i at age x. The delay 'h' can be
537: split into an exact number (nh*stepm) of unobserved intermediate
538: states. This elementary transition (by month, quarter,
539: semester or year) is modelled as a multinomial logistic. The hPx
540: matrix is simply the matrix product of nh*stepm elementary matrices
541: and the contribution of each individual to the likelihood is simply
542: hPijx.
543:
544: Also this programme outputs the covariance matrix of the parameters but also
545: of the life expectancies. It also computes the period (stable) prevalence.
546:
1.133 brouard 547: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
548: Institut national d'études démographiques, Paris.
1.126 brouard 549: This software have been partly granted by Euro-REVES, a concerted action
550: from the European Union.
551: It is copyrighted identically to a GNU software product, ie programme and
552: software can be distributed freely for non commercial use. Latest version
553: can be accessed at http://euroreves.ined.fr/imach .
554:
555: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
556: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
557:
558: **********************************************************************/
559: /*
560: main
561: read parameterfile
562: read datafile
563: concatwav
564: freqsummary
565: if (mle >= 1)
566: mlikeli
567: print results files
568: if mle==1
569: computes hessian
570: read end of parameter file: agemin, agemax, bage, fage, estepm
571: begin-prev-date,...
572: open gnuplot file
573: open html file
1.145 brouard 574: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
575: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
576: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
577: freexexit2 possible for memory heap.
578:
579: h Pij x | pij_nom ficrestpij
580: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
581: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
582: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
583:
584: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
585: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
586: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
587: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
588: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
589:
1.126 brouard 590: forecasting if prevfcast==1 prevforecast call prevalence()
591: health expectancies
592: Variance-covariance of DFLE
593: prevalence()
594: movingaverage()
595: varevsij()
596: if popbased==1 varevsij(,popbased)
597: total life expectancies
598: Variance of period (stable) prevalence
599: end
600: */
601:
1.187 brouard 602: /* #define DEBUG */
603: /* #define DEBUGBRENT */
1.165 brouard 604: #define POWELL /* Instead of NLOPT */
1.186 brouard 605: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
606: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 607:
608: #include <math.h>
609: #include <stdio.h>
610: #include <stdlib.h>
611: #include <string.h>
1.159 brouard 612:
613: #ifdef _WIN32
614: #include <io.h>
1.172 brouard 615: #include <windows.h>
616: #include <tchar.h>
1.159 brouard 617: #else
1.126 brouard 618: #include <unistd.h>
1.159 brouard 619: #endif
1.126 brouard 620:
621: #include <limits.h>
622: #include <sys/types.h>
1.171 brouard 623:
624: #if defined(__GNUC__)
625: #include <sys/utsname.h> /* Doesn't work on Windows */
626: #endif
627:
1.126 brouard 628: #include <sys/stat.h>
629: #include <errno.h>
1.159 brouard 630: /* extern int errno; */
1.126 brouard 631:
1.157 brouard 632: /* #ifdef LINUX */
633: /* #include <time.h> */
634: /* #include "timeval.h" */
635: /* #else */
636: /* #include <sys/time.h> */
637: /* #endif */
638:
1.126 brouard 639: #include <time.h>
640:
1.136 brouard 641: #ifdef GSL
642: #include <gsl/gsl_errno.h>
643: #include <gsl/gsl_multimin.h>
644: #endif
645:
1.167 brouard 646:
1.162 brouard 647: #ifdef NLOPT
648: #include <nlopt.h>
649: typedef struct {
650: double (* function)(double [] );
651: } myfunc_data ;
652: #endif
653:
1.126 brouard 654: /* #include <libintl.h> */
655: /* #define _(String) gettext (String) */
656:
1.141 brouard 657: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 658:
659: #define GNUPLOTPROGRAM "gnuplot"
660: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
661: #define FILENAMELENGTH 132
662:
663: #define GLOCK_ERROR_NOPATH -1 /* empty path */
664: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
665:
1.144 brouard 666: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
667: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 668:
669: #define NINTERVMAX 8
1.144 brouard 670: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
671: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
672: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 673: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 674: #define MAXN 20000
1.144 brouard 675: #define YEARM 12. /**< Number of months per year */
1.126 brouard 676: #define AGESUP 130
677: #define AGEBASE 40
1.164 brouard 678: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 679: #ifdef _WIN32
680: #define DIRSEPARATOR '\\'
681: #define CHARSEPARATOR "\\"
682: #define ODIRSEPARATOR '/'
683: #else
1.126 brouard 684: #define DIRSEPARATOR '/'
685: #define CHARSEPARATOR "/"
686: #define ODIRSEPARATOR '\\'
687: #endif
688:
1.191 ! brouard 689: /* $Id: imach.c,v 1.190 2015/05/05 08:51:13 brouard Exp $ */
1.126 brouard 690: /* $State: Exp $ */
691:
1.189 brouard 692: char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.191 ! brouard 693: char fullversion[]="$Revision: 1.190 $ $Date: 2015/05/05 08:51:13 $";
1.126 brouard 694: char strstart[80];
695: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 696: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 697: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 698: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
699: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
700: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
701: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
702: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
703: int cptcovprodnoage=0; /**< Number of covariate products without age */
704: int cptcoveff=0; /* Total number of covariates to vary for printing results */
705: int cptcov=0; /* Working variable */
1.126 brouard 706: int npar=NPARMAX;
707: int nlstate=2; /* Number of live states */
708: int ndeath=1; /* Number of dead states */
1.130 brouard 709: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 710: int popbased=0;
711:
712: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 713: int maxwav=0; /* Maxim number of waves */
714: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
715: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
716: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 717: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 718: int mle=1, weightopt=0;
1.126 brouard 719: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
720: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
721: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
722: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 723: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 724: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 725: double **matprod2(); /* test */
1.126 brouard 726: double **oldm, **newm, **savm; /* Working pointers to matrices */
727: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 728: /*FILE *fic ; */ /* Used in readdata only */
729: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 730: FILE *ficlog, *ficrespow;
1.130 brouard 731: int globpr=0; /* Global variable for printing or not */
1.126 brouard 732: double fretone; /* Only one call to likelihood */
1.130 brouard 733: long ipmx=0; /* Number of contributions */
1.126 brouard 734: double sw; /* Sum of weights */
735: char filerespow[FILENAMELENGTH];
736: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
737: FILE *ficresilk;
738: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
739: FILE *ficresprobmorprev;
740: FILE *fichtm, *fichtmcov; /* Html File */
741: FILE *ficreseij;
742: char filerese[FILENAMELENGTH];
743: FILE *ficresstdeij;
744: char fileresstde[FILENAMELENGTH];
745: FILE *ficrescveij;
746: char filerescve[FILENAMELENGTH];
747: FILE *ficresvij;
748: char fileresv[FILENAMELENGTH];
749: FILE *ficresvpl;
750: char fileresvpl[FILENAMELENGTH];
751: char title[MAXLINE];
752: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
753: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
754: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
755: char command[FILENAMELENGTH];
756: int outcmd=0;
757:
758: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
759:
760: char filelog[FILENAMELENGTH]; /* Log file */
761: char filerest[FILENAMELENGTH];
762: char fileregp[FILENAMELENGTH];
763: char popfile[FILENAMELENGTH];
764:
765: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
766:
1.157 brouard 767: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
768: /* struct timezone tzp; */
769: /* extern int gettimeofday(); */
770: struct tm tml, *gmtime(), *localtime();
771:
772: extern time_t time();
773:
774: struct tm start_time, end_time, curr_time, last_time, forecast_time;
775: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
776: struct tm tm;
777:
1.126 brouard 778: char strcurr[80], strfor[80];
779:
780: char *endptr;
781: long lval;
782: double dval;
783:
784: #define NR_END 1
785: #define FREE_ARG char*
786: #define FTOL 1.0e-10
787:
788: #define NRANSI
789: #define ITMAX 200
790:
791: #define TOL 2.0e-4
792:
793: #define CGOLD 0.3819660
794: #define ZEPS 1.0e-10
795: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
796:
797: #define GOLD 1.618034
798: #define GLIMIT 100.0
799: #define TINY 1.0e-20
800:
801: static double maxarg1,maxarg2;
802: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
803: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
804:
805: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
806: #define rint(a) floor(a+0.5)
1.166 brouard 807: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 808: #define mytinydouble 1.0e-16
1.166 brouard 809: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
810: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
811: /* static double dsqrarg; */
812: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 813: static double sqrarg;
814: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
815: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
816: int agegomp= AGEGOMP;
817:
818: int imx;
819: int stepm=1;
820: /* Stepm, step in month: minimum step interpolation*/
821:
822: int estepm;
823: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
824:
825: int m,nb;
826: long *num;
827: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
828: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
829: double **pmmij, ***probs;
830: double *ageexmed,*agecens;
831: double dateintmean=0;
832:
833: double *weight;
834: int **s; /* Status */
1.141 brouard 835: double *agedc;
1.145 brouard 836: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 837: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 838: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 839: double idx;
840: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 841: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 842: int **codtab; /**< codtab=imatrix(1,100,1,10); */
843: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 844: double *lsurv, *lpop, *tpop;
845:
1.143 brouard 846: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
847: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 848:
849: /**************** split *************************/
850: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
851: {
852: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
853: the name of the file (name), its extension only (ext) and its first part of the name (finame)
854: */
855: char *ss; /* pointer */
1.186 brouard 856: int l1=0, l2=0; /* length counters */
1.126 brouard 857:
858: l1 = strlen(path ); /* length of path */
859: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
860: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
861: if ( ss == NULL ) { /* no directory, so determine current directory */
862: strcpy( name, path ); /* we got the fullname name because no directory */
863: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
864: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
865: /* get current working directory */
866: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 867: #ifdef WIN32
868: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
869: #else
870: if (getcwd(dirc, FILENAME_MAX) == NULL) {
871: #endif
1.126 brouard 872: return( GLOCK_ERROR_GETCWD );
873: }
874: /* got dirc from getcwd*/
875: printf(" DIRC = %s \n",dirc);
876: } else { /* strip direcotry from path */
877: ss++; /* after this, the filename */
878: l2 = strlen( ss ); /* length of filename */
879: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
880: strcpy( name, ss ); /* save file name */
881: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 882: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 883: printf(" DIRC2 = %s \n",dirc);
884: }
885: /* We add a separator at the end of dirc if not exists */
886: l1 = strlen( dirc ); /* length of directory */
887: if( dirc[l1-1] != DIRSEPARATOR ){
888: dirc[l1] = DIRSEPARATOR;
889: dirc[l1+1] = 0;
890: printf(" DIRC3 = %s \n",dirc);
891: }
892: ss = strrchr( name, '.' ); /* find last / */
893: if (ss >0){
894: ss++;
895: strcpy(ext,ss); /* save extension */
896: l1= strlen( name);
897: l2= strlen(ss)+1;
898: strncpy( finame, name, l1-l2);
899: finame[l1-l2]= 0;
900: }
901:
902: return( 0 ); /* we're done */
903: }
904:
905:
906: /******************************************/
907:
908: void replace_back_to_slash(char *s, char*t)
909: {
910: int i;
911: int lg=0;
912: i=0;
913: lg=strlen(t);
914: for(i=0; i<= lg; i++) {
915: (s[i] = t[i]);
916: if (t[i]== '\\') s[i]='/';
917: }
918: }
919:
1.132 brouard 920: char *trimbb(char *out, char *in)
1.137 brouard 921: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 922: char *s;
923: s=out;
924: while (*in != '\0'){
1.137 brouard 925: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 926: in++;
927: }
928: *out++ = *in++;
929: }
930: *out='\0';
931: return s;
932: }
933:
1.187 brouard 934: /* char *substrchaine(char *out, char *in, char *chain) */
935: /* { */
936: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
937: /* char *s, *t; */
938: /* t=in;s=out; */
939: /* while ((*in != *chain) && (*in != '\0')){ */
940: /* *out++ = *in++; */
941: /* } */
942:
943: /* /\* *in matches *chain *\/ */
944: /* while ((*in++ == *chain++) && (*in != '\0')){ */
945: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
946: /* } */
947: /* in--; chain--; */
948: /* while ( (*in != '\0')){ */
949: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
950: /* *out++ = *in++; */
951: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
952: /* } */
953: /* *out='\0'; */
954: /* out=s; */
955: /* return out; */
956: /* } */
957: char *substrchaine(char *out, char *in, char *chain)
958: {
959: /* Substract chain 'chain' from 'in', return and output 'out' */
960: /* in="V1+V1*age+age*age+V2", chain="age*age" */
961:
962: char *strloc;
963:
964: strcpy (out, in);
965: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
966: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
967: if(strloc != NULL){
968: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
969: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
970: /* strcpy (strloc, strloc +strlen(chain));*/
971: }
972: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
973: return out;
974: }
975:
976:
1.145 brouard 977: char *cutl(char *blocc, char *alocc, char *in, char occ)
978: {
1.187 brouard 979: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 980: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 981: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 982: If occ is not found blocc is null and alocc is equal to in. Returns blocc
983: */
1.160 brouard 984: char *s, *t;
1.145 brouard 985: t=in;s=in;
986: while ((*in != occ) && (*in != '\0')){
987: *alocc++ = *in++;
988: }
989: if( *in == occ){
990: *(alocc)='\0';
991: s=++in;
992: }
993:
994: if (s == t) {/* occ not found */
995: *(alocc-(in-s))='\0';
996: in=s;
997: }
998: while ( *in != '\0'){
999: *blocc++ = *in++;
1000: }
1001:
1002: *blocc='\0';
1003: return t;
1004: }
1.137 brouard 1005: char *cutv(char *blocc, char *alocc, char *in, char occ)
1006: {
1.187 brouard 1007: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1008: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1009: gives blocc="abcdef2ghi" and alocc="j".
1010: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1011: */
1012: char *s, *t;
1013: t=in;s=in;
1014: while (*in != '\0'){
1015: while( *in == occ){
1016: *blocc++ = *in++;
1017: s=in;
1018: }
1019: *blocc++ = *in++;
1020: }
1021: if (s == t) /* occ not found */
1022: *(blocc-(in-s))='\0';
1023: else
1024: *(blocc-(in-s)-1)='\0';
1025: in=s;
1026: while ( *in != '\0'){
1027: *alocc++ = *in++;
1028: }
1029:
1030: *alocc='\0';
1031: return s;
1032: }
1033:
1.126 brouard 1034: int nbocc(char *s, char occ)
1035: {
1036: int i,j=0;
1037: int lg=20;
1038: i=0;
1039: lg=strlen(s);
1040: for(i=0; i<= lg; i++) {
1041: if (s[i] == occ ) j++;
1042: }
1043: return j;
1044: }
1045:
1.137 brouard 1046: /* void cutv(char *u,char *v, char*t, char occ) */
1047: /* { */
1048: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1049: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1050: /* gives u="abcdef2ghi" and v="j" *\/ */
1051: /* int i,lg,j,p=0; */
1052: /* i=0; */
1053: /* lg=strlen(t); */
1054: /* for(j=0; j<=lg-1; j++) { */
1055: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1056: /* } */
1.126 brouard 1057:
1.137 brouard 1058: /* for(j=0; j<p; j++) { */
1059: /* (u[j] = t[j]); */
1060: /* } */
1061: /* u[p]='\0'; */
1.126 brouard 1062:
1.137 brouard 1063: /* for(j=0; j<= lg; j++) { */
1064: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1065: /* } */
1066: /* } */
1.126 brouard 1067:
1.160 brouard 1068: #ifdef _WIN32
1069: char * strsep(char **pp, const char *delim)
1070: {
1071: char *p, *q;
1072:
1073: if ((p = *pp) == NULL)
1074: return 0;
1075: if ((q = strpbrk (p, delim)) != NULL)
1076: {
1077: *pp = q + 1;
1078: *q = '\0';
1079: }
1080: else
1081: *pp = 0;
1082: return p;
1083: }
1084: #endif
1085:
1.126 brouard 1086: /********************** nrerror ********************/
1087:
1088: void nrerror(char error_text[])
1089: {
1090: fprintf(stderr,"ERREUR ...\n");
1091: fprintf(stderr,"%s\n",error_text);
1092: exit(EXIT_FAILURE);
1093: }
1094: /*********************** vector *******************/
1095: double *vector(int nl, int nh)
1096: {
1097: double *v;
1098: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1099: if (!v) nrerror("allocation failure in vector");
1100: return v-nl+NR_END;
1101: }
1102:
1103: /************************ free vector ******************/
1104: void free_vector(double*v, int nl, int nh)
1105: {
1106: free((FREE_ARG)(v+nl-NR_END));
1107: }
1108:
1109: /************************ivector *******************************/
1110: int *ivector(long nl,long nh)
1111: {
1112: int *v;
1113: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1114: if (!v) nrerror("allocation failure in ivector");
1115: return v-nl+NR_END;
1116: }
1117:
1118: /******************free ivector **************************/
1119: void free_ivector(int *v, long nl, long nh)
1120: {
1121: free((FREE_ARG)(v+nl-NR_END));
1122: }
1123:
1124: /************************lvector *******************************/
1125: long *lvector(long nl,long nh)
1126: {
1127: long *v;
1128: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1129: if (!v) nrerror("allocation failure in ivector");
1130: return v-nl+NR_END;
1131: }
1132:
1133: /******************free lvector **************************/
1134: void free_lvector(long *v, long nl, long nh)
1135: {
1136: free((FREE_ARG)(v+nl-NR_END));
1137: }
1138:
1139: /******************* imatrix *******************************/
1140: int **imatrix(long nrl, long nrh, long ncl, long nch)
1141: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1142: {
1143: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1144: int **m;
1145:
1146: /* allocate pointers to rows */
1147: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1148: if (!m) nrerror("allocation failure 1 in matrix()");
1149: m += NR_END;
1150: m -= nrl;
1151:
1152:
1153: /* allocate rows and set pointers to them */
1154: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1155: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1156: m[nrl] += NR_END;
1157: m[nrl] -= ncl;
1158:
1159: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1160:
1161: /* return pointer to array of pointers to rows */
1162: return m;
1163: }
1164:
1165: /****************** free_imatrix *************************/
1166: void free_imatrix(m,nrl,nrh,ncl,nch)
1167: int **m;
1168: long nch,ncl,nrh,nrl;
1169: /* free an int matrix allocated by imatrix() */
1170: {
1171: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1172: free((FREE_ARG) (m+nrl-NR_END));
1173: }
1174:
1175: /******************* matrix *******************************/
1176: double **matrix(long nrl, long nrh, long ncl, long nch)
1177: {
1178: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1179: double **m;
1180:
1181: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1182: if (!m) nrerror("allocation failure 1 in matrix()");
1183: m += NR_END;
1184: m -= nrl;
1185:
1186: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1187: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1188: m[nrl] += NR_END;
1189: m[nrl] -= ncl;
1190:
1191: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1192: return m;
1.145 brouard 1193: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1194: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1195: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1196: */
1197: }
1198:
1199: /*************************free matrix ************************/
1200: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1201: {
1202: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1203: free((FREE_ARG)(m+nrl-NR_END));
1204: }
1205:
1206: /******************* ma3x *******************************/
1207: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1208: {
1209: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1210: double ***m;
1211:
1212: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1213: if (!m) nrerror("allocation failure 1 in matrix()");
1214: m += NR_END;
1215: m -= nrl;
1216:
1217: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1218: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1219: m[nrl] += NR_END;
1220: m[nrl] -= ncl;
1221:
1222: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1223:
1224: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1225: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1226: m[nrl][ncl] += NR_END;
1227: m[nrl][ncl] -= nll;
1228: for (j=ncl+1; j<=nch; j++)
1229: m[nrl][j]=m[nrl][j-1]+nlay;
1230:
1231: for (i=nrl+1; i<=nrh; i++) {
1232: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1233: for (j=ncl+1; j<=nch; j++)
1234: m[i][j]=m[i][j-1]+nlay;
1235: }
1236: return m;
1237: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1238: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1239: */
1240: }
1241:
1242: /*************************free ma3x ************************/
1243: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1244: {
1245: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1246: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1247: free((FREE_ARG)(m+nrl-NR_END));
1248: }
1249:
1250: /*************** function subdirf ***********/
1251: char *subdirf(char fileres[])
1252: {
1253: /* Caution optionfilefiname is hidden */
1254: strcpy(tmpout,optionfilefiname);
1255: strcat(tmpout,"/"); /* Add to the right */
1256: strcat(tmpout,fileres);
1257: return tmpout;
1258: }
1259:
1260: /*************** function subdirf2 ***********/
1261: char *subdirf2(char fileres[], char *preop)
1262: {
1263:
1264: /* Caution optionfilefiname is hidden */
1265: strcpy(tmpout,optionfilefiname);
1266: strcat(tmpout,"/");
1267: strcat(tmpout,preop);
1268: strcat(tmpout,fileres);
1269: return tmpout;
1270: }
1271:
1272: /*************** function subdirf3 ***********/
1273: char *subdirf3(char fileres[], char *preop, char *preop2)
1274: {
1275:
1276: /* Caution optionfilefiname is hidden */
1277: strcpy(tmpout,optionfilefiname);
1278: strcat(tmpout,"/");
1279: strcat(tmpout,preop);
1280: strcat(tmpout,preop2);
1281: strcat(tmpout,fileres);
1282: return tmpout;
1283: }
1284:
1.162 brouard 1285: char *asc_diff_time(long time_sec, char ascdiff[])
1286: {
1287: long sec_left, days, hours, minutes;
1288: days = (time_sec) / (60*60*24);
1289: sec_left = (time_sec) % (60*60*24);
1290: hours = (sec_left) / (60*60) ;
1291: sec_left = (sec_left) %(60*60);
1292: minutes = (sec_left) /60;
1293: sec_left = (sec_left) % (60);
1294: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1295: return ascdiff;
1296: }
1297:
1.126 brouard 1298: /***************** f1dim *************************/
1299: extern int ncom;
1300: extern double *pcom,*xicom;
1301: extern double (*nrfunc)(double []);
1302:
1303: double f1dim(double x)
1304: {
1305: int j;
1306: double f;
1307: double *xt;
1308:
1309: xt=vector(1,ncom);
1310: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1311: f=(*nrfunc)(xt);
1312: free_vector(xt,1,ncom);
1313: return f;
1314: }
1315:
1316: /*****************brent *************************/
1317: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1318: {
1319: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1320: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1321: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1322: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1323: * returned function value.
1324: */
1.126 brouard 1325: int iter;
1326: double a,b,d,etemp;
1.159 brouard 1327: double fu=0,fv,fw,fx;
1.164 brouard 1328: double ftemp=0.;
1.126 brouard 1329: double p,q,r,tol1,tol2,u,v,w,x,xm;
1330: double e=0.0;
1331:
1332: a=(ax < cx ? ax : cx);
1333: b=(ax > cx ? ax : cx);
1334: x=w=v=bx;
1335: fw=fv=fx=(*f)(x);
1336: for (iter=1;iter<=ITMAX;iter++) {
1337: xm=0.5*(a+b);
1338: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1339: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1340: printf(".");fflush(stdout);
1341: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1342: #ifdef DEBUGBRENT
1.126 brouard 1343: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1344: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1345: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1346: #endif
1347: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1348: *xmin=x;
1349: return fx;
1350: }
1351: ftemp=fu;
1352: if (fabs(e) > tol1) {
1353: r=(x-w)*(fx-fv);
1354: q=(x-v)*(fx-fw);
1355: p=(x-v)*q-(x-w)*r;
1356: q=2.0*(q-r);
1357: if (q > 0.0) p = -p;
1358: q=fabs(q);
1359: etemp=e;
1360: e=d;
1361: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1362: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1363: else {
1364: d=p/q;
1365: u=x+d;
1366: if (u-a < tol2 || b-u < tol2)
1367: d=SIGN(tol1,xm-x);
1368: }
1369: } else {
1370: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1371: }
1372: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1373: fu=(*f)(u);
1374: if (fu <= fx) {
1375: if (u >= x) a=x; else b=x;
1376: SHFT(v,w,x,u)
1.183 brouard 1377: SHFT(fv,fw,fx,fu)
1378: } else {
1379: if (u < x) a=u; else b=u;
1380: if (fu <= fw || w == x) {
1381: v=w;
1382: w=u;
1383: fv=fw;
1384: fw=fu;
1385: } else if (fu <= fv || v == x || v == w) {
1386: v=u;
1387: fv=fu;
1388: }
1389: }
1.126 brouard 1390: }
1391: nrerror("Too many iterations in brent");
1392: *xmin=x;
1393: return fx;
1394: }
1395:
1396: /****************** mnbrak ***********************/
1397:
1398: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1399: double (*func)(double))
1.183 brouard 1400: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1401: the downhill direction (defined by the function as evaluated at the initial points) and returns
1402: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1403: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1404: */
1.126 brouard 1405: double ulim,u,r,q, dum;
1406: double fu;
1.187 brouard 1407:
1408: double scale=10.;
1409: int iterscale=0;
1410:
1411: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1412: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1413:
1414:
1415: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1416: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1417: /* *bx = *ax - (*ax - *bx)/scale; */
1418: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1419: /* } */
1420:
1.126 brouard 1421: if (*fb > *fa) {
1422: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1423: SHFT(dum,*fb,*fa,dum)
1424: }
1.126 brouard 1425: *cx=(*bx)+GOLD*(*bx-*ax);
1426: *fc=(*func)(*cx);
1.183 brouard 1427: #ifdef DEBUG
1428: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1429: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1430: #endif
1431: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1432: r=(*bx-*ax)*(*fb-*fc);
1433: q=(*bx-*cx)*(*fb-*fa);
1434: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1435: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1436: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1437: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1438: fu=(*func)(u);
1.163 brouard 1439: #ifdef DEBUG
1440: /* f(x)=A(x-u)**2+f(u) */
1441: double A, fparabu;
1442: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1443: fparabu= *fa - A*(*ax-u)*(*ax-u);
1444: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1445: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183 brouard 1446: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1447: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1448: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1449: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1450: #endif
1.184 brouard 1451: #ifdef MNBRAKORIGINAL
1.183 brouard 1452: #else
1.191 ! brouard 1453: /* if (fu > *fc) { */
! 1454: /* #ifdef DEBUG */
! 1455: /* printf("mnbrak4 fu > fc \n"); */
! 1456: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
! 1457: /* #endif */
! 1458: /* /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/ *\/ */
! 1459: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
! 1460: /* dum=u; /\* Shifting c and u *\/ */
! 1461: /* u = *cx; */
! 1462: /* *cx = dum; */
! 1463: /* dum = fu; */
! 1464: /* fu = *fc; */
! 1465: /* *fc =dum; */
! 1466: /* } else { /\* end *\/ */
! 1467: /* #ifdef DEBUG */
! 1468: /* printf("mnbrak3 fu < fc \n"); */
! 1469: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
! 1470: /* #endif */
! 1471: /* dum=u; /\* Shifting c and u *\/ */
! 1472: /* u = *cx; */
! 1473: /* *cx = dum; */
! 1474: /* dum = fu; */
! 1475: /* fu = *fc; */
! 1476: /* *fc =dum; */
! 1477: /* } */
1.183 brouard 1478: #ifdef DEBUG
1.191 ! brouard 1479: printf("mnbrak34 fu < or >= fc \n");
! 1480: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1481: #endif
1.191 ! brouard 1482: dum=u; /* Shifting c and u */
! 1483: u = *cx;
! 1484: *cx = dum;
! 1485: dum = fu;
! 1486: fu = *fc;
! 1487: *fc =dum;
1.183 brouard 1488: #endif
1.162 brouard 1489: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1490: #ifdef DEBUG
1491: printf("mnbrak2 u after c but before ulim\n");
1492: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1493: #endif
1.126 brouard 1494: fu=(*func)(u);
1495: if (fu < *fc) {
1.183 brouard 1496: #ifdef DEBUG
1497: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1498: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1499: #endif
1.126 brouard 1500: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1501: SHFT(*fb,*fc,fu,(*func)(u))
1502: }
1.162 brouard 1503: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1504: #ifdef DEBUG
1505: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1506: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1507: #endif
1.126 brouard 1508: u=ulim;
1509: fu=(*func)(u);
1.183 brouard 1510: } else { /* u could be left to b (if r > q parabola has a maximum) */
1511: #ifdef DEBUG
1512: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1513: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1514: #endif
1.126 brouard 1515: u=(*cx)+GOLD*(*cx-*bx);
1516: fu=(*func)(u);
1.183 brouard 1517: } /* end tests */
1.126 brouard 1518: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1519: SHFT(*fa,*fb,*fc,fu)
1520: #ifdef DEBUG
1521: 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);
1522: 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);
1523: #endif
1524: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126 brouard 1525: }
1526:
1527: /*************** linmin ************************/
1.162 brouard 1528: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1529: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1530: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1531: the value of func at the returned location p . This is actually all accomplished by calling the
1532: routines mnbrak and brent .*/
1.126 brouard 1533: int ncom;
1534: double *pcom,*xicom;
1535: double (*nrfunc)(double []);
1536:
1537: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1538: {
1539: double brent(double ax, double bx, double cx,
1540: double (*f)(double), double tol, double *xmin);
1541: double f1dim(double x);
1542: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1543: double *fc, double (*func)(double));
1544: int j;
1545: double xx,xmin,bx,ax;
1546: double fx,fb,fa;
1.187 brouard 1547:
1548: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1549:
1550: ncom=n;
1551: pcom=vector(1,n);
1552: xicom=vector(1,n);
1553: nrfunc=func;
1554: for (j=1;j<=n;j++) {
1555: pcom[j]=p[j];
1556: xicom[j]=xi[j];
1557: }
1.187 brouard 1558:
1559: axs=0.0;
1560: xxss=1; /* 1 and using scale */
1561: xxs=1;
1562: do{
1563: ax=0.;
1564: xx= xxs;
1565: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1566: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1567: /* 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)) */
1568: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1569: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1570: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1571: /* 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]]*/
1572: if (fx != fx){
1573: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1574: 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);
1575: }
1576: }while(fx != fx);
1577:
1.191 ! brouard 1578: #ifdef DEBUGLINMIN
! 1579: 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);
! 1580: #endif
1.187 brouard 1581: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1582: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1583: /* fmin = f(p[j] + xmin * xi[j]) */
1584: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1585: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1586: #ifdef DEBUG
1587: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1588: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1589: #endif
1.191 ! brouard 1590: #ifdef DEBUGLINMIN
! 1591: printf("linmin end ");
! 1592: #endif
1.126 brouard 1593: for (j=1;j<=n;j++) {
1.188 brouard 1594: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1595: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1596: /* if(xxs <1.0) */
1597: /* 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 ); */
1.187 brouard 1598: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1599: }
1.189 brouard 1600: /* printf("\n"); */
1.191 ! brouard 1601: #ifdef DEBUGLINMIN
! 1602: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
! 1603: for (j=1;j<=n;j++) {
! 1604: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
! 1605: if(j % ncovmodel == 0)
! 1606: printf("\n");
! 1607: }
! 1608: #endif
1.126 brouard 1609: free_vector(xicom,1,n);
1610: free_vector(pcom,1,n);
1611: }
1612:
1613:
1614: /*************** powell ************************/
1.162 brouard 1615: /*
1616: Minimization of a function func of n variables. Input consists of an initial starting point
1617: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1618: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1619: such that failure to decrease by more than this amount on one iteration signals doneness. On
1620: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1621: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1622: */
1.126 brouard 1623: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1624: double (*func)(double []))
1625: {
1626: void linmin(double p[], double xi[], int n, double *fret,
1627: double (*func)(double []));
1628: int i,ibig,j;
1629: double del,t,*pt,*ptt,*xit;
1.181 brouard 1630: double directest;
1.126 brouard 1631: double fp,fptt;
1632: double *xits;
1633: int niterf, itmp;
1634:
1635: pt=vector(1,n);
1636: ptt=vector(1,n);
1637: xit=vector(1,n);
1638: xits=vector(1,n);
1639: *fret=(*func)(p);
1640: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1641: rcurr_time = time(NULL);
1.126 brouard 1642: for (*iter=1;;++(*iter)) {
1.187 brouard 1643: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1644: ibig=0;
1645: del=0.0;
1.157 brouard 1646: rlast_time=rcurr_time;
1647: /* (void) gettimeofday(&curr_time,&tzp); */
1648: rcurr_time = time(NULL);
1649: curr_time = *localtime(&rcurr_time);
1650: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1651: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1652: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1653: for (i=1;i<=n;i++) {
1654: printf(" %d %.12f",i, p[i]);
1655: fprintf(ficlog," %d %.12lf",i, p[i]);
1656: fprintf(ficrespow," %.12lf", p[i]);
1657: }
1658: printf("\n");
1659: fprintf(ficlog,"\n");
1660: fprintf(ficrespow,"\n");fflush(ficrespow);
1661: if(*iter <=3){
1.157 brouard 1662: tml = *localtime(&rcurr_time);
1663: strcpy(strcurr,asctime(&tml));
1664: rforecast_time=rcurr_time;
1.126 brouard 1665: itmp = strlen(strcurr);
1666: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1667: strcurr[itmp-1]='\0';
1.162 brouard 1668: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1669: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1670: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1671: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1672: forecast_time = *localtime(&rforecast_time);
1673: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1674: itmp = strlen(strfor);
1675: if(strfor[itmp-1]=='\n')
1676: strfor[itmp-1]='\0';
1.157 brouard 1677: 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);
1678: 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);
1.126 brouard 1679: }
1680: }
1.187 brouard 1681: for (i=1;i<=n;i++) { /* For each direction i */
1682: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1683: fptt=(*fret);
1684: #ifdef DEBUG
1.164 brouard 1685: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1686: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1687: #endif
1.187 brouard 1688: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1689: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1690: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1691: /* Outputs are fret(new point p) p is updated and xit rescaled */
1692: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1693: /* because that direction will be replaced unless the gain del is small */
1694: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1695: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1696: /* with the new direction. */
1.126 brouard 1697: del=fabs(fptt-(*fret));
1698: ibig=i;
1699: }
1700: #ifdef DEBUG
1701: printf("%d %.12e",i,(*fret));
1702: fprintf(ficlog,"%d %.12e",i,(*fret));
1703: for (j=1;j<=n;j++) {
1704: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1705: printf(" x(%d)=%.12e",j,xit[j]);
1706: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1707: }
1708: for(j=1;j<=n;j++) {
1.162 brouard 1709: printf(" p(%d)=%.12e",j,p[j]);
1710: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1711: }
1712: printf("\n");
1713: fprintf(ficlog,"\n");
1714: #endif
1.187 brouard 1715: } /* end loop on each direction i */
1716: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1717: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1718: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1719: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1720: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1721: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1722: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1723: /* decreased of more than 3.84 */
1724: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1725: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1726: /* By adding 10 parameters more the gain should be 18.31 */
1727:
1728: /* Starting the program with initial values given by a former maximization will simply change */
1729: /* the scales of the directions and the directions, because the are reset to canonical directions */
1730: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1731: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1732: #ifdef DEBUG
1733: int k[2],l;
1734: k[0]=1;
1735: k[1]=-1;
1736: printf("Max: %.12e",(*func)(p));
1737: fprintf(ficlog,"Max: %.12e",(*func)(p));
1738: for (j=1;j<=n;j++) {
1739: printf(" %.12e",p[j]);
1740: fprintf(ficlog," %.12e",p[j]);
1741: }
1742: printf("\n");
1743: fprintf(ficlog,"\n");
1744: for(l=0;l<=1;l++) {
1745: for (j=1;j<=n;j++) {
1746: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1747: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1748: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1749: }
1750: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1751: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1752: }
1753: #endif
1754:
1755:
1756: free_vector(xit,1,n);
1757: free_vector(xits,1,n);
1758: free_vector(ptt,1,n);
1759: free_vector(pt,1,n);
1760: return;
1761: }
1762: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1763: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1764: ptt[j]=2.0*p[j]-pt[j];
1765: xit[j]=p[j]-pt[j];
1766: pt[j]=p[j];
1767: }
1.181 brouard 1768: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1769: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1770: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1771: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1772: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1773: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1774: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1775: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1776: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1777: #ifdef NRCORIGINAL
1778: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1779: #else
1780: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1.161 brouard 1781: t= t- del*SQR(fp-fptt);
1.183 brouard 1782: #endif
1.182 brouard 1783: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1784: #ifdef DEBUG
1.181 brouard 1785: 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);
1786: 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);
1.161 brouard 1787: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1788: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1789: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1790: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1791: 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);
1792: 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);
1793: #endif
1.183 brouard 1794: #ifdef POWELLORIGINAL
1795: if (t < 0.0) { /* Then we use it for new direction */
1796: #else
1.182 brouard 1797: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 brouard 1798: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1799: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.184 brouard 1800: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1801: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1802: }
1.181 brouard 1803: if (directest < 0.0) { /* Then we use it for new direction */
1804: #endif
1.191 ! brouard 1805: #ifdef DEBUGLINMIN
! 1806: printf("Before linmin in direction P%d-P0\n",n);
! 1807: for (j=1;j<=n;j++) {
! 1808: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 1809: if(j % ncovmodel == 0)
! 1810: printf("\n");
! 1811: }
! 1812: #endif
1.187 brouard 1813: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 ! brouard 1814: #ifdef DEBUGLINMIN
! 1815: for (j=1;j<=n;j++) {
! 1816: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
! 1817: if(j % ncovmodel == 0)
! 1818: printf("\n");
! 1819: }
! 1820: #endif
1.126 brouard 1821: for (j=1;j<=n;j++) {
1.181 brouard 1822: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1823: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1824: }
1.181 brouard 1825: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1826: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1827:
1.126 brouard 1828: #ifdef DEBUG
1.164 brouard 1829: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1830: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1831: for(j=1;j<=n;j++){
1832: printf(" %.12e",xit[j]);
1833: fprintf(ficlog," %.12e",xit[j]);
1834: }
1835: printf("\n");
1836: fprintf(ficlog,"\n");
1837: #endif
1.162 brouard 1838: } /* end of t negative */
1839: } /* end if (fptt < fp) */
1.126 brouard 1840: }
1841: }
1842:
1843: /**** Prevalence limit (stable or period prevalence) ****************/
1844:
1845: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1846: {
1847: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1848: matrix by transitions matrix until convergence is reached */
1.169 brouard 1849:
1.126 brouard 1850: int i, ii,j,k;
1851: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1852: /* double **matprod2(); */ /* test */
1.131 brouard 1853: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1854: double **newm;
1855: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1856:
1.126 brouard 1857: for (ii=1;ii<=nlstate+ndeath;ii++)
1858: for (j=1;j<=nlstate+ndeath;j++){
1859: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1860: }
1.169 brouard 1861:
1862: cov[1]=1.;
1863:
1864: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1865: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1866: newm=savm;
1867: /* Covariates have to be included here again */
1.138 brouard 1868: cov[2]=agefin;
1.187 brouard 1869: if(nagesqr==1)
1870: cov[3]= agefin*agefin;;
1.138 brouard 1871: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1872: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1873: /*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]]);*/
1.138 brouard 1874: }
1.186 brouard 1875: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1876: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1877: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1878: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1879:
1880: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1881: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1882: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1883: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1884: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1885: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1886:
1.126 brouard 1887: savm=oldm;
1888: oldm=newm;
1889: maxmax=0.;
1890: for(j=1;j<=nlstate;j++){
1891: min=1.;
1892: max=0.;
1893: for(i=1; i<=nlstate; i++) {
1894: sumnew=0;
1895: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1896: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1897: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1898: max=FMAX(max,prlim[i][j]);
1899: min=FMIN(min,prlim[i][j]);
1900: }
1901: maxmin=max-min;
1902: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1903: } /* j loop */
1.126 brouard 1904: if(maxmax < ftolpl){
1905: return prlim;
1906: }
1.169 brouard 1907: } /* age loop */
1908: return prlim; /* should not reach here */
1.126 brouard 1909: }
1910:
1911: /*************** transition probabilities ***************/
1912:
1913: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1914: {
1.138 brouard 1915: /* According to parameters values stored in x and the covariate's values stored in cov,
1916: computes the probability to be observed in state j being in state i by appying the
1917: model to the ncovmodel covariates (including constant and age).
1918: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1919: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1920: ncth covariate in the global vector x is given by the formula:
1921: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1922: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1923: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1924: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1925: Outputs ps[i][j] the probability to be observed in j being in j according to
1926: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1927: */
1928: double s1, lnpijopii;
1.126 brouard 1929: /*double t34;*/
1.164 brouard 1930: int i,j, nc, ii, jj;
1.126 brouard 1931:
1932: for(i=1; i<= nlstate; i++){
1933: for(j=1; j<i;j++){
1.138 brouard 1934: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1935: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1936: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1937: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1938: }
1.138 brouard 1939: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1940: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1941: }
1942: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1943: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1944: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1945: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1946: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1947: }
1.138 brouard 1948: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1949: }
1950: }
1951:
1952: for(i=1; i<= nlstate; i++){
1953: s1=0;
1.131 brouard 1954: for(j=1; j<i; j++){
1.138 brouard 1955: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1956: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1957: }
1958: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1959: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1960: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1961: }
1.138 brouard 1962: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1963: ps[i][i]=1./(s1+1.);
1.138 brouard 1964: /* Computing other pijs */
1.126 brouard 1965: for(j=1; j<i; j++)
1966: ps[i][j]= exp(ps[i][j])*ps[i][i];
1967: for(j=i+1; j<=nlstate+ndeath; j++)
1968: ps[i][j]= exp(ps[i][j])*ps[i][i];
1969: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1970: } /* end i */
1971:
1972: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1973: for(jj=1; jj<= nlstate+ndeath; jj++){
1974: ps[ii][jj]=0;
1975: ps[ii][ii]=1;
1976: }
1977: }
1978:
1.145 brouard 1979:
1980: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1981: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1982: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1983: /* } */
1984: /* printf("\n "); */
1985: /* } */
1986: /* printf("\n ");printf("%lf ",cov[2]);*/
1987: /*
1.126 brouard 1988: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1989: goto end;*/
1990: return ps;
1991: }
1992:
1993: /**************** Product of 2 matrices ******************/
1994:
1.145 brouard 1995: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1996: {
1997: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1998: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1999: /* in, b, out are matrice of pointers which should have been initialized
2000: before: only the contents of out is modified. The function returns
2001: a pointer to pointers identical to out */
1.145 brouard 2002: int i, j, k;
1.126 brouard 2003: for(i=nrl; i<= nrh; i++)
1.145 brouard 2004: for(k=ncolol; k<=ncoloh; k++){
2005: out[i][k]=0.;
2006: for(j=ncl; j<=nch; j++)
2007: out[i][k] +=in[i][j]*b[j][k];
2008: }
1.126 brouard 2009: return out;
2010: }
2011:
2012:
2013: /************* Higher Matrix Product ***************/
2014:
2015: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2016: {
2017: /* Computes the transition matrix starting at age 'age' over
2018: 'nhstepm*hstepm*stepm' months (i.e. until
2019: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2020: nhstepm*hstepm matrices.
2021: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2022: (typically every 2 years instead of every month which is too big
2023: for the memory).
2024: Model is determined by parameters x and covariates have to be
2025: included manually here.
2026:
2027: */
2028:
2029: int i, j, d, h, k;
1.131 brouard 2030: double **out, cov[NCOVMAX+1];
1.126 brouard 2031: double **newm;
1.187 brouard 2032: double agexact;
1.126 brouard 2033:
2034: /* Hstepm could be zero and should return the unit matrix */
2035: for (i=1;i<=nlstate+ndeath;i++)
2036: for (j=1;j<=nlstate+ndeath;j++){
2037: oldm[i][j]=(i==j ? 1.0 : 0.0);
2038: po[i][j][0]=(i==j ? 1.0 : 0.0);
2039: }
2040: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2041: for(h=1; h <=nhstepm; h++){
2042: for(d=1; d <=hstepm; d++){
2043: newm=savm;
2044: /* Covariates have to be included here again */
2045: cov[1]=1.;
1.187 brouard 2046: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2047: cov[2]=agexact;
2048: if(nagesqr==1)
2049: cov[3]= agexact*agexact;
1.131 brouard 2050: for (k=1; k<=cptcovn;k++)
1.187 brouard 2051: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2052: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2053: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2054: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2055: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2056: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 2057:
2058:
2059: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2060: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2061: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2062: pmij(pmmij,cov,ncovmodel,x,nlstate));
2063: savm=oldm;
2064: oldm=newm;
2065: }
2066: for(i=1; i<=nlstate+ndeath; i++)
2067: for(j=1;j<=nlstate+ndeath;j++) {
2068: po[i][j][h]=newm[i][j];
1.128 brouard 2069: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2070: }
1.128 brouard 2071: /*printf("h=%d ",h);*/
1.126 brouard 2072: } /* end h */
1.128 brouard 2073: /* printf("\n H=%d \n",h); */
1.126 brouard 2074: return po;
2075: }
2076:
1.162 brouard 2077: #ifdef NLOPT
2078: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2079: double fret;
2080: double *xt;
2081: int j;
2082: myfunc_data *d2 = (myfunc_data *) pd;
2083: /* xt = (p1-1); */
2084: xt=vector(1,n);
2085: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2086:
2087: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2088: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2089: printf("Function = %.12lf ",fret);
2090: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2091: printf("\n");
2092: free_vector(xt,1,n);
2093: return fret;
2094: }
2095: #endif
1.126 brouard 2096:
2097: /*************** log-likelihood *************/
2098: double func( double *x)
2099: {
2100: int i, ii, j, k, mi, d, kk;
1.131 brouard 2101: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2102: double **out;
2103: double sw; /* Sum of weights */
2104: double lli; /* Individual log likelihood */
2105: int s1, s2;
2106: double bbh, survp;
2107: long ipmx;
1.187 brouard 2108: double agexact;
1.126 brouard 2109: /*extern weight */
2110: /* We are differentiating ll according to initial status */
2111: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2112: /*for(i=1;i<imx;i++)
2113: printf(" %d\n",s[4][i]);
2114: */
1.162 brouard 2115:
2116: ++countcallfunc;
2117:
1.126 brouard 2118: cov[1]=1.;
2119:
2120: for(k=1; k<=nlstate; k++) ll[k]=0.;
2121:
2122: if(mle==1){
2123: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2124: /* Computes the values of the ncovmodel covariates of the model
2125: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2126: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2127: to be observed in j being in i according to the model.
2128: */
1.145 brouard 2129: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2130: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2131: }
1.137 brouard 2132: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2133: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2134: has been calculated etc */
1.126 brouard 2135: for(mi=1; mi<= wav[i]-1; mi++){
2136: for (ii=1;ii<=nlstate+ndeath;ii++)
2137: for (j=1;j<=nlstate+ndeath;j++){
2138: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2139: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2140: }
2141: for(d=0; d<dh[mi][i]; d++){
2142: newm=savm;
1.187 brouard 2143: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2144: cov[2]=agexact;
2145: if(nagesqr==1)
2146: cov[3]= agexact*agexact;
1.126 brouard 2147: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2148: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2149: }
2150: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2151: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2152: savm=oldm;
2153: oldm=newm;
2154: } /* end mult */
2155:
2156: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2157: /* But now since version 0.9 we anticipate for bias at large stepm.
2158: * If stepm is larger than one month (smallest stepm) and if the exact delay
2159: * (in months) between two waves is not a multiple of stepm, we rounded to
2160: * the nearest (and in case of equal distance, to the lowest) interval but now
2161: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2162: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2163: * probability in order to take into account the bias as a fraction of the way
2164: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2165: * -stepm/2 to stepm/2 .
2166: * For stepm=1 the results are the same as for previous versions of Imach.
2167: * For stepm > 1 the results are less biased than in previous versions.
2168: */
2169: s1=s[mw[mi][i]][i];
2170: s2=s[mw[mi+1][i]][i];
2171: bbh=(double)bh[mi][i]/(double)stepm;
2172: /* bias bh is positive if real duration
2173: * is higher than the multiple of stepm and negative otherwise.
2174: */
2175: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2176: if( s2 > nlstate){
2177: /* i.e. if s2 is a death state and if the date of death is known
2178: then the contribution to the likelihood is the probability to
2179: die between last step unit time and current step unit time,
2180: which is also equal to probability to die before dh
2181: minus probability to die before dh-stepm .
2182: In version up to 0.92 likelihood was computed
2183: as if date of death was unknown. Death was treated as any other
2184: health state: the date of the interview describes the actual state
2185: and not the date of a change in health state. The former idea was
2186: to consider that at each interview the state was recorded
2187: (healthy, disable or death) and IMaCh was corrected; but when we
2188: introduced the exact date of death then we should have modified
2189: the contribution of an exact death to the likelihood. This new
2190: contribution is smaller and very dependent of the step unit
2191: stepm. It is no more the probability to die between last interview
2192: and month of death but the probability to survive from last
2193: interview up to one month before death multiplied by the
2194: probability to die within a month. Thanks to Chris
2195: Jackson for correcting this bug. Former versions increased
2196: mortality artificially. The bad side is that we add another loop
2197: which slows down the processing. The difference can be up to 10%
2198: lower mortality.
2199: */
1.183 brouard 2200: /* If, at the beginning of the maximization mostly, the
2201: cumulative probability or probability to be dead is
2202: constant (ie = 1) over time d, the difference is equal to
2203: 0. out[s1][3] = savm[s1][3]: probability, being at state
2204: s1 at precedent wave, to be dead a month before current
2205: wave is equal to probability, being at state s1 at
2206: precedent wave, to be dead at mont of the current
2207: wave. Then the observed probability (that this person died)
2208: is null according to current estimated parameter. In fact,
2209: it should be very low but not zero otherwise the log go to
2210: infinity.
2211: */
2212: /* #ifdef INFINITYORIGINAL */
2213: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2214: /* #else */
2215: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2216: /* lli=log(mytinydouble); */
2217: /* else */
2218: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2219: /* #endif */
2220: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2221:
2222: } else if (s2==-2) {
2223: for (j=1,survp=0. ; j<=nlstate; j++)
2224: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2225: /*survp += out[s1][j]; */
2226: lli= log(survp);
2227: }
2228:
2229: else if (s2==-4) {
2230: for (j=3,survp=0. ; j<=nlstate; j++)
2231: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2232: lli= log(survp);
2233: }
2234:
2235: else if (s2==-5) {
2236: for (j=1,survp=0. ; j<=2; j++)
2237: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2238: lli= log(survp);
2239: }
2240:
2241: else{
2242: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2243: /* 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 */
2244: }
2245: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2246: /*if(lli ==000.0)*/
2247: /*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); */
2248: ipmx +=1;
2249: sw += weight[i];
2250: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2251: /* if (lli < log(mytinydouble)){ */
2252: /* 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); */
2253: /* 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]); */
2254: /* } */
1.126 brouard 2255: } /* end of wave */
2256: } /* end of individual */
2257: } else if(mle==2){
2258: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2259: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2260: for(mi=1; mi<= wav[i]-1; mi++){
2261: for (ii=1;ii<=nlstate+ndeath;ii++)
2262: for (j=1;j<=nlstate+ndeath;j++){
2263: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2264: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2265: }
2266: for(d=0; d<=dh[mi][i]; d++){
2267: newm=savm;
1.187 brouard 2268: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2269: cov[2]=agexact;
2270: if(nagesqr==1)
2271: cov[3]= agexact*agexact;
1.126 brouard 2272: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2273: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2274: }
2275: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2276: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2277: savm=oldm;
2278: oldm=newm;
2279: } /* end mult */
2280:
2281: s1=s[mw[mi][i]][i];
2282: s2=s[mw[mi+1][i]][i];
2283: bbh=(double)bh[mi][i]/(double)stepm;
2284: 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 */
2285: ipmx +=1;
2286: sw += weight[i];
2287: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2288: } /* end of wave */
2289: } /* end of individual */
2290: } else if(mle==3){ /* exponential inter-extrapolation */
2291: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2292: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2293: for(mi=1; mi<= wav[i]-1; mi++){
2294: for (ii=1;ii<=nlstate+ndeath;ii++)
2295: for (j=1;j<=nlstate+ndeath;j++){
2296: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2297: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2298: }
2299: for(d=0; d<dh[mi][i]; d++){
2300: newm=savm;
1.187 brouard 2301: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2302: cov[2]=agexact;
2303: if(nagesqr==1)
2304: cov[3]= agexact*agexact;
1.126 brouard 2305: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2306: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2307: }
2308: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2309: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2310: savm=oldm;
2311: oldm=newm;
2312: } /* end mult */
2313:
2314: s1=s[mw[mi][i]][i];
2315: s2=s[mw[mi+1][i]][i];
2316: bbh=(double)bh[mi][i]/(double)stepm;
2317: 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 */
2318: ipmx +=1;
2319: sw += weight[i];
2320: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2321: } /* end of wave */
2322: } /* end of individual */
2323: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2324: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2325: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2326: for(mi=1; mi<= wav[i]-1; mi++){
2327: for (ii=1;ii<=nlstate+ndeath;ii++)
2328: for (j=1;j<=nlstate+ndeath;j++){
2329: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2330: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2331: }
2332: for(d=0; d<dh[mi][i]; d++){
2333: newm=savm;
1.187 brouard 2334: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2335: cov[2]=agexact;
2336: if(nagesqr==1)
2337: cov[3]= agexact*agexact;
1.126 brouard 2338: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2339: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2340: }
2341:
2342: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2343: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2344: savm=oldm;
2345: oldm=newm;
2346: } /* end mult */
2347:
2348: s1=s[mw[mi][i]][i];
2349: s2=s[mw[mi+1][i]][i];
2350: if( s2 > nlstate){
2351: lli=log(out[s1][s2] - savm[s1][s2]);
2352: }else{
2353: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2354: }
2355: ipmx +=1;
2356: sw += weight[i];
2357: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2358: /* 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]); */
2359: } /* end of wave */
2360: } /* end of individual */
2361: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2362: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2363: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2364: for(mi=1; mi<= wav[i]-1; mi++){
2365: for (ii=1;ii<=nlstate+ndeath;ii++)
2366: for (j=1;j<=nlstate+ndeath;j++){
2367: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2368: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2369: }
2370: for(d=0; d<dh[mi][i]; d++){
2371: newm=savm;
1.187 brouard 2372: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2373: cov[2]=agexact;
2374: if(nagesqr==1)
2375: cov[3]= agexact*agexact;
1.126 brouard 2376: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2377: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2378: }
2379:
2380: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2381: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2382: savm=oldm;
2383: oldm=newm;
2384: } /* end mult */
2385:
2386: s1=s[mw[mi][i]][i];
2387: s2=s[mw[mi+1][i]][i];
2388: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2389: ipmx +=1;
2390: sw += weight[i];
2391: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2392: /*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]);*/
2393: } /* end of wave */
2394: } /* end of individual */
2395: } /* End of if */
2396: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2397: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2398: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2399: return -l;
2400: }
2401:
2402: /*************** log-likelihood *************/
2403: double funcone( double *x)
2404: {
2405: /* Same as likeli but slower because of a lot of printf and if */
2406: int i, ii, j, k, mi, d, kk;
1.131 brouard 2407: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2408: double **out;
2409: double lli; /* Individual log likelihood */
2410: double llt;
2411: int s1, s2;
2412: double bbh, survp;
1.187 brouard 2413: double agexact;
1.126 brouard 2414: /*extern weight */
2415: /* We are differentiating ll according to initial status */
2416: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2417: /*for(i=1;i<imx;i++)
2418: printf(" %d\n",s[4][i]);
2419: */
2420: cov[1]=1.;
2421:
2422: for(k=1; k<=nlstate; k++) ll[k]=0.;
2423:
2424: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2425: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2426: for(mi=1; mi<= wav[i]-1; mi++){
2427: for (ii=1;ii<=nlstate+ndeath;ii++)
2428: for (j=1;j<=nlstate+ndeath;j++){
2429: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2430: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2431: }
2432: for(d=0; d<dh[mi][i]; d++){
2433: newm=savm;
1.187 brouard 2434: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2435: cov[2]=agexact;
2436: if(nagesqr==1)
2437: cov[3]= agexact*agexact;
1.126 brouard 2438: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2439: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2440: }
1.187 brouard 2441:
1.145 brouard 2442: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2443: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2444: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2445: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2446: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2447: savm=oldm;
2448: oldm=newm;
2449: } /* end mult */
2450:
2451: s1=s[mw[mi][i]][i];
2452: s2=s[mw[mi+1][i]][i];
2453: bbh=(double)bh[mi][i]/(double)stepm;
2454: /* bias is positive if real duration
2455: * is higher than the multiple of stepm and negative otherwise.
2456: */
2457: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2458: lli=log(out[s1][s2] - savm[s1][s2]);
2459: } else if (s2==-2) {
2460: for (j=1,survp=0. ; j<=nlstate; j++)
2461: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2462: lli= log(survp);
2463: }else if (mle==1){
2464: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2465: } else if(mle==2){
2466: 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 */
2467: } else if(mle==3){ /* exponential inter-extrapolation */
2468: 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 */
2469: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2470: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2471: } else{ /* mle=0 back to 1 */
2472: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2473: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2474: } /* End of if */
2475: ipmx +=1;
2476: sw += weight[i];
2477: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2478: /*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]); */
1.126 brouard 2479: if(globpr){
1.141 brouard 2480: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2481: %11.6f %11.6f %11.6f ", \
2482: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2483: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2484: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2485: llt +=ll[k]*gipmx/gsw;
2486: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2487: }
2488: fprintf(ficresilk," %10.6f\n", -llt);
2489: }
2490: } /* end of wave */
2491: } /* end of individual */
2492: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2493: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2494: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2495: if(globpr==0){ /* First time we count the contributions and weights */
2496: gipmx=ipmx;
2497: gsw=sw;
2498: }
2499: return -l;
2500: }
2501:
2502:
2503: /*************** function likelione ***********/
2504: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2505: {
2506: /* This routine should help understanding what is done with
2507: the selection of individuals/waves and
2508: to check the exact contribution to the likelihood.
2509: Plotting could be done.
2510: */
2511: int k;
2512:
2513: if(*globpri !=0){ /* Just counts and sums, no printings */
2514: strcpy(fileresilk,"ilk");
2515: strcat(fileresilk,fileres);
2516: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2517: printf("Problem with resultfile: %s\n", fileresilk);
2518: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2519: }
2520: 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");
2521: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2522: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2523: for(k=1; k<=nlstate; k++)
2524: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2525: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2526: }
2527:
2528: *fretone=(*funcone)(p);
2529: if(*globpri !=0){
2530: fclose(ficresilk);
2531: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2532: fflush(fichtm);
2533: }
2534: return;
2535: }
2536:
2537:
2538: /*********** Maximum Likelihood Estimation ***************/
2539:
2540: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2541: {
1.165 brouard 2542: int i,j, iter=0;
1.126 brouard 2543: double **xi;
2544: double fret;
2545: double fretone; /* Only one call to likelihood */
2546: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2547:
2548: #ifdef NLOPT
2549: int creturn;
2550: nlopt_opt opt;
2551: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2552: double *lb;
2553: double minf; /* the minimum objective value, upon return */
2554: double * p1; /* Shifted parameters from 0 instead of 1 */
2555: myfunc_data dinst, *d = &dinst;
2556: #endif
2557:
2558:
1.126 brouard 2559: xi=matrix(1,npar,1,npar);
2560: for (i=1;i<=npar;i++)
2561: for (j=1;j<=npar;j++)
2562: xi[i][j]=(i==j ? 1.0 : 0.0);
2563: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2564: strcpy(filerespow,"pow");
2565: strcat(filerespow,fileres);
2566: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2567: printf("Problem with resultfile: %s\n", filerespow);
2568: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2569: }
2570: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2571: for (i=1;i<=nlstate;i++)
2572: for(j=1;j<=nlstate+ndeath;j++)
2573: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2574: fprintf(ficrespow,"\n");
1.162 brouard 2575: #ifdef POWELL
1.126 brouard 2576: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2577: #endif
1.126 brouard 2578:
1.162 brouard 2579: #ifdef NLOPT
2580: #ifdef NEWUOA
2581: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2582: #else
2583: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2584: #endif
2585: lb=vector(0,npar-1);
2586: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2587: nlopt_set_lower_bounds(opt, lb);
2588: nlopt_set_initial_step1(opt, 0.1);
2589:
2590: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2591: d->function = func;
2592: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2593: nlopt_set_min_objective(opt, myfunc, d);
2594: nlopt_set_xtol_rel(opt, ftol);
2595: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2596: printf("nlopt failed! %d\n",creturn);
2597: }
2598: else {
2599: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2600: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2601: iter=1; /* not equal */
2602: }
2603: nlopt_destroy(opt);
2604: #endif
1.126 brouard 2605: free_matrix(xi,1,npar,1,npar);
2606: fclose(ficrespow);
1.180 brouard 2607: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2608: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2609: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2610:
2611: }
2612:
2613: /**** Computes Hessian and covariance matrix ***/
2614: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2615: {
2616: double **a,**y,*x,pd;
2617: double **hess;
1.164 brouard 2618: int i, j;
1.126 brouard 2619: int *indx;
2620:
2621: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2622: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2623: void lubksb(double **a, int npar, int *indx, double b[]) ;
2624: void ludcmp(double **a, int npar, int *indx, double *d) ;
2625: double gompertz(double p[]);
2626: hess=matrix(1,npar,1,npar);
2627:
2628: printf("\nCalculation of the hessian matrix. Wait...\n");
2629: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2630: for (i=1;i<=npar;i++){
2631: printf("%d",i);fflush(stdout);
2632: fprintf(ficlog,"%d",i);fflush(ficlog);
2633:
2634: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2635:
2636: /* printf(" %f ",p[i]);
2637: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2638: }
2639:
2640: for (i=1;i<=npar;i++) {
2641: for (j=1;j<=npar;j++) {
2642: if (j>i) {
2643: printf(".%d%d",i,j);fflush(stdout);
2644: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2645: hess[i][j]=hessij(p,delti,i,j,func,npar);
2646:
2647: hess[j][i]=hess[i][j];
2648: /*printf(" %lf ",hess[i][j]);*/
2649: }
2650: }
2651: }
2652: printf("\n");
2653: fprintf(ficlog,"\n");
2654:
2655: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2656: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2657:
2658: a=matrix(1,npar,1,npar);
2659: y=matrix(1,npar,1,npar);
2660: x=vector(1,npar);
2661: indx=ivector(1,npar);
2662: for (i=1;i<=npar;i++)
2663: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2664: ludcmp(a,npar,indx,&pd);
2665:
2666: for (j=1;j<=npar;j++) {
2667: for (i=1;i<=npar;i++) x[i]=0;
2668: x[j]=1;
2669: lubksb(a,npar,indx,x);
2670: for (i=1;i<=npar;i++){
2671: matcov[i][j]=x[i];
2672: }
2673: }
2674:
2675: printf("\n#Hessian matrix#\n");
2676: fprintf(ficlog,"\n#Hessian matrix#\n");
2677: for (i=1;i<=npar;i++) {
2678: for (j=1;j<=npar;j++) {
2679: printf("%.3e ",hess[i][j]);
2680: fprintf(ficlog,"%.3e ",hess[i][j]);
2681: }
2682: printf("\n");
2683: fprintf(ficlog,"\n");
2684: }
2685:
2686: /* Recompute Inverse */
2687: for (i=1;i<=npar;i++)
2688: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2689: ludcmp(a,npar,indx,&pd);
2690:
2691: /* printf("\n#Hessian matrix recomputed#\n");
2692:
2693: for (j=1;j<=npar;j++) {
2694: for (i=1;i<=npar;i++) x[i]=0;
2695: x[j]=1;
2696: lubksb(a,npar,indx,x);
2697: for (i=1;i<=npar;i++){
2698: y[i][j]=x[i];
2699: printf("%.3e ",y[i][j]);
2700: fprintf(ficlog,"%.3e ",y[i][j]);
2701: }
2702: printf("\n");
2703: fprintf(ficlog,"\n");
2704: }
2705: */
2706:
2707: free_matrix(a,1,npar,1,npar);
2708: free_matrix(y,1,npar,1,npar);
2709: free_vector(x,1,npar);
2710: free_ivector(indx,1,npar);
2711: free_matrix(hess,1,npar,1,npar);
2712:
2713:
2714: }
2715:
2716: /*************** hessian matrix ****************/
2717: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2718: {
2719: int i;
2720: int l=1, lmax=20;
2721: double k1,k2;
1.132 brouard 2722: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2723: double res;
2724: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2725: double fx;
2726: int k=0,kmax=10;
2727: double l1;
2728:
2729: fx=func(x);
2730: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2731: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2732: l1=pow(10,l);
2733: delts=delt;
2734: for(k=1 ; k <kmax; k=k+1){
2735: delt = delta*(l1*k);
2736: p2[theta]=x[theta] +delt;
1.145 brouard 2737: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2738: p2[theta]=x[theta]-delt;
2739: k2=func(p2)-fx;
2740: /*res= (k1-2.0*fx+k2)/delt/delt; */
2741: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2742:
1.132 brouard 2743: #ifdef DEBUGHESS
1.126 brouard 2744: 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);
2745: 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);
2746: #endif
2747: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2748: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2749: k=kmax;
2750: }
2751: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2752: k=kmax; l=lmax*10;
1.126 brouard 2753: }
2754: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2755: delts=delt;
2756: }
2757: }
2758: }
2759: delti[theta]=delts;
2760: return res;
2761:
2762: }
2763:
2764: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2765: {
2766: int i;
1.164 brouard 2767: int l=1, lmax=20;
1.126 brouard 2768: double k1,k2,k3,k4,res,fx;
1.132 brouard 2769: double p2[MAXPARM+1];
1.126 brouard 2770: int k;
2771:
2772: fx=func(x);
2773: for (k=1; k<=2; k++) {
2774: for (i=1;i<=npar;i++) p2[i]=x[i];
2775: p2[thetai]=x[thetai]+delti[thetai]/k;
2776: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2777: k1=func(p2)-fx;
2778:
2779: p2[thetai]=x[thetai]+delti[thetai]/k;
2780: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2781: k2=func(p2)-fx;
2782:
2783: p2[thetai]=x[thetai]-delti[thetai]/k;
2784: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2785: k3=func(p2)-fx;
2786:
2787: p2[thetai]=x[thetai]-delti[thetai]/k;
2788: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2789: k4=func(p2)-fx;
2790: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2791: #ifdef DEBUG
2792: 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);
2793: 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);
2794: #endif
2795: }
2796: return res;
2797: }
2798:
2799: /************** Inverse of matrix **************/
2800: void ludcmp(double **a, int n, int *indx, double *d)
2801: {
2802: int i,imax,j,k;
2803: double big,dum,sum,temp;
2804: double *vv;
2805:
2806: vv=vector(1,n);
2807: *d=1.0;
2808: for (i=1;i<=n;i++) {
2809: big=0.0;
2810: for (j=1;j<=n;j++)
2811: if ((temp=fabs(a[i][j])) > big) big=temp;
2812: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2813: vv[i]=1.0/big;
2814: }
2815: for (j=1;j<=n;j++) {
2816: for (i=1;i<j;i++) {
2817: sum=a[i][j];
2818: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2819: a[i][j]=sum;
2820: }
2821: big=0.0;
2822: for (i=j;i<=n;i++) {
2823: sum=a[i][j];
2824: for (k=1;k<j;k++)
2825: sum -= a[i][k]*a[k][j];
2826: a[i][j]=sum;
2827: if ( (dum=vv[i]*fabs(sum)) >= big) {
2828: big=dum;
2829: imax=i;
2830: }
2831: }
2832: if (j != imax) {
2833: for (k=1;k<=n;k++) {
2834: dum=a[imax][k];
2835: a[imax][k]=a[j][k];
2836: a[j][k]=dum;
2837: }
2838: *d = -(*d);
2839: vv[imax]=vv[j];
2840: }
2841: indx[j]=imax;
2842: if (a[j][j] == 0.0) a[j][j]=TINY;
2843: if (j != n) {
2844: dum=1.0/(a[j][j]);
2845: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2846: }
2847: }
2848: free_vector(vv,1,n); /* Doesn't work */
2849: ;
2850: }
2851:
2852: void lubksb(double **a, int n, int *indx, double b[])
2853: {
2854: int i,ii=0,ip,j;
2855: double sum;
2856:
2857: for (i=1;i<=n;i++) {
2858: ip=indx[i];
2859: sum=b[ip];
2860: b[ip]=b[i];
2861: if (ii)
2862: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2863: else if (sum) ii=i;
2864: b[i]=sum;
2865: }
2866: for (i=n;i>=1;i--) {
2867: sum=b[i];
2868: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2869: b[i]=sum/a[i][i];
2870: }
2871: }
2872:
2873: void pstamp(FILE *fichier)
2874: {
2875: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2876: }
2877:
2878: /************ Frequencies ********************/
2879: 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[])
2880: { /* Some frequencies */
2881:
1.164 brouard 2882: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2883: int first;
2884: double ***freq; /* Frequencies */
2885: double *pp, **prop;
2886: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2887: char fileresp[FILENAMELENGTH];
2888:
2889: pp=vector(1,nlstate);
2890: prop=matrix(1,nlstate,iagemin,iagemax+3);
2891: strcpy(fileresp,"p");
2892: strcat(fileresp,fileres);
2893: if((ficresp=fopen(fileresp,"w"))==NULL) {
2894: printf("Problem with prevalence resultfile: %s\n", fileresp);
2895: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2896: exit(0);
2897: }
2898: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2899: j1=0;
2900:
2901: j=cptcoveff;
2902: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2903:
2904: first=1;
2905:
1.169 brouard 2906: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2907: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2908: /* j1++; */
1.145 brouard 2909: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2910: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2911: scanf("%d", i);*/
2912: for (i=-5; i<=nlstate+ndeath; i++)
2913: for (jk=-5; jk<=nlstate+ndeath; jk++)
2914: for(m=iagemin; m <= iagemax+3; m++)
2915: freq[i][jk][m]=0;
1.143 brouard 2916:
2917: for (i=1; i<=nlstate; i++)
2918: for(m=iagemin; m <= iagemax+3; m++)
2919: prop[i][m]=0;
1.126 brouard 2920:
2921: dateintsum=0;
2922: k2cpt=0;
2923: for (i=1; i<=imx; i++) {
2924: bool=1;
1.144 brouard 2925: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2926: for (z1=1; z1<=cptcoveff; z1++)
2927: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2928: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2929: bool=0;
1.145 brouard 2930: /* 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",
2931: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2932: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2933: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2934: }
1.126 brouard 2935: }
1.144 brouard 2936:
1.126 brouard 2937: if (bool==1){
2938: for(m=firstpass; m<=lastpass; m++){
2939: k2=anint[m][i]+(mint[m][i]/12.);
2940: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2941: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2942: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2943: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2944: if (m<lastpass) {
2945: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2946: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2947: }
2948:
2949: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2950: dateintsum=dateintsum+k2;
2951: k2cpt++;
2952: }
2953: /*}*/
2954: }
2955: }
1.145 brouard 2956: } /* end i */
1.126 brouard 2957:
2958: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2959: pstamp(ficresp);
2960: if (cptcovn>0) {
2961: fprintf(ficresp, "\n#********** Variable ");
2962: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2963: fprintf(ficresp, "**********\n#");
1.143 brouard 2964: fprintf(ficlog, "\n#********** Variable ");
2965: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2966: fprintf(ficlog, "**********\n#");
1.126 brouard 2967: }
2968: for(i=1; i<=nlstate;i++)
2969: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2970: fprintf(ficresp, "\n");
2971:
2972: for(i=iagemin; i <= iagemax+3; i++){
2973: if(i==iagemax+3){
2974: fprintf(ficlog,"Total");
2975: }else{
2976: if(first==1){
2977: first=0;
2978: printf("See log file for details...\n");
2979: }
2980: fprintf(ficlog,"Age %d", i);
2981: }
2982: for(jk=1; jk <=nlstate ; jk++){
2983: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2984: pp[jk] += freq[jk][m][i];
2985: }
2986: for(jk=1; jk <=nlstate ; jk++){
2987: for(m=-1, pos=0; m <=0 ; m++)
2988: pos += freq[jk][m][i];
2989: if(pp[jk]>=1.e-10){
2990: if(first==1){
1.132 brouard 2991: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2992: }
2993: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2994: }else{
2995: if(first==1)
2996: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2997: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2998: }
2999: }
3000:
3001: for(jk=1; jk <=nlstate ; jk++){
3002: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3003: pp[jk] += freq[jk][m][i];
3004: }
3005: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3006: pos += pp[jk];
3007: posprop += prop[jk][i];
3008: }
3009: for(jk=1; jk <=nlstate ; jk++){
3010: if(pos>=1.e-5){
3011: if(first==1)
3012: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3013: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3014: }else{
3015: if(first==1)
3016: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3017: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3018: }
3019: if( i <= iagemax){
3020: if(pos>=1.e-5){
3021: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3022: /*probs[i][jk][j1]= pp[jk]/pos;*/
3023: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3024: }
3025: else
3026: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3027: }
3028: }
3029:
3030: for(jk=-1; jk <=nlstate+ndeath; jk++)
3031: for(m=-1; m <=nlstate+ndeath; m++)
3032: if(freq[jk][m][i] !=0 ) {
3033: if(first==1)
3034: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3035: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3036: }
3037: if(i <= iagemax)
3038: fprintf(ficresp,"\n");
3039: if(first==1)
3040: printf("Others in log...\n");
3041: fprintf(ficlog,"\n");
3042: }
1.145 brouard 3043: /*}*/
1.126 brouard 3044: }
3045: dateintmean=dateintsum/k2cpt;
3046:
3047: fclose(ficresp);
3048: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3049: free_vector(pp,1,nlstate);
3050: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3051: /* End of Freq */
3052: }
3053:
3054: /************ Prevalence ********************/
3055: 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)
3056: {
3057: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3058: in each health status at the date of interview (if between dateprev1 and dateprev2).
3059: We still use firstpass and lastpass as another selection.
3060: */
3061:
1.164 brouard 3062: int i, m, jk, j1, bool, z1,j;
3063:
3064: double **prop;
3065: double posprop;
1.126 brouard 3066: double y2; /* in fractional years */
3067: int iagemin, iagemax;
1.145 brouard 3068: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3069:
3070: iagemin= (int) agemin;
3071: iagemax= (int) agemax;
3072: /*pp=vector(1,nlstate);*/
3073: prop=matrix(1,nlstate,iagemin,iagemax+3);
3074: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3075: j1=0;
3076:
1.145 brouard 3077: /*j=cptcoveff;*/
1.126 brouard 3078: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3079:
1.145 brouard 3080: first=1;
3081: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3082: /*for(i1=1; i1<=ncodemax[k1];i1++){
3083: j1++;*/
1.126 brouard 3084:
3085: for (i=1; i<=nlstate; i++)
3086: for(m=iagemin; m <= iagemax+3; m++)
3087: prop[i][m]=0.0;
3088:
3089: for (i=1; i<=imx; i++) { /* Each individual */
3090: bool=1;
3091: if (cptcovn>0) {
3092: for (z1=1; z1<=cptcoveff; z1++)
3093: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3094: bool=0;
3095: }
3096: if (bool==1) {
3097: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3098: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3099: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3100: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3101: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3102: 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);
3103: if (s[m][i]>0 && s[m][i]<=nlstate) {
3104: /*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]]);*/
3105: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3106: prop[s[m][i]][iagemax+3] += weight[i];
3107: }
3108: }
3109: } /* end selection of waves */
3110: }
3111: }
3112: for(i=iagemin; i <= iagemax+3; i++){
3113: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3114: posprop += prop[jk][i];
3115: }
1.145 brouard 3116:
1.126 brouard 3117: for(jk=1; jk <=nlstate ; jk++){
3118: if( i <= iagemax){
3119: if(posprop>=1.e-5){
3120: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3121: } else{
3122: if(first==1){
3123: first=0;
3124: 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]);
3125: }
3126: }
1.126 brouard 3127: }
3128: }/* end jk */
3129: }/* end i */
1.145 brouard 3130: /*} *//* end i1 */
3131: } /* end j1 */
1.126 brouard 3132:
3133: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3134: /*free_vector(pp,1,nlstate);*/
3135: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3136: } /* End of prevalence */
3137:
3138: /************* Waves Concatenation ***************/
3139:
3140: 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)
3141: {
3142: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3143: Death is a valid wave (if date is known).
3144: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3145: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3146: and mw[mi+1][i]. dh depends on stepm.
3147: */
3148:
3149: int i, mi, m;
3150: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3151: double sum=0., jmean=0.;*/
3152: int first;
3153: int j, k=0,jk, ju, jl;
3154: double sum=0.;
3155: first=0;
1.164 brouard 3156: jmin=100000;
1.126 brouard 3157: jmax=-1;
3158: jmean=0.;
3159: for(i=1; i<=imx; i++){
3160: mi=0;
3161: m=firstpass;
3162: while(s[m][i] <= nlstate){
3163: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3164: mw[++mi][i]=m;
3165: if(m >=lastpass)
3166: break;
3167: else
3168: m++;
3169: }/* end while */
3170: if (s[m][i] > nlstate){
3171: mi++; /* Death is another wave */
3172: /* if(mi==0) never been interviewed correctly before death */
3173: /* Only death is a correct wave */
3174: mw[mi][i]=m;
3175: }
3176:
3177: wav[i]=mi;
3178: if(mi==0){
3179: nbwarn++;
3180: if(first==0){
3181: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3182: first=1;
3183: }
3184: if(first==1){
3185: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3186: }
3187: } /* end mi==0 */
3188: } /* End individuals */
3189:
3190: for(i=1; i<=imx; i++){
3191: for(mi=1; mi<wav[i];mi++){
3192: if (stepm <=0)
3193: dh[mi][i]=1;
3194: else{
3195: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3196: if (agedc[i] < 2*AGESUP) {
3197: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3198: if(j==0) j=1; /* Survives at least one month after exam */
3199: else if(j<0){
3200: nberr++;
3201: 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]);
3202: j=1; /* Temporary Dangerous patch */
3203: 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);
3204: 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]);
3205: 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);
3206: }
3207: k=k+1;
3208: if (j >= jmax){
3209: jmax=j;
3210: ijmax=i;
3211: }
3212: if (j <= jmin){
3213: jmin=j;
3214: ijmin=i;
3215: }
3216: sum=sum+j;
3217: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3218: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3219: }
3220: }
3221: else{
3222: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3223: /* 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]); */
3224:
3225: k=k+1;
3226: if (j >= jmax) {
3227: jmax=j;
3228: ijmax=i;
3229: }
3230: else if (j <= jmin){
3231: jmin=j;
3232: ijmin=i;
3233: }
3234: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3235: /*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]);*/
3236: if(j<0){
3237: nberr++;
3238: 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]);
3239: 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]);
3240: }
3241: sum=sum+j;
3242: }
3243: jk= j/stepm;
3244: jl= j -jk*stepm;
3245: ju= j -(jk+1)*stepm;
3246: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3247: if(jl==0){
3248: dh[mi][i]=jk;
3249: bh[mi][i]=0;
3250: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3251: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3252: dh[mi][i]=jk+1;
3253: bh[mi][i]=ju;
3254: }
3255: }else{
3256: if(jl <= -ju){
3257: dh[mi][i]=jk;
3258: bh[mi][i]=jl; /* bias is positive if real duration
3259: * is higher than the multiple of stepm and negative otherwise.
3260: */
3261: }
3262: else{
3263: dh[mi][i]=jk+1;
3264: bh[mi][i]=ju;
3265: }
3266: if(dh[mi][i]==0){
3267: dh[mi][i]=1; /* At least one step */
3268: bh[mi][i]=ju; /* At least one step */
3269: /* 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);*/
3270: }
3271: } /* end if mle */
3272: }
3273: } /* end wave */
3274: }
3275: jmean=sum/k;
3276: 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);
1.141 brouard 3277: 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);
1.126 brouard 3278: }
3279:
3280: /*********** Tricode ****************************/
1.145 brouard 3281: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3282: {
1.144 brouard 3283: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3284: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
1.169 brouard 3285: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3286: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3287: * nbcode[Tvar[j]][1]=
1.144 brouard 3288: */
1.130 brouard 3289:
1.145 brouard 3290: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3291: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3292: int cptcode=0; /* Modality max of covariates j */
3293: int modmincovj=0; /* Modality min of covariates j */
3294:
3295:
1.126 brouard 3296: cptcoveff=0;
3297:
1.145 brouard 3298: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3299: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3300:
1.145 brouard 3301: /* Loop on covariates without age and products */
1.186 brouard 3302: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3303: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3304: modality of this covariate Vj*/
1.145 brouard 3305: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3306: * If product of Vn*Vm, still boolean *:
3307: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3308: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3309: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3310: modality of the nth covariate of individual i. */
1.145 brouard 3311: if (ij > modmaxcovj)
3312: modmaxcovj=ij;
3313: else if (ij < modmincovj)
3314: modmincovj=ij;
3315: if ((ij < -1) && (ij > NCOVMAX)){
3316: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3317: exit(1);
3318: }else
1.136 brouard 3319: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3320: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3321: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3322: /* getting the maximum value of the modality of the covariate
3323: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3324: female is 1, then modmaxcovj=1.*/
1.187 brouard 3325: } /* end for loop on individuals */
1.145 brouard 3326: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3327: cptcode=modmaxcovj;
1.137 brouard 3328: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3329: /*for (i=0; i<=cptcode; i++) {*/
3330: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
1.187 brouard 3331: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
1.145 brouard 3332: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3333: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3334: }
3335: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3336: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3337: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3338:
1.136 brouard 3339: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3340: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3341: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 3342: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3343: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3344: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3345: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3346: nbcode[Tvar[j]][ij]=k;
3347: nbcode[Tvar[j]][1]=0;
3348: nbcode[Tvar[j]][2]=1;
3349: nbcode[Tvar[j]][3]=2;
3350: */
3351: ij=1; /* ij is similar to i but can jumps over null modalities */
3352: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3353: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3354: /*recode from 0 */
1.131 brouard 3355: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
1.186 brouard 3356: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
1.131 brouard 3357: k is a modality. If we have model=V1+V1*sex
3358: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3359: ij++;
3360: }
3361: if (ij > ncodemax[j]) break;
1.137 brouard 3362: } /* end of loop on */
3363: } /* end of loop on modality */
3364: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3365:
1.145 brouard 3366: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3367:
1.187 brouard 3368: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3369: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3370: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3371: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3372: }
1.126 brouard 3373:
3374: ij=1;
1.145 brouard 3375: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3376: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3377: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3378: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3379: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3380: ij++;
1.145 brouard 3381: }else
3382: Tvaraff[ij]=0;
1.126 brouard 3383: }
1.131 brouard 3384: ij--;
1.144 brouard 3385: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3386:
1.126 brouard 3387: }
3388:
1.145 brouard 3389:
1.126 brouard 3390: /*********** Health Expectancies ****************/
3391:
1.127 brouard 3392: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 3393:
3394: {
3395: /* Health expectancies, no variances */
1.164 brouard 3396: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3397: int nhstepma, nstepma; /* Decreasing with age */
3398: double age, agelim, hf;
3399: double ***p3mat;
3400: double eip;
3401:
3402: pstamp(ficreseij);
3403: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3404: fprintf(ficreseij,"# Age");
3405: for(i=1; i<=nlstate;i++){
3406: for(j=1; j<=nlstate;j++){
3407: fprintf(ficreseij," e%1d%1d ",i,j);
3408: }
3409: fprintf(ficreseij," e%1d. ",i);
3410: }
3411: fprintf(ficreseij,"\n");
3412:
3413:
3414: if(estepm < stepm){
3415: printf ("Problem %d lower than %d\n",estepm, stepm);
3416: }
3417: else hstepm=estepm;
3418: /* We compute the life expectancy from trapezoids spaced every estepm months
3419: * This is mainly to measure the difference between two models: for example
3420: * if stepm=24 months pijx are given only every 2 years and by summing them
3421: * we are calculating an estimate of the Life Expectancy assuming a linear
3422: * progression in between and thus overestimating or underestimating according
3423: * to the curvature of the survival function. If, for the same date, we
3424: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3425: * to compare the new estimate of Life expectancy with the same linear
3426: * hypothesis. A more precise result, taking into account a more precise
3427: * curvature will be obtained if estepm is as small as stepm. */
3428:
3429: /* For example we decided to compute the life expectancy with the smallest unit */
3430: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3431: nhstepm is the number of hstepm from age to agelim
3432: nstepm is the number of stepm from age to agelin.
3433: Look at hpijx to understand the reason of that which relies in memory size
3434: and note for a fixed period like estepm months */
3435: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3436: survival function given by stepm (the optimization length). Unfortunately it
3437: means that if the survival funtion is printed only each two years of age and if
3438: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3439: results. So we changed our mind and took the option of the best precision.
3440: */
3441: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3442:
3443: agelim=AGESUP;
3444: /* If stepm=6 months */
3445: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3446: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3447:
3448: /* nhstepm age range expressed in number of stepm */
3449: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3450: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3451: /* if (stepm >= YEARM) hstepm=1;*/
3452: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3453: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3454:
3455: for (age=bage; age<=fage; age ++){
3456: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3457: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3458: /* if (stepm >= YEARM) hstepm=1;*/
3459: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3460:
3461: /* If stepm=6 months */
3462: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3463: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3464:
3465: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3466:
3467: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3468:
3469: printf("%d|",(int)age);fflush(stdout);
3470: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3471:
3472: /* Computing expectancies */
3473: for(i=1; i<=nlstate;i++)
3474: for(j=1; j<=nlstate;j++)
3475: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3476: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3477:
3478: /* 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]);*/
3479:
3480: }
3481:
3482: fprintf(ficreseij,"%3.0f",age );
3483: for(i=1; i<=nlstate;i++){
3484: eip=0;
3485: for(j=1; j<=nlstate;j++){
3486: eip +=eij[i][j][(int)age];
3487: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3488: }
3489: fprintf(ficreseij,"%9.4f", eip );
3490: }
3491: fprintf(ficreseij,"\n");
3492:
3493: }
3494: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3495: printf("\n");
3496: fprintf(ficlog,"\n");
3497:
3498: }
3499:
1.127 brouard 3500: 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[] )
1.126 brouard 3501:
3502: {
3503: /* Covariances of health expectancies eij and of total life expectancies according
3504: to initial status i, ei. .
3505: */
3506: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3507: int nhstepma, nstepma; /* Decreasing with age */
3508: double age, agelim, hf;
3509: double ***p3matp, ***p3matm, ***varhe;
3510: double **dnewm,**doldm;
3511: double *xp, *xm;
3512: double **gp, **gm;
3513: double ***gradg, ***trgradg;
3514: int theta;
3515:
3516: double eip, vip;
3517:
3518: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3519: xp=vector(1,npar);
3520: xm=vector(1,npar);
3521: dnewm=matrix(1,nlstate*nlstate,1,npar);
3522: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3523:
3524: pstamp(ficresstdeij);
3525: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3526: fprintf(ficresstdeij,"# Age");
3527: for(i=1; i<=nlstate;i++){
3528: for(j=1; j<=nlstate;j++)
3529: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3530: fprintf(ficresstdeij," e%1d. ",i);
3531: }
3532: fprintf(ficresstdeij,"\n");
3533:
3534: pstamp(ficrescveij);
3535: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3536: fprintf(ficrescveij,"# Age");
3537: for(i=1; i<=nlstate;i++)
3538: for(j=1; j<=nlstate;j++){
3539: cptj= (j-1)*nlstate+i;
3540: for(i2=1; i2<=nlstate;i2++)
3541: for(j2=1; j2<=nlstate;j2++){
3542: cptj2= (j2-1)*nlstate+i2;
3543: if(cptj2 <= cptj)
3544: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3545: }
3546: }
3547: fprintf(ficrescveij,"\n");
3548:
3549: if(estepm < stepm){
3550: printf ("Problem %d lower than %d\n",estepm, stepm);
3551: }
3552: else hstepm=estepm;
3553: /* We compute the life expectancy from trapezoids spaced every estepm months
3554: * This is mainly to measure the difference between two models: for example
3555: * if stepm=24 months pijx are given only every 2 years and by summing them
3556: * we are calculating an estimate of the Life Expectancy assuming a linear
3557: * progression in between and thus overestimating or underestimating according
3558: * to the curvature of the survival function. If, for the same date, we
3559: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3560: * to compare the new estimate of Life expectancy with the same linear
3561: * hypothesis. A more precise result, taking into account a more precise
3562: * curvature will be obtained if estepm is as small as stepm. */
3563:
3564: /* For example we decided to compute the life expectancy with the smallest unit */
3565: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3566: nhstepm is the number of hstepm from age to agelim
3567: nstepm is the number of stepm from age to agelin.
3568: Look at hpijx to understand the reason of that which relies in memory size
3569: and note for a fixed period like estepm months */
3570: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3571: survival function given by stepm (the optimization length). Unfortunately it
3572: means that if the survival funtion is printed only each two years of age and if
3573: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3574: results. So we changed our mind and took the option of the best precision.
3575: */
3576: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3577:
3578: /* If stepm=6 months */
3579: /* nhstepm age range expressed in number of stepm */
3580: agelim=AGESUP;
3581: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3582: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3583: /* if (stepm >= YEARM) hstepm=1;*/
3584: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3585:
3586: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3587: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3588: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3589: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3590: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3591: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3592:
3593: for (age=bage; age<=fage; age ++){
3594: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3595: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3596: /* if (stepm >= YEARM) hstepm=1;*/
3597: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3598:
3599: /* If stepm=6 months */
3600: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3601: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3602:
3603: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3604:
3605: /* Computing Variances of health expectancies */
3606: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3607: decrease memory allocation */
3608: for(theta=1; theta <=npar; theta++){
3609: for(i=1; i<=npar; i++){
3610: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3611: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3612: }
3613: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3614: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3615:
3616: for(j=1; j<= nlstate; j++){
3617: for(i=1; i<=nlstate; i++){
3618: for(h=0; h<=nhstepm-1; h++){
3619: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3620: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3621: }
3622: }
3623: }
3624:
3625: for(ij=1; ij<= nlstate*nlstate; ij++)
3626: for(h=0; h<=nhstepm-1; h++){
3627: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3628: }
3629: }/* End theta */
3630:
3631:
3632: for(h=0; h<=nhstepm-1; h++)
3633: for(j=1; j<=nlstate*nlstate;j++)
3634: for(theta=1; theta <=npar; theta++)
3635: trgradg[h][j][theta]=gradg[h][theta][j];
3636:
3637:
3638: for(ij=1;ij<=nlstate*nlstate;ij++)
3639: for(ji=1;ji<=nlstate*nlstate;ji++)
3640: varhe[ij][ji][(int)age] =0.;
3641:
3642: printf("%d|",(int)age);fflush(stdout);
3643: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3644: for(h=0;h<=nhstepm-1;h++){
3645: for(k=0;k<=nhstepm-1;k++){
3646: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3647: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3648: for(ij=1;ij<=nlstate*nlstate;ij++)
3649: for(ji=1;ji<=nlstate*nlstate;ji++)
3650: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3651: }
3652: }
3653:
3654: /* Computing expectancies */
3655: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3656: for(i=1; i<=nlstate;i++)
3657: for(j=1; j<=nlstate;j++)
3658: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3659: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3660:
3661: /* 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]);*/
3662:
3663: }
3664:
3665: fprintf(ficresstdeij,"%3.0f",age );
3666: for(i=1; i<=nlstate;i++){
3667: eip=0.;
3668: vip=0.;
3669: for(j=1; j<=nlstate;j++){
3670: eip += eij[i][j][(int)age];
3671: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3672: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3673: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3674: }
3675: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3676: }
3677: fprintf(ficresstdeij,"\n");
3678:
3679: fprintf(ficrescveij,"%3.0f",age );
3680: for(i=1; i<=nlstate;i++)
3681: for(j=1; j<=nlstate;j++){
3682: cptj= (j-1)*nlstate+i;
3683: for(i2=1; i2<=nlstate;i2++)
3684: for(j2=1; j2<=nlstate;j2++){
3685: cptj2= (j2-1)*nlstate+i2;
3686: if(cptj2 <= cptj)
3687: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3688: }
3689: }
3690: fprintf(ficrescveij,"\n");
3691:
3692: }
3693: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3694: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3695: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3696: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3697: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3698: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3699: printf("\n");
3700: fprintf(ficlog,"\n");
3701:
3702: free_vector(xm,1,npar);
3703: free_vector(xp,1,npar);
3704: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3705: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3706: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3707: }
3708:
3709: /************ Variance ******************/
3710: 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[])
3711: {
3712: /* Variance of health expectancies */
3713: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3714: /* double **newm;*/
1.169 brouard 3715: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3716:
3717: int movingaverage();
1.126 brouard 3718: double **dnewm,**doldm;
3719: double **dnewmp,**doldmp;
3720: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3721: int k;
1.126 brouard 3722: double *xp;
3723: double **gp, **gm; /* for var eij */
3724: double ***gradg, ***trgradg; /*for var eij */
3725: double **gradgp, **trgradgp; /* for var p point j */
3726: double *gpp, *gmp; /* for var p point j */
3727: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3728: double ***p3mat;
3729: double age,agelim, hf;
3730: double ***mobaverage;
3731: int theta;
3732: char digit[4];
3733: char digitp[25];
3734:
3735: char fileresprobmorprev[FILENAMELENGTH];
3736:
3737: if(popbased==1){
3738: if(mobilav!=0)
3739: strcpy(digitp,"-populbased-mobilav-");
3740: else strcpy(digitp,"-populbased-nomobil-");
3741: }
3742: else
3743: strcpy(digitp,"-stablbased-");
3744:
3745: if (mobilav!=0) {
3746: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3747: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3748: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3749: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3750: }
3751: }
3752:
3753: strcpy(fileresprobmorprev,"prmorprev");
3754: sprintf(digit,"%-d",ij);
3755: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3756: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3757: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3758: strcat(fileresprobmorprev,fileres);
3759: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3760: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3761: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3762: }
3763: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3764:
3765: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3766: pstamp(ficresprobmorprev);
3767: 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);
3768: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3769: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3770: fprintf(ficresprobmorprev," p.%-d SE",j);
3771: for(i=1; i<=nlstate;i++)
3772: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3773: }
3774: fprintf(ficresprobmorprev,"\n");
3775: fprintf(ficgp,"\n# Routine varevsij");
3776: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3777: 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");
3778: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3779: /* } */
3780: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3781: pstamp(ficresvij);
3782: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3783: if(popbased==1)
1.128 brouard 3784: 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);
1.126 brouard 3785: else
3786: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3787: fprintf(ficresvij,"# Age");
3788: for(i=1; i<=nlstate;i++)
3789: for(j=1; j<=nlstate;j++)
3790: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3791: fprintf(ficresvij,"\n");
3792:
3793: xp=vector(1,npar);
3794: dnewm=matrix(1,nlstate,1,npar);
3795: doldm=matrix(1,nlstate,1,nlstate);
3796: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3797: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3798:
3799: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3800: gpp=vector(nlstate+1,nlstate+ndeath);
3801: gmp=vector(nlstate+1,nlstate+ndeath);
3802: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3803:
3804: if(estepm < stepm){
3805: printf ("Problem %d lower than %d\n",estepm, stepm);
3806: }
3807: else hstepm=estepm;
3808: /* For example we decided to compute the life expectancy with the smallest unit */
3809: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3810: nhstepm is the number of hstepm from age to agelim
3811: nstepm is the number of stepm from age to agelin.
1.128 brouard 3812: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3813: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3814: survival function given by stepm (the optimization length). Unfortunately it
3815: means that if the survival funtion is printed every two years of age and if
3816: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3817: results. So we changed our mind and took the option of the best precision.
3818: */
3819: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3820: agelim = AGESUP;
3821: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3822: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3823: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3824: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3825: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3826: gp=matrix(0,nhstepm,1,nlstate);
3827: gm=matrix(0,nhstepm,1,nlstate);
3828:
3829:
3830: for(theta=1; theta <=npar; theta++){
3831: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3832: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3833: }
3834: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3835: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3836:
3837: if (popbased==1) {
3838: if(mobilav ==0){
3839: for(i=1; i<=nlstate;i++)
3840: prlim[i][i]=probs[(int)age][i][ij];
3841: }else{ /* mobilav */
3842: for(i=1; i<=nlstate;i++)
3843: prlim[i][i]=mobaverage[(int)age][i][ij];
3844: }
3845: }
3846:
3847: for(j=1; j<= nlstate; j++){
3848: for(h=0; h<=nhstepm; h++){
3849: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3850: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3851: }
3852: }
3853: /* This for computing probability of death (h=1 means
3854: computed over hstepm matrices product = hstepm*stepm months)
3855: as a weighted average of prlim.
3856: */
3857: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3858: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3859: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3860: }
3861: /* end probability of death */
3862:
3863: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3864: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3865: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3866: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3867:
3868: if (popbased==1) {
3869: if(mobilav ==0){
3870: for(i=1; i<=nlstate;i++)
3871: prlim[i][i]=probs[(int)age][i][ij];
3872: }else{ /* mobilav */
3873: for(i=1; i<=nlstate;i++)
3874: prlim[i][i]=mobaverage[(int)age][i][ij];
3875: }
3876: }
3877:
1.128 brouard 3878: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3879: for(h=0; h<=nhstepm; h++){
3880: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3881: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3882: }
3883: }
3884: /* This for computing probability of death (h=1 means
3885: computed over hstepm matrices product = hstepm*stepm months)
3886: as a weighted average of prlim.
3887: */
3888: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3889: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3890: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3891: }
3892: /* end probability of death */
3893:
3894: for(j=1; j<= nlstate; j++) /* vareij */
3895: for(h=0; h<=nhstepm; h++){
3896: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3897: }
3898:
3899: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3900: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3901: }
3902:
3903: } /* End theta */
3904:
3905: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3906:
3907: for(h=0; h<=nhstepm; h++) /* veij */
3908: for(j=1; j<=nlstate;j++)
3909: for(theta=1; theta <=npar; theta++)
3910: trgradg[h][j][theta]=gradg[h][theta][j];
3911:
3912: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3913: for(theta=1; theta <=npar; theta++)
3914: trgradgp[j][theta]=gradgp[theta][j];
3915:
3916:
3917: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3918: for(i=1;i<=nlstate;i++)
3919: for(j=1;j<=nlstate;j++)
3920: vareij[i][j][(int)age] =0.;
3921:
3922: for(h=0;h<=nhstepm;h++){
3923: for(k=0;k<=nhstepm;k++){
3924: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3925: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3926: for(i=1;i<=nlstate;i++)
3927: for(j=1;j<=nlstate;j++)
3928: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3929: }
3930: }
3931:
3932: /* pptj */
3933: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3934: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3935: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3936: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3937: varppt[j][i]=doldmp[j][i];
3938: /* end ppptj */
3939: /* x centered again */
3940: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3941: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3942:
3943: if (popbased==1) {
3944: if(mobilav ==0){
3945: for(i=1; i<=nlstate;i++)
3946: prlim[i][i]=probs[(int)age][i][ij];
3947: }else{ /* mobilav */
3948: for(i=1; i<=nlstate;i++)
3949: prlim[i][i]=mobaverage[(int)age][i][ij];
3950: }
3951: }
3952:
3953: /* This for computing probability of death (h=1 means
3954: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3955: as a weighted average of prlim.
3956: */
3957: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3958: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3959: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3960: }
3961: /* end probability of death */
3962:
3963: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3964: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3965: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3966: for(i=1; i<=nlstate;i++){
3967: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3968: }
3969: }
3970: fprintf(ficresprobmorprev,"\n");
3971:
3972: fprintf(ficresvij,"%.0f ",age );
3973: for(i=1; i<=nlstate;i++)
3974: for(j=1; j<=nlstate;j++){
3975: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3976: }
3977: fprintf(ficresvij,"\n");
3978: free_matrix(gp,0,nhstepm,1,nlstate);
3979: free_matrix(gm,0,nhstepm,1,nlstate);
3980: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3981: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3982: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3983: } /* End age */
3984: free_vector(gpp,nlstate+1,nlstate+ndeath);
3985: free_vector(gmp,nlstate+1,nlstate+ndeath);
3986: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3987: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3988: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3989: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3990: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3991: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3992: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3993: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3994: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3995: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3996: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3997: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3998: 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);
3999: /* 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);
4000: */
4001: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4002: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4003:
4004: free_vector(xp,1,npar);
4005: free_matrix(doldm,1,nlstate,1,nlstate);
4006: free_matrix(dnewm,1,nlstate,1,npar);
4007: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4008: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4009: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4010: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4011: fclose(ficresprobmorprev);
4012: fflush(ficgp);
4013: fflush(fichtm);
4014: } /* end varevsij */
4015:
4016: /************ Variance of prevlim ******************/
4017: 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[])
4018: {
4019: /* Variance of prevalence limit */
4020: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4021:
1.126 brouard 4022: double **dnewm,**doldm;
4023: int i, j, nhstepm, hstepm;
4024: double *xp;
4025: double *gp, *gm;
4026: double **gradg, **trgradg;
4027: double age,agelim;
4028: int theta;
4029:
4030: pstamp(ficresvpl);
4031: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4032: fprintf(ficresvpl,"# Age");
4033: for(i=1; i<=nlstate;i++)
4034: fprintf(ficresvpl," %1d-%1d",i,i);
4035: fprintf(ficresvpl,"\n");
4036:
4037: xp=vector(1,npar);
4038: dnewm=matrix(1,nlstate,1,npar);
4039: doldm=matrix(1,nlstate,1,nlstate);
4040:
4041: hstepm=1*YEARM; /* Every year of age */
4042: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4043: agelim = AGESUP;
4044: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4045: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4046: if (stepm >= YEARM) hstepm=1;
4047: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4048: gradg=matrix(1,npar,1,nlstate);
4049: gp=vector(1,nlstate);
4050: gm=vector(1,nlstate);
4051:
4052: for(theta=1; theta <=npar; theta++){
4053: for(i=1; i<=npar; i++){ /* Computes gradient */
4054: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4055: }
4056: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4057: for(i=1;i<=nlstate;i++)
4058: gp[i] = prlim[i][i];
4059:
4060: for(i=1; i<=npar; i++) /* Computes gradient */
4061: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4062: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4063: for(i=1;i<=nlstate;i++)
4064: gm[i] = prlim[i][i];
4065:
4066: for(i=1;i<=nlstate;i++)
4067: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4068: } /* End theta */
4069:
4070: trgradg =matrix(1,nlstate,1,npar);
4071:
4072: for(j=1; j<=nlstate;j++)
4073: for(theta=1; theta <=npar; theta++)
4074: trgradg[j][theta]=gradg[theta][j];
4075:
4076: for(i=1;i<=nlstate;i++)
4077: varpl[i][(int)age] =0.;
4078: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4079: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4080: for(i=1;i<=nlstate;i++)
4081: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4082:
4083: fprintf(ficresvpl,"%.0f ",age );
4084: for(i=1; i<=nlstate;i++)
4085: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4086: fprintf(ficresvpl,"\n");
4087: free_vector(gp,1,nlstate);
4088: free_vector(gm,1,nlstate);
4089: free_matrix(gradg,1,npar,1,nlstate);
4090: free_matrix(trgradg,1,nlstate,1,npar);
4091: } /* End age */
4092:
4093: free_vector(xp,1,npar);
4094: free_matrix(doldm,1,nlstate,1,npar);
4095: free_matrix(dnewm,1,nlstate,1,nlstate);
4096:
4097: }
4098:
4099: /************ Variance of one-step probabilities ******************/
4100: 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[])
4101: {
1.164 brouard 4102: int i, j=0, k1, l1, tj;
1.126 brouard 4103: int k2, l2, j1, z1;
1.164 brouard 4104: int k=0, l;
1.145 brouard 4105: int first=1, first1, first2;
1.126 brouard 4106: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4107: double **dnewm,**doldm;
4108: double *xp;
4109: double *gp, *gm;
4110: double **gradg, **trgradg;
4111: double **mu;
1.164 brouard 4112: double age, cov[NCOVMAX+1];
1.126 brouard 4113: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4114: int theta;
4115: char fileresprob[FILENAMELENGTH];
4116: char fileresprobcov[FILENAMELENGTH];
4117: char fileresprobcor[FILENAMELENGTH];
4118: double ***varpij;
4119:
4120: strcpy(fileresprob,"prob");
4121: strcat(fileresprob,fileres);
4122: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4123: printf("Problem with resultfile: %s\n", fileresprob);
4124: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4125: }
4126: strcpy(fileresprobcov,"probcov");
4127: strcat(fileresprobcov,fileres);
4128: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4129: printf("Problem with resultfile: %s\n", fileresprobcov);
4130: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4131: }
4132: strcpy(fileresprobcor,"probcor");
4133: strcat(fileresprobcor,fileres);
4134: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4135: printf("Problem with resultfile: %s\n", fileresprobcor);
4136: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4137: }
4138: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4139: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4140: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4141: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4142: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4143: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4144: pstamp(ficresprob);
4145: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4146: fprintf(ficresprob,"# Age");
4147: pstamp(ficresprobcov);
4148: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4149: fprintf(ficresprobcov,"# Age");
4150: pstamp(ficresprobcor);
4151: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4152: fprintf(ficresprobcor,"# Age");
4153:
4154:
4155: for(i=1; i<=nlstate;i++)
4156: for(j=1; j<=(nlstate+ndeath);j++){
4157: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4158: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4159: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4160: }
4161: /* fprintf(ficresprob,"\n");
4162: fprintf(ficresprobcov,"\n");
4163: fprintf(ficresprobcor,"\n");
4164: */
1.131 brouard 4165: xp=vector(1,npar);
1.126 brouard 4166: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4167: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4168: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4169: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4170: first=1;
4171: fprintf(ficgp,"\n# Routine varprob");
4172: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4173: fprintf(fichtm,"\n");
4174:
4175: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4176: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4177: file %s<br>\n",optionfilehtmcov);
4178: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4179: and drawn. It helps understanding how is the covariance between two incidences.\
4180: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4181: 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. \
4182: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4183: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4184: standard deviations wide on each axis. <br>\
4185: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4186: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4187: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4188:
4189: cov[1]=1;
1.145 brouard 4190: /* tj=cptcoveff; */
4191: tj = (int) pow(2,cptcoveff);
1.126 brouard 4192: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4193: j1=0;
1.145 brouard 4194: for(j1=1; j1<=tj;j1++){
4195: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4196: /*j1++;*/
1.126 brouard 4197: if (cptcovn>0) {
4198: fprintf(ficresprob, "\n#********** Variable ");
4199: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4200: fprintf(ficresprob, "**********\n#\n");
4201: fprintf(ficresprobcov, "\n#********** Variable ");
4202: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4203: fprintf(ficresprobcov, "**********\n#\n");
4204:
4205: fprintf(ficgp, "\n#********** Variable ");
4206: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4207: fprintf(ficgp, "**********\n#\n");
4208:
4209:
4210: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4211: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4212: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4213:
4214: fprintf(ficresprobcor, "\n#********** Variable ");
4215: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4216: fprintf(ficresprobcor, "**********\n#");
4217: }
4218:
1.145 brouard 4219: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4220: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4221: gp=vector(1,(nlstate)*(nlstate+ndeath));
4222: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4223: for (age=bage; age<=fage; age ++){
4224: cov[2]=age;
1.187 brouard 4225: if(nagesqr==1)
4226: cov[3]= age*age;
1.126 brouard 4227: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4228: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4229: * 1 1 1 1 1
4230: * 2 2 1 1 1
4231: * 3 1 2 1 1
4232: */
4233: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4234: }
1.186 brouard 4235: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4236: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4237: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4238: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 4239:
4240:
4241: for(theta=1; theta <=npar; theta++){
4242: for(i=1; i<=npar; i++)
4243: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4244:
4245: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4246:
4247: k=0;
4248: for(i=1; i<= (nlstate); i++){
4249: for(j=1; j<=(nlstate+ndeath);j++){
4250: k=k+1;
4251: gp[k]=pmmij[i][j];
4252: }
4253: }
4254:
4255: for(i=1; i<=npar; i++)
4256: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4257:
4258: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4259: k=0;
4260: for(i=1; i<=(nlstate); i++){
4261: for(j=1; j<=(nlstate+ndeath);j++){
4262: k=k+1;
4263: gm[k]=pmmij[i][j];
4264: }
4265: }
4266:
4267: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4268: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4269: }
4270:
4271: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4272: for(theta=1; theta <=npar; theta++)
4273: trgradg[j][theta]=gradg[theta][j];
4274:
4275: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4276: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4277:
4278: pmij(pmmij,cov,ncovmodel,x,nlstate);
4279:
4280: k=0;
4281: for(i=1; i<=(nlstate); i++){
4282: for(j=1; j<=(nlstate+ndeath);j++){
4283: k=k+1;
4284: mu[k][(int) age]=pmmij[i][j];
4285: }
4286: }
4287: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4288: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4289: varpij[i][j][(int)age] = doldm[i][j];
4290:
4291: /*printf("\n%d ",(int)age);
4292: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4293: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4294: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4295: }*/
4296:
4297: fprintf(ficresprob,"\n%d ",(int)age);
4298: fprintf(ficresprobcov,"\n%d ",(int)age);
4299: fprintf(ficresprobcor,"\n%d ",(int)age);
4300:
4301: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4302: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4303: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4304: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4305: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4306: }
4307: i=0;
4308: for (k=1; k<=(nlstate);k++){
4309: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4310: i++;
1.126 brouard 4311: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4312: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4313: for (j=1; j<=i;j++){
1.145 brouard 4314: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4315: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4316: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4317: }
4318: }
4319: }/* end of loop for state */
4320: } /* end of loop for age */
1.145 brouard 4321: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4322: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4323: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4324: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4325:
1.126 brouard 4326: /* Confidence intervalle of pij */
4327: /*
1.131 brouard 4328: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4329: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4330: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4331: 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);
4332: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4333: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4334: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4335: */
4336:
4337: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4338: first1=1;first2=2;
1.126 brouard 4339: for (k2=1; k2<=(nlstate);k2++){
4340: for (l2=1; l2<=(nlstate+ndeath);l2++){
4341: if(l2==k2) continue;
4342: j=(k2-1)*(nlstate+ndeath)+l2;
4343: for (k1=1; k1<=(nlstate);k1++){
4344: for (l1=1; l1<=(nlstate+ndeath);l1++){
4345: if(l1==k1) continue;
4346: i=(k1-1)*(nlstate+ndeath)+l1;
4347: if(i<=j) continue;
4348: for (age=bage; age<=fage; age ++){
4349: if ((int)age %5==0){
4350: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4351: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4352: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4353: mu1=mu[i][(int) age]/stepm*YEARM ;
4354: mu2=mu[j][(int) age]/stepm*YEARM;
4355: c12=cv12/sqrt(v1*v2);
4356: /* Computing eigen value of matrix of covariance */
4357: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4358: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4359: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4360: if(first2==1){
4361: first1=0;
4362: 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);
4363: }
4364: 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);
4365: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4366: /* lc2=fabs(lc2); */
1.135 brouard 4367: }
4368:
1.126 brouard 4369: /* Eigen vectors */
4370: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4371: /*v21=sqrt(1.-v11*v11); *//* error */
4372: v21=(lc1-v1)/cv12*v11;
4373: v12=-v21;
4374: v22=v11;
4375: tnalp=v21/v11;
4376: if(first1==1){
4377: first1=0;
4378: 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);
4379: }
4380: 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);
4381: /*printf(fignu*/
4382: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4383: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4384: if(first==1){
4385: first=0;
4386: fprintf(ficgp,"\nset parametric;unset label");
4387: 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);
1.145 brouard 4388: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4389: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4390: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4391: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4392: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4393: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4394: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4395: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4396: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4397: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4398: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4399: 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",\
4400: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4401: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4402: }else{
4403: first=0;
4404: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4405: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4406: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4407: 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",\
4408: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4409: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4410: }/* if first */
4411: } /* age mod 5 */
4412: } /* end loop age */
4413: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4414: first=1;
4415: } /*l12 */
4416: } /* k12 */
4417: } /*l1 */
4418: }/* k1 */
1.169 brouard 4419: /* } */ /* loop covariates */
1.126 brouard 4420: }
4421: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4422: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4423: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4424: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4425: free_vector(xp,1,npar);
4426: fclose(ficresprob);
4427: fclose(ficresprobcov);
4428: fclose(ficresprobcor);
4429: fflush(ficgp);
4430: fflush(fichtmcov);
4431: }
4432:
4433:
4434: /******************* Printing html file ***********/
4435: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4436: int lastpass, int stepm, int weightopt, char model[],\
4437: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4438: int popforecast, int estepm ,\
4439: double jprev1, double mprev1,double anprev1, \
4440: double jprev2, double mprev2,double anprev2){
4441: int jj1, k1, i1, cpt;
4442:
4443: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4444: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4445: </ul>");
4446: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4447: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4448: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4449: fprintf(fichtm,"\
4450: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4451: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4452: fprintf(fichtm,"\
4453: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4454: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4455: fprintf(fichtm,"\
1.128 brouard 4456: - (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): \
1.126 brouard 4457: <a href=\"%s\">%s</a> <br>\n",
4458: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4459: fprintf(fichtm,"\
4460: - Population projections by age and states: \
4461: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4462:
4463: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4464:
1.145 brouard 4465: m=pow(2,cptcoveff);
1.126 brouard 4466: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4467:
4468: jj1=0;
4469: for(k1=1; k1<=m;k1++){
4470: for(i1=1; i1<=ncodemax[k1];i1++){
4471: jj1++;
4472: if (cptcovn > 0) {
4473: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4474: for (cpt=1; cpt<=cptcoveff;cpt++)
4475: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4476: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4477: }
4478: /* Pij */
1.145 brouard 4479: 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> \
4480: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4481: /* Quasi-incidences */
4482: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4483: 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> \
4484: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4485: /* Period (stable) prevalence in each health state */
1.154 brouard 4486: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4487: 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> \
4488: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4489: }
4490: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4491: 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> \
4492: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4493: }
4494: } /* end i1 */
4495: }/* End k1 */
4496: fprintf(fichtm,"</ul>");
4497:
4498:
4499: fprintf(fichtm,"\
4500: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4501: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4502:
4503: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4504: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4505: fprintf(fichtm,"\
4506: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4507: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4508:
4509: fprintf(fichtm,"\
4510: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4511: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4512: fprintf(fichtm,"\
4513: - 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): \
4514: <a href=\"%s\">%s</a> <br>\n</li>",
4515: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4516: fprintf(fichtm,"\
4517: - (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): \
4518: <a href=\"%s\">%s</a> <br>\n</li>",
4519: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4520: fprintf(fichtm,"\
1.128 brouard 4521: - 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",
1.126 brouard 4522: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4523: fprintf(fichtm,"\
1.128 brouard 4524: - 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",
4525: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4526: fprintf(fichtm,"\
4527: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4528: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4529:
4530: /* if(popforecast==1) fprintf(fichtm,"\n */
4531: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4532: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4533: /* <br>",fileres,fileres,fileres,fileres); */
4534: /* else */
4535: /* 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); */
4536: fflush(fichtm);
4537: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4538:
1.145 brouard 4539: m=pow(2,cptcoveff);
1.126 brouard 4540: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4541:
4542: jj1=0;
4543: for(k1=1; k1<=m;k1++){
4544: for(i1=1; i1<=ncodemax[k1];i1++){
4545: jj1++;
4546: if (cptcovn > 0) {
4547: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4548: for (cpt=1; cpt<=cptcoveff;cpt++)
4549: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4550: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4551: }
4552: for(cpt=1; cpt<=nlstate;cpt++) {
4553: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4554: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4555: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4556: }
4557: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4558: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4559: true period expectancies (those weighted with period prevalences are also\
4560: drawn in addition to the population based expectancies computed using\
4561: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4562: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4563: } /* end i1 */
4564: }/* End k1 */
4565: fprintf(fichtm,"</ul>");
4566: fflush(fichtm);
4567: }
4568:
4569: /******************* Gnuplot file **************/
4570: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4571:
4572: char dirfileres[132],optfileres[132];
1.164 brouard 4573: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4574: int ng=0;
1.126 brouard 4575: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4576: /* printf("Problem with file %s",optionfilegnuplot); */
4577: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4578: /* } */
4579:
4580: /*#ifdef windows */
4581: fprintf(ficgp,"cd \"%s\" \n",pathc);
4582: /*#endif */
4583: m=pow(2,cptcoveff);
4584:
4585: strcpy(dirfileres,optionfilefiname);
4586: strcpy(optfileres,"vpl");
4587: /* 1eme*/
1.153 brouard 4588: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4589: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4590: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4591: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4592: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4593: fprintf(ficgp,"set xlabel \"Age\" \n\
4594: set ylabel \"Probability\" \n\
1.145 brouard 4595: set ter png small size 320, 240\n\
1.170 brouard 4596: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4597:
4598: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4599: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4600: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4601: }
1.170 brouard 4602: 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);
1.126 brouard 4603: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4604: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4605: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4606: }
1.170 brouard 4607: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4608: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4609: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4610: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4611: }
1.145 brouard 4612: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4613: }
4614: }
4615: /*2 eme*/
1.153 brouard 4616: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4617: for (k1=1; k1<= m ; k1 ++) {
4618: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4619: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4620:
4621: for (i=1; i<= nlstate+1 ; i ++) {
4622: k=2*i;
1.170 brouard 4623: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4624: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4625: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4626: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4627: }
4628: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4629: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4630: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4631: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4632: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4633: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4634: }
1.145 brouard 4635: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4636: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4637: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4638: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4639: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4640: }
1.145 brouard 4641: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4642: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4643: }
4644: }
4645:
4646: /*3eme*/
4647:
4648: for (k1=1; k1<= m ; k1 ++) {
4649: for (cpt=1; cpt<= nlstate ; cpt ++) {
4650: /* k=2+nlstate*(2*cpt-2); */
4651: k=2+(nlstate+1)*(cpt-1);
4652: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4653: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4654: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4655: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4656: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4657: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4658: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4659: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4660: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4661:
4662: */
4663: for (i=1; i< nlstate ; i ++) {
4664: 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);
4665: /* 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);*/
4666:
4667: }
4668: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4669: }
4670: }
4671:
4672: /* CV preval stable (period) */
1.153 brouard 4673: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4674: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4675: k=3;
1.153 brouard 4676: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4677: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4678: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4679: set ter png small size 320, 240\n\
1.126 brouard 4680: unset log y\n\
1.153 brouard 4681: plot [%.f:%.f] ", ageminpar, agemaxpar);
4682: for (i=1; i<= nlstate ; i ++){
4683: if(i==1)
4684: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4685: else
4686: fprintf(ficgp,", '' ");
1.154 brouard 4687: l=(nlstate+ndeath)*(i-1)+1;
4688: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4689: for (j=1; j<= (nlstate-1) ; j ++)
4690: fprintf(ficgp,"+$%d",k+l+j);
4691: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4692: } /* nlstate */
4693: fprintf(ficgp,"\n");
4694: } /* end cpt state*/
4695: } /* end covariate */
1.126 brouard 4696:
4697: /* proba elementaires */
1.187 brouard 4698: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4699: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4700: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4701: for(k=1; k <=(nlstate+ndeath); k++){
4702: if (k != i) {
1.187 brouard 4703: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4704: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4705: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4706: jk++;
4707: }
1.187 brouard 4708: fprintf(ficgp,"\n");
1.126 brouard 4709: }
4710: }
4711: }
1.187 brouard 4712: fprintf(ficgp,"##############\n#\n");
4713:
1.145 brouard 4714: /*goto avoid;*/
1.187 brouard 4715: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4716: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4717: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4718: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4719: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4720: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4721: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4722: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4723: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4724: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4725: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4726: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4727: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4728: fprintf(ficgp,"#\n");
1.126 brouard 4729: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4730: fprintf(ficgp,"# ng=%d\n",ng);
4731: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4732: for(jk=1; jk <=m; jk++) {
1.187 brouard 4733: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4734: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4735: if (ng==2)
4736: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4737: else
4738: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4739: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4740: i=1;
4741: for(k2=1; k2<=nlstate; k2++) {
4742: k3=i;
4743: for(k=1; k<=(nlstate+ndeath); k++) {
4744: if (k != k2){
4745: if(ng==2)
1.187 brouard 4746: if(nagesqr==0)
4747: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4748: else /* nagesqr =1 */
4749: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4750: else
1.187 brouard 4751: if(nagesqr==0)
4752: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4753: else /* nagesqr =1 */
4754: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4755: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4756: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4757: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 brouard 4758: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4759: ij++;
4760: }
4761: else
1.187 brouard 4762: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4763: }
4764: fprintf(ficgp,")/(1");
4765:
1.187 brouard 4766: for(k1=1; k1 <=nlstate; k1++){
4767: if(nagesqr==0)
4768: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4769: else /* nagesqr =1 */
4770: 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);
4771:
1.126 brouard 4772: ij=1;
1.187 brouard 4773: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4774: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 brouard 4775: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4776: ij++;
4777: }
4778: else
1.187 brouard 4779: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4780: }
4781: fprintf(ficgp,")");
4782: }
4783: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4784: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4785: i=i+ncovmodel;
4786: }
4787: } /* end k */
4788: } /* end k2 */
4789: } /* end jk */
4790: } /* end ng */
1.164 brouard 4791: /* avoid: */
1.126 brouard 4792: fflush(ficgp);
4793: } /* end gnuplot */
4794:
4795:
4796: /*************** Moving average **************/
4797: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4798:
4799: int i, cpt, cptcod;
4800: int modcovmax =1;
4801: int mobilavrange, mob;
4802: double age;
4803:
4804: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4805: a covariate has 2 modalities */
4806: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4807:
4808: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4809: if(mobilav==1) mobilavrange=5; /* default */
4810: else mobilavrange=mobilav;
4811: for (age=bage; age<=fage; age++)
4812: for (i=1; i<=nlstate;i++)
4813: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4814: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4815: /* We keep the original values on the extreme ages bage, fage and for
4816: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4817: we use a 5 terms etc. until the borders are no more concerned.
4818: */
4819: for (mob=3;mob <=mobilavrange;mob=mob+2){
4820: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4821: for (i=1; i<=nlstate;i++){
4822: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4823: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4824: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4825: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4826: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4827: }
4828: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4829: }
4830: }
4831: }/* end age */
4832: }/* end mob */
4833: }else return -1;
4834: return 0;
4835: }/* End movingaverage */
4836:
4837:
4838: /************** Forecasting ******************/
1.169 brouard 4839: 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){
1.126 brouard 4840: /* proj1, year, month, day of starting projection
4841: agemin, agemax range of age
4842: dateprev1 dateprev2 range of dates during which prevalence is computed
4843: anproj2 year of en of projection (same day and month as proj1).
4844: */
1.164 brouard 4845: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4846: double agec; /* generic age */
4847: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4848: double *popeffectif,*popcount;
4849: double ***p3mat;
4850: double ***mobaverage;
4851: char fileresf[FILENAMELENGTH];
4852:
4853: agelim=AGESUP;
4854: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4855:
4856: strcpy(fileresf,"f");
4857: strcat(fileresf,fileres);
4858: if((ficresf=fopen(fileresf,"w"))==NULL) {
4859: printf("Problem with forecast resultfile: %s\n", fileresf);
4860: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4861: }
4862: printf("Computing forecasting: result on file '%s' \n", fileresf);
4863: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4864:
4865: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4866:
4867: if (mobilav!=0) {
4868: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4869: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4870: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4871: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4872: }
4873: }
4874:
4875: stepsize=(int) (stepm+YEARM-1)/YEARM;
4876: if (stepm<=12) stepsize=1;
4877: if(estepm < stepm){
4878: printf ("Problem %d lower than %d\n",estepm, stepm);
4879: }
4880: else hstepm=estepm;
4881:
4882: hstepm=hstepm/stepm;
4883: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4884: fractional in yp1 */
4885: anprojmean=yp;
4886: yp2=modf((yp1*12),&yp);
4887: mprojmean=yp;
4888: yp1=modf((yp2*30.5),&yp);
4889: jprojmean=yp;
4890: if(jprojmean==0) jprojmean=1;
4891: if(mprojmean==0) jprojmean=1;
4892:
4893: i1=cptcoveff;
4894: if (cptcovn < 1){i1=1;}
4895:
4896: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4897:
4898: fprintf(ficresf,"#****** Routine prevforecast **\n");
4899:
4900: /* if (h==(int)(YEARM*yearp)){ */
4901: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4902: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4903: k=k+1;
4904: fprintf(ficresf,"\n#******");
4905: for(j=1;j<=cptcoveff;j++) {
4906: 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]]);
4907: }
4908: fprintf(ficresf,"******\n");
4909: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4910: for(j=1; j<=nlstate+ndeath;j++){
4911: for(i=1; i<=nlstate;i++)
4912: fprintf(ficresf," p%d%d",i,j);
4913: fprintf(ficresf," p.%d",j);
4914: }
4915: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4916: fprintf(ficresf,"\n");
4917: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4918:
4919: for (agec=fage; agec>=(ageminpar-1); agec--){
4920: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4921: nhstepm = nhstepm/hstepm;
4922: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4923: oldm=oldms;savm=savms;
4924: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4925:
4926: for (h=0; h<=nhstepm; h++){
4927: if (h*hstepm/YEARM*stepm ==yearp) {
4928: fprintf(ficresf,"\n");
4929: for(j=1;j<=cptcoveff;j++)
4930: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4931: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4932: }
4933: for(j=1; j<=nlstate+ndeath;j++) {
4934: ppij=0.;
4935: for(i=1; i<=nlstate;i++) {
4936: if (mobilav==1)
4937: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4938: else {
4939: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4940: }
4941: if (h*hstepm/YEARM*stepm== yearp) {
4942: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4943: }
4944: } /* end i */
4945: if (h*hstepm/YEARM*stepm==yearp) {
4946: fprintf(ficresf," %.3f", ppij);
4947: }
4948: }/* end j */
4949: } /* end h */
4950: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4951: } /* end agec */
4952: } /* end yearp */
4953: } /* end cptcod */
4954: } /* end cptcov */
4955:
4956: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4957:
4958: fclose(ficresf);
4959: }
4960:
4961: /************** Forecasting *****not tested NB*************/
1.169 brouard 4962: 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){
1.126 brouard 4963:
4964: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4965: int *popage;
4966: double calagedatem, agelim, kk1, kk2;
4967: double *popeffectif,*popcount;
4968: double ***p3mat,***tabpop,***tabpopprev;
4969: double ***mobaverage;
4970: char filerespop[FILENAMELENGTH];
4971:
4972: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4973: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4974: agelim=AGESUP;
4975: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4976:
4977: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4978:
4979:
4980: strcpy(filerespop,"pop");
4981: strcat(filerespop,fileres);
4982: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4983: printf("Problem with forecast resultfile: %s\n", filerespop);
4984: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4985: }
4986: printf("Computing forecasting: result on file '%s' \n", filerespop);
4987: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4988:
4989: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4990:
4991: if (mobilav!=0) {
4992: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4993: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4994: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4995: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4996: }
4997: }
4998:
4999: stepsize=(int) (stepm+YEARM-1)/YEARM;
5000: if (stepm<=12) stepsize=1;
5001:
5002: agelim=AGESUP;
5003:
5004: hstepm=1;
5005: hstepm=hstepm/stepm;
5006:
5007: if (popforecast==1) {
5008: if((ficpop=fopen(popfile,"r"))==NULL) {
5009: printf("Problem with population file : %s\n",popfile);exit(0);
5010: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5011: }
5012: popage=ivector(0,AGESUP);
5013: popeffectif=vector(0,AGESUP);
5014: popcount=vector(0,AGESUP);
5015:
5016: i=1;
5017: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5018:
5019: imx=i;
5020: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5021: }
5022:
5023: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5024: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5025: k=k+1;
5026: fprintf(ficrespop,"\n#******");
5027: for(j=1;j<=cptcoveff;j++) {
5028: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5029: }
5030: fprintf(ficrespop,"******\n");
5031: fprintf(ficrespop,"# Age");
5032: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5033: if (popforecast==1) fprintf(ficrespop," [Population]");
5034:
5035: for (cpt=0; cpt<=0;cpt++) {
5036: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5037:
5038: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5039: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5040: nhstepm = nhstepm/hstepm;
5041:
5042: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5043: oldm=oldms;savm=savms;
5044: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5045:
5046: for (h=0; h<=nhstepm; h++){
5047: if (h==(int) (calagedatem+YEARM*cpt)) {
5048: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5049: }
5050: for(j=1; j<=nlstate+ndeath;j++) {
5051: kk1=0.;kk2=0;
5052: for(i=1; i<=nlstate;i++) {
5053: if (mobilav==1)
5054: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5055: else {
5056: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5057: }
5058: }
5059: if (h==(int)(calagedatem+12*cpt)){
5060: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5061: /*fprintf(ficrespop," %.3f", kk1);
5062: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5063: }
5064: }
5065: for(i=1; i<=nlstate;i++){
5066: kk1=0.;
5067: for(j=1; j<=nlstate;j++){
5068: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5069: }
5070: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5071: }
5072:
5073: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5074: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5075: }
5076: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5077: }
5078: }
5079:
5080: /******/
5081:
5082: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5083: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5084: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5085: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5086: nhstepm = nhstepm/hstepm;
5087:
5088: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5089: oldm=oldms;savm=savms;
5090: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5091: for (h=0; h<=nhstepm; h++){
5092: if (h==(int) (calagedatem+YEARM*cpt)) {
5093: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5094: }
5095: for(j=1; j<=nlstate+ndeath;j++) {
5096: kk1=0.;kk2=0;
5097: for(i=1; i<=nlstate;i++) {
5098: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5099: }
5100: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5101: }
5102: }
5103: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5104: }
5105: }
5106: }
5107: }
5108:
5109: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5110:
5111: if (popforecast==1) {
5112: free_ivector(popage,0,AGESUP);
5113: free_vector(popeffectif,0,AGESUP);
5114: free_vector(popcount,0,AGESUP);
5115: }
5116: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5117: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5118: fclose(ficrespop);
5119: } /* End of popforecast */
5120:
5121: int fileappend(FILE *fichier, char *optionfich)
5122: {
5123: if((fichier=fopen(optionfich,"a"))==NULL) {
5124: printf("Problem with file: %s\n", optionfich);
5125: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5126: return (0);
5127: }
5128: fflush(fichier);
5129: return (1);
5130: }
5131:
5132:
5133: /**************** function prwizard **********************/
5134: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5135: {
5136:
5137: /* Wizard to print covariance matrix template */
5138:
1.164 brouard 5139: char ca[32], cb[32];
5140: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5141: int numlinepar;
5142:
5143: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5144: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5145: for(i=1; i <=nlstate; i++){
5146: jj=0;
5147: for(j=1; j <=nlstate+ndeath; j++){
5148: if(j==i) continue;
5149: jj++;
5150: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5151: printf("%1d%1d",i,j);
5152: fprintf(ficparo,"%1d%1d",i,j);
5153: for(k=1; k<=ncovmodel;k++){
5154: /* printf(" %lf",param[i][j][k]); */
5155: /* fprintf(ficparo," %lf",param[i][j][k]); */
5156: printf(" 0.");
5157: fprintf(ficparo," 0.");
5158: }
5159: printf("\n");
5160: fprintf(ficparo,"\n");
5161: }
5162: }
5163: printf("# Scales (for hessian or gradient estimation)\n");
5164: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5165: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5166: for(i=1; i <=nlstate; i++){
5167: jj=0;
5168: for(j=1; j <=nlstate+ndeath; j++){
5169: if(j==i) continue;
5170: jj++;
5171: fprintf(ficparo,"%1d%1d",i,j);
5172: printf("%1d%1d",i,j);
5173: fflush(stdout);
5174: for(k=1; k<=ncovmodel;k++){
5175: /* printf(" %le",delti3[i][j][k]); */
5176: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5177: printf(" 0.");
5178: fprintf(ficparo," 0.");
5179: }
5180: numlinepar++;
5181: printf("\n");
5182: fprintf(ficparo,"\n");
5183: }
5184: }
5185: printf("# Covariance matrix\n");
5186: /* # 121 Var(a12)\n\ */
5187: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5188: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5189: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5190: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5191: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5192: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5193: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5194: fflush(stdout);
5195: fprintf(ficparo,"# Covariance matrix\n");
5196: /* # 121 Var(a12)\n\ */
5197: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5198: /* # ...\n\ */
5199: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5200:
5201: for(itimes=1;itimes<=2;itimes++){
5202: jj=0;
5203: for(i=1; i <=nlstate; i++){
5204: for(j=1; j <=nlstate+ndeath; j++){
5205: if(j==i) continue;
5206: for(k=1; k<=ncovmodel;k++){
5207: jj++;
5208: ca[0]= k+'a'-1;ca[1]='\0';
5209: if(itimes==1){
5210: printf("#%1d%1d%d",i,j,k);
5211: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5212: }else{
5213: printf("%1d%1d%d",i,j,k);
5214: fprintf(ficparo,"%1d%1d%d",i,j,k);
5215: /* printf(" %.5le",matcov[i][j]); */
5216: }
5217: ll=0;
5218: for(li=1;li <=nlstate; li++){
5219: for(lj=1;lj <=nlstate+ndeath; lj++){
5220: if(lj==li) continue;
5221: for(lk=1;lk<=ncovmodel;lk++){
5222: ll++;
5223: if(ll<=jj){
5224: cb[0]= lk +'a'-1;cb[1]='\0';
5225: if(ll<jj){
5226: if(itimes==1){
5227: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5228: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5229: }else{
5230: printf(" 0.");
5231: fprintf(ficparo," 0.");
5232: }
5233: }else{
5234: if(itimes==1){
5235: printf(" Var(%s%1d%1d)",ca,i,j);
5236: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5237: }else{
5238: printf(" 0.");
5239: fprintf(ficparo," 0.");
5240: }
5241: }
5242: }
5243: } /* end lk */
5244: } /* end lj */
5245: } /* end li */
5246: printf("\n");
5247: fprintf(ficparo,"\n");
5248: numlinepar++;
5249: } /* end k*/
5250: } /*end j */
5251: } /* end i */
5252: } /* end itimes */
5253:
5254: } /* end of prwizard */
5255: /******************* Gompertz Likelihood ******************************/
5256: double gompertz(double x[])
5257: {
5258: double A,B,L=0.0,sump=0.,num=0.;
5259: int i,n=0; /* n is the size of the sample */
5260:
5261: for (i=0;i<=imx-1 ; i++) {
5262: sump=sump+weight[i];
5263: /* sump=sump+1;*/
5264: num=num+1;
5265: }
5266:
5267:
5268: /* for (i=0; i<=imx; i++)
5269: 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]);*/
5270:
5271: for (i=1;i<=imx ; i++)
5272: {
5273: if (cens[i] == 1 && wav[i]>1)
5274: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5275:
5276: if (cens[i] == 0 && wav[i]>1)
5277: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5278: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5279:
5280: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5281: if (wav[i] > 1 ) { /* ??? */
5282: L=L+A*weight[i];
5283: /* 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]);*/
5284: }
5285: }
5286:
5287: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5288:
5289: return -2*L*num/sump;
5290: }
5291:
1.136 brouard 5292: #ifdef GSL
5293: /******************* Gompertz_f Likelihood ******************************/
5294: double gompertz_f(const gsl_vector *v, void *params)
5295: {
5296: double A,B,LL=0.0,sump=0.,num=0.;
5297: double *x= (double *) v->data;
5298: int i,n=0; /* n is the size of the sample */
5299:
5300: for (i=0;i<=imx-1 ; i++) {
5301: sump=sump+weight[i];
5302: /* sump=sump+1;*/
5303: num=num+1;
5304: }
5305:
5306:
5307: /* for (i=0; i<=imx; i++)
5308: 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]);*/
5309: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5310: for (i=1;i<=imx ; i++)
5311: {
5312: if (cens[i] == 1 && wav[i]>1)
5313: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5314:
5315: if (cens[i] == 0 && wav[i]>1)
5316: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5317: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5318:
5319: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5320: if (wav[i] > 1 ) { /* ??? */
5321: LL=LL+A*weight[i];
5322: /* 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]);*/
5323: }
5324: }
5325:
5326: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5327: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5328:
5329: return -2*LL*num/sump;
5330: }
5331: #endif
5332:
1.126 brouard 5333: /******************* Printing html file ***********/
5334: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5335: int lastpass, int stepm, int weightopt, char model[],\
5336: int imx, double p[],double **matcov,double agemortsup){
5337: int i,k;
5338:
5339: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5340: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5341: for (i=1;i<=2;i++)
5342: 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]));
5343: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5344: fprintf(fichtm,"</ul>");
5345:
5346: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5347:
5348: 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>");
5349:
5350: for (k=agegomp;k<(agemortsup-2);k++)
5351: 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]);
5352:
5353:
5354: fflush(fichtm);
5355: }
5356:
5357: /******************* Gnuplot file **************/
5358: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5359:
5360: char dirfileres[132],optfileres[132];
1.164 brouard 5361:
1.126 brouard 5362: int ng;
5363:
5364:
5365: /*#ifdef windows */
5366: fprintf(ficgp,"cd \"%s\" \n",pathc);
5367: /*#endif */
5368:
5369:
5370: strcpy(dirfileres,optionfilefiname);
5371: strcpy(optfileres,"vpl");
5372: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5373: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5374: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5375: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5376: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5377:
5378: }
5379:
1.136 brouard 5380: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5381: {
1.126 brouard 5382:
1.136 brouard 5383: /*-------- data file ----------*/
5384: FILE *fic;
5385: char dummy[]=" ";
1.164 brouard 5386: int i=0, j=0, n=0;
1.136 brouard 5387: int linei, month, year,iout;
5388: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5389: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5390: char *stratrunc;
5391: int lstra;
1.126 brouard 5392:
5393:
1.136 brouard 5394: if((fic=fopen(datafile,"r"))==NULL) {
5395: printf("Problem while opening datafile: %s\n", datafile);return 1;
5396: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5397: }
1.126 brouard 5398:
1.136 brouard 5399: i=1;
5400: linei=0;
5401: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5402: linei=linei+1;
5403: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5404: if(line[j] == '\t')
5405: line[j] = ' ';
5406: }
5407: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5408: ;
5409: };
5410: line[j+1]=0; /* Trims blanks at end of line */
5411: if(line[0]=='#'){
5412: fprintf(ficlog,"Comment line\n%s\n",line);
5413: printf("Comment line\n%s\n",line);
5414: continue;
5415: }
5416: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5417: strcpy(line, linetmp);
1.136 brouard 5418:
1.126 brouard 5419:
1.136 brouard 5420: for (j=maxwav;j>=1;j--){
1.137 brouard 5421: cutv(stra, strb, line, ' ');
1.136 brouard 5422: if(strb[0]=='.') { /* Missing status */
5423: lval=-1;
5424: }else{
5425: errno=0;
5426: lval=strtol(strb,&endptr,10);
5427: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5428: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5429: 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);
5430: 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);
1.136 brouard 5431: return 1;
5432: }
5433: }
5434: s[j][i]=lval;
5435:
5436: strcpy(line,stra);
5437: cutv(stra, strb,line,' ');
1.169 brouard 5438: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5439: }
1.169 brouard 5440: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5441: month=99;
5442: year=9999;
5443: }else{
1.141 brouard 5444: 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);
5445: 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);
1.136 brouard 5446: return 1;
5447: }
5448: anint[j][i]= (double) year;
5449: mint[j][i]= (double)month;
5450: strcpy(line,stra);
5451: } /* ENd Waves */
5452:
5453: cutv(stra, strb,line,' ');
1.169 brouard 5454: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5455: }
1.169 brouard 5456: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5457: month=99;
5458: year=9999;
5459: }else{
1.141 brouard 5460: 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);
5461: 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);
1.136 brouard 5462: return 1;
5463: }
5464: andc[i]=(double) year;
5465: moisdc[i]=(double) month;
5466: strcpy(line,stra);
5467:
5468: cutv(stra, strb,line,' ');
1.169 brouard 5469: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5470: }
1.169 brouard 5471: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5472: month=99;
5473: year=9999;
5474: }else{
1.141 brouard 5475: 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);
5476: 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);
1.136 brouard 5477: return 1;
5478: }
5479: if (year==9999) {
1.141 brouard 5480: 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);
5481: 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);
1.136 brouard 5482: return 1;
1.126 brouard 5483:
1.136 brouard 5484: }
5485: annais[i]=(double)(year);
5486: moisnais[i]=(double)(month);
5487: strcpy(line,stra);
5488:
5489: cutv(stra, strb,line,' ');
5490: errno=0;
5491: dval=strtod(strb,&endptr);
5492: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5493: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5494: 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);
1.136 brouard 5495: fflush(ficlog);
5496: return 1;
5497: }
5498: weight[i]=dval;
5499: strcpy(line,stra);
5500:
5501: for (j=ncovcol;j>=1;j--){
5502: cutv(stra, strb,line,' ');
5503: if(strb[0]=='.') { /* Missing status */
5504: lval=-1;
5505: }else{
5506: errno=0;
5507: lval=strtol(strb,&endptr,10);
5508: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5509: 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);
5510: 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);
1.136 brouard 5511: return 1;
5512: }
5513: }
5514: if(lval <-1 || lval >1){
1.141 brouard 5515: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5516: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5517: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5518: For example, for multinomial values like 1, 2 and 3,\n \
5519: build V1=0 V2=0 for the reference value (1),\n \
5520: V1=1 V2=0 for (2) \n \
5521: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5522: output of IMaCh is often meaningless.\n \
5523: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5524: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5525: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5526: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5527: For example, for multinomial values like 1, 2 and 3,\n \
5528: build V1=0 V2=0 for the reference value (1),\n \
5529: V1=1 V2=0 for (2) \n \
5530: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5531: output of IMaCh is often meaningless.\n \
5532: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5533: return 1;
5534: }
5535: covar[j][i]=(double)(lval);
5536: strcpy(line,stra);
5537: }
5538: lstra=strlen(stra);
5539:
5540: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5541: stratrunc = &(stra[lstra-9]);
5542: num[i]=atol(stratrunc);
5543: }
5544: else
5545: num[i]=atol(stra);
5546: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5547: 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;}*/
5548:
5549: i=i+1;
5550: } /* End loop reading data */
1.126 brouard 5551:
1.136 brouard 5552: *imax=i-1; /* Number of individuals */
5553: fclose(fic);
5554:
5555: return (0);
1.164 brouard 5556: /* endread: */
1.136 brouard 5557: printf("Exiting readdata: ");
5558: fclose(fic);
5559: return (1);
1.126 brouard 5560:
5561:
5562:
1.136 brouard 5563: }
1.145 brouard 5564: void removespace(char *str) {
5565: char *p1 = str, *p2 = str;
5566: do
5567: while (*p2 == ' ')
5568: p2++;
1.169 brouard 5569: while (*p1++ == *p2++);
1.145 brouard 5570: }
5571:
5572: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5573: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5574: * - nagesqr = 1 if age*age in the model, otherwise 0.
5575: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5576: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5577: * - cptcovage number of covariates with age*products =2
5578: * - cptcovs number of simple covariates
5579: * - 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
5580: * which is a new column after the 9 (ncovcol) variables.
5581: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5582: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5583: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5584: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5585: */
1.136 brouard 5586: {
1.145 brouard 5587: int i, j, k, ks;
1.164 brouard 5588: int j1, k1, k2;
1.136 brouard 5589: char modelsav[80];
1.145 brouard 5590: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5591: char *strpt;
1.136 brouard 5592:
1.145 brouard 5593: /*removespace(model);*/
1.136 brouard 5594: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5595: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5596: if (strstr(model,"AGE") !=0){
1.187 brouard 5597: printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
5598: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
1.136 brouard 5599: return 1;
5600: }
1.141 brouard 5601: if (strstr(model,"v") !=0){
5602: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5603: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5604: return 1;
5605: }
1.187 brouard 5606: strcpy(modelsav,model);
5607: if ((strpt=strstr(model,"age*age")) !=0){
5608: printf(" strpt=%s, model=%s\n",strpt, model);
5609: if(strpt != model){
5610: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5611: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5612: corresponding column of parameters.\n",model);
5613: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5614: 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
5615: corresponding column of parameters.\n",model); fflush(ficlog);
5616: return 1;
5617: }
5618:
5619: nagesqr=1;
5620: if (strstr(model,"+age*age") !=0)
5621: substrchaine(modelsav, model, "+age*age");
5622: else if (strstr(model,"age*age+") !=0)
5623: substrchaine(modelsav, model, "age*age+");
5624: else
5625: substrchaine(modelsav, model, "age*age");
5626: }else
5627: nagesqr=0;
5628: if (strlen(modelsav) >1){
5629: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5630: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5631: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5632: cptcovt= j+1; /* Number of total covariates in the model, not including
5633: * cst, age and age*age
5634: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5635: /* including age products which are counted in cptcovage.
5636: * but the covariates which are products must be treated
5637: * separately: ncovn=4- 2=2 (V1+V3). */
5638: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5639: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5640:
5641:
5642: /* Design
5643: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5644: * < ncovcol=8 >
5645: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5646: * k= 1 2 3 4 5 6 7 8
5647: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5648: * covar[k,i], value of kth covariate if not including age for individual i:
5649: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5650: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5651: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5652: * Tage[++cptcovage]=k
5653: * if products, new covar are created after ncovcol with k1
5654: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5655: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5656: * 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
5657: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5658: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5659: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5660: * < ncovcol=8 >
5661: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5662: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5663: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5664: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5665: * p Tprod[1]@2={ 6, 5}
5666: *p Tvard[1][1]@4= {7, 8, 5, 6}
5667: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5668: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5669: *How to reorganize?
5670: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5671: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5672: * {2, 1, 4, 8, 5, 6, 3, 7}
5673: * Struct []
5674: */
1.145 brouard 5675:
1.187 brouard 5676: /* This loop fills the array Tvar from the string 'model'.*/
5677: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5678: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5679: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5680: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5681: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5682: /* k=1 Tvar[1]=2 (from V2) */
5683: /* k=5 Tvar[5] */
5684: /* for (k=1; k<=cptcovn;k++) { */
5685: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5686: /* } */
5687: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5688: /*
5689: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5690: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5691: Tvar[k]=0;
1.187 brouard 5692: cptcovage=0;
5693: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5694: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5695: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5696: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5697: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5698: /*scanf("%d",i);*/
5699: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5700: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5701: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5702: /* covar is not filled and then is empty */
5703: cptcovprod--;
5704: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5705: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5706: cptcovage++; /* Sums the number of covariates which include age as a product */
5707: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5708: /*printf("stre=%s ", stre);*/
5709: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5710: cptcovprod--;
5711: cutl(stre,strb,strc,'V');
5712: Tvar[k]=atoi(stre);
5713: cptcovage++;
5714: Tage[cptcovage]=k;
5715: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5716: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5717: cptcovn++;
5718: cptcovprodnoage++;k1++;
5719: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5720: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5721: because this model-covariate is a construction we invent a new column
5722: ncovcol + k1
5723: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5724: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5725: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5726: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5727: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5728: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5729: k2=k2+2;
5730: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5731: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5732: for (i=1; i<=lastobs;i++){
5733: /* Computes the new covariate which is a product of
5734: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5735: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5736: }
5737: } /* End age is not in the model */
5738: } /* End if model includes a product */
5739: else { /* no more sum */
5740: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5741: /* scanf("%d",i);*/
5742: cutl(strd,strc,strb,'V');
5743: ks++; /**< Number of simple covariates */
1.145 brouard 5744: cptcovn++;
1.187 brouard 5745: Tvar[k]=atoi(strd);
5746: }
5747: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5748: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5749: scanf("%d",i);*/
5750: } /* end of loop + on total covariates */
5751: } /* end if strlen(modelsave == 0) age*age might exist */
5752: } /* end if strlen(model == 0) */
1.136 brouard 5753:
5754: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5755: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5756:
5757: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5758: printf("cptcovprod=%d ", cptcovprod);
5759: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5760:
5761: scanf("%d ",i);*/
5762:
5763:
1.137 brouard 5764: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5765: /*endread:*/
1.136 brouard 5766: printf("Exiting decodemodel: ");
5767: return (1);
5768: }
5769:
1.169 brouard 5770: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5771: {
5772: int i, m;
5773:
5774: for (i=1; i<=imx; i++) {
5775: for(m=2; (m<= maxwav); m++) {
5776: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5777: anint[m][i]=9999;
5778: s[m][i]=-1;
5779: }
5780: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5781: *nberr = *nberr + 1;
5782: 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);
5783: 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);
1.136 brouard 5784: s[m][i]=-1;
5785: }
5786: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5787: (*nberr)++;
1.136 brouard 5788: 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]);
5789: 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]);
5790: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5791: }
5792: }
5793: }
5794:
5795: for (i=1; i<=imx; i++) {
5796: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5797: for(m=firstpass; (m<= lastpass); m++){
5798: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5799: if (s[m][i] >= nlstate+1) {
1.169 brouard 5800: if(agedc[i]>0){
5801: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5802: agev[m][i]=agedc[i];
5803: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5804: }else {
1.136 brouard 5805: if ((int)andc[i]!=9999){
5806: nbwarn++;
5807: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5808: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5809: agev[m][i]=-1;
5810: }
5811: }
1.169 brouard 5812: } /* agedc > 0 */
1.136 brouard 5813: }
5814: else if(s[m][i] !=9){ /* Standard case, age in fractional
5815: years but with the precision of a month */
5816: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5817: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5818: agev[m][i]=1;
5819: else if(agev[m][i] < *agemin){
5820: *agemin=agev[m][i];
5821: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5822: }
5823: else if(agev[m][i] >*agemax){
5824: *agemax=agev[m][i];
1.156 brouard 5825: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5826: }
5827: /*agev[m][i]=anint[m][i]-annais[i];*/
5828: /* agev[m][i] = age[i]+2*m;*/
5829: }
5830: else { /* =9 */
5831: agev[m][i]=1;
5832: s[m][i]=-1;
5833: }
5834: }
5835: else /*= 0 Unknown */
5836: agev[m][i]=1;
5837: }
5838:
5839: }
5840: for (i=1; i<=imx; i++) {
5841: for(m=firstpass; (m<=lastpass); m++){
5842: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5843: (*nberr)++;
1.136 brouard 5844: 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);
5845: 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);
5846: return 1;
5847: }
5848: }
5849: }
5850:
5851: /*for (i=1; i<=imx; i++){
5852: for (m=firstpass; (m<lastpass); m++){
5853: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5854: }
5855:
5856: }*/
5857:
5858:
1.139 brouard 5859: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5860: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5861:
5862: return (0);
1.164 brouard 5863: /* endread:*/
1.136 brouard 5864: printf("Exiting calandcheckages: ");
5865: return (1);
5866: }
5867:
1.172 brouard 5868: #if defined(_MSC_VER)
5869: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5870: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5871: //#include "stdafx.h"
5872: //#include <stdio.h>
5873: //#include <tchar.h>
5874: //#include <windows.h>
5875: //#include <iostream>
5876: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5877:
5878: LPFN_ISWOW64PROCESS fnIsWow64Process;
5879:
5880: BOOL IsWow64()
5881: {
5882: BOOL bIsWow64 = FALSE;
5883:
5884: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5885: // (HANDLE, PBOOL);
5886:
5887: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5888:
5889: HMODULE module = GetModuleHandle(_T("kernel32"));
5890: const char funcName[] = "IsWow64Process";
5891: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5892: GetProcAddress(module, funcName);
5893:
5894: if (NULL != fnIsWow64Process)
5895: {
5896: if (!fnIsWow64Process(GetCurrentProcess(),
5897: &bIsWow64))
5898: //throw std::exception("Unknown error");
5899: printf("Unknown error\n");
5900: }
5901: return bIsWow64 != FALSE;
5902: }
5903: #endif
1.177 brouard 5904:
1.191 ! brouard 5905: void syscompilerinfo(int logged)
1.167 brouard 5906: {
5907: /* #include "syscompilerinfo.h"*/
1.185 brouard 5908: /* command line Intel compiler 32bit windows, XP compatible:*/
5909: /* /GS /W3 /Gy
5910: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5911: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5912: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5913: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5914: */
5915: /* 64 bits */
1.185 brouard 5916: /*
5917: /GS /W3 /Gy
5918: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5919: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5920: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5921: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5922: /* Optimization are useless and O3 is slower than O2 */
5923: /*
5924: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5925: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5926: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5927: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5928: */
1.186 brouard 5929: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5930: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5931: /PDB:"visual studio
5932: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5933: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5934: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5935: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5936: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5937: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5938: uiAccess='false'"
5939: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5940: /NOLOGO /TLBID:1
5941: */
1.177 brouard 5942: #if defined __INTEL_COMPILER
1.178 brouard 5943: #if defined(__GNUC__)
5944: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5945: #endif
1.177 brouard 5946: #elif defined(__GNUC__)
1.179 brouard 5947: #ifndef __APPLE__
1.174 brouard 5948: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5949: #endif
1.177 brouard 5950: struct utsname sysInfo;
1.178 brouard 5951: int cross = CROSS;
5952: if (cross){
5953: printf("Cross-");
1.191 ! brouard 5954: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 5955: }
1.174 brouard 5956: #endif
5957:
1.171 brouard 5958: #include <stdint.h>
1.178 brouard 5959:
1.191 ! brouard 5960: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 5961: #if defined(__clang__)
1.191 ! brouard 5962: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 5963: #endif
5964: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 ! brouard 5965: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 5966: #endif
5967: #if defined(__GNUC__) || defined(__GNUG__)
1.191 ! brouard 5968: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 5969: #endif
5970: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 ! brouard 5971: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 5972: #endif
5973: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 ! brouard 5974: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 5975: #endif
5976: #if defined(_MSC_VER)
1.191 ! brouard 5977: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 5978: #endif
5979: #if defined(__PGI)
1.191 ! brouard 5980: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 5981: #endif
5982: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 ! brouard 5983: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5984: #endif
1.191 ! brouard 5985: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 5986:
1.167 brouard 5987: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5988: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5989: // Windows (x64 and x86)
1.191 ! brouard 5990: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5991: #elif __unix__ // all unices, not all compilers
5992: // Unix
1.191 ! brouard 5993: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 5994: #elif __linux__
5995: // linux
1.191 ! brouard 5996: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 5997: #elif __APPLE__
1.174 brouard 5998: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 ! brouard 5999: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6000: #endif
6001:
6002: /* __MINGW32__ */
6003: /* __CYGWIN__ */
6004: /* __MINGW64__ */
6005: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6006: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6007: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6008: /* _WIN64 // Defined for applications for Win64. */
6009: /* _M_X64 // Defined for compilations that target x64 processors. */
6010: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6011:
1.167 brouard 6012: #if UINTPTR_MAX == 0xffffffff
1.191 ! brouard 6013: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6014: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 ! brouard 6015: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6016: #else
1.191 ! brouard 6017: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6018: #endif
6019:
1.169 brouard 6020: #if defined(__GNUC__)
6021: # if defined(__GNUC_PATCHLEVEL__)
6022: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6023: + __GNUC_MINOR__ * 100 \
6024: + __GNUC_PATCHLEVEL__)
6025: # else
6026: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6027: + __GNUC_MINOR__ * 100)
6028: # endif
1.174 brouard 6029: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 ! brouard 6030: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6031:
6032: if (uname(&sysInfo) != -1) {
6033: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 ! brouard 6034: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.176 brouard 6035: }
6036: else
6037: perror("uname() error");
1.179 brouard 6038: //#ifndef __INTEL_COMPILER
6039: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6040: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 ! brouard 6041: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6042: #endif
1.169 brouard 6043: #endif
1.172 brouard 6044:
6045: // void main()
6046: // {
1.169 brouard 6047: #if defined(_MSC_VER)
1.174 brouard 6048: if (IsWow64()){
1.191 ! brouard 6049: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
! 6050: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6051: }
6052: else{
1.191 ! brouard 6053: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
! 6054: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6055: }
1.172 brouard 6056: // printf("\nPress Enter to continue...");
6057: // getchar();
6058: // }
6059:
1.169 brouard 6060: #endif
6061:
1.167 brouard 6062:
6063: }
1.136 brouard 6064:
1.180 brouard 6065: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6066: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6067: int i, j, k, i1 ;
6068: double ftolpl = 1.e-10;
6069: double age, agebase, agelim;
6070:
6071: strcpy(filerespl,"pl");
6072: strcat(filerespl,fileres);
6073: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6074: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6075: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6076: }
6077: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6078: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6079: pstamp(ficrespl);
6080: fprintf(ficrespl,"# Period (stable) prevalence \n");
6081: fprintf(ficrespl,"#Age ");
6082: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6083: fprintf(ficrespl,"\n");
6084:
6085: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6086:
6087: agebase=ageminpar;
6088: agelim=agemaxpar;
6089:
6090: i1=pow(2,cptcoveff);
6091: if (cptcovn < 1){i1=1;}
6092:
6093: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6094: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6095: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6096: k=k+1;
6097: /* to clean */
6098: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6099: fprintf(ficrespl,"\n#******");
6100: printf("\n#******");
6101: fprintf(ficlog,"\n#******");
6102: for(j=1;j<=cptcoveff;j++) {
6103: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6104: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6105: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6106: }
6107: fprintf(ficrespl,"******\n");
6108: printf("******\n");
6109: fprintf(ficlog,"******\n");
6110:
6111: fprintf(ficrespl,"#Age ");
6112: for(j=1;j<=cptcoveff;j++) {
6113: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6114: }
6115: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6116: fprintf(ficrespl,"\n");
6117:
6118: for (age=agebase; age<=agelim; age++){
6119: /* for (age=agebase; age<=agebase; age++){ */
6120: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6121: fprintf(ficrespl,"%.0f ",age );
6122: for(j=1;j<=cptcoveff;j++)
6123: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6124: for(i=1; i<=nlstate;i++)
6125: fprintf(ficrespl," %.5f", prlim[i][i]);
6126: fprintf(ficrespl,"\n");
6127: } /* Age */
6128: /* was end of cptcod */
6129: } /* cptcov */
1.184 brouard 6130: return 0;
1.180 brouard 6131: }
6132:
6133: int hPijx(double *p, int bage, int fage){
6134: /*------------- h Pij x at various ages ------------*/
6135:
6136: int stepsize;
6137: int agelim;
6138: int hstepm;
6139: int nhstepm;
6140: int h, i, i1, j, k;
6141:
6142: double agedeb;
6143: double ***p3mat;
6144:
6145: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6146: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6147: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6148: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6149: }
6150: printf("Computing pij: result on file '%s' \n", filerespij);
6151: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6152:
6153: stepsize=(int) (stepm+YEARM-1)/YEARM;
6154: /*if (stepm<=24) stepsize=2;*/
6155:
6156: agelim=AGESUP;
6157: hstepm=stepsize*YEARM; /* Every year of age */
6158: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6159:
6160: /* hstepm=1; aff par mois*/
6161: pstamp(ficrespij);
6162: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6163: i1= pow(2,cptcoveff);
1.183 brouard 6164: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6165: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6166: /* k=k+1; */
6167: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6168: fprintf(ficrespij,"\n#****** ");
6169: for(j=1;j<=cptcoveff;j++)
6170: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6171: fprintf(ficrespij,"******\n");
6172:
6173: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6174: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6175: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6176:
6177: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6178:
1.183 brouard 6179: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6180: oldm=oldms;savm=savms;
6181: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6182: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6183: for(i=1; i<=nlstate;i++)
6184: for(j=1; j<=nlstate+ndeath;j++)
6185: fprintf(ficrespij," %1d-%1d",i,j);
6186: fprintf(ficrespij,"\n");
6187: for (h=0; h<=nhstepm; h++){
6188: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6189: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6190: for(i=1; i<=nlstate;i++)
6191: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6192: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6193: fprintf(ficrespij,"\n");
6194: }
1.183 brouard 6195: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6196: fprintf(ficrespij,"\n");
6197: }
1.180 brouard 6198: /*}*/
6199: }
1.184 brouard 6200: return 0;
1.180 brouard 6201: }
6202:
6203:
1.136 brouard 6204: /***********************************************/
6205: /**************** Main Program *****************/
6206: /***********************************************/
6207:
6208: int main(int argc, char *argv[])
6209: {
6210: #ifdef GSL
6211: const gsl_multimin_fminimizer_type *T;
6212: size_t iteri = 0, it;
6213: int rval = GSL_CONTINUE;
6214: int status = GSL_SUCCESS;
6215: double ssval;
6216: #endif
6217: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6218: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6219:
6220: int jj, ll, li, lj, lk;
1.136 brouard 6221: int numlinepar=0; /* Current linenumber of parameter file */
6222: int itimes;
6223: int NDIM=2;
6224: int vpopbased=0;
6225:
1.164 brouard 6226: char ca[32], cb[32];
1.136 brouard 6227: /* FILE *fichtm; *//* Html File */
6228: /* FILE *ficgp;*/ /*Gnuplot File */
6229: struct stat info;
1.191 ! brouard 6230: double agedeb=0.;
1.136 brouard 6231: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6232:
1.165 brouard 6233: double fret;
1.191 ! brouard 6234: double dum=0.; /* Dummy variable */
1.136 brouard 6235: double ***p3mat;
6236: double ***mobaverage;
1.164 brouard 6237:
6238: char line[MAXLINE];
1.136 brouard 6239: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6240: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6241: char *tok, *val; /* pathtot */
1.136 brouard 6242: int firstobs=1, lastobs=10;
1.164 brouard 6243: int c, h , cpt;
1.191 ! brouard 6244: int jl=0;
! 6245: int i1, j1, jk, stepsize=0;
1.164 brouard 6246: int *tab;
1.136 brouard 6247: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6248: int mobilav=0,popforecast=0;
1.191 ! brouard 6249: int hstepm=0, nhstepm=0;
1.136 brouard 6250: int agemortsup;
6251: float sumlpop=0.;
6252: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6253: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6254:
1.191 ! brouard 6255: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6256: double ftolpl=FTOL;
6257: double **prlim;
6258: double ***param; /* Matrix of parameters */
6259: double *p;
6260: double **matcov; /* Matrix of covariance */
6261: double ***delti3; /* Scale */
6262: double *delti; /* Scale */
6263: double ***eij, ***vareij;
6264: double **varpl; /* Variances of prevalence limits by age */
6265: double *epj, vepp;
1.164 brouard 6266:
1.136 brouard 6267: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6268: double **ximort;
1.145 brouard 6269: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6270: int *dcwave;
6271:
1.164 brouard 6272: char z[1]="c";
1.136 brouard 6273:
6274: /*char *strt;*/
6275: char strtend[80];
1.126 brouard 6276:
1.164 brouard 6277:
1.126 brouard 6278: /* setlocale (LC_ALL, ""); */
6279: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6280: /* textdomain (PACKAGE); */
6281: /* setlocale (LC_CTYPE, ""); */
6282: /* setlocale (LC_MESSAGES, ""); */
6283:
6284: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6285: rstart_time = time(NULL);
6286: /* (void) gettimeofday(&start_time,&tzp);*/
6287: start_time = *localtime(&rstart_time);
1.126 brouard 6288: curr_time=start_time;
1.157 brouard 6289: /*tml = *localtime(&start_time.tm_sec);*/
6290: /* strcpy(strstart,asctime(&tml)); */
6291: strcpy(strstart,asctime(&start_time));
1.126 brouard 6292:
6293: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6294: /* tp.tm_sec = tp.tm_sec +86400; */
6295: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6296: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6297: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6298: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6299: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6300: /* strt=asctime(&tmg); */
6301: /* printf("Time(after) =%s",strstart); */
6302: /* (void) time (&time_value);
6303: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6304: * tm = *localtime(&time_value);
6305: * strstart=asctime(&tm);
6306: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6307: */
6308:
6309: nberr=0; /* Number of errors and warnings */
6310: nbwarn=0;
1.184 brouard 6311: #ifdef WIN32
6312: _getcwd(pathcd, size);
6313: #else
1.126 brouard 6314: getcwd(pathcd, size);
1.184 brouard 6315: #endif
1.191 ! brouard 6316: syscompilerinfo(0);
1.126 brouard 6317: printf("\n%s\n%s",version,fullversion);
6318: if(argc <=1){
6319: printf("\nEnter the parameter file name: ");
6320: fgets(pathr,FILENAMELENGTH,stdin);
6321: i=strlen(pathr);
6322: if(pathr[i-1]=='\n')
6323: pathr[i-1]='\0';
1.156 brouard 6324: i=strlen(pathr);
6325: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6326: pathr[i-1]='\0';
1.126 brouard 6327: for (tok = pathr; tok != NULL; ){
6328: printf("Pathr |%s|\n",pathr);
6329: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6330: printf("val= |%s| pathr=%s\n",val,pathr);
6331: strcpy (pathtot, val);
6332: if(pathr[0] == '\0') break; /* Dirty */
6333: }
6334: }
6335: else{
6336: strcpy(pathtot,argv[1]);
6337: }
6338: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6339: /*cygwin_split_path(pathtot,path,optionfile);
6340: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6341: /* cutv(path,optionfile,pathtot,'\\');*/
6342:
6343: /* Split argv[0], imach program to get pathimach */
6344: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6345: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6346: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6347: /* strcpy(pathimach,argv[0]); */
6348: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6349: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6350: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6351: #ifdef WIN32
6352: _chdir(path); /* Can be a relative path */
6353: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6354: #else
1.126 brouard 6355: chdir(path); /* Can be a relative path */
1.184 brouard 6356: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6357: #endif
6358: printf("Current directory %s!\n",pathcd);
1.126 brouard 6359: strcpy(command,"mkdir ");
6360: strcat(command,optionfilefiname);
6361: if((outcmd=system(command)) != 0){
1.169 brouard 6362: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6363: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6364: /* fclose(ficlog); */
6365: /* exit(1); */
6366: }
6367: /* if((imk=mkdir(optionfilefiname))<0){ */
6368: /* perror("mkdir"); */
6369: /* } */
6370:
6371: /*-------- arguments in the command line --------*/
6372:
1.186 brouard 6373: /* Main Log file */
1.126 brouard 6374: strcat(filelog, optionfilefiname);
6375: strcat(filelog,".log"); /* */
6376: if((ficlog=fopen(filelog,"w"))==NULL) {
6377: printf("Problem with logfile %s\n",filelog);
6378: goto end;
6379: }
6380: fprintf(ficlog,"Log filename:%s\n",filelog);
6381: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6382: fprintf(ficlog,"\nEnter the parameter file name: \n");
6383: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6384: path=%s \n\
6385: optionfile=%s\n\
6386: optionfilext=%s\n\
1.156 brouard 6387: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6388:
1.191 ! brouard 6389: syscompilerinfo(0);
1.167 brouard 6390:
1.126 brouard 6391: printf("Local time (at start):%s",strstart);
6392: fprintf(ficlog,"Local time (at start): %s",strstart);
6393: fflush(ficlog);
6394: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6395: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6396:
6397: /* */
6398: strcpy(fileres,"r");
6399: strcat(fileres, optionfilefiname);
6400: strcat(fileres,".txt"); /* Other files have txt extension */
6401:
1.186 brouard 6402: /* Main ---------arguments file --------*/
1.126 brouard 6403:
6404: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6405: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6406: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6407: fflush(ficlog);
1.149 brouard 6408: /* goto end; */
6409: exit(70);
1.126 brouard 6410: }
6411:
6412:
6413:
6414: strcpy(filereso,"o");
6415: strcat(filereso,fileres);
6416: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6417: printf("Problem with Output resultfile: %s\n", filereso);
6418: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6419: fflush(ficlog);
6420: goto end;
6421: }
6422:
6423: /* Reads comments: lines beginning with '#' */
6424: numlinepar=0;
6425: while((c=getc(ficpar))=='#' && c!= EOF){
6426: ungetc(c,ficpar);
6427: fgets(line, MAXLINE, ficpar);
6428: numlinepar++;
1.141 brouard 6429: fputs(line,stdout);
1.126 brouard 6430: fputs(line,ficparo);
6431: fputs(line,ficlog);
6432: }
6433: ungetc(c,ficpar);
6434:
1.187 brouard 6435: 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);
1.126 brouard 6436: numlinepar++;
1.187 brouard 6437: 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);
6438: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6439: model[strlen(model)-1]='\0';
6440: 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);
6441: 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);
1.126 brouard 6442: fflush(ficlog);
1.190 brouard 6443: /* if(model[0]=='#'|| model[0]== '\0'){ */
6444: if(model[0]=='#'){
1.187 brouard 6445: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6446: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6447: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6448: if(mle != -1){
6449: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6450: exit(1);
6451: }
6452: }
1.126 brouard 6453: while((c=getc(ficpar))=='#' && c!= EOF){
6454: ungetc(c,ficpar);
6455: fgets(line, MAXLINE, ficpar);
6456: numlinepar++;
1.141 brouard 6457: fputs(line, stdout);
6458: //puts(line);
1.126 brouard 6459: fputs(line,ficparo);
6460: fputs(line,ficlog);
6461: }
6462: ungetc(c,ficpar);
6463:
6464:
1.145 brouard 6465: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6466: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6467: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6468: v1+v2*age+v2*v3 makes cptcovn = 3
6469: */
6470: if (strlen(model)>1)
1.187 brouard 6471: 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*/
1.145 brouard 6472: else
1.187 brouard 6473: ncovmodel=2; /* Constant and age */
1.133 brouard 6474: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6475: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6476: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6477: 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);
6478: 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);
6479: fflush(stdout);
6480: fclose (ficlog);
6481: goto end;
6482: }
1.126 brouard 6483: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6484: delti=delti3[1][1];
6485: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6486: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6487: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 ! brouard 6488: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
! 6489: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6490: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6491: fclose (ficparo);
6492: fclose (ficlog);
6493: goto end;
6494: exit(0);
6495: }
1.186 brouard 6496: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6497: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6498: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6499: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6500: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6501: matcov=matrix(1,npar,1,npar);
6502: }
6503: else{
1.145 brouard 6504: /* Read guessed parameters */
1.126 brouard 6505: /* Reads comments: lines beginning with '#' */
6506: while((c=getc(ficpar))=='#' && c!= EOF){
6507: ungetc(c,ficpar);
6508: fgets(line, MAXLINE, ficpar);
6509: numlinepar++;
1.141 brouard 6510: fputs(line,stdout);
1.126 brouard 6511: fputs(line,ficparo);
6512: fputs(line,ficlog);
6513: }
6514: ungetc(c,ficpar);
6515:
6516: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6517: for(i=1; i <=nlstate; i++){
6518: j=0;
6519: for(jj=1; jj <=nlstate+ndeath; jj++){
6520: if(jj==i) continue;
6521: j++;
6522: fscanf(ficpar,"%1d%1d",&i1,&j1);
6523: if ((i1 != i) && (j1 != j)){
6524: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6525: It might be a problem of design; if ncovcol and the model are correct\n \
6526: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6527: exit(1);
6528: }
6529: fprintf(ficparo,"%1d%1d",i1,j1);
6530: if(mle==1)
6531: printf("%1d%1d",i,j);
6532: fprintf(ficlog,"%1d%1d",i,j);
6533: for(k=1; k<=ncovmodel;k++){
6534: fscanf(ficpar," %lf",¶m[i][j][k]);
6535: if(mle==1){
6536: printf(" %lf",param[i][j][k]);
6537: fprintf(ficlog," %lf",param[i][j][k]);
6538: }
6539: else
6540: fprintf(ficlog," %lf",param[i][j][k]);
6541: fprintf(ficparo," %lf",param[i][j][k]);
6542: }
6543: fscanf(ficpar,"\n");
6544: numlinepar++;
6545: if(mle==1)
6546: printf("\n");
6547: fprintf(ficlog,"\n");
6548: fprintf(ficparo,"\n");
6549: }
6550: }
6551: fflush(ficlog);
6552:
1.145 brouard 6553: /* Reads scales values */
1.126 brouard 6554: p=param[1][1];
6555:
6556: /* Reads comments: lines beginning with '#' */
6557: while((c=getc(ficpar))=='#' && c!= EOF){
6558: ungetc(c,ficpar);
6559: fgets(line, MAXLINE, ficpar);
6560: numlinepar++;
1.141 brouard 6561: fputs(line,stdout);
1.126 brouard 6562: fputs(line,ficparo);
6563: fputs(line,ficlog);
6564: }
6565: ungetc(c,ficpar);
6566:
6567: for(i=1; i <=nlstate; i++){
6568: for(j=1; j <=nlstate+ndeath-1; j++){
6569: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6570: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6571: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6572: exit(1);
6573: }
6574: printf("%1d%1d",i,j);
6575: fprintf(ficparo,"%1d%1d",i1,j1);
6576: fprintf(ficlog,"%1d%1d",i1,j1);
6577: for(k=1; k<=ncovmodel;k++){
6578: fscanf(ficpar,"%le",&delti3[i][j][k]);
6579: printf(" %le",delti3[i][j][k]);
6580: fprintf(ficparo," %le",delti3[i][j][k]);
6581: fprintf(ficlog," %le",delti3[i][j][k]);
6582: }
6583: fscanf(ficpar,"\n");
6584: numlinepar++;
6585: printf("\n");
6586: fprintf(ficparo,"\n");
6587: fprintf(ficlog,"\n");
6588: }
6589: }
6590: fflush(ficlog);
6591:
1.145 brouard 6592: /* Reads covariance matrix */
1.126 brouard 6593: delti=delti3[1][1];
6594:
6595:
6596: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6597:
6598: /* Reads comments: lines beginning with '#' */
6599: while((c=getc(ficpar))=='#' && c!= EOF){
6600: ungetc(c,ficpar);
6601: fgets(line, MAXLINE, ficpar);
6602: numlinepar++;
1.141 brouard 6603: fputs(line,stdout);
1.126 brouard 6604: fputs(line,ficparo);
6605: fputs(line,ficlog);
6606: }
6607: ungetc(c,ficpar);
6608:
6609: matcov=matrix(1,npar,1,npar);
1.131 brouard 6610: for(i=1; i <=npar; i++)
6611: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6612:
1.126 brouard 6613: for(i=1; i <=npar; i++){
1.145 brouard 6614: fscanf(ficpar,"%s",str);
1.126 brouard 6615: if(mle==1)
6616: printf("%s",str);
6617: fprintf(ficlog,"%s",str);
6618: fprintf(ficparo,"%s",str);
6619: for(j=1; j <=i; j++){
6620: fscanf(ficpar," %le",&matcov[i][j]);
6621: if(mle==1){
6622: printf(" %.5le",matcov[i][j]);
6623: }
6624: fprintf(ficlog," %.5le",matcov[i][j]);
6625: fprintf(ficparo," %.5le",matcov[i][j]);
6626: }
6627: fscanf(ficpar,"\n");
6628: numlinepar++;
6629: if(mle==1)
6630: printf("\n");
6631: fprintf(ficlog,"\n");
6632: fprintf(ficparo,"\n");
6633: }
6634: for(i=1; i <=npar; i++)
6635: for(j=i+1;j<=npar;j++)
6636: matcov[i][j]=matcov[j][i];
6637:
6638: if(mle==1)
6639: printf("\n");
6640: fprintf(ficlog,"\n");
6641:
6642: fflush(ficlog);
6643:
6644: /*-------- Rewriting parameter file ----------*/
6645: strcpy(rfileres,"r"); /* "Rparameterfile */
6646: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6647: strcat(rfileres,"."); /* */
6648: strcat(rfileres,optionfilext); /* Other files have txt extension */
6649: if((ficres =fopen(rfileres,"w"))==NULL) {
6650: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6651: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6652: }
6653: fprintf(ficres,"#%s\n",version);
6654: } /* End of mle != -3 */
6655:
1.186 brouard 6656: /* Main data
6657: */
1.126 brouard 6658: n= lastobs;
6659: num=lvector(1,n);
6660: moisnais=vector(1,n);
6661: annais=vector(1,n);
6662: moisdc=vector(1,n);
6663: andc=vector(1,n);
6664: agedc=vector(1,n);
6665: cod=ivector(1,n);
6666: weight=vector(1,n);
6667: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6668: mint=matrix(1,maxwav,1,n);
6669: anint=matrix(1,maxwav,1,n);
1.131 brouard 6670: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6671: tab=ivector(1,NCOVMAX);
1.144 brouard 6672: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6673:
1.136 brouard 6674: /* Reads data from file datafile */
6675: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6676: goto end;
6677:
6678: /* Calculation of the number of parameters from char model */
1.137 brouard 6679: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6680: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6681: k=3 V4 Tvar[k=3]= 4 (from V4)
6682: k=2 V1 Tvar[k=2]= 1 (from V1)
6683: k=1 Tvar[1]=2 (from V2)
6684: */
6685: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6686: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6687: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6688: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6689: */
6690: /* For model-covariate k tells which data-covariate to use but
6691: because this model-covariate is a construction we invent a new column
6692: ncovcol + k1
6693: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6694: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6695: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6696: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6697: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6698: */
1.145 brouard 6699: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6700: 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
1.141 brouard 6701: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6702: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6703: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6704: 4 covariates (3 plus signs)
6705: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6706: */
1.136 brouard 6707:
1.186 brouard 6708: /* Main decodemodel */
6709:
1.187 brouard 6710:
1.136 brouard 6711: if(decodemodel(model, lastobs) == 1)
6712: goto end;
6713:
1.137 brouard 6714: if((double)(lastobs-imx)/(double)imx > 1.10){
6715: nbwarn++;
6716: 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);
6717: 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);
6718: }
1.136 brouard 6719: /* if(mle==1){*/
1.137 brouard 6720: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6721: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6722: }
6723:
6724: /*-calculation of age at interview from date of interview and age at death -*/
6725: agev=matrix(1,maxwav,1,imx);
6726:
6727: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6728: goto end;
6729:
1.126 brouard 6730:
1.136 brouard 6731: agegomp=(int)agemin;
6732: free_vector(moisnais,1,n);
6733: free_vector(annais,1,n);
1.126 brouard 6734: /* free_matrix(mint,1,maxwav,1,n);
6735: free_matrix(anint,1,maxwav,1,n);*/
6736: free_vector(moisdc,1,n);
6737: free_vector(andc,1,n);
1.145 brouard 6738: /* */
6739:
1.126 brouard 6740: wav=ivector(1,imx);
6741: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6742: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6743: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6744:
6745: /* Concatenates waves */
6746: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6747: /* */
6748:
1.126 brouard 6749: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6750:
6751: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6752: ncodemax[1]=1;
1.145 brouard 6753: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6754: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6755: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6756: /* Nbcode gives the value of the lth modality of jth covariate, in
6757: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6758: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6759:
6760: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6761: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6762: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6763: h=0;
6764:
6765:
6766: /*if (cptcovn > 0) */
1.126 brouard 6767:
1.145 brouard 6768:
1.126 brouard 6769: m=pow(2,cptcoveff);
6770:
1.131 brouard 6771: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6772: 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 */
6773: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6774: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 6775: h++;
1.141 brouard 6776: if (h>m)
1.136 brouard 6777: h=1;
1.144 brouard 6778: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6779: * For k=4 covariates, h goes from 1 to 2**k
6780: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6781: * h\k 1 2 3 4
1.143 brouard 6782: *______________________________
6783: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6784: * 2 2 1 1 1
6785: * 3 i=2 1 2 1 1
6786: * 4 2 2 1 1
6787: * 5 i=3 1 i=2 1 2 1
6788: * 6 2 1 2 1
6789: * 7 i=4 1 2 2 1
6790: * 8 2 2 2 1
6791: * 9 i=5 1 i=3 1 i=2 1 1
6792: * 10 2 1 1 1
6793: * 11 i=6 1 2 1 1
6794: * 12 2 2 1 1
6795: * 13 i=7 1 i=4 1 2 1
6796: * 14 2 1 2 1
6797: * 15 i=8 1 2 2 1
6798: * 16 2 2 2 1
6799: */
1.141 brouard 6800: codtab[h][k]=j;
1.186 brouard 6801: /* codtab[12][3]=1; */
1.145 brouard 6802: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6803: 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]]);
1.126 brouard 6804: }
6805: }
6806: }
6807: }
6808: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6809: codtab[1][2]=1;codtab[2][2]=2; */
6810: /* for(i=1; i <=m ;i++){
6811: for(k=1; k <=cptcovn; k++){
1.131 brouard 6812: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6813: }
6814: printf("\n");
6815: }
6816: scanf("%d",i);*/
1.145 brouard 6817:
6818: free_ivector(Ndum,-1,NCOVMAX);
6819:
6820:
1.126 brouard 6821:
1.186 brouard 6822: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6823: strcpy(optionfilegnuplot,optionfilefiname);
6824: if(mle==-3)
6825: strcat(optionfilegnuplot,"-mort");
6826: strcat(optionfilegnuplot,".gp");
6827:
6828: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6829: printf("Problem with file %s",optionfilegnuplot);
6830: }
6831: else{
6832: fprintf(ficgp,"\n# %s\n", version);
6833: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6834: //fprintf(ficgp,"set missing 'NaNq'\n");
6835: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6836: }
6837: /* fclose(ficgp);*/
1.186 brouard 6838:
6839:
6840: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6841:
6842: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6843: if(mle==-3)
6844: strcat(optionfilehtm,"-mort");
6845: strcat(optionfilehtm,".htm");
6846: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6847: printf("Problem with %s \n",optionfilehtm);
6848: exit(0);
1.126 brouard 6849: }
6850:
6851: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6852: strcat(optionfilehtmcov,"-cov.htm");
6853: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6854: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6855: }
6856: else{
6857: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6858: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6859: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6860: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6861: }
6862:
6863: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6864: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6865: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6866: \n\
6867: <hr size=\"2\" color=\"#EC5E5E\">\
6868: <ul><li><h4>Parameter files</h4>\n\
6869: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6870: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6871: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6872: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6873: - Date and time at start: %s</ul>\n",\
6874: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6875: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6876: fileres,fileres,\
6877: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6878: fflush(fichtm);
6879:
6880: strcpy(pathr,path);
6881: strcat(pathr,optionfilefiname);
1.184 brouard 6882: #ifdef WIN32
6883: _chdir(optionfilefiname); /* Move to directory named optionfile */
6884: #else
1.126 brouard 6885: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6886: #endif
6887:
1.126 brouard 6888:
6889: /* Calculates basic frequencies. Computes observed prevalence at single age
6890: and prints on file fileres'p'. */
6891: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6892:
6893: fprintf(fichtm,"\n");
6894: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6895: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6896: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6897: imx,agemin,agemax,jmin,jmax,jmean);
6898: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6899: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6900: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6901: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6902: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6903:
6904:
6905: /* For Powell, parameters are in a vector p[] starting at p[1]
6906: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6907: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6908:
6909: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6910: /* For mortality only */
1.126 brouard 6911: if (mle==-3){
1.136 brouard 6912: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6913: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6914: cens=ivector(1,n);
6915: ageexmed=vector(1,n);
6916: agecens=vector(1,n);
6917: dcwave=ivector(1,n);
6918:
6919: for (i=1; i<=imx; i++){
6920: dcwave[i]=-1;
6921: for (m=firstpass; m<=lastpass; m++)
6922: if (s[m][i]>nlstate) {
6923: dcwave[i]=m;
6924: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6925: break;
6926: }
6927: }
6928:
6929: for (i=1; i<=imx; i++) {
6930: if (wav[i]>0){
6931: ageexmed[i]=agev[mw[1][i]][i];
6932: j=wav[i];
6933: agecens[i]=1.;
6934:
6935: if (ageexmed[i]> 1 && wav[i] > 0){
6936: agecens[i]=agev[mw[j][i]][i];
6937: cens[i]= 1;
6938: }else if (ageexmed[i]< 1)
6939: cens[i]= -1;
6940: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6941: cens[i]=0 ;
6942: }
6943: else cens[i]=-1;
6944: }
6945:
6946: for (i=1;i<=NDIM;i++) {
6947: for (j=1;j<=NDIM;j++)
6948: ximort[i][j]=(i == j ? 1.0 : 0.0);
6949: }
6950:
1.145 brouard 6951: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6952: /*printf("%lf %lf", p[1], p[2]);*/
6953:
6954:
1.136 brouard 6955: #ifdef GSL
6956: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6957: #else
1.126 brouard 6958: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6959: #endif
1.126 brouard 6960: strcpy(filerespow,"pow-mort");
6961: strcat(filerespow,fileres);
6962: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6963: printf("Problem with resultfile: %s\n", filerespow);
6964: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6965: }
1.136 brouard 6966: #ifdef GSL
6967: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6968: #else
1.126 brouard 6969: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6970: #endif
1.126 brouard 6971: /* for (i=1;i<=nlstate;i++)
6972: for(j=1;j<=nlstate+ndeath;j++)
6973: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6974: */
6975: fprintf(ficrespow,"\n");
1.136 brouard 6976: #ifdef GSL
6977: /* gsl starts here */
6978: T = gsl_multimin_fminimizer_nmsimplex;
6979: gsl_multimin_fminimizer *sfm = NULL;
6980: gsl_vector *ss, *x;
6981: gsl_multimin_function minex_func;
6982:
6983: /* Initial vertex size vector */
6984: ss = gsl_vector_alloc (NDIM);
6985:
6986: if (ss == NULL){
6987: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6988: }
6989: /* Set all step sizes to 1 */
6990: gsl_vector_set_all (ss, 0.001);
6991:
6992: /* Starting point */
1.126 brouard 6993:
1.136 brouard 6994: x = gsl_vector_alloc (NDIM);
6995:
6996: if (x == NULL){
6997: gsl_vector_free(ss);
6998: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6999: }
7000:
7001: /* Initialize method and iterate */
7002: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7003: /* gsl_vector_set(x, 0, 0.0268); */
7004: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7005: gsl_vector_set(x, 0, p[1]);
7006: gsl_vector_set(x, 1, p[2]);
7007:
7008: minex_func.f = &gompertz_f;
7009: minex_func.n = NDIM;
7010: minex_func.params = (void *)&p; /* ??? */
7011:
7012: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7013: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7014:
7015: printf("Iterations beginning .....\n\n");
7016: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7017:
7018: iteri=0;
7019: while (rval == GSL_CONTINUE){
7020: iteri++;
7021: status = gsl_multimin_fminimizer_iterate(sfm);
7022:
7023: if (status) printf("error: %s\n", gsl_strerror (status));
7024: fflush(0);
7025:
7026: if (status)
7027: break;
7028:
7029: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7030: ssval = gsl_multimin_fminimizer_size (sfm);
7031:
7032: if (rval == GSL_SUCCESS)
7033: printf ("converged to a local maximum at\n");
7034:
7035: printf("%5d ", iteri);
7036: for (it = 0; it < NDIM; it++){
7037: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7038: }
7039: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7040: }
7041:
7042: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7043:
7044: gsl_vector_free(x); /* initial values */
7045: gsl_vector_free(ss); /* inital step size */
7046: for (it=0; it<NDIM; it++){
7047: p[it+1]=gsl_vector_get(sfm->x,it);
7048: fprintf(ficrespow," %.12lf", p[it]);
7049: }
7050: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7051: #endif
7052: #ifdef POWELL
7053: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7054: #endif
1.126 brouard 7055: fclose(ficrespow);
7056:
7057: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7058:
7059: for(i=1; i <=NDIM; i++)
7060: for(j=i+1;j<=NDIM;j++)
7061: matcov[i][j]=matcov[j][i];
7062:
7063: printf("\nCovariance matrix\n ");
7064: for(i=1; i <=NDIM; i++) {
7065: for(j=1;j<=NDIM;j++){
7066: printf("%f ",matcov[i][j]);
7067: }
7068: printf("\n ");
7069: }
7070:
7071: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7072: for (i=1;i<=NDIM;i++)
7073: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7074:
7075: lsurv=vector(1,AGESUP);
7076: lpop=vector(1,AGESUP);
7077: tpop=vector(1,AGESUP);
7078: lsurv[agegomp]=100000;
7079:
7080: for (k=agegomp;k<=AGESUP;k++) {
7081: agemortsup=k;
7082: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7083: }
7084:
7085: for (k=agegomp;k<agemortsup;k++)
7086: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7087:
7088: for (k=agegomp;k<agemortsup;k++){
7089: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7090: sumlpop=sumlpop+lpop[k];
7091: }
7092:
7093: tpop[agegomp]=sumlpop;
7094: for (k=agegomp;k<(agemortsup-3);k++){
7095: /* tpop[k+1]=2;*/
7096: tpop[k+1]=tpop[k]-lpop[k];
7097: }
7098:
7099:
7100: printf("\nAge lx qx dx Lx Tx e(x)\n");
7101: for (k=agegomp;k<(agemortsup-2);k++)
7102: 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]);
7103:
7104:
7105: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7106: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7107:
7108: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7109: stepm, weightopt,\
7110: model,imx,p,matcov,agemortsup);
7111:
7112: free_vector(lsurv,1,AGESUP);
7113: free_vector(lpop,1,AGESUP);
7114: free_vector(tpop,1,AGESUP);
1.136 brouard 7115: #ifdef GSL
7116: free_ivector(cens,1,n);
7117: free_vector(agecens,1,n);
7118: free_ivector(dcwave,1,n);
7119: free_matrix(ximort,1,NDIM,1,NDIM);
7120: #endif
1.186 brouard 7121: } /* Endof if mle==-3 mortality only */
7122: /* Standard maximisation */
1.126 brouard 7123: else{ /* For mle >=1 */
1.132 brouard 7124: globpr=0;/* debug */
1.186 brouard 7125: /* Computes likelihood for initial parameters */
1.132 brouard 7126: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7127: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7128: for (k=1; k<=npar;k++)
7129: printf(" %d %8.5f",k,p[k]);
7130: printf("\n");
1.186 brouard 7131: globpr=1; /* again, to print the contributions */
1.126 brouard 7132: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7133: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7134: for (k=1; k<=npar;k++)
7135: printf(" %d %8.5f",k,p[k]);
7136: printf("\n");
1.186 brouard 7137: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7138: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7139: }
7140:
7141: /*--------- results files --------------*/
1.187 brouard 7142: 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);
1.126 brouard 7143:
7144:
7145: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7146: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7147: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7148: for(i=1,jk=1; i <=nlstate; i++){
7149: for(k=1; k <=(nlstate+ndeath); k++){
7150: if (k != i) {
7151: printf("%d%d ",i,k);
7152: fprintf(ficlog,"%d%d ",i,k);
7153: fprintf(ficres,"%1d%1d ",i,k);
7154: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7155: printf("%12.7f ",p[jk]);
7156: fprintf(ficlog,"%12.7f ",p[jk]);
7157: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7158: jk++;
7159: }
7160: printf("\n");
7161: fprintf(ficlog,"\n");
7162: fprintf(ficres,"\n");
7163: }
7164: }
7165: }
7166: if(mle!=0){
7167: /* Computing hessian and covariance matrix */
7168: ftolhess=ftol; /* Usually correct */
7169: hesscov(matcov, p, npar, delti, ftolhess, func);
7170: }
7171: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7172: printf("# Scales (for hessian or gradient estimation)\n");
7173: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7174: for(i=1,jk=1; i <=nlstate; i++){
7175: for(j=1; j <=nlstate+ndeath; j++){
7176: if (j!=i) {
7177: fprintf(ficres,"%1d%1d",i,j);
7178: printf("%1d%1d",i,j);
7179: fprintf(ficlog,"%1d%1d",i,j);
7180: for(k=1; k<=ncovmodel;k++){
7181: printf(" %.5e",delti[jk]);
7182: fprintf(ficlog," %.5e",delti[jk]);
7183: fprintf(ficres," %.5e",delti[jk]);
7184: jk++;
7185: }
7186: printf("\n");
7187: fprintf(ficlog,"\n");
7188: fprintf(ficres,"\n");
7189: }
7190: }
7191: }
7192:
7193: 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");
7194: if(mle>=1)
7195: 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");
7196: 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");
7197: /* # 121 Var(a12)\n\ */
7198: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7199: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7200: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7201: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7202: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7203: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7204: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7205:
7206:
7207: /* Just to have a covariance matrix which will be more understandable
7208: even is we still don't want to manage dictionary of variables
7209: */
7210: for(itimes=1;itimes<=2;itimes++){
7211: jj=0;
7212: for(i=1; i <=nlstate; i++){
7213: for(j=1; j <=nlstate+ndeath; j++){
7214: if(j==i) continue;
7215: for(k=1; k<=ncovmodel;k++){
7216: jj++;
7217: ca[0]= k+'a'-1;ca[1]='\0';
7218: if(itimes==1){
7219: if(mle>=1)
7220: printf("#%1d%1d%d",i,j,k);
7221: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7222: fprintf(ficres,"#%1d%1d%d",i,j,k);
7223: }else{
7224: if(mle>=1)
7225: printf("%1d%1d%d",i,j,k);
7226: fprintf(ficlog,"%1d%1d%d",i,j,k);
7227: fprintf(ficres,"%1d%1d%d",i,j,k);
7228: }
7229: ll=0;
7230: for(li=1;li <=nlstate; li++){
7231: for(lj=1;lj <=nlstate+ndeath; lj++){
7232: if(lj==li) continue;
7233: for(lk=1;lk<=ncovmodel;lk++){
7234: ll++;
7235: if(ll<=jj){
7236: cb[0]= lk +'a'-1;cb[1]='\0';
7237: if(ll<jj){
7238: if(itimes==1){
7239: if(mle>=1)
7240: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7241: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7242: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7243: }else{
7244: if(mle>=1)
7245: printf(" %.5e",matcov[jj][ll]);
7246: fprintf(ficlog," %.5e",matcov[jj][ll]);
7247: fprintf(ficres," %.5e",matcov[jj][ll]);
7248: }
7249: }else{
7250: if(itimes==1){
7251: if(mle>=1)
7252: printf(" Var(%s%1d%1d)",ca,i,j);
7253: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7254: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7255: }else{
7256: if(mle>=1)
7257: printf(" %.5e",matcov[jj][ll]);
7258: fprintf(ficlog," %.5e",matcov[jj][ll]);
7259: fprintf(ficres," %.5e",matcov[jj][ll]);
7260: }
7261: }
7262: }
7263: } /* end lk */
7264: } /* end lj */
7265: } /* end li */
7266: if(mle>=1)
7267: printf("\n");
7268: fprintf(ficlog,"\n");
7269: fprintf(ficres,"\n");
7270: numlinepar++;
7271: } /* end k*/
7272: } /*end j */
7273: } /* end i */
7274: } /* end itimes */
7275:
7276: fflush(ficlog);
7277: fflush(ficres);
7278:
7279: while((c=getc(ficpar))=='#' && c!= EOF){
7280: ungetc(c,ficpar);
7281: fgets(line, MAXLINE, ficpar);
1.141 brouard 7282: fputs(line,stdout);
1.126 brouard 7283: fputs(line,ficparo);
7284: }
7285: ungetc(c,ficpar);
7286:
7287: estepm=0;
7288: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7289: if (estepm==0 || estepm < stepm) estepm=stepm;
7290: if (fage <= 2) {
7291: bage = ageminpar;
7292: fage = agemaxpar;
7293: }
7294:
7295: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7296: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7297: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7298:
7299: /* Other stuffs, more or less useful */
1.126 brouard 7300: while((c=getc(ficpar))=='#' && c!= EOF){
7301: ungetc(c,ficpar);
7302: fgets(line, MAXLINE, ficpar);
1.141 brouard 7303: fputs(line,stdout);
1.126 brouard 7304: fputs(line,ficparo);
7305: }
7306: ungetc(c,ficpar);
7307:
7308: 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);
7309: 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);
7310: 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);
7311: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7312: 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);
7313:
7314: while((c=getc(ficpar))=='#' && c!= EOF){
7315: ungetc(c,ficpar);
7316: fgets(line, MAXLINE, ficpar);
1.141 brouard 7317: fputs(line,stdout);
1.126 brouard 7318: fputs(line,ficparo);
7319: }
7320: ungetc(c,ficpar);
7321:
7322:
7323: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7324: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7325:
7326: fscanf(ficpar,"pop_based=%d\n",&popbased);
7327: fprintf(ficparo,"pop_based=%d\n",popbased);
7328: fprintf(ficres,"pop_based=%d\n",popbased);
7329:
7330: while((c=getc(ficpar))=='#' && c!= EOF){
7331: ungetc(c,ficpar);
7332: fgets(line, MAXLINE, ficpar);
1.141 brouard 7333: fputs(line,stdout);
1.126 brouard 7334: fputs(line,ficparo);
7335: }
7336: ungetc(c,ficpar);
7337:
7338: 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);
7339: 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);
7340: 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);
7341: 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);
7342: 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);
7343: /* day and month of proj2 are not used but only year anproj2.*/
7344:
7345:
7346:
1.145 brouard 7347: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7348: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7349:
7350: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7351: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7352:
7353: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7354: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7355: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7356:
7357: /*------------ free_vector -------------*/
7358: /* chdir(path); */
7359:
7360: free_ivector(wav,1,imx);
7361: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7362: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7363: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7364: free_lvector(num,1,n);
7365: free_vector(agedc,1,n);
7366: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7367: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7368: fclose(ficparo);
7369: fclose(ficres);
7370:
7371:
1.186 brouard 7372: /* Other results (useful)*/
7373:
7374:
1.126 brouard 7375: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7376: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7377: prlim=matrix(1,nlstate,1,nlstate);
7378: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7379: fclose(ficrespl);
7380:
1.145 brouard 7381: #ifdef FREEEXIT2
7382: #include "freeexit2.h"
7383: #endif
7384:
1.126 brouard 7385: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7386: /*#include "hpijx.h"*/
7387: hPijx(p, bage, fage);
1.145 brouard 7388: fclose(ficrespij);
1.126 brouard 7389:
1.145 brouard 7390: /*-------------- Variance of one-step probabilities---*/
7391: k=1;
1.126 brouard 7392: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7393:
7394:
7395: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7396: for(i=1;i<=AGESUP;i++)
7397: for(j=1;j<=NCOVMAX;j++)
7398: for(k=1;k<=NCOVMAX;k++)
7399: probs[i][j][k]=0.;
7400:
7401: /*---------- Forecasting ------------------*/
7402: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7403: if(prevfcast==1){
7404: /* if(stepm ==1){*/
7405: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7406: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7407: /* } */
7408: /* else{ */
7409: /* erreur=108; */
7410: /* 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); */
7411: /* 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); */
7412: /* } */
7413: }
1.186 brouard 7414:
7415: /* ------ Other prevalence ratios------------ */
1.126 brouard 7416:
1.127 brouard 7417: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7418:
7419: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7420: /* 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",\
7421: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7422: */
1.126 brouard 7423:
1.127 brouard 7424: if (mobilav!=0) {
7425: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7426: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7427: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7428: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7429: }
1.126 brouard 7430: }
7431:
7432:
1.127 brouard 7433: /*---------- Health expectancies, no variances ------------*/
7434:
1.126 brouard 7435: strcpy(filerese,"e");
7436: strcat(filerese,fileres);
7437: if((ficreseij=fopen(filerese,"w"))==NULL) {
7438: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7439: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7440: }
7441: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7442: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7443: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7444: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7445:
7446: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7447: fprintf(ficreseij,"\n#****** ");
7448: for(j=1;j<=cptcoveff;j++) {
7449: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7450: }
7451: fprintf(ficreseij,"******\n");
7452:
7453: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7454: oldm=oldms;savm=savms;
7455: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7456:
7457: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7458: /*}*/
1.127 brouard 7459: }
7460: fclose(ficreseij);
7461:
7462:
7463: /*---------- Health expectancies and variances ------------*/
7464:
7465:
7466: strcpy(filerest,"t");
7467: strcat(filerest,fileres);
7468: if((ficrest=fopen(filerest,"w"))==NULL) {
7469: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7470: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7471: }
7472: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7473: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7474:
1.126 brouard 7475:
7476: strcpy(fileresstde,"stde");
7477: strcat(fileresstde,fileres);
7478: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7479: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7480: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7481: }
7482: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7483: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7484:
7485: strcpy(filerescve,"cve");
7486: strcat(filerescve,fileres);
7487: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7488: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7489: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7490: }
7491: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7492: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7493:
7494: strcpy(fileresv,"v");
7495: strcat(fileresv,fileres);
7496: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7497: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7498: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7499: }
7500: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7501: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7502:
1.145 brouard 7503: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7504: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7505:
7506: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7507: fprintf(ficrest,"\n#****** ");
1.126 brouard 7508: for(j=1;j<=cptcoveff;j++)
7509: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7510: fprintf(ficrest,"******\n");
7511:
7512: fprintf(ficresstdeij,"\n#****** ");
7513: fprintf(ficrescveij,"\n#****** ");
7514: for(j=1;j<=cptcoveff;j++) {
7515: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7516: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7517: }
7518: fprintf(ficresstdeij,"******\n");
7519: fprintf(ficrescveij,"******\n");
7520:
7521: fprintf(ficresvij,"\n#****** ");
7522: for(j=1;j<=cptcoveff;j++)
7523: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7524: fprintf(ficresvij,"******\n");
7525:
7526: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7527: oldm=oldms;savm=savms;
1.127 brouard 7528: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7529: /*
7530: */
7531: /* goto endfree; */
1.126 brouard 7532:
7533: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7534: pstamp(ficrest);
1.145 brouard 7535:
7536:
1.128 brouard 7537: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7538: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7539: cptcod= 0; /* To be deleted */
7540: 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 */
1.145 brouard 7541: 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 ");
1.128 brouard 7542: if(vpopbased==1)
7543: 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);
7544: else
7545: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7546: fprintf(ficrest,"# Age e.. (std) ");
7547: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7548: fprintf(ficrest,"\n");
1.126 brouard 7549:
1.128 brouard 7550: epj=vector(1,nlstate+1);
7551: for(age=bage; age <=fage ;age++){
7552: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7553: if (vpopbased==1) {
7554: if(mobilav ==0){
7555: for(i=1; i<=nlstate;i++)
7556: prlim[i][i]=probs[(int)age][i][k];
7557: }else{ /* mobilav */
7558: for(i=1; i<=nlstate;i++)
7559: prlim[i][i]=mobaverage[(int)age][i][k];
7560: }
1.126 brouard 7561: }
7562:
1.128 brouard 7563: fprintf(ficrest," %4.0f",age);
7564: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7565: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7566: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7567: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7568: }
7569: epj[nlstate+1] +=epj[j];
1.126 brouard 7570: }
7571:
1.128 brouard 7572: for(i=1, vepp=0.;i <=nlstate;i++)
7573: for(j=1;j <=nlstate;j++)
7574: vepp += vareij[i][j][(int)age];
7575: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7576: for(j=1;j <=nlstate;j++){
7577: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7578: }
7579: fprintf(ficrest,"\n");
1.126 brouard 7580: }
7581: }
7582: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7583: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7584: free_vector(epj,1,nlstate+1);
1.145 brouard 7585: /*}*/
1.126 brouard 7586: }
7587: free_vector(weight,1,n);
1.145 brouard 7588: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7589: free_imatrix(s,1,maxwav+1,1,n);
7590: free_matrix(anint,1,maxwav,1,n);
7591: free_matrix(mint,1,maxwav,1,n);
7592: free_ivector(cod,1,n);
7593: free_ivector(tab,1,NCOVMAX);
7594: fclose(ficresstdeij);
7595: fclose(ficrescveij);
7596: fclose(ficresvij);
7597: fclose(ficrest);
7598: fclose(ficpar);
7599:
7600: /*------- Variance of period (stable) prevalence------*/
7601:
7602: strcpy(fileresvpl,"vpl");
7603: strcat(fileresvpl,fileres);
7604: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7605: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7606: exit(0);
7607: }
7608: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7609:
1.145 brouard 7610: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7611: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7612:
7613: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7614: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7615: for(j=1;j<=cptcoveff;j++)
7616: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7617: fprintf(ficresvpl,"******\n");
7618:
7619: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7620: oldm=oldms;savm=savms;
7621: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7622: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7623: /*}*/
1.126 brouard 7624: }
7625:
7626: fclose(ficresvpl);
7627:
7628: /*---------- End : free ----------------*/
7629: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7630: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7631: } /* mle==-3 arrives here for freeing */
1.164 brouard 7632: /* endfree:*/
1.141 brouard 7633: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7634: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7635: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7636: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7637: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7638: free_matrix(covar,0,NCOVMAX,1,n);
7639: free_matrix(matcov,1,npar,1,npar);
7640: /*free_vector(delti,1,npar);*/
7641: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7642: free_matrix(agev,1,maxwav,1,imx);
7643: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7644:
1.145 brouard 7645: free_ivector(ncodemax,1,NCOVMAX);
7646: free_ivector(Tvar,1,NCOVMAX);
7647: free_ivector(Tprod,1,NCOVMAX);
7648: free_ivector(Tvaraff,1,NCOVMAX);
7649: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7650:
7651: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7652: free_imatrix(codtab,1,100,1,10);
7653: fflush(fichtm);
7654: fflush(ficgp);
7655:
7656:
7657: if((nberr >0) || (nbwarn>0)){
7658: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7659: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7660: }else{
7661: printf("End of Imach\n");
7662: fprintf(ficlog,"End of Imach\n");
7663: }
7664: printf("See log file on %s\n",filelog);
7665: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7666: /*(void) gettimeofday(&end_time,&tzp);*/
7667: rend_time = time(NULL);
7668: end_time = *localtime(&rend_time);
7669: /* tml = *localtime(&end_time.tm_sec); */
7670: strcpy(strtend,asctime(&end_time));
1.126 brouard 7671: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7672: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7673: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7674:
1.157 brouard 7675: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7676: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7677: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7678: /* printf("Total time was %d uSec.\n", total_usecs);*/
7679: /* if(fileappend(fichtm,optionfilehtm)){ */
7680: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7681: fclose(fichtm);
7682: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7683: fclose(fichtmcov);
7684: fclose(ficgp);
7685: fclose(ficlog);
7686: /*------ End -----------*/
7687:
7688:
7689: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7690: #ifdef WIN32
7691: if (_chdir(pathcd) != 0)
7692: printf("Can't move to directory %s!\n",path);
7693: if(_getcwd(pathcd,MAXLINE) > 0)
7694: #else
1.126 brouard 7695: if(chdir(pathcd) != 0)
1.184 brouard 7696: printf("Can't move to directory %s!\n", path);
7697: if (getcwd(pathcd, MAXLINE) > 0)
7698: #endif
1.126 brouard 7699: printf("Current directory %s!\n",pathcd);
7700: /*strcat(plotcmd,CHARSEPARATOR);*/
7701: sprintf(plotcmd,"gnuplot");
1.157 brouard 7702: #ifdef _WIN32
1.126 brouard 7703: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7704: #endif
7705: if(!stat(plotcmd,&info)){
1.158 brouard 7706: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7707: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7708: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7709: }else
7710: strcpy(pplotcmd,plotcmd);
1.157 brouard 7711: #ifdef __unix
1.126 brouard 7712: strcpy(plotcmd,GNUPLOTPROGRAM);
7713: if(!stat(plotcmd,&info)){
1.158 brouard 7714: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7715: }else
7716: strcpy(pplotcmd,plotcmd);
7717: #endif
7718: }else
7719: strcpy(pplotcmd,plotcmd);
7720:
7721: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7722: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7723:
7724: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7725: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7726: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7727: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7728: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7729: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7730: }
1.158 brouard 7731: printf(" Successful, please wait...");
1.126 brouard 7732: while (z[0] != 'q') {
7733: /* chdir(path); */
1.154 brouard 7734: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7735: scanf("%s",z);
7736: /* if (z[0] == 'c') system("./imach"); */
7737: if (z[0] == 'e') {
1.158 brouard 7738: #ifdef __APPLE__
1.152 brouard 7739: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7740: #elif __linux
7741: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7742: #else
1.152 brouard 7743: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7744: #endif
7745: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7746: system(pplotcmd);
1.126 brouard 7747: }
7748: else if (z[0] == 'g') system(plotcmd);
7749: else if (z[0] == 'q') exit(0);
7750: }
7751: end:
7752: while (z[0] != 'q') {
7753: printf("\nType q for exiting: ");
7754: scanf("%s",z);
7755: }
7756: }
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src