Annotation of imach/src/imach.c, revision 1.193
1.193 ! brouard 1: /* $Id: imach.c,v 1.192 2015/07/16 16:49:02 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.193 ! brouard 4: Revision 1.192 2015/07/16 16:49:02 brouard
! 5: Summary: Fixing some outputs
! 6:
1.192 brouard 7: Revision 1.191 2015/07/14 10:00:33 brouard
8: Summary: Some fixes
9:
1.191 brouard 10: Revision 1.190 2015/05/05 08:51:13 brouard
11: Summary: Adding digits in output parameters (7 digits instead of 6)
12:
13: Fix 1+age+.
14:
1.190 brouard 15: Revision 1.189 2015/04/30 14:45:16 brouard
16: Summary: 0.98q2
17:
1.189 brouard 18: Revision 1.188 2015/04/30 08:27:53 brouard
19: *** empty log message ***
20:
1.188 brouard 21: Revision 1.187 2015/04/29 09:11:15 brouard
22: *** empty log message ***
23:
1.187 brouard 24: Revision 1.186 2015/04/23 12:01:52 brouard
25: Summary: V1*age is working now, version 0.98q1
26:
27: Some codes had been disabled in order to simplify and Vn*age was
28: working in the optimization phase, ie, giving correct MLE parameters,
29: but, as usual, outputs were not correct and program core dumped.
30:
1.186 brouard 31: Revision 1.185 2015/03/11 13:26:42 brouard
32: Summary: Inclusion of compile and links command line for Intel Compiler
33:
1.185 brouard 34: Revision 1.184 2015/03/11 11:52:39 brouard
35: Summary: Back from Windows 8. Intel Compiler
36:
1.184 brouard 37: Revision 1.183 2015/03/10 20:34:32 brouard
38: Summary: 0.98q0, trying with directest, mnbrak fixed
39:
40: We use directest instead of original Powell test; probably no
41: incidence on the results, but better justifications;
42: We fixed Numerical Recipes mnbrak routine which was wrong and gave
43: wrong results.
44:
1.183 brouard 45: Revision 1.182 2015/02/12 08:19:57 brouard
46: Summary: Trying to keep directest which seems simpler and more general
47: Author: Nicolas Brouard
48:
1.182 brouard 49: Revision 1.181 2015/02/11 23:22:24 brouard
50: Summary: Comments on Powell added
51:
52: Author:
53:
1.181 brouard 54: Revision 1.180 2015/02/11 17:33:45 brouard
55: Summary: Finishing move from main to function (hpijx and prevalence_limit)
56:
1.180 brouard 57: Revision 1.179 2015/01/04 09:57:06 brouard
58: Summary: back to OS/X
59:
1.179 brouard 60: Revision 1.178 2015/01/04 09:35:48 brouard
61: *** empty log message ***
62:
1.178 brouard 63: Revision 1.177 2015/01/03 18:40:56 brouard
64: Summary: Still testing ilc32 on OSX
65:
1.177 brouard 66: Revision 1.176 2015/01/03 16:45:04 brouard
67: *** empty log message ***
68:
1.176 brouard 69: Revision 1.175 2015/01/03 16:33:42 brouard
70: *** empty log message ***
71:
1.175 brouard 72: Revision 1.174 2015/01/03 16:15:49 brouard
73: Summary: Still in cross-compilation
74:
1.174 brouard 75: Revision 1.173 2015/01/03 12:06:26 brouard
76: Summary: trying to detect cross-compilation
77:
1.173 brouard 78: Revision 1.172 2014/12/27 12:07:47 brouard
79: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
80:
1.172 brouard 81: Revision 1.171 2014/12/23 13:26:59 brouard
82: Summary: Back from Visual C
83:
84: Still problem with utsname.h on Windows
85:
1.171 brouard 86: Revision 1.170 2014/12/23 11:17:12 brouard
87: Summary: Cleaning some \%% back to %%
88:
89: The escape was mandatory for a specific compiler (which one?), but too many warnings.
90:
1.170 brouard 91: Revision 1.169 2014/12/22 23:08:31 brouard
92: Summary: 0.98p
93:
94: Outputs some informations on compiler used, OS etc. Testing on different platforms.
95:
1.169 brouard 96: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 97: Summary: update
1.169 brouard 98:
1.168 brouard 99: Revision 1.167 2014/12/22 13:50:56 brouard
100: Summary: Testing uname and compiler version and if compiled 32 or 64
101:
102: Testing on Linux 64
103:
1.167 brouard 104: Revision 1.166 2014/12/22 11:40:47 brouard
105: *** empty log message ***
106:
1.166 brouard 107: Revision 1.165 2014/12/16 11:20:36 brouard
108: Summary: After compiling on Visual C
109:
110: * imach.c (Module): Merging 1.61 to 1.162
111:
1.165 brouard 112: Revision 1.164 2014/12/16 10:52:11 brouard
113: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
114:
115: * imach.c (Module): Merging 1.61 to 1.162
116:
1.164 brouard 117: Revision 1.163 2014/12/16 10:30:11 brouard
118: * imach.c (Module): Merging 1.61 to 1.162
119:
1.163 brouard 120: Revision 1.162 2014/09/25 11:43:39 brouard
121: Summary: temporary backup 0.99!
122:
1.162 brouard 123: Revision 1.1 2014/09/16 11:06:58 brouard
124: Summary: With some code (wrong) for nlopt
125:
126: Author:
127:
128: Revision 1.161 2014/09/15 20:41:41 brouard
129: Summary: Problem with macro SQR on Intel compiler
130:
1.161 brouard 131: Revision 1.160 2014/09/02 09:24:05 brouard
132: *** empty log message ***
133:
1.160 brouard 134: Revision 1.159 2014/09/01 10:34:10 brouard
135: Summary: WIN32
136: Author: Brouard
137:
1.159 brouard 138: Revision 1.158 2014/08/27 17:11:51 brouard
139: *** empty log message ***
140:
1.158 brouard 141: Revision 1.157 2014/08/27 16:26:55 brouard
142: Summary: Preparing windows Visual studio version
143: Author: Brouard
144:
145: In order to compile on Visual studio, time.h is now correct and time_t
146: and tm struct should be used. difftime should be used but sometimes I
147: just make the differences in raw time format (time(&now).
148: Trying to suppress #ifdef LINUX
149: Add xdg-open for __linux in order to open default browser.
150:
1.157 brouard 151: Revision 1.156 2014/08/25 20:10:10 brouard
152: *** empty log message ***
153:
1.156 brouard 154: Revision 1.155 2014/08/25 18:32:34 brouard
155: Summary: New compile, minor changes
156: Author: Brouard
157:
1.155 brouard 158: Revision 1.154 2014/06/20 17:32:08 brouard
159: Summary: Outputs now all graphs of convergence to period prevalence
160:
1.154 brouard 161: Revision 1.153 2014/06/20 16:45:46 brouard
162: Summary: If 3 live state, convergence to period prevalence on same graph
163: Author: Brouard
164:
1.153 brouard 165: Revision 1.152 2014/06/18 17:54:09 brouard
166: Summary: open browser, use gnuplot on same dir than imach if not found in the path
167:
1.152 brouard 168: Revision 1.151 2014/06/18 16:43:30 brouard
169: *** empty log message ***
170:
1.151 brouard 171: Revision 1.150 2014/06/18 16:42:35 brouard
172: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
173: Author: brouard
174:
1.150 brouard 175: Revision 1.149 2014/06/18 15:51:14 brouard
176: Summary: Some fixes in parameter files errors
177: Author: Nicolas Brouard
178:
1.149 brouard 179: Revision 1.148 2014/06/17 17:38:48 brouard
180: Summary: Nothing new
181: Author: Brouard
182:
183: Just a new packaging for OS/X version 0.98nS
184:
1.148 brouard 185: Revision 1.147 2014/06/16 10:33:11 brouard
186: *** empty log message ***
187:
1.147 brouard 188: Revision 1.146 2014/06/16 10:20:28 brouard
189: Summary: Merge
190: Author: Brouard
191:
192: Merge, before building revised version.
193:
1.146 brouard 194: Revision 1.145 2014/06/10 21:23:15 brouard
195: Summary: Debugging with valgrind
196: Author: Nicolas Brouard
197:
198: Lot of changes in order to output the results with some covariates
199: After the Edimburgh REVES conference 2014, it seems mandatory to
200: improve the code.
201: No more memory valgrind error but a lot has to be done in order to
202: continue the work of splitting the code into subroutines.
203: Also, decodemodel has been improved. Tricode is still not
204: optimal. nbcode should be improved. Documentation has been added in
205: the source code.
206:
1.144 brouard 207: Revision 1.143 2014/01/26 09:45:38 brouard
208: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
209:
210: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
211: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
212:
1.143 brouard 213: Revision 1.142 2014/01/26 03:57:36 brouard
214: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
215:
216: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
217:
1.142 brouard 218: Revision 1.141 2014/01/26 02:42:01 brouard
219: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
220:
1.141 brouard 221: Revision 1.140 2011/09/02 10:37:54 brouard
222: Summary: times.h is ok with mingw32 now.
223:
1.140 brouard 224: Revision 1.139 2010/06/14 07:50:17 brouard
225: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
226: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
227:
1.139 brouard 228: Revision 1.138 2010/04/30 18:19:40 brouard
229: *** empty log message ***
230:
1.138 brouard 231: Revision 1.137 2010/04/29 18:11:38 brouard
232: (Module): Checking covariates for more complex models
233: than V1+V2. A lot of change to be done. Unstable.
234:
1.137 brouard 235: Revision 1.136 2010/04/26 20:30:53 brouard
236: (Module): merging some libgsl code. Fixing computation
237: of likelione (using inter/intrapolation if mle = 0) in order to
238: get same likelihood as if mle=1.
239: Some cleaning of code and comments added.
240:
1.136 brouard 241: Revision 1.135 2009/10/29 15:33:14 brouard
242: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
243:
1.135 brouard 244: Revision 1.134 2009/10/29 13:18:53 brouard
245: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
246:
1.134 brouard 247: Revision 1.133 2009/07/06 10:21:25 brouard
248: just nforces
249:
1.133 brouard 250: Revision 1.132 2009/07/06 08:22:05 brouard
251: Many tings
252:
1.132 brouard 253: Revision 1.131 2009/06/20 16:22:47 brouard
254: Some dimensions resccaled
255:
1.131 brouard 256: Revision 1.130 2009/05/26 06:44:34 brouard
257: (Module): Max Covariate is now set to 20 instead of 8. A
258: lot of cleaning with variables initialized to 0. Trying to make
259: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
260:
1.130 brouard 261: Revision 1.129 2007/08/31 13:49:27 lievre
262: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
263:
1.129 lievre 264: Revision 1.128 2006/06/30 13:02:05 brouard
265: (Module): Clarifications on computing e.j
266:
1.128 brouard 267: Revision 1.127 2006/04/28 18:11:50 brouard
268: (Module): Yes the sum of survivors was wrong since
269: imach-114 because nhstepm was no more computed in the age
270: loop. Now we define nhstepma in the age loop.
271: (Module): In order to speed up (in case of numerous covariates) we
272: compute health expectancies (without variances) in a first step
273: and then all the health expectancies with variances or standard
274: deviation (needs data from the Hessian matrices) which slows the
275: computation.
276: In the future we should be able to stop the program is only health
277: expectancies and graph are needed without standard deviations.
278:
1.127 brouard 279: Revision 1.126 2006/04/28 17:23:28 brouard
280: (Module): Yes the sum of survivors was wrong since
281: imach-114 because nhstepm was no more computed in the age
282: loop. Now we define nhstepma in the age loop.
283: Version 0.98h
284:
1.126 brouard 285: Revision 1.125 2006/04/04 15:20:31 lievre
286: Errors in calculation of health expectancies. Age was not initialized.
287: Forecasting file added.
288:
289: Revision 1.124 2006/03/22 17:13:53 lievre
290: Parameters are printed with %lf instead of %f (more numbers after the comma).
291: The log-likelihood is printed in the log file
292:
293: Revision 1.123 2006/03/20 10:52:43 brouard
294: * imach.c (Module): <title> changed, corresponds to .htm file
295: name. <head> headers where missing.
296:
297: * imach.c (Module): Weights can have a decimal point as for
298: English (a comma might work with a correct LC_NUMERIC environment,
299: otherwise the weight is truncated).
300: Modification of warning when the covariates values are not 0 or
301: 1.
302: Version 0.98g
303:
304: Revision 1.122 2006/03/20 09:45:41 brouard
305: (Module): Weights can have a decimal point as for
306: English (a comma might work with a correct LC_NUMERIC environment,
307: otherwise the weight is truncated).
308: Modification of warning when the covariates values are not 0 or
309: 1.
310: Version 0.98g
311:
312: Revision 1.121 2006/03/16 17:45:01 lievre
313: * imach.c (Module): Comments concerning covariates added
314:
315: * imach.c (Module): refinements in the computation of lli if
316: status=-2 in order to have more reliable computation if stepm is
317: not 1 month. Version 0.98f
318:
319: Revision 1.120 2006/03/16 15:10:38 lievre
320: (Module): refinements in the computation of lli if
321: status=-2 in order to have more reliable computation if stepm is
322: not 1 month. Version 0.98f
323:
324: Revision 1.119 2006/03/15 17:42:26 brouard
325: (Module): Bug if status = -2, the loglikelihood was
326: computed as likelihood omitting the logarithm. Version O.98e
327:
328: Revision 1.118 2006/03/14 18:20:07 brouard
329: (Module): varevsij Comments added explaining the second
330: table of variances if popbased=1 .
331: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
332: (Module): Function pstamp added
333: (Module): Version 0.98d
334:
335: Revision 1.117 2006/03/14 17:16:22 brouard
336: (Module): varevsij Comments added explaining the second
337: table of variances if popbased=1 .
338: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
339: (Module): Function pstamp added
340: (Module): Version 0.98d
341:
342: Revision 1.116 2006/03/06 10:29:27 brouard
343: (Module): Variance-covariance wrong links and
344: varian-covariance of ej. is needed (Saito).
345:
346: Revision 1.115 2006/02/27 12:17:45 brouard
347: (Module): One freematrix added in mlikeli! 0.98c
348:
349: Revision 1.114 2006/02/26 12:57:58 brouard
350: (Module): Some improvements in processing parameter
351: filename with strsep.
352:
353: Revision 1.113 2006/02/24 14:20:24 brouard
354: (Module): Memory leaks checks with valgrind and:
355: datafile was not closed, some imatrix were not freed and on matrix
356: allocation too.
357:
358: Revision 1.112 2006/01/30 09:55:26 brouard
359: (Module): Back to gnuplot.exe instead of wgnuplot.exe
360:
361: Revision 1.111 2006/01/25 20:38:18 brouard
362: (Module): Lots of cleaning and bugs added (Gompertz)
363: (Module): Comments can be added in data file. Missing date values
364: can be a simple dot '.'.
365:
366: Revision 1.110 2006/01/25 00:51:50 brouard
367: (Module): Lots of cleaning and bugs added (Gompertz)
368:
369: Revision 1.109 2006/01/24 19:37:15 brouard
370: (Module): Comments (lines starting with a #) are allowed in data.
371:
372: Revision 1.108 2006/01/19 18:05:42 lievre
373: Gnuplot problem appeared...
374: To be fixed
375:
376: Revision 1.107 2006/01/19 16:20:37 brouard
377: Test existence of gnuplot in imach path
378:
379: Revision 1.106 2006/01/19 13:24:36 brouard
380: Some cleaning and links added in html output
381:
382: Revision 1.105 2006/01/05 20:23:19 lievre
383: *** empty log message ***
384:
385: Revision 1.104 2005/09/30 16:11:43 lievre
386: (Module): sump fixed, loop imx fixed, and simplifications.
387: (Module): If the status is missing at the last wave but we know
388: that the person is alive, then we can code his/her status as -2
389: (instead of missing=-1 in earlier versions) and his/her
390: contributions to the likelihood is 1 - Prob of dying from last
391: health status (= 1-p13= p11+p12 in the easiest case of somebody in
392: the healthy state at last known wave). Version is 0.98
393:
394: Revision 1.103 2005/09/30 15:54:49 lievre
395: (Module): sump fixed, loop imx fixed, and simplifications.
396:
397: Revision 1.102 2004/09/15 17:31:30 brouard
398: Add the possibility to read data file including tab characters.
399:
400: Revision 1.101 2004/09/15 10:38:38 brouard
401: Fix on curr_time
402:
403: Revision 1.100 2004/07/12 18:29:06 brouard
404: Add version for Mac OS X. Just define UNIX in Makefile
405:
406: Revision 1.99 2004/06/05 08:57:40 brouard
407: *** empty log message ***
408:
409: Revision 1.98 2004/05/16 15:05:56 brouard
410: New version 0.97 . First attempt to estimate force of mortality
411: directly from the data i.e. without the need of knowing the health
412: state at each age, but using a Gompertz model: log u =a + b*age .
413: This is the basic analysis of mortality and should be done before any
414: other analysis, in order to test if the mortality estimated from the
415: cross-longitudinal survey is different from the mortality estimated
416: from other sources like vital statistic data.
417:
418: The same imach parameter file can be used but the option for mle should be -3.
419:
1.133 brouard 420: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 421: former routines in order to include the new code within the former code.
422:
423: The output is very simple: only an estimate of the intercept and of
424: the slope with 95% confident intervals.
425:
426: Current limitations:
427: A) Even if you enter covariates, i.e. with the
428: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
429: B) There is no computation of Life Expectancy nor Life Table.
430:
431: Revision 1.97 2004/02/20 13:25:42 lievre
432: Version 0.96d. Population forecasting command line is (temporarily)
433: suppressed.
434:
435: Revision 1.96 2003/07/15 15:38:55 brouard
436: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
437: rewritten within the same printf. Workaround: many printfs.
438:
439: Revision 1.95 2003/07/08 07:54:34 brouard
440: * imach.c (Repository):
441: (Repository): Using imachwizard code to output a more meaningful covariance
442: matrix (cov(a12,c31) instead of numbers.
443:
444: Revision 1.94 2003/06/27 13:00:02 brouard
445: Just cleaning
446:
447: Revision 1.93 2003/06/25 16:33:55 brouard
448: (Module): On windows (cygwin) function asctime_r doesn't
449: exist so I changed back to asctime which exists.
450: (Module): Version 0.96b
451:
452: Revision 1.92 2003/06/25 16:30:45 brouard
453: (Module): On windows (cygwin) function asctime_r doesn't
454: exist so I changed back to asctime which exists.
455:
456: Revision 1.91 2003/06/25 15:30:29 brouard
457: * imach.c (Repository): Duplicated warning errors corrected.
458: (Repository): Elapsed time after each iteration is now output. It
459: helps to forecast when convergence will be reached. Elapsed time
460: is stamped in powell. We created a new html file for the graphs
461: concerning matrix of covariance. It has extension -cov.htm.
462:
463: Revision 1.90 2003/06/24 12:34:15 brouard
464: (Module): Some bugs corrected for windows. Also, when
465: mle=-1 a template is output in file "or"mypar.txt with the design
466: of the covariance matrix to be input.
467:
468: Revision 1.89 2003/06/24 12:30:52 brouard
469: (Module): Some bugs corrected for windows. Also, when
470: mle=-1 a template is output in file "or"mypar.txt with the design
471: of the covariance matrix to be input.
472:
473: Revision 1.88 2003/06/23 17:54:56 brouard
474: * 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.
475:
476: Revision 1.87 2003/06/18 12:26:01 brouard
477: Version 0.96
478:
479: Revision 1.86 2003/06/17 20:04:08 brouard
480: (Module): Change position of html and gnuplot routines and added
481: routine fileappend.
482:
483: Revision 1.85 2003/06/17 13:12:43 brouard
484: * imach.c (Repository): Check when date of death was earlier that
485: current date of interview. It may happen when the death was just
486: prior to the death. In this case, dh was negative and likelihood
487: was wrong (infinity). We still send an "Error" but patch by
488: assuming that the date of death was just one stepm after the
489: interview.
490: (Repository): Because some people have very long ID (first column)
491: we changed int to long in num[] and we added a new lvector for
492: memory allocation. But we also truncated to 8 characters (left
493: truncation)
494: (Repository): No more line truncation errors.
495:
496: Revision 1.84 2003/06/13 21:44:43 brouard
497: * imach.c (Repository): Replace "freqsummary" at a correct
498: place. It differs from routine "prevalence" which may be called
499: many times. Probs is memory consuming and must be used with
500: parcimony.
501: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
502:
503: Revision 1.83 2003/06/10 13:39:11 lievre
504: *** empty log message ***
505:
506: Revision 1.82 2003/06/05 15:57:20 brouard
507: Add log in imach.c and fullversion number is now printed.
508:
509: */
510: /*
511: Interpolated Markov Chain
512:
513: Short summary of the programme:
514:
515: This program computes Healthy Life Expectancies from
516: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
517: first survey ("cross") where individuals from different ages are
518: interviewed on their health status or degree of disability (in the
519: case of a health survey which is our main interest) -2- at least a
520: second wave of interviews ("longitudinal") which measure each change
521: (if any) in individual health status. Health expectancies are
522: computed from the time spent in each health state according to a
523: model. More health states you consider, more time is necessary to reach the
524: Maximum Likelihood of the parameters involved in the model. The
525: simplest model is the multinomial logistic model where pij is the
526: probability to be observed in state j at the second wave
527: conditional to be observed in state i at the first wave. Therefore
528: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
529: 'age' is age and 'sex' is a covariate. If you want to have a more
530: complex model than "constant and age", you should modify the program
531: where the markup *Covariates have to be included here again* invites
532: you to do it. More covariates you add, slower the
533: convergence.
534:
535: The advantage of this computer programme, compared to a simple
536: multinomial logistic model, is clear when the delay between waves is not
537: identical for each individual. Also, if a individual missed an
538: intermediate interview, the information is lost, but taken into
539: account using an interpolation or extrapolation.
540:
541: hPijx is the probability to be observed in state i at age x+h
542: conditional to the observed state i at age x. The delay 'h' can be
543: split into an exact number (nh*stepm) of unobserved intermediate
544: states. This elementary transition (by month, quarter,
545: semester or year) is modelled as a multinomial logistic. The hPx
546: matrix is simply the matrix product of nh*stepm elementary matrices
547: and the contribution of each individual to the likelihood is simply
548: hPijx.
549:
550: Also this programme outputs the covariance matrix of the parameters but also
551: of the life expectancies. It also computes the period (stable) prevalence.
552:
1.133 brouard 553: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
554: Institut national d'études démographiques, Paris.
1.126 brouard 555: This software have been partly granted by Euro-REVES, a concerted action
556: from the European Union.
557: It is copyrighted identically to a GNU software product, ie programme and
558: software can be distributed freely for non commercial use. Latest version
559: can be accessed at http://euroreves.ined.fr/imach .
560:
561: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
562: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
563:
564: **********************************************************************/
565: /*
566: main
567: read parameterfile
568: read datafile
569: concatwav
570: freqsummary
571: if (mle >= 1)
572: mlikeli
573: print results files
574: if mle==1
575: computes hessian
576: read end of parameter file: agemin, agemax, bage, fage, estepm
577: begin-prev-date,...
578: open gnuplot file
579: open html file
1.145 brouard 580: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
581: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
582: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
583: freexexit2 possible for memory heap.
584:
585: h Pij x | pij_nom ficrestpij
586: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
587: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
588: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
589:
590: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
591: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
592: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
593: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
594: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
595:
1.126 brouard 596: forecasting if prevfcast==1 prevforecast call prevalence()
597: health expectancies
598: Variance-covariance of DFLE
599: prevalence()
600: movingaverage()
601: varevsij()
602: if popbased==1 varevsij(,popbased)
603: total life expectancies
604: Variance of period (stable) prevalence
605: end
606: */
607:
1.187 brouard 608: /* #define DEBUG */
609: /* #define DEBUGBRENT */
1.165 brouard 610: #define POWELL /* Instead of NLOPT */
1.192 brouard 611: #define POWELLF1F3 /* Skip test */
1.186 brouard 612: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
613: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 614:
615: #include <math.h>
616: #include <stdio.h>
617: #include <stdlib.h>
618: #include <string.h>
1.159 brouard 619:
620: #ifdef _WIN32
621: #include <io.h>
1.172 brouard 622: #include <windows.h>
623: #include <tchar.h>
1.159 brouard 624: #else
1.126 brouard 625: #include <unistd.h>
1.159 brouard 626: #endif
1.126 brouard 627:
628: #include <limits.h>
629: #include <sys/types.h>
1.171 brouard 630:
631: #if defined(__GNUC__)
632: #include <sys/utsname.h> /* Doesn't work on Windows */
633: #endif
634:
1.126 brouard 635: #include <sys/stat.h>
636: #include <errno.h>
1.159 brouard 637: /* extern int errno; */
1.126 brouard 638:
1.157 brouard 639: /* #ifdef LINUX */
640: /* #include <time.h> */
641: /* #include "timeval.h" */
642: /* #else */
643: /* #include <sys/time.h> */
644: /* #endif */
645:
1.126 brouard 646: #include <time.h>
647:
1.136 brouard 648: #ifdef GSL
649: #include <gsl/gsl_errno.h>
650: #include <gsl/gsl_multimin.h>
651: #endif
652:
1.167 brouard 653:
1.162 brouard 654: #ifdef NLOPT
655: #include <nlopt.h>
656: typedef struct {
657: double (* function)(double [] );
658: } myfunc_data ;
659: #endif
660:
1.126 brouard 661: /* #include <libintl.h> */
662: /* #define _(String) gettext (String) */
663:
1.141 brouard 664: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 665:
666: #define GNUPLOTPROGRAM "gnuplot"
667: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
668: #define FILENAMELENGTH 132
669:
670: #define GLOCK_ERROR_NOPATH -1 /* empty path */
671: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
672:
1.144 brouard 673: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
674: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 675:
676: #define NINTERVMAX 8
1.144 brouard 677: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
678: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
679: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 680: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 681: #define MAXN 20000
1.144 brouard 682: #define YEARM 12. /**< Number of months per year */
1.126 brouard 683: #define AGESUP 130
684: #define AGEBASE 40
1.164 brouard 685: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 686: #ifdef _WIN32
687: #define DIRSEPARATOR '\\'
688: #define CHARSEPARATOR "\\"
689: #define ODIRSEPARATOR '/'
690: #else
1.126 brouard 691: #define DIRSEPARATOR '/'
692: #define CHARSEPARATOR "/"
693: #define ODIRSEPARATOR '\\'
694: #endif
695:
1.193 ! brouard 696: /* $Id: imach.c,v 1.192 2015/07/16 16:49:02 brouard Exp $ */
1.126 brouard 697: /* $State: Exp $ */
698:
1.193 ! brouard 699: char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
! 700: char fullversion[]="$Revision: 1.192 $ $Date: 2015/07/16 16:49:02 $";
1.126 brouard 701: char strstart[80];
702: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 703: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 704: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 705: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
706: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
707: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
708: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
709: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
710: int cptcovprodnoage=0; /**< Number of covariate products without age */
711: int cptcoveff=0; /* Total number of covariates to vary for printing results */
712: int cptcov=0; /* Working variable */
1.126 brouard 713: int npar=NPARMAX;
714: int nlstate=2; /* Number of live states */
715: int ndeath=1; /* Number of dead states */
1.130 brouard 716: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 717: int popbased=0;
718:
719: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 720: int maxwav=0; /* Maxim number of waves */
721: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
722: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
723: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 724: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 725: int mle=1, weightopt=0;
1.126 brouard 726: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
727: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
728: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
729: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 730: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 731: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 732: double **matprod2(); /* test */
1.126 brouard 733: double **oldm, **newm, **savm; /* Working pointers to matrices */
734: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 735: /*FILE *fic ; */ /* Used in readdata only */
736: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 737: FILE *ficlog, *ficrespow;
1.130 brouard 738: int globpr=0; /* Global variable for printing or not */
1.126 brouard 739: double fretone; /* Only one call to likelihood */
1.130 brouard 740: long ipmx=0; /* Number of contributions */
1.126 brouard 741: double sw; /* Sum of weights */
742: char filerespow[FILENAMELENGTH];
743: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
744: FILE *ficresilk;
745: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
746: FILE *ficresprobmorprev;
747: FILE *fichtm, *fichtmcov; /* Html File */
748: FILE *ficreseij;
749: char filerese[FILENAMELENGTH];
750: FILE *ficresstdeij;
751: char fileresstde[FILENAMELENGTH];
752: FILE *ficrescveij;
753: char filerescve[FILENAMELENGTH];
754: FILE *ficresvij;
755: char fileresv[FILENAMELENGTH];
756: FILE *ficresvpl;
757: char fileresvpl[FILENAMELENGTH];
758: char title[MAXLINE];
759: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
760: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
761: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
762: char command[FILENAMELENGTH];
763: int outcmd=0;
764:
765: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
766:
767: char filelog[FILENAMELENGTH]; /* Log file */
768: char filerest[FILENAMELENGTH];
769: char fileregp[FILENAMELENGTH];
770: char popfile[FILENAMELENGTH];
771:
772: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
773:
1.157 brouard 774: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
775: /* struct timezone tzp; */
776: /* extern int gettimeofday(); */
777: struct tm tml, *gmtime(), *localtime();
778:
779: extern time_t time();
780:
781: struct tm start_time, end_time, curr_time, last_time, forecast_time;
782: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
783: struct tm tm;
784:
1.126 brouard 785: char strcurr[80], strfor[80];
786:
787: char *endptr;
788: long lval;
789: double dval;
790:
791: #define NR_END 1
792: #define FREE_ARG char*
793: #define FTOL 1.0e-10
794:
795: #define NRANSI
796: #define ITMAX 200
797:
798: #define TOL 2.0e-4
799:
800: #define CGOLD 0.3819660
801: #define ZEPS 1.0e-10
802: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
803:
804: #define GOLD 1.618034
805: #define GLIMIT 100.0
806: #define TINY 1.0e-20
807:
808: static double maxarg1,maxarg2;
809: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
810: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
811:
812: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
813: #define rint(a) floor(a+0.5)
1.166 brouard 814: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 815: #define mytinydouble 1.0e-16
1.166 brouard 816: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
817: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
818: /* static double dsqrarg; */
819: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 820: static double sqrarg;
821: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
822: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
823: int agegomp= AGEGOMP;
824:
825: int imx;
826: int stepm=1;
827: /* Stepm, step in month: minimum step interpolation*/
828:
829: int estepm;
830: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
831:
832: int m,nb;
833: long *num;
1.192 brouard 834: int firstpass=0, lastpass=4,*cod, *Tage,*cens;
835: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
836: covariate for which somebody answered excluding
837: undefined. Usually 2: 0 and 1. */
838: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
839: covariate for which somebody answered including
840: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 841: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
842: double **pmmij, ***probs;
843: double *ageexmed,*agecens;
844: double dateintmean=0;
845:
846: double *weight;
847: int **s; /* Status */
1.141 brouard 848: double *agedc;
1.145 brouard 849: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 850: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 851: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 852: double idx;
853: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 854: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 855: int **codtab; /**< codtab=imatrix(1,100,1,10); */
856: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 857: double *lsurv, *lpop, *tpop;
858:
1.143 brouard 859: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
860: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 861:
862: /**************** split *************************/
863: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
864: {
865: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
866: the name of the file (name), its extension only (ext) and its first part of the name (finame)
867: */
868: char *ss; /* pointer */
1.186 brouard 869: int l1=0, l2=0; /* length counters */
1.126 brouard 870:
871: l1 = strlen(path ); /* length of path */
872: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
873: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
874: if ( ss == NULL ) { /* no directory, so determine current directory */
875: strcpy( name, path ); /* we got the fullname name because no directory */
876: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
877: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
878: /* get current working directory */
879: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 880: #ifdef WIN32
881: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
882: #else
883: if (getcwd(dirc, FILENAME_MAX) == NULL) {
884: #endif
1.126 brouard 885: return( GLOCK_ERROR_GETCWD );
886: }
887: /* got dirc from getcwd*/
888: printf(" DIRC = %s \n",dirc);
889: } else { /* strip direcotry from path */
890: ss++; /* after this, the filename */
891: l2 = strlen( ss ); /* length of filename */
892: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
893: strcpy( name, ss ); /* save file name */
894: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 895: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 896: printf(" DIRC2 = %s \n",dirc);
897: }
898: /* We add a separator at the end of dirc if not exists */
899: l1 = strlen( dirc ); /* length of directory */
900: if( dirc[l1-1] != DIRSEPARATOR ){
901: dirc[l1] = DIRSEPARATOR;
902: dirc[l1+1] = 0;
903: printf(" DIRC3 = %s \n",dirc);
904: }
905: ss = strrchr( name, '.' ); /* find last / */
906: if (ss >0){
907: ss++;
908: strcpy(ext,ss); /* save extension */
909: l1= strlen( name);
910: l2= strlen(ss)+1;
911: strncpy( finame, name, l1-l2);
912: finame[l1-l2]= 0;
913: }
914:
915: return( 0 ); /* we're done */
916: }
917:
918:
919: /******************************************/
920:
921: void replace_back_to_slash(char *s, char*t)
922: {
923: int i;
924: int lg=0;
925: i=0;
926: lg=strlen(t);
927: for(i=0; i<= lg; i++) {
928: (s[i] = t[i]);
929: if (t[i]== '\\') s[i]='/';
930: }
931: }
932:
1.132 brouard 933: char *trimbb(char *out, char *in)
1.137 brouard 934: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 935: char *s;
936: s=out;
937: while (*in != '\0'){
1.137 brouard 938: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 939: in++;
940: }
941: *out++ = *in++;
942: }
943: *out='\0';
944: return s;
945: }
946:
1.187 brouard 947: /* char *substrchaine(char *out, char *in, char *chain) */
948: /* { */
949: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
950: /* char *s, *t; */
951: /* t=in;s=out; */
952: /* while ((*in != *chain) && (*in != '\0')){ */
953: /* *out++ = *in++; */
954: /* } */
955:
956: /* /\* *in matches *chain *\/ */
957: /* while ((*in++ == *chain++) && (*in != '\0')){ */
958: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
959: /* } */
960: /* in--; chain--; */
961: /* while ( (*in != '\0')){ */
962: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
963: /* *out++ = *in++; */
964: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
965: /* } */
966: /* *out='\0'; */
967: /* out=s; */
968: /* return out; */
969: /* } */
970: char *substrchaine(char *out, char *in, char *chain)
971: {
972: /* Substract chain 'chain' from 'in', return and output 'out' */
973: /* in="V1+V1*age+age*age+V2", chain="age*age" */
974:
975: char *strloc;
976:
977: strcpy (out, in);
978: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
979: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
980: if(strloc != NULL){
981: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
982: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
983: /* strcpy (strloc, strloc +strlen(chain));*/
984: }
985: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
986: return out;
987: }
988:
989:
1.145 brouard 990: char *cutl(char *blocc, char *alocc, char *in, char occ)
991: {
1.187 brouard 992: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 993: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 994: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 995: If occ is not found blocc is null and alocc is equal to in. Returns blocc
996: */
1.160 brouard 997: char *s, *t;
1.145 brouard 998: t=in;s=in;
999: while ((*in != occ) && (*in != '\0')){
1000: *alocc++ = *in++;
1001: }
1002: if( *in == occ){
1003: *(alocc)='\0';
1004: s=++in;
1005: }
1006:
1007: if (s == t) {/* occ not found */
1008: *(alocc-(in-s))='\0';
1009: in=s;
1010: }
1011: while ( *in != '\0'){
1012: *blocc++ = *in++;
1013: }
1014:
1015: *blocc='\0';
1016: return t;
1017: }
1.137 brouard 1018: char *cutv(char *blocc, char *alocc, char *in, char occ)
1019: {
1.187 brouard 1020: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1021: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1022: gives blocc="abcdef2ghi" and alocc="j".
1023: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1024: */
1025: char *s, *t;
1026: t=in;s=in;
1027: while (*in != '\0'){
1028: while( *in == occ){
1029: *blocc++ = *in++;
1030: s=in;
1031: }
1032: *blocc++ = *in++;
1033: }
1034: if (s == t) /* occ not found */
1035: *(blocc-(in-s))='\0';
1036: else
1037: *(blocc-(in-s)-1)='\0';
1038: in=s;
1039: while ( *in != '\0'){
1040: *alocc++ = *in++;
1041: }
1042:
1043: *alocc='\0';
1044: return s;
1045: }
1046:
1.126 brouard 1047: int nbocc(char *s, char occ)
1048: {
1049: int i,j=0;
1050: int lg=20;
1051: i=0;
1052: lg=strlen(s);
1053: for(i=0; i<= lg; i++) {
1054: if (s[i] == occ ) j++;
1055: }
1056: return j;
1057: }
1058:
1.137 brouard 1059: /* void cutv(char *u,char *v, char*t, char occ) */
1060: /* { */
1061: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1062: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1063: /* gives u="abcdef2ghi" and v="j" *\/ */
1064: /* int i,lg,j,p=0; */
1065: /* i=0; */
1066: /* lg=strlen(t); */
1067: /* for(j=0; j<=lg-1; j++) { */
1068: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1069: /* } */
1.126 brouard 1070:
1.137 brouard 1071: /* for(j=0; j<p; j++) { */
1072: /* (u[j] = t[j]); */
1073: /* } */
1074: /* u[p]='\0'; */
1.126 brouard 1075:
1.137 brouard 1076: /* for(j=0; j<= lg; j++) { */
1077: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1078: /* } */
1079: /* } */
1.126 brouard 1080:
1.160 brouard 1081: #ifdef _WIN32
1082: char * strsep(char **pp, const char *delim)
1083: {
1084: char *p, *q;
1085:
1086: if ((p = *pp) == NULL)
1087: return 0;
1088: if ((q = strpbrk (p, delim)) != NULL)
1089: {
1090: *pp = q + 1;
1091: *q = '\0';
1092: }
1093: else
1094: *pp = 0;
1095: return p;
1096: }
1097: #endif
1098:
1.126 brouard 1099: /********************** nrerror ********************/
1100:
1101: void nrerror(char error_text[])
1102: {
1103: fprintf(stderr,"ERREUR ...\n");
1104: fprintf(stderr,"%s\n",error_text);
1105: exit(EXIT_FAILURE);
1106: }
1107: /*********************** vector *******************/
1108: double *vector(int nl, int nh)
1109: {
1110: double *v;
1111: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1112: if (!v) nrerror("allocation failure in vector");
1113: return v-nl+NR_END;
1114: }
1115:
1116: /************************ free vector ******************/
1117: void free_vector(double*v, int nl, int nh)
1118: {
1119: free((FREE_ARG)(v+nl-NR_END));
1120: }
1121:
1122: /************************ivector *******************************/
1123: int *ivector(long nl,long nh)
1124: {
1125: int *v;
1126: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1127: if (!v) nrerror("allocation failure in ivector");
1128: return v-nl+NR_END;
1129: }
1130:
1131: /******************free ivector **************************/
1132: void free_ivector(int *v, long nl, long nh)
1133: {
1134: free((FREE_ARG)(v+nl-NR_END));
1135: }
1136:
1137: /************************lvector *******************************/
1138: long *lvector(long nl,long nh)
1139: {
1140: long *v;
1141: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1142: if (!v) nrerror("allocation failure in ivector");
1143: return v-nl+NR_END;
1144: }
1145:
1146: /******************free lvector **************************/
1147: void free_lvector(long *v, long nl, long nh)
1148: {
1149: free((FREE_ARG)(v+nl-NR_END));
1150: }
1151:
1152: /******************* imatrix *******************************/
1153: int **imatrix(long nrl, long nrh, long ncl, long nch)
1154: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1155: {
1156: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1157: int **m;
1158:
1159: /* allocate pointers to rows */
1160: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1161: if (!m) nrerror("allocation failure 1 in matrix()");
1162: m += NR_END;
1163: m -= nrl;
1164:
1165:
1166: /* allocate rows and set pointers to them */
1167: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1168: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1169: m[nrl] += NR_END;
1170: m[nrl] -= ncl;
1171:
1172: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1173:
1174: /* return pointer to array of pointers to rows */
1175: return m;
1176: }
1177:
1178: /****************** free_imatrix *************************/
1179: void free_imatrix(m,nrl,nrh,ncl,nch)
1180: int **m;
1181: long nch,ncl,nrh,nrl;
1182: /* free an int matrix allocated by imatrix() */
1183: {
1184: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1185: free((FREE_ARG) (m+nrl-NR_END));
1186: }
1187:
1188: /******************* matrix *******************************/
1189: double **matrix(long nrl, long nrh, long ncl, long nch)
1190: {
1191: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1192: double **m;
1193:
1194: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1195: if (!m) nrerror("allocation failure 1 in matrix()");
1196: m += NR_END;
1197: m -= nrl;
1198:
1199: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1200: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1201: m[nrl] += NR_END;
1202: m[nrl] -= ncl;
1203:
1204: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1205: return m;
1.145 brouard 1206: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1207: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1208: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1209: */
1210: }
1211:
1212: /*************************free matrix ************************/
1213: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1214: {
1215: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1216: free((FREE_ARG)(m+nrl-NR_END));
1217: }
1218:
1219: /******************* ma3x *******************************/
1220: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1221: {
1222: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1223: double ***m;
1224:
1225: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1226: if (!m) nrerror("allocation failure 1 in matrix()");
1227: m += NR_END;
1228: m -= nrl;
1229:
1230: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1231: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1232: m[nrl] += NR_END;
1233: m[nrl] -= ncl;
1234:
1235: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1236:
1237: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1238: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1239: m[nrl][ncl] += NR_END;
1240: m[nrl][ncl] -= nll;
1241: for (j=ncl+1; j<=nch; j++)
1242: m[nrl][j]=m[nrl][j-1]+nlay;
1243:
1244: for (i=nrl+1; i<=nrh; i++) {
1245: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1246: for (j=ncl+1; j<=nch; j++)
1247: m[i][j]=m[i][j-1]+nlay;
1248: }
1249: return m;
1250: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1251: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1252: */
1253: }
1254:
1255: /*************************free ma3x ************************/
1256: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1257: {
1258: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1259: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1260: free((FREE_ARG)(m+nrl-NR_END));
1261: }
1262:
1263: /*************** function subdirf ***********/
1264: char *subdirf(char fileres[])
1265: {
1266: /* Caution optionfilefiname is hidden */
1267: strcpy(tmpout,optionfilefiname);
1268: strcat(tmpout,"/"); /* Add to the right */
1269: strcat(tmpout,fileres);
1270: return tmpout;
1271: }
1272:
1273: /*************** function subdirf2 ***********/
1274: char *subdirf2(char fileres[], char *preop)
1275: {
1276:
1277: /* Caution optionfilefiname is hidden */
1278: strcpy(tmpout,optionfilefiname);
1279: strcat(tmpout,"/");
1280: strcat(tmpout,preop);
1281: strcat(tmpout,fileres);
1282: return tmpout;
1283: }
1284:
1285: /*************** function subdirf3 ***********/
1286: char *subdirf3(char fileres[], char *preop, char *preop2)
1287: {
1288:
1289: /* Caution optionfilefiname is hidden */
1290: strcpy(tmpout,optionfilefiname);
1291: strcat(tmpout,"/");
1292: strcat(tmpout,preop);
1293: strcat(tmpout,preop2);
1294: strcat(tmpout,fileres);
1295: return tmpout;
1296: }
1297:
1.162 brouard 1298: char *asc_diff_time(long time_sec, char ascdiff[])
1299: {
1300: long sec_left, days, hours, minutes;
1301: days = (time_sec) / (60*60*24);
1302: sec_left = (time_sec) % (60*60*24);
1303: hours = (sec_left) / (60*60) ;
1304: sec_left = (sec_left) %(60*60);
1305: minutes = (sec_left) /60;
1306: sec_left = (sec_left) % (60);
1307: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1308: return ascdiff;
1309: }
1310:
1.126 brouard 1311: /***************** f1dim *************************/
1312: extern int ncom;
1313: extern double *pcom,*xicom;
1314: extern double (*nrfunc)(double []);
1315:
1316: double f1dim(double x)
1317: {
1318: int j;
1319: double f;
1320: double *xt;
1321:
1322: xt=vector(1,ncom);
1323: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1324: f=(*nrfunc)(xt);
1325: free_vector(xt,1,ncom);
1326: return f;
1327: }
1328:
1329: /*****************brent *************************/
1330: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1331: {
1332: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1333: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1334: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1335: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1336: * returned function value.
1337: */
1.126 brouard 1338: int iter;
1339: double a,b,d,etemp;
1.159 brouard 1340: double fu=0,fv,fw,fx;
1.164 brouard 1341: double ftemp=0.;
1.126 brouard 1342: double p,q,r,tol1,tol2,u,v,w,x,xm;
1343: double e=0.0;
1344:
1345: a=(ax < cx ? ax : cx);
1346: b=(ax > cx ? ax : cx);
1347: x=w=v=bx;
1348: fw=fv=fx=(*f)(x);
1349: for (iter=1;iter<=ITMAX;iter++) {
1350: xm=0.5*(a+b);
1351: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1352: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1353: printf(".");fflush(stdout);
1354: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1355: #ifdef DEBUGBRENT
1.126 brouard 1356: 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);
1357: 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);
1358: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1359: #endif
1360: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1361: *xmin=x;
1362: return fx;
1363: }
1364: ftemp=fu;
1365: if (fabs(e) > tol1) {
1366: r=(x-w)*(fx-fv);
1367: q=(x-v)*(fx-fw);
1368: p=(x-v)*q-(x-w)*r;
1369: q=2.0*(q-r);
1370: if (q > 0.0) p = -p;
1371: q=fabs(q);
1372: etemp=e;
1373: e=d;
1374: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1375: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1376: else {
1377: d=p/q;
1378: u=x+d;
1379: if (u-a < tol2 || b-u < tol2)
1380: d=SIGN(tol1,xm-x);
1381: }
1382: } else {
1383: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1384: }
1385: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1386: fu=(*f)(u);
1387: if (fu <= fx) {
1388: if (u >= x) a=x; else b=x;
1389: SHFT(v,w,x,u)
1.183 brouard 1390: SHFT(fv,fw,fx,fu)
1391: } else {
1392: if (u < x) a=u; else b=u;
1393: if (fu <= fw || w == x) {
1394: v=w;
1395: w=u;
1396: fv=fw;
1397: fw=fu;
1398: } else if (fu <= fv || v == x || v == w) {
1399: v=u;
1400: fv=fu;
1401: }
1402: }
1.126 brouard 1403: }
1404: nrerror("Too many iterations in brent");
1405: *xmin=x;
1406: return fx;
1407: }
1408:
1409: /****************** mnbrak ***********************/
1410:
1411: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1412: double (*func)(double))
1.183 brouard 1413: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1414: the downhill direction (defined by the function as evaluated at the initial points) and returns
1415: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1416: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1417: */
1.126 brouard 1418: double ulim,u,r,q, dum;
1419: double fu;
1.187 brouard 1420:
1421: double scale=10.;
1422: int iterscale=0;
1423:
1424: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1425: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1426:
1427:
1428: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1429: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1430: /* *bx = *ax - (*ax - *bx)/scale; */
1431: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1432: /* } */
1433:
1.126 brouard 1434: if (*fb > *fa) {
1435: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1436: SHFT(dum,*fb,*fa,dum)
1437: }
1.126 brouard 1438: *cx=(*bx)+GOLD*(*bx-*ax);
1439: *fc=(*func)(*cx);
1.183 brouard 1440: #ifdef DEBUG
1441: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1442: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1443: #endif
1444: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1445: r=(*bx-*ax)*(*fb-*fc);
1446: q=(*bx-*cx)*(*fb-*fa);
1447: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1448: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1449: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1450: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1451: fu=(*func)(u);
1.163 brouard 1452: #ifdef DEBUG
1453: /* f(x)=A(x-u)**2+f(u) */
1454: double A, fparabu;
1455: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1456: fparabu= *fa - A*(*ax-u)*(*ax-u);
1457: 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);
1458: 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 1459: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1460: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1461: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1462: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1463: #endif
1.184 brouard 1464: #ifdef MNBRAKORIGINAL
1.183 brouard 1465: #else
1.191 brouard 1466: /* if (fu > *fc) { */
1467: /* #ifdef DEBUG */
1468: /* printf("mnbrak4 fu > fc \n"); */
1469: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1470: /* #endif */
1471: /* /\* 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 *\\/ *\/ */
1472: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1473: /* dum=u; /\* Shifting c and u *\/ */
1474: /* u = *cx; */
1475: /* *cx = dum; */
1476: /* dum = fu; */
1477: /* fu = *fc; */
1478: /* *fc =dum; */
1479: /* } else { /\* end *\/ */
1480: /* #ifdef DEBUG */
1481: /* printf("mnbrak3 fu < fc \n"); */
1482: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1483: /* #endif */
1484: /* dum=u; /\* Shifting c and u *\/ */
1485: /* u = *cx; */
1486: /* *cx = dum; */
1487: /* dum = fu; */
1488: /* fu = *fc; */
1489: /* *fc =dum; */
1490: /* } */
1.183 brouard 1491: #ifdef DEBUG
1.191 brouard 1492: printf("mnbrak34 fu < or >= fc \n");
1493: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1494: #endif
1.191 brouard 1495: dum=u; /* Shifting c and u */
1496: u = *cx;
1497: *cx = dum;
1498: dum = fu;
1499: fu = *fc;
1500: *fc =dum;
1.183 brouard 1501: #endif
1.162 brouard 1502: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1503: #ifdef DEBUG
1504: printf("mnbrak2 u after c but before ulim\n");
1505: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1506: #endif
1.126 brouard 1507: fu=(*func)(u);
1508: if (fu < *fc) {
1.183 brouard 1509: #ifdef DEBUG
1510: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1511: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1512: #endif
1.126 brouard 1513: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1514: SHFT(*fb,*fc,fu,(*func)(u))
1515: }
1.162 brouard 1516: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1517: #ifdef DEBUG
1518: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1519: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1520: #endif
1.126 brouard 1521: u=ulim;
1522: fu=(*func)(u);
1.183 brouard 1523: } else { /* u could be left to b (if r > q parabola has a maximum) */
1524: #ifdef DEBUG
1525: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1526: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1527: #endif
1.126 brouard 1528: u=(*cx)+GOLD*(*cx-*bx);
1529: fu=(*func)(u);
1.183 brouard 1530: } /* end tests */
1.126 brouard 1531: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1532: SHFT(*fa,*fb,*fc,fu)
1533: #ifdef DEBUG
1534: 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);
1535: 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);
1536: #endif
1537: } /* 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 1538: }
1539:
1540: /*************** linmin ************************/
1.162 brouard 1541: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1542: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1543: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1544: the value of func at the returned location p . This is actually all accomplished by calling the
1545: routines mnbrak and brent .*/
1.126 brouard 1546: int ncom;
1547: double *pcom,*xicom;
1548: double (*nrfunc)(double []);
1549:
1550: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1551: {
1552: double brent(double ax, double bx, double cx,
1553: double (*f)(double), double tol, double *xmin);
1554: double f1dim(double x);
1555: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1556: double *fc, double (*func)(double));
1557: int j;
1558: double xx,xmin,bx,ax;
1559: double fx,fb,fa;
1.187 brouard 1560:
1561: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1562:
1563: ncom=n;
1564: pcom=vector(1,n);
1565: xicom=vector(1,n);
1566: nrfunc=func;
1567: for (j=1;j<=n;j++) {
1568: pcom[j]=p[j];
1569: xicom[j]=xi[j];
1570: }
1.187 brouard 1571:
1.192 brouard 1572: /* axs=0.0; */
1573: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1574: xxs=1;
1.192 brouard 1575: /* do{ */
1.187 brouard 1576: ax=0.;
1577: xx= xxs;
1578: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1579: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1580: /* 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)) */
1581: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1582: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1583: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1584: /* 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]]*/
1.192 brouard 1585: /* if (fx != fx){ */
1586: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1587: /* 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); */
1588: /* } */
1589: /* }while(fx != fx); */
1.187 brouard 1590:
1.191 brouard 1591: #ifdef DEBUGLINMIN
1592: 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);
1593: #endif
1.187 brouard 1594: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1595: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1596: /* fmin = f(p[j] + xmin * xi[j]) */
1597: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1598: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1599: #ifdef DEBUG
1600: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1601: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1602: #endif
1.191 brouard 1603: #ifdef DEBUGLINMIN
1604: printf("linmin end ");
1605: #endif
1.126 brouard 1606: for (j=1;j<=n;j++) {
1.188 brouard 1607: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1608: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1609: /* if(xxs <1.0) */
1610: /* 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 1611: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1612: }
1.189 brouard 1613: /* printf("\n"); */
1.191 brouard 1614: #ifdef DEBUGLINMIN
1615: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1616: for (j=1;j<=n;j++) {
1617: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1618: if(j % ncovmodel == 0)
1619: printf("\n");
1620: }
1621: #endif
1.126 brouard 1622: free_vector(xicom,1,n);
1623: free_vector(pcom,1,n);
1624: }
1625:
1626:
1627: /*************** powell ************************/
1.162 brouard 1628: /*
1629: Minimization of a function func of n variables. Input consists of an initial starting point
1630: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1631: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1632: such that failure to decrease by more than this amount on one iteration signals doneness. On
1633: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1634: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1635: */
1.126 brouard 1636: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1637: double (*func)(double []))
1638: {
1639: void linmin(double p[], double xi[], int n, double *fret,
1640: double (*func)(double []));
1641: int i,ibig,j;
1642: double del,t,*pt,*ptt,*xit;
1.181 brouard 1643: double directest;
1.126 brouard 1644: double fp,fptt;
1645: double *xits;
1646: int niterf, itmp;
1647:
1648: pt=vector(1,n);
1649: ptt=vector(1,n);
1650: xit=vector(1,n);
1651: xits=vector(1,n);
1652: *fret=(*func)(p);
1653: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1654: rcurr_time = time(NULL);
1.126 brouard 1655: for (*iter=1;;++(*iter)) {
1.187 brouard 1656: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1657: ibig=0;
1658: del=0.0;
1.157 brouard 1659: rlast_time=rcurr_time;
1660: /* (void) gettimeofday(&curr_time,&tzp); */
1661: rcurr_time = time(NULL);
1662: curr_time = *localtime(&rcurr_time);
1663: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1664: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1665: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1666: for (i=1;i<=n;i++) {
1.126 brouard 1667: printf(" %d %.12f",i, p[i]);
1668: fprintf(ficlog," %d %.12lf",i, p[i]);
1669: fprintf(ficrespow," %.12lf", p[i]);
1670: }
1671: printf("\n");
1672: fprintf(ficlog,"\n");
1673: fprintf(ficrespow,"\n");fflush(ficrespow);
1674: if(*iter <=3){
1.157 brouard 1675: tml = *localtime(&rcurr_time);
1676: strcpy(strcurr,asctime(&tml));
1677: rforecast_time=rcurr_time;
1.126 brouard 1678: itmp = strlen(strcurr);
1679: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1680: strcurr[itmp-1]='\0';
1.162 brouard 1681: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1682: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1683: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1684: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1685: forecast_time = *localtime(&rforecast_time);
1686: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1687: itmp = strlen(strfor);
1688: if(strfor[itmp-1]=='\n')
1689: strfor[itmp-1]='\0';
1.157 brouard 1690: 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);
1691: 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 1692: }
1693: }
1.187 brouard 1694: for (i=1;i<=n;i++) { /* For each direction i */
1695: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1696: fptt=(*fret);
1697: #ifdef DEBUG
1.164 brouard 1698: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1699: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1700: #endif
1.187 brouard 1701: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1702: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1703: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1704: /* Outputs are fret(new point p) p is updated and xit rescaled */
1705: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1706: /* because that direction will be replaced unless the gain del is small */
1707: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1708: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1709: /* with the new direction. */
1.126 brouard 1710: del=fabs(fptt-(*fret));
1711: ibig=i;
1712: }
1713: #ifdef DEBUG
1714: printf("%d %.12e",i,(*fret));
1715: fprintf(ficlog,"%d %.12e",i,(*fret));
1716: for (j=1;j<=n;j++) {
1717: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1718: printf(" x(%d)=%.12e",j,xit[j]);
1719: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1720: }
1721: for(j=1;j<=n;j++) {
1.162 brouard 1722: printf(" p(%d)=%.12e",j,p[j]);
1723: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1724: }
1725: printf("\n");
1726: fprintf(ficlog,"\n");
1727: #endif
1.187 brouard 1728: } /* end loop on each direction i */
1729: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1730: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1731: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1732: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1733: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1734: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1735: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1736: /* decreased of more than 3.84 */
1737: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1738: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1739: /* By adding 10 parameters more the gain should be 18.31 */
1740:
1741: /* Starting the program with initial values given by a former maximization will simply change */
1742: /* the scales of the directions and the directions, because the are reset to canonical directions */
1743: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1744: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1745: #ifdef DEBUG
1746: int k[2],l;
1747: k[0]=1;
1748: k[1]=-1;
1749: printf("Max: %.12e",(*func)(p));
1750: fprintf(ficlog,"Max: %.12e",(*func)(p));
1751: for (j=1;j<=n;j++) {
1752: printf(" %.12e",p[j]);
1753: fprintf(ficlog," %.12e",p[j]);
1754: }
1755: printf("\n");
1756: fprintf(ficlog,"\n");
1757: for(l=0;l<=1;l++) {
1758: for (j=1;j<=n;j++) {
1759: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1760: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1761: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1762: }
1763: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1764: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1765: }
1766: #endif
1767:
1768:
1769: free_vector(xit,1,n);
1770: free_vector(xits,1,n);
1771: free_vector(ptt,1,n);
1772: free_vector(pt,1,n);
1773: return;
1.192 brouard 1774: } /* enough precision */
1.126 brouard 1775: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1776: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1777: ptt[j]=2.0*p[j]-pt[j];
1778: xit[j]=p[j]-pt[j];
1779: pt[j]=p[j];
1780: }
1.181 brouard 1781: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1782: #ifdef POWELLF1F3
1783: #else
1.161 brouard 1784: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1785: #endif
1.162 brouard 1786: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1787: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1788: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1789: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1790: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1791: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1792: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1793: #ifdef NRCORIGINAL
1794: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1795: #else
1796: 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 1797: t= t- del*SQR(fp-fptt);
1.183 brouard 1798: #endif
1.182 brouard 1799: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1800: #ifdef DEBUG
1.181 brouard 1801: 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);
1802: 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 1803: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1804: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1805: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1806: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1807: 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);
1808: 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);
1809: #endif
1.183 brouard 1810: #ifdef POWELLORIGINAL
1811: if (t < 0.0) { /* Then we use it for new direction */
1812: #else
1.182 brouard 1813: if (directest*t < 0.0) { /* Contradiction between both tests */
1.192 brouard 1814: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1815: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1816: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1817: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1818: }
1.181 brouard 1819: if (directest < 0.0) { /* Then we use it for new direction */
1820: #endif
1.191 brouard 1821: #ifdef DEBUGLINMIN
1822: printf("Before linmin in direction P%d-P0\n",n);
1823: for (j=1;j<=n;j++) {
1824: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1825: if(j % ncovmodel == 0)
1826: printf("\n");
1827: }
1828: #endif
1.187 brouard 1829: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1830: #ifdef DEBUGLINMIN
1831: for (j=1;j<=n;j++) {
1832: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1833: if(j % ncovmodel == 0)
1834: printf("\n");
1835: }
1836: #endif
1.126 brouard 1837: for (j=1;j<=n;j++) {
1.181 brouard 1838: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1839: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1840: }
1.181 brouard 1841: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1842: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1843:
1.126 brouard 1844: #ifdef DEBUG
1.164 brouard 1845: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1846: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1847: for(j=1;j<=n;j++){
1848: printf(" %.12e",xit[j]);
1849: fprintf(ficlog," %.12e",xit[j]);
1850: }
1851: printf("\n");
1852: fprintf(ficlog,"\n");
1853: #endif
1.192 brouard 1854: } /* end of t or directest negative */
1855: #ifdef POWELLF1F3
1856: #else
1.162 brouard 1857: } /* end if (fptt < fp) */
1.192 brouard 1858: #endif
1859: } /* loop iteration */
1.126 brouard 1860: }
1861:
1862: /**** Prevalence limit (stable or period prevalence) ****************/
1863:
1864: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1865: {
1866: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1867: matrix by transitions matrix until convergence is reached */
1.169 brouard 1868:
1.126 brouard 1869: int i, ii,j,k;
1870: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1871: /* double **matprod2(); */ /* test */
1.131 brouard 1872: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1873: double **newm;
1874: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1875:
1.126 brouard 1876: for (ii=1;ii<=nlstate+ndeath;ii++)
1877: for (j=1;j<=nlstate+ndeath;j++){
1878: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1879: }
1.169 brouard 1880:
1881: cov[1]=1.;
1882:
1883: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1884: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1885: newm=savm;
1886: /* Covariates have to be included here again */
1.138 brouard 1887: cov[2]=agefin;
1.187 brouard 1888: if(nagesqr==1)
1889: cov[3]= agefin*agefin;;
1.138 brouard 1890: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1891: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1892: /*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 1893: }
1.186 brouard 1894: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1895: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1896: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1897: 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 1898:
1899: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1900: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1901: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1902: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1903: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1904: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1905:
1.126 brouard 1906: savm=oldm;
1907: oldm=newm;
1908: maxmax=0.;
1909: for(j=1;j<=nlstate;j++){
1910: min=1.;
1911: max=0.;
1912: for(i=1; i<=nlstate; i++) {
1913: sumnew=0;
1914: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1915: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1916: /*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 1917: max=FMAX(max,prlim[i][j]);
1918: min=FMIN(min,prlim[i][j]);
1919: }
1920: maxmin=max-min;
1921: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1922: } /* j loop */
1.126 brouard 1923: if(maxmax < ftolpl){
1924: return prlim;
1925: }
1.169 brouard 1926: } /* age loop */
1927: return prlim; /* should not reach here */
1.126 brouard 1928: }
1929:
1930: /*************** transition probabilities ***************/
1931:
1932: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1933: {
1.138 brouard 1934: /* According to parameters values stored in x and the covariate's values stored in cov,
1935: computes the probability to be observed in state j being in state i by appying the
1936: model to the ncovmodel covariates (including constant and age).
1937: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1938: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1939: ncth covariate in the global vector x is given by the formula:
1940: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1941: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1942: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1943: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1944: Outputs ps[i][j] the probability to be observed in j being in j according to
1945: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1946: */
1947: double s1, lnpijopii;
1.126 brouard 1948: /*double t34;*/
1.164 brouard 1949: int i,j, nc, ii, jj;
1.126 brouard 1950:
1951: for(i=1; i<= nlstate; i++){
1952: for(j=1; j<i;j++){
1.138 brouard 1953: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1954: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1955: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1956: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1957: }
1.138 brouard 1958: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1959: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1960: }
1961: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1962: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1963: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1964: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1965: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1966: }
1.138 brouard 1967: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1968: }
1969: }
1970:
1971: for(i=1; i<= nlstate; i++){
1972: s1=0;
1.131 brouard 1973: for(j=1; j<i; j++){
1.138 brouard 1974: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1975: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1976: }
1977: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1978: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1979: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1980: }
1.138 brouard 1981: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1982: ps[i][i]=1./(s1+1.);
1.138 brouard 1983: /* Computing other pijs */
1.126 brouard 1984: for(j=1; j<i; j++)
1985: ps[i][j]= exp(ps[i][j])*ps[i][i];
1986: for(j=i+1; j<=nlstate+ndeath; j++)
1987: ps[i][j]= exp(ps[i][j])*ps[i][i];
1988: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1989: } /* end i */
1990:
1991: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1992: for(jj=1; jj<= nlstate+ndeath; jj++){
1993: ps[ii][jj]=0;
1994: ps[ii][ii]=1;
1995: }
1996: }
1997:
1.145 brouard 1998:
1999: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2000: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2001: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2002: /* } */
2003: /* printf("\n "); */
2004: /* } */
2005: /* printf("\n ");printf("%lf ",cov[2]);*/
2006: /*
1.126 brouard 2007: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2008: goto end;*/
2009: return ps;
2010: }
2011:
2012: /**************** Product of 2 matrices ******************/
2013:
1.145 brouard 2014: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2015: {
2016: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2017: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2018: /* in, b, out are matrice of pointers which should have been initialized
2019: before: only the contents of out is modified. The function returns
2020: a pointer to pointers identical to out */
1.145 brouard 2021: int i, j, k;
1.126 brouard 2022: for(i=nrl; i<= nrh; i++)
1.145 brouard 2023: for(k=ncolol; k<=ncoloh; k++){
2024: out[i][k]=0.;
2025: for(j=ncl; j<=nch; j++)
2026: out[i][k] +=in[i][j]*b[j][k];
2027: }
1.126 brouard 2028: return out;
2029: }
2030:
2031:
2032: /************* Higher Matrix Product ***************/
2033:
2034: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2035: {
2036: /* Computes the transition matrix starting at age 'age' over
2037: 'nhstepm*hstepm*stepm' months (i.e. until
2038: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2039: nhstepm*hstepm matrices.
2040: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2041: (typically every 2 years instead of every month which is too big
2042: for the memory).
2043: Model is determined by parameters x and covariates have to be
2044: included manually here.
2045:
2046: */
2047:
2048: int i, j, d, h, k;
1.131 brouard 2049: double **out, cov[NCOVMAX+1];
1.126 brouard 2050: double **newm;
1.187 brouard 2051: double agexact;
1.126 brouard 2052:
2053: /* Hstepm could be zero and should return the unit matrix */
2054: for (i=1;i<=nlstate+ndeath;i++)
2055: for (j=1;j<=nlstate+ndeath;j++){
2056: oldm[i][j]=(i==j ? 1.0 : 0.0);
2057: po[i][j][0]=(i==j ? 1.0 : 0.0);
2058: }
2059: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2060: for(h=1; h <=nhstepm; h++){
2061: for(d=1; d <=hstepm; d++){
2062: newm=savm;
2063: /* Covariates have to be included here again */
2064: cov[1]=1.;
1.187 brouard 2065: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2066: cov[2]=agexact;
2067: if(nagesqr==1)
2068: cov[3]= agexact*agexact;
1.131 brouard 2069: for (k=1; k<=cptcovn;k++)
1.187 brouard 2070: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2071: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2072: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2073: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2074: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2075: 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 2076:
2077:
2078: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2079: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2080: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2081: pmij(pmmij,cov,ncovmodel,x,nlstate));
2082: savm=oldm;
2083: oldm=newm;
2084: }
2085: for(i=1; i<=nlstate+ndeath; i++)
2086: for(j=1;j<=nlstate+ndeath;j++) {
2087: po[i][j][h]=newm[i][j];
1.128 brouard 2088: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2089: }
1.128 brouard 2090: /*printf("h=%d ",h);*/
1.126 brouard 2091: } /* end h */
1.128 brouard 2092: /* printf("\n H=%d \n",h); */
1.126 brouard 2093: return po;
2094: }
2095:
1.162 brouard 2096: #ifdef NLOPT
2097: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2098: double fret;
2099: double *xt;
2100: int j;
2101: myfunc_data *d2 = (myfunc_data *) pd;
2102: /* xt = (p1-1); */
2103: xt=vector(1,n);
2104: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2105:
2106: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2107: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2108: printf("Function = %.12lf ",fret);
2109: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2110: printf("\n");
2111: free_vector(xt,1,n);
2112: return fret;
2113: }
2114: #endif
1.126 brouard 2115:
2116: /*************** log-likelihood *************/
2117: double func( double *x)
2118: {
2119: int i, ii, j, k, mi, d, kk;
1.131 brouard 2120: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2121: double **out;
2122: double sw; /* Sum of weights */
2123: double lli; /* Individual log likelihood */
2124: int s1, s2;
2125: double bbh, survp;
2126: long ipmx;
1.187 brouard 2127: double agexact;
1.126 brouard 2128: /*extern weight */
2129: /* We are differentiating ll according to initial status */
2130: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2131: /*for(i=1;i<imx;i++)
2132: printf(" %d\n",s[4][i]);
2133: */
1.162 brouard 2134:
2135: ++countcallfunc;
2136:
1.126 brouard 2137: cov[1]=1.;
2138:
2139: for(k=1; k<=nlstate; k++) ll[k]=0.;
2140:
2141: if(mle==1){
2142: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2143: /* Computes the values of the ncovmodel covariates of the model
2144: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2145: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2146: to be observed in j being in i according to the model.
2147: */
1.145 brouard 2148: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2149: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2150: }
1.137 brouard 2151: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2152: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2153: has been calculated etc */
1.126 brouard 2154: for(mi=1; mi<= wav[i]-1; mi++){
2155: for (ii=1;ii<=nlstate+ndeath;ii++)
2156: for (j=1;j<=nlstate+ndeath;j++){
2157: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2158: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2159: }
2160: for(d=0; d<dh[mi][i]; d++){
2161: newm=savm;
1.187 brouard 2162: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2163: cov[2]=agexact;
2164: if(nagesqr==1)
2165: cov[3]= agexact*agexact;
1.126 brouard 2166: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2167: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2168: }
2169: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2170: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2171: savm=oldm;
2172: oldm=newm;
2173: } /* end mult */
2174:
2175: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2176: /* But now since version 0.9 we anticipate for bias at large stepm.
2177: * If stepm is larger than one month (smallest stepm) and if the exact delay
2178: * (in months) between two waves is not a multiple of stepm, we rounded to
2179: * the nearest (and in case of equal distance, to the lowest) interval but now
2180: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2181: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2182: * probability in order to take into account the bias as a fraction of the way
2183: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2184: * -stepm/2 to stepm/2 .
2185: * For stepm=1 the results are the same as for previous versions of Imach.
2186: * For stepm > 1 the results are less biased than in previous versions.
2187: */
2188: s1=s[mw[mi][i]][i];
2189: s2=s[mw[mi+1][i]][i];
2190: bbh=(double)bh[mi][i]/(double)stepm;
2191: /* bias bh is positive if real duration
2192: * is higher than the multiple of stepm and negative otherwise.
2193: */
2194: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2195: if( s2 > nlstate){
2196: /* i.e. if s2 is a death state and if the date of death is known
2197: then the contribution to the likelihood is the probability to
2198: die between last step unit time and current step unit time,
2199: which is also equal to probability to die before dh
2200: minus probability to die before dh-stepm .
2201: In version up to 0.92 likelihood was computed
2202: as if date of death was unknown. Death was treated as any other
2203: health state: the date of the interview describes the actual state
2204: and not the date of a change in health state. The former idea was
2205: to consider that at each interview the state was recorded
2206: (healthy, disable or death) and IMaCh was corrected; but when we
2207: introduced the exact date of death then we should have modified
2208: the contribution of an exact death to the likelihood. This new
2209: contribution is smaller and very dependent of the step unit
2210: stepm. It is no more the probability to die between last interview
2211: and month of death but the probability to survive from last
2212: interview up to one month before death multiplied by the
2213: probability to die within a month. Thanks to Chris
2214: Jackson for correcting this bug. Former versions increased
2215: mortality artificially. The bad side is that we add another loop
2216: which slows down the processing. The difference can be up to 10%
2217: lower mortality.
2218: */
1.183 brouard 2219: /* If, at the beginning of the maximization mostly, the
2220: cumulative probability or probability to be dead is
2221: constant (ie = 1) over time d, the difference is equal to
2222: 0. out[s1][3] = savm[s1][3]: probability, being at state
2223: s1 at precedent wave, to be dead a month before current
2224: wave is equal to probability, being at state s1 at
2225: precedent wave, to be dead at mont of the current
2226: wave. Then the observed probability (that this person died)
2227: is null according to current estimated parameter. In fact,
2228: it should be very low but not zero otherwise the log go to
2229: infinity.
2230: */
2231: /* #ifdef INFINITYORIGINAL */
2232: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2233: /* #else */
2234: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2235: /* lli=log(mytinydouble); */
2236: /* else */
2237: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2238: /* #endif */
2239: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2240:
2241: } else if (s2==-2) {
2242: for (j=1,survp=0. ; j<=nlstate; j++)
2243: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2244: /*survp += out[s1][j]; */
2245: lli= log(survp);
2246: }
2247:
2248: else if (s2==-4) {
2249: for (j=3,survp=0. ; j<=nlstate; j++)
2250: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2251: lli= log(survp);
2252: }
2253:
2254: else if (s2==-5) {
2255: for (j=1,survp=0. ; j<=2; j++)
2256: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2257: lli= log(survp);
2258: }
2259:
2260: else{
2261: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2262: /* 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 */
2263: }
2264: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2265: /*if(lli ==000.0)*/
2266: /*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); */
2267: ipmx +=1;
2268: sw += weight[i];
2269: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2270: /* if (lli < log(mytinydouble)){ */
2271: /* 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); */
2272: /* 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]); */
2273: /* } */
1.126 brouard 2274: } /* end of wave */
2275: } /* end of individual */
2276: } else if(mle==2){
2277: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2278: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2279: for(mi=1; mi<= wav[i]-1; mi++){
2280: for (ii=1;ii<=nlstate+ndeath;ii++)
2281: for (j=1;j<=nlstate+ndeath;j++){
2282: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2283: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2284: }
2285: for(d=0; d<=dh[mi][i]; d++){
2286: newm=savm;
1.187 brouard 2287: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2288: cov[2]=agexact;
2289: if(nagesqr==1)
2290: cov[3]= agexact*agexact;
1.126 brouard 2291: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2292: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2293: }
2294: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2295: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2296: savm=oldm;
2297: oldm=newm;
2298: } /* end mult */
2299:
2300: s1=s[mw[mi][i]][i];
2301: s2=s[mw[mi+1][i]][i];
2302: bbh=(double)bh[mi][i]/(double)stepm;
2303: 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 */
2304: ipmx +=1;
2305: sw += weight[i];
2306: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2307: } /* end of wave */
2308: } /* end of individual */
2309: } else if(mle==3){ /* exponential inter-extrapolation */
2310: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2311: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2312: for(mi=1; mi<= wav[i]-1; mi++){
2313: for (ii=1;ii<=nlstate+ndeath;ii++)
2314: for (j=1;j<=nlstate+ndeath;j++){
2315: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2316: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2317: }
2318: for(d=0; d<dh[mi][i]; d++){
2319: newm=savm;
1.187 brouard 2320: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2321: cov[2]=agexact;
2322: if(nagesqr==1)
2323: cov[3]= agexact*agexact;
1.126 brouard 2324: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2325: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2326: }
2327: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2328: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2329: savm=oldm;
2330: oldm=newm;
2331: } /* end mult */
2332:
2333: s1=s[mw[mi][i]][i];
2334: s2=s[mw[mi+1][i]][i];
2335: bbh=(double)bh[mi][i]/(double)stepm;
2336: 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 */
2337: ipmx +=1;
2338: sw += weight[i];
2339: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2340: } /* end of wave */
2341: } /* end of individual */
2342: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2343: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2344: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2345: for(mi=1; mi<= wav[i]-1; mi++){
2346: for (ii=1;ii<=nlstate+ndeath;ii++)
2347: for (j=1;j<=nlstate+ndeath;j++){
2348: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2349: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2350: }
2351: for(d=0; d<dh[mi][i]; d++){
2352: newm=savm;
1.187 brouard 2353: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2354: cov[2]=agexact;
2355: if(nagesqr==1)
2356: cov[3]= agexact*agexact;
1.126 brouard 2357: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2358: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2359: }
2360:
2361: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2362: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2363: savm=oldm;
2364: oldm=newm;
2365: } /* end mult */
2366:
2367: s1=s[mw[mi][i]][i];
2368: s2=s[mw[mi+1][i]][i];
2369: if( s2 > nlstate){
2370: lli=log(out[s1][s2] - savm[s1][s2]);
2371: }else{
2372: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2373: }
2374: ipmx +=1;
2375: sw += weight[i];
2376: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2377: /* 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]); */
2378: } /* end of wave */
2379: } /* end of individual */
2380: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2381: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2382: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2383: for(mi=1; mi<= wav[i]-1; mi++){
2384: for (ii=1;ii<=nlstate+ndeath;ii++)
2385: for (j=1;j<=nlstate+ndeath;j++){
2386: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2387: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2388: }
2389: for(d=0; d<dh[mi][i]; d++){
2390: newm=savm;
1.187 brouard 2391: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2392: cov[2]=agexact;
2393: if(nagesqr==1)
2394: cov[3]= agexact*agexact;
1.126 brouard 2395: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2396: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2397: }
2398:
2399: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2400: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2401: savm=oldm;
2402: oldm=newm;
2403: } /* end mult */
2404:
2405: s1=s[mw[mi][i]][i];
2406: s2=s[mw[mi+1][i]][i];
2407: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2408: ipmx +=1;
2409: sw += weight[i];
2410: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2411: /*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]);*/
2412: } /* end of wave */
2413: } /* end of individual */
2414: } /* End of if */
2415: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2416: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2417: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2418: return -l;
2419: }
2420:
2421: /*************** log-likelihood *************/
2422: double funcone( double *x)
2423: {
2424: /* Same as likeli but slower because of a lot of printf and if */
2425: int i, ii, j, k, mi, d, kk;
1.131 brouard 2426: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2427: double **out;
2428: double lli; /* Individual log likelihood */
2429: double llt;
2430: int s1, s2;
2431: double bbh, survp;
1.187 brouard 2432: double agexact;
1.126 brouard 2433: /*extern weight */
2434: /* We are differentiating ll according to initial status */
2435: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2436: /*for(i=1;i<imx;i++)
2437: printf(" %d\n",s[4][i]);
2438: */
2439: cov[1]=1.;
2440:
2441: for(k=1; k<=nlstate; k++) ll[k]=0.;
2442:
2443: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2444: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2445: for(mi=1; mi<= wav[i]-1; mi++){
2446: for (ii=1;ii<=nlstate+ndeath;ii++)
2447: for (j=1;j<=nlstate+ndeath;j++){
2448: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2449: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2450: }
2451: for(d=0; d<dh[mi][i]; d++){
2452: newm=savm;
1.187 brouard 2453: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2454: cov[2]=agexact;
2455: if(nagesqr==1)
2456: cov[3]= agexact*agexact;
1.126 brouard 2457: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2458: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2459: }
1.187 brouard 2460:
1.145 brouard 2461: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2462: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2463: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2464: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2465: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2466: savm=oldm;
2467: oldm=newm;
2468: } /* end mult */
2469:
2470: s1=s[mw[mi][i]][i];
2471: s2=s[mw[mi+1][i]][i];
2472: bbh=(double)bh[mi][i]/(double)stepm;
2473: /* bias is positive if real duration
2474: * is higher than the multiple of stepm and negative otherwise.
2475: */
2476: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2477: lli=log(out[s1][s2] - savm[s1][s2]);
2478: } else if (s2==-2) {
2479: for (j=1,survp=0. ; j<=nlstate; j++)
2480: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2481: lli= log(survp);
2482: }else if (mle==1){
2483: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2484: } else if(mle==2){
2485: 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 */
2486: } else if(mle==3){ /* exponential inter-extrapolation */
2487: 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 */
2488: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2489: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2490: } else{ /* mle=0 back to 1 */
2491: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2492: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2493: } /* End of if */
2494: ipmx +=1;
2495: sw += weight[i];
2496: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2497: /*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 2498: if(globpr){
1.141 brouard 2499: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2500: %11.6f %11.6f %11.6f ", \
2501: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2502: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2503: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2504: llt +=ll[k]*gipmx/gsw;
2505: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2506: }
2507: fprintf(ficresilk," %10.6f\n", -llt);
2508: }
2509: } /* end of wave */
2510: } /* end of individual */
2511: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2512: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2513: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2514: if(globpr==0){ /* First time we count the contributions and weights */
2515: gipmx=ipmx;
2516: gsw=sw;
2517: }
2518: return -l;
2519: }
2520:
2521:
2522: /*************** function likelione ***********/
2523: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2524: {
2525: /* This routine should help understanding what is done with
2526: the selection of individuals/waves and
2527: to check the exact contribution to the likelihood.
2528: Plotting could be done.
2529: */
2530: int k;
2531:
2532: if(*globpri !=0){ /* Just counts and sums, no printings */
2533: strcpy(fileresilk,"ilk");
2534: strcat(fileresilk,fileres);
2535: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2536: printf("Problem with resultfile: %s\n", fileresilk);
2537: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2538: }
2539: 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");
2540: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2541: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2542: for(k=1; k<=nlstate; k++)
2543: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2544: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2545: }
2546:
2547: *fretone=(*funcone)(p);
2548: if(*globpri !=0){
2549: fclose(ficresilk);
2550: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2551: fflush(fichtm);
2552: }
2553: return;
2554: }
2555:
2556:
2557: /*********** Maximum Likelihood Estimation ***************/
2558:
2559: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2560: {
1.165 brouard 2561: int i,j, iter=0;
1.126 brouard 2562: double **xi;
2563: double fret;
2564: double fretone; /* Only one call to likelihood */
2565: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2566:
2567: #ifdef NLOPT
2568: int creturn;
2569: nlopt_opt opt;
2570: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2571: double *lb;
2572: double minf; /* the minimum objective value, upon return */
2573: double * p1; /* Shifted parameters from 0 instead of 1 */
2574: myfunc_data dinst, *d = &dinst;
2575: #endif
2576:
2577:
1.126 brouard 2578: xi=matrix(1,npar,1,npar);
2579: for (i=1;i<=npar;i++)
2580: for (j=1;j<=npar;j++)
2581: xi[i][j]=(i==j ? 1.0 : 0.0);
2582: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2583: strcpy(filerespow,"pow");
2584: strcat(filerespow,fileres);
2585: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2586: printf("Problem with resultfile: %s\n", filerespow);
2587: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2588: }
2589: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2590: for (i=1;i<=nlstate;i++)
2591: for(j=1;j<=nlstate+ndeath;j++)
2592: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2593: fprintf(ficrespow,"\n");
1.162 brouard 2594: #ifdef POWELL
1.126 brouard 2595: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2596: #endif
1.126 brouard 2597:
1.162 brouard 2598: #ifdef NLOPT
2599: #ifdef NEWUOA
2600: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2601: #else
2602: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2603: #endif
2604: lb=vector(0,npar-1);
2605: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2606: nlopt_set_lower_bounds(opt, lb);
2607: nlopt_set_initial_step1(opt, 0.1);
2608:
2609: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2610: d->function = func;
2611: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2612: nlopt_set_min_objective(opt, myfunc, d);
2613: nlopt_set_xtol_rel(opt, ftol);
2614: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2615: printf("nlopt failed! %d\n",creturn);
2616: }
2617: else {
2618: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2619: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2620: iter=1; /* not equal */
2621: }
2622: nlopt_destroy(opt);
2623: #endif
1.126 brouard 2624: free_matrix(xi,1,npar,1,npar);
2625: fclose(ficrespow);
1.180 brouard 2626: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2627: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2628: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2629:
2630: }
2631:
2632: /**** Computes Hessian and covariance matrix ***/
2633: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2634: {
2635: double **a,**y,*x,pd;
2636: double **hess;
1.164 brouard 2637: int i, j;
1.126 brouard 2638: int *indx;
2639:
2640: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2641: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2642: void lubksb(double **a, int npar, int *indx, double b[]) ;
2643: void ludcmp(double **a, int npar, int *indx, double *d) ;
2644: double gompertz(double p[]);
2645: hess=matrix(1,npar,1,npar);
2646:
2647: printf("\nCalculation of the hessian matrix. Wait...\n");
2648: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2649: for (i=1;i<=npar;i++){
2650: printf("%d",i);fflush(stdout);
2651: fprintf(ficlog,"%d",i);fflush(ficlog);
2652:
2653: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2654:
2655: /* printf(" %f ",p[i]);
2656: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2657: }
2658:
2659: for (i=1;i<=npar;i++) {
2660: for (j=1;j<=npar;j++) {
2661: if (j>i) {
2662: printf(".%d%d",i,j);fflush(stdout);
2663: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2664: hess[i][j]=hessij(p,delti,i,j,func,npar);
2665:
2666: hess[j][i]=hess[i][j];
2667: /*printf(" %lf ",hess[i][j]);*/
2668: }
2669: }
2670: }
2671: printf("\n");
2672: fprintf(ficlog,"\n");
2673:
2674: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2675: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2676:
2677: a=matrix(1,npar,1,npar);
2678: y=matrix(1,npar,1,npar);
2679: x=vector(1,npar);
2680: indx=ivector(1,npar);
2681: for (i=1;i<=npar;i++)
2682: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2683: ludcmp(a,npar,indx,&pd);
2684:
2685: for (j=1;j<=npar;j++) {
2686: for (i=1;i<=npar;i++) x[i]=0;
2687: x[j]=1;
2688: lubksb(a,npar,indx,x);
2689: for (i=1;i<=npar;i++){
2690: matcov[i][j]=x[i];
2691: }
2692: }
2693:
2694: printf("\n#Hessian matrix#\n");
2695: fprintf(ficlog,"\n#Hessian matrix#\n");
2696: for (i=1;i<=npar;i++) {
2697: for (j=1;j<=npar;j++) {
2698: printf("%.3e ",hess[i][j]);
2699: fprintf(ficlog,"%.3e ",hess[i][j]);
2700: }
2701: printf("\n");
2702: fprintf(ficlog,"\n");
2703: }
2704:
2705: /* Recompute Inverse */
2706: for (i=1;i<=npar;i++)
2707: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2708: ludcmp(a,npar,indx,&pd);
2709:
2710: /* printf("\n#Hessian matrix recomputed#\n");
2711:
2712: for (j=1;j<=npar;j++) {
2713: for (i=1;i<=npar;i++) x[i]=0;
2714: x[j]=1;
2715: lubksb(a,npar,indx,x);
2716: for (i=1;i<=npar;i++){
2717: y[i][j]=x[i];
2718: printf("%.3e ",y[i][j]);
2719: fprintf(ficlog,"%.3e ",y[i][j]);
2720: }
2721: printf("\n");
2722: fprintf(ficlog,"\n");
2723: }
2724: */
2725:
2726: free_matrix(a,1,npar,1,npar);
2727: free_matrix(y,1,npar,1,npar);
2728: free_vector(x,1,npar);
2729: free_ivector(indx,1,npar);
2730: free_matrix(hess,1,npar,1,npar);
2731:
2732:
2733: }
2734:
2735: /*************** hessian matrix ****************/
2736: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2737: {
2738: int i;
2739: int l=1, lmax=20;
2740: double k1,k2;
1.132 brouard 2741: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2742: double res;
2743: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2744: double fx;
2745: int k=0,kmax=10;
2746: double l1;
2747:
2748: fx=func(x);
2749: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2750: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2751: l1=pow(10,l);
2752: delts=delt;
2753: for(k=1 ; k <kmax; k=k+1){
2754: delt = delta*(l1*k);
2755: p2[theta]=x[theta] +delt;
1.145 brouard 2756: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2757: p2[theta]=x[theta]-delt;
2758: k2=func(p2)-fx;
2759: /*res= (k1-2.0*fx+k2)/delt/delt; */
2760: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2761:
1.132 brouard 2762: #ifdef DEBUGHESS
1.126 brouard 2763: 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);
2764: 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);
2765: #endif
2766: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2767: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2768: k=kmax;
2769: }
2770: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2771: k=kmax; l=lmax*10;
1.126 brouard 2772: }
2773: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2774: delts=delt;
2775: }
2776: }
2777: }
2778: delti[theta]=delts;
2779: return res;
2780:
2781: }
2782:
2783: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2784: {
2785: int i;
1.164 brouard 2786: int l=1, lmax=20;
1.126 brouard 2787: double k1,k2,k3,k4,res,fx;
1.132 brouard 2788: double p2[MAXPARM+1];
1.126 brouard 2789: int k;
2790:
2791: fx=func(x);
2792: for (k=1; k<=2; k++) {
2793: for (i=1;i<=npar;i++) p2[i]=x[i];
2794: p2[thetai]=x[thetai]+delti[thetai]/k;
2795: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2796: k1=func(p2)-fx;
2797:
2798: p2[thetai]=x[thetai]+delti[thetai]/k;
2799: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2800: k2=func(p2)-fx;
2801:
2802: p2[thetai]=x[thetai]-delti[thetai]/k;
2803: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2804: k3=func(p2)-fx;
2805:
2806: p2[thetai]=x[thetai]-delti[thetai]/k;
2807: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2808: k4=func(p2)-fx;
2809: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2810: #ifdef DEBUG
2811: 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);
2812: 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);
2813: #endif
2814: }
2815: return res;
2816: }
2817:
2818: /************** Inverse of matrix **************/
2819: void ludcmp(double **a, int n, int *indx, double *d)
2820: {
2821: int i,imax,j,k;
2822: double big,dum,sum,temp;
2823: double *vv;
2824:
2825: vv=vector(1,n);
2826: *d=1.0;
2827: for (i=1;i<=n;i++) {
2828: big=0.0;
2829: for (j=1;j<=n;j++)
2830: if ((temp=fabs(a[i][j])) > big) big=temp;
2831: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2832: vv[i]=1.0/big;
2833: }
2834: for (j=1;j<=n;j++) {
2835: for (i=1;i<j;i++) {
2836: sum=a[i][j];
2837: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2838: a[i][j]=sum;
2839: }
2840: big=0.0;
2841: for (i=j;i<=n;i++) {
2842: sum=a[i][j];
2843: for (k=1;k<j;k++)
2844: sum -= a[i][k]*a[k][j];
2845: a[i][j]=sum;
2846: if ( (dum=vv[i]*fabs(sum)) >= big) {
2847: big=dum;
2848: imax=i;
2849: }
2850: }
2851: if (j != imax) {
2852: for (k=1;k<=n;k++) {
2853: dum=a[imax][k];
2854: a[imax][k]=a[j][k];
2855: a[j][k]=dum;
2856: }
2857: *d = -(*d);
2858: vv[imax]=vv[j];
2859: }
2860: indx[j]=imax;
2861: if (a[j][j] == 0.0) a[j][j]=TINY;
2862: if (j != n) {
2863: dum=1.0/(a[j][j]);
2864: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2865: }
2866: }
2867: free_vector(vv,1,n); /* Doesn't work */
2868: ;
2869: }
2870:
2871: void lubksb(double **a, int n, int *indx, double b[])
2872: {
2873: int i,ii=0,ip,j;
2874: double sum;
2875:
2876: for (i=1;i<=n;i++) {
2877: ip=indx[i];
2878: sum=b[ip];
2879: b[ip]=b[i];
2880: if (ii)
2881: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2882: else if (sum) ii=i;
2883: b[i]=sum;
2884: }
2885: for (i=n;i>=1;i--) {
2886: sum=b[i];
2887: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2888: b[i]=sum/a[i][i];
2889: }
2890: }
2891:
2892: void pstamp(FILE *fichier)
2893: {
2894: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2895: }
2896:
2897: /************ Frequencies ********************/
2898: 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[])
2899: { /* Some frequencies */
2900:
1.164 brouard 2901: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2902: int first;
2903: double ***freq; /* Frequencies */
2904: double *pp, **prop;
2905: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2906: char fileresp[FILENAMELENGTH];
2907:
2908: pp=vector(1,nlstate);
2909: prop=matrix(1,nlstate,iagemin,iagemax+3);
2910: strcpy(fileresp,"p");
2911: strcat(fileresp,fileres);
2912: if((ficresp=fopen(fileresp,"w"))==NULL) {
2913: printf("Problem with prevalence resultfile: %s\n", fileresp);
2914: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2915: exit(0);
2916: }
2917: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2918: j1=0;
2919:
2920: j=cptcoveff;
2921: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2922:
2923: first=1;
2924:
1.169 brouard 2925: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2926: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2927: /* j1++; */
1.145 brouard 2928: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2929: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2930: scanf("%d", i);*/
2931: for (i=-5; i<=nlstate+ndeath; i++)
2932: for (jk=-5; jk<=nlstate+ndeath; jk++)
2933: for(m=iagemin; m <= iagemax+3; m++)
2934: freq[i][jk][m]=0;
1.143 brouard 2935:
2936: for (i=1; i<=nlstate; i++)
2937: for(m=iagemin; m <= iagemax+3; m++)
2938: prop[i][m]=0;
1.126 brouard 2939:
2940: dateintsum=0;
2941: k2cpt=0;
2942: for (i=1; i<=imx; i++) {
2943: bool=1;
1.144 brouard 2944: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2945: for (z1=1; z1<=cptcoveff; z1++)
2946: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2947: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2948: bool=0;
1.145 brouard 2949: /* 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",
2950: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2951: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2952: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2953: }
1.126 brouard 2954: }
1.144 brouard 2955:
1.126 brouard 2956: if (bool==1){
2957: for(m=firstpass; m<=lastpass; m++){
2958: k2=anint[m][i]+(mint[m][i]/12.);
2959: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2960: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2961: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2962: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2963: if (m<lastpass) {
2964: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2965: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2966: }
2967:
2968: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2969: dateintsum=dateintsum+k2;
2970: k2cpt++;
2971: }
2972: /*}*/
2973: }
2974: }
1.145 brouard 2975: } /* end i */
1.126 brouard 2976:
2977: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2978: pstamp(ficresp);
2979: if (cptcovn>0) {
2980: fprintf(ficresp, "\n#********** Variable ");
2981: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2982: fprintf(ficresp, "**********\n#");
1.143 brouard 2983: fprintf(ficlog, "\n#********** Variable ");
2984: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2985: fprintf(ficlog, "**********\n#");
1.126 brouard 2986: }
2987: for(i=1; i<=nlstate;i++)
2988: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2989: fprintf(ficresp, "\n");
2990:
2991: for(i=iagemin; i <= iagemax+3; i++){
2992: if(i==iagemax+3){
2993: fprintf(ficlog,"Total");
2994: }else{
2995: if(first==1){
2996: first=0;
2997: printf("See log file for details...\n");
2998: }
2999: fprintf(ficlog,"Age %d", i);
3000: }
3001: for(jk=1; jk <=nlstate ; jk++){
3002: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3003: pp[jk] += freq[jk][m][i];
3004: }
3005: for(jk=1; jk <=nlstate ; jk++){
3006: for(m=-1, pos=0; m <=0 ; m++)
3007: pos += freq[jk][m][i];
3008: if(pp[jk]>=1.e-10){
3009: if(first==1){
1.132 brouard 3010: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3011: }
3012: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3013: }else{
3014: if(first==1)
3015: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3016: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3017: }
3018: }
3019:
3020: for(jk=1; jk <=nlstate ; jk++){
3021: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3022: pp[jk] += freq[jk][m][i];
3023: }
3024: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3025: pos += pp[jk];
3026: posprop += prop[jk][i];
3027: }
3028: for(jk=1; jk <=nlstate ; jk++){
3029: if(pos>=1.e-5){
3030: if(first==1)
3031: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3032: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3033: }else{
3034: if(first==1)
3035: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3036: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3037: }
3038: if( i <= iagemax){
3039: if(pos>=1.e-5){
3040: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3041: /*probs[i][jk][j1]= pp[jk]/pos;*/
3042: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3043: }
3044: else
3045: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3046: }
3047: }
3048:
3049: for(jk=-1; jk <=nlstate+ndeath; jk++)
3050: for(m=-1; m <=nlstate+ndeath; m++)
3051: if(freq[jk][m][i] !=0 ) {
3052: if(first==1)
3053: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3054: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3055: }
3056: if(i <= iagemax)
3057: fprintf(ficresp,"\n");
3058: if(first==1)
3059: printf("Others in log...\n");
3060: fprintf(ficlog,"\n");
3061: }
1.145 brouard 3062: /*}*/
1.126 brouard 3063: }
3064: dateintmean=dateintsum/k2cpt;
3065:
3066: fclose(ficresp);
3067: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3068: free_vector(pp,1,nlstate);
3069: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3070: /* End of Freq */
3071: }
3072:
3073: /************ Prevalence ********************/
3074: 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)
3075: {
3076: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3077: in each health status at the date of interview (if between dateprev1 and dateprev2).
3078: We still use firstpass and lastpass as another selection.
3079: */
3080:
1.164 brouard 3081: int i, m, jk, j1, bool, z1,j;
3082:
3083: double **prop;
3084: double posprop;
1.126 brouard 3085: double y2; /* in fractional years */
3086: int iagemin, iagemax;
1.145 brouard 3087: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3088:
3089: iagemin= (int) agemin;
3090: iagemax= (int) agemax;
3091: /*pp=vector(1,nlstate);*/
3092: prop=matrix(1,nlstate,iagemin,iagemax+3);
3093: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3094: j1=0;
3095:
1.145 brouard 3096: /*j=cptcoveff;*/
1.126 brouard 3097: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3098:
1.145 brouard 3099: first=1;
3100: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3101: /*for(i1=1; i1<=ncodemax[k1];i1++){
3102: j1++;*/
1.126 brouard 3103:
3104: for (i=1; i<=nlstate; i++)
3105: for(m=iagemin; m <= iagemax+3; m++)
3106: prop[i][m]=0.0;
3107:
3108: for (i=1; i<=imx; i++) { /* Each individual */
3109: bool=1;
3110: if (cptcovn>0) {
3111: for (z1=1; z1<=cptcoveff; z1++)
3112: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3113: bool=0;
3114: }
3115: if (bool==1) {
3116: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3117: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3118: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3119: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3120: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3121: 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);
3122: if (s[m][i]>0 && s[m][i]<=nlstate) {
3123: /*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]]);*/
3124: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3125: prop[s[m][i]][iagemax+3] += weight[i];
3126: }
3127: }
3128: } /* end selection of waves */
3129: }
3130: }
3131: for(i=iagemin; i <= iagemax+3; i++){
3132: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3133: posprop += prop[jk][i];
3134: }
1.145 brouard 3135:
1.126 brouard 3136: for(jk=1; jk <=nlstate ; jk++){
3137: if( i <= iagemax){
3138: if(posprop>=1.e-5){
3139: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3140: } else{
3141: if(first==1){
3142: first=0;
3143: 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]);
3144: }
3145: }
1.126 brouard 3146: }
3147: }/* end jk */
3148: }/* end i */
1.145 brouard 3149: /*} *//* end i1 */
3150: } /* end j1 */
1.126 brouard 3151:
3152: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3153: /*free_vector(pp,1,nlstate);*/
3154: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3155: } /* End of prevalence */
3156:
3157: /************* Waves Concatenation ***************/
3158:
3159: 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)
3160: {
3161: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3162: Death is a valid wave (if date is known).
3163: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3164: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3165: and mw[mi+1][i]. dh depends on stepm.
3166: */
3167:
3168: int i, mi, m;
3169: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3170: double sum=0., jmean=0.;*/
3171: int first;
3172: int j, k=0,jk, ju, jl;
3173: double sum=0.;
3174: first=0;
1.164 brouard 3175: jmin=100000;
1.126 brouard 3176: jmax=-1;
3177: jmean=0.;
3178: for(i=1; i<=imx; i++){
3179: mi=0;
3180: m=firstpass;
3181: while(s[m][i] <= nlstate){
3182: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3183: mw[++mi][i]=m;
3184: if(m >=lastpass)
3185: break;
3186: else
3187: m++;
3188: }/* end while */
3189: if (s[m][i] > nlstate){
3190: mi++; /* Death is another wave */
3191: /* if(mi==0) never been interviewed correctly before death */
3192: /* Only death is a correct wave */
3193: mw[mi][i]=m;
3194: }
3195:
3196: wav[i]=mi;
3197: if(mi==0){
3198: nbwarn++;
3199: if(first==0){
3200: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3201: first=1;
3202: }
3203: if(first==1){
3204: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3205: }
3206: } /* end mi==0 */
3207: } /* End individuals */
3208:
3209: for(i=1; i<=imx; i++){
3210: for(mi=1; mi<wav[i];mi++){
3211: if (stepm <=0)
3212: dh[mi][i]=1;
3213: else{
3214: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3215: if (agedc[i] < 2*AGESUP) {
3216: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3217: if(j==0) j=1; /* Survives at least one month after exam */
3218: else if(j<0){
3219: nberr++;
3220: 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]);
3221: j=1; /* Temporary Dangerous patch */
3222: 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);
3223: 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]);
3224: 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);
3225: }
3226: k=k+1;
3227: if (j >= jmax){
3228: jmax=j;
3229: ijmax=i;
3230: }
3231: if (j <= jmin){
3232: jmin=j;
3233: ijmin=i;
3234: }
3235: sum=sum+j;
3236: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3237: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3238: }
3239: }
3240: else{
3241: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3242: /* 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]); */
3243:
3244: k=k+1;
3245: if (j >= jmax) {
3246: jmax=j;
3247: ijmax=i;
3248: }
3249: else if (j <= jmin){
3250: jmin=j;
3251: ijmin=i;
3252: }
3253: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3254: /*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]);*/
3255: if(j<0){
3256: nberr++;
3257: 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]);
3258: 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]);
3259: }
3260: sum=sum+j;
3261: }
3262: jk= j/stepm;
3263: jl= j -jk*stepm;
3264: ju= j -(jk+1)*stepm;
3265: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3266: if(jl==0){
3267: dh[mi][i]=jk;
3268: bh[mi][i]=0;
3269: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3270: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3271: dh[mi][i]=jk+1;
3272: bh[mi][i]=ju;
3273: }
3274: }else{
3275: if(jl <= -ju){
3276: dh[mi][i]=jk;
3277: bh[mi][i]=jl; /* bias is positive if real duration
3278: * is higher than the multiple of stepm and negative otherwise.
3279: */
3280: }
3281: else{
3282: dh[mi][i]=jk+1;
3283: bh[mi][i]=ju;
3284: }
3285: if(dh[mi][i]==0){
3286: dh[mi][i]=1; /* At least one step */
3287: bh[mi][i]=ju; /* At least one step */
3288: /* 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);*/
3289: }
3290: } /* end if mle */
3291: }
3292: } /* end wave */
3293: }
3294: jmean=sum/k;
3295: 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 3296: 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 3297: }
3298:
3299: /*********** Tricode ****************************/
1.145 brouard 3300: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3301: {
1.144 brouard 3302: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3303: /* 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 3304: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3305: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3306: * nbcode[Tvar[j]][1]=
1.144 brouard 3307: */
1.130 brouard 3308:
1.145 brouard 3309: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3310: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3311: int cptcode=0; /* Modality max of covariates j */
3312: int modmincovj=0; /* Modality min of covariates j */
3313:
3314:
1.126 brouard 3315: cptcoveff=0;
3316:
1.144 brouard 3317: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3318:
1.145 brouard 3319: /* Loop on covariates without age and products */
1.186 brouard 3320: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3321: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3322: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3323: modality of this covariate Vj*/
1.145 brouard 3324: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3325: * If product of Vn*Vm, still boolean *:
3326: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3327: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3328: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3329: modality of the nth covariate of individual i. */
1.145 brouard 3330: if (ij > modmaxcovj)
3331: modmaxcovj=ij;
3332: else if (ij < modmincovj)
3333: modmincovj=ij;
3334: if ((ij < -1) && (ij > NCOVMAX)){
3335: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3336: exit(1);
3337: }else
1.136 brouard 3338: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3339: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3340: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3341: /* getting the maximum value of the modality of the covariate
3342: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3343: female is 1, then modmaxcovj=1.*/
1.192 brouard 3344: } /* end for loop on individuals i */
1.145 brouard 3345: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3346: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 3347: cptcode=modmaxcovj;
1.137 brouard 3348: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3349: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3350: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3351: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3352: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3353: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3354: if( k != -1){
3355: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3356: covariate for which somebody answered excluding
3357: undefined. Usually 2: 0 and 1. */
3358: }
3359: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3360: covariate for which somebody answered including
3361: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3362: }
3363: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3364: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3365: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3366:
1.136 brouard 3367: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3368: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3369: 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 3370: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3371: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3372: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3373: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3374: nbcode[Tvar[j]][ij]=k;
3375: nbcode[Tvar[j]][1]=0;
3376: nbcode[Tvar[j]][2]=1;
3377: nbcode[Tvar[j]][3]=2;
3378: */
1.192 brouard 3379: ij=0; /* ij is similar to i but can jumps over null modalities */
3380: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
3381: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
3382: break;
3383: }
3384: ij++;
3385: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
3386: cptcode = ij; /* New max modality for covar j */
3387: } /* end of loop on modality i=-1 to 1 or more */
3388:
3389: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3390: /* /\*recode from 0 *\/ */
3391: /* k is a modality. If we have model=V1+V1*sex */
3392: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3393: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3394: /* } */
3395: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3396: /* if (ij > ncodemax[j]) { */
3397: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3398: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3399: /* break; */
3400: /* } */
3401: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3402: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3403:
1.145 brouard 3404: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3405:
1.187 brouard 3406: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3407: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3408: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3409: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3410: }
1.126 brouard 3411:
1.192 brouard 3412: ij=0;
1.145 brouard 3413: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3414: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3415: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3416: ij++;
1.145 brouard 3417: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3418: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3419: }else{
3420: /* Tvaraff[ij]=0; */
3421: }
1.126 brouard 3422: }
1.192 brouard 3423: /* ij--; */
1.144 brouard 3424: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3425:
1.126 brouard 3426: }
3427:
1.145 brouard 3428:
1.126 brouard 3429: /*********** Health Expectancies ****************/
3430:
1.127 brouard 3431: 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 3432:
3433: {
3434: /* Health expectancies, no variances */
1.164 brouard 3435: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3436: int nhstepma, nstepma; /* Decreasing with age */
3437: double age, agelim, hf;
3438: double ***p3mat;
3439: double eip;
3440:
3441: pstamp(ficreseij);
3442: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3443: fprintf(ficreseij,"# Age");
3444: for(i=1; i<=nlstate;i++){
3445: for(j=1; j<=nlstate;j++){
3446: fprintf(ficreseij," e%1d%1d ",i,j);
3447: }
3448: fprintf(ficreseij," e%1d. ",i);
3449: }
3450: fprintf(ficreseij,"\n");
3451:
3452:
3453: if(estepm < stepm){
3454: printf ("Problem %d lower than %d\n",estepm, stepm);
3455: }
3456: else hstepm=estepm;
3457: /* We compute the life expectancy from trapezoids spaced every estepm months
3458: * This is mainly to measure the difference between two models: for example
3459: * if stepm=24 months pijx are given only every 2 years and by summing them
3460: * we are calculating an estimate of the Life Expectancy assuming a linear
3461: * progression in between and thus overestimating or underestimating according
3462: * to the curvature of the survival function. If, for the same date, we
3463: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3464: * to compare the new estimate of Life expectancy with the same linear
3465: * hypothesis. A more precise result, taking into account a more precise
3466: * curvature will be obtained if estepm is as small as stepm. */
3467:
3468: /* For example we decided to compute the life expectancy with the smallest unit */
3469: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3470: nhstepm is the number of hstepm from age to agelim
3471: nstepm is the number of stepm from age to agelin.
3472: Look at hpijx to understand the reason of that which relies in memory size
3473: and note for a fixed period like estepm months */
3474: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3475: survival function given by stepm (the optimization length). Unfortunately it
3476: means that if the survival funtion is printed only each two years of age and if
3477: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3478: results. So we changed our mind and took the option of the best precision.
3479: */
3480: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3481:
3482: agelim=AGESUP;
3483: /* If stepm=6 months */
3484: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3485: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3486:
3487: /* nhstepm age range expressed in number of stepm */
3488: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3489: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3490: /* if (stepm >= YEARM) hstepm=1;*/
3491: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3492: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3493:
3494: for (age=bage; age<=fage; age ++){
3495: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3496: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3497: /* if (stepm >= YEARM) hstepm=1;*/
3498: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3499:
3500: /* If stepm=6 months */
3501: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3502: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3503:
3504: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3505:
3506: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3507:
3508: printf("%d|",(int)age);fflush(stdout);
3509: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3510:
3511: /* Computing expectancies */
3512: for(i=1; i<=nlstate;i++)
3513: for(j=1; j<=nlstate;j++)
3514: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3515: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3516:
3517: /* 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]);*/
3518:
3519: }
3520:
3521: fprintf(ficreseij,"%3.0f",age );
3522: for(i=1; i<=nlstate;i++){
3523: eip=0;
3524: for(j=1; j<=nlstate;j++){
3525: eip +=eij[i][j][(int)age];
3526: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3527: }
3528: fprintf(ficreseij,"%9.4f", eip );
3529: }
3530: fprintf(ficreseij,"\n");
3531:
3532: }
3533: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3534: printf("\n");
3535: fprintf(ficlog,"\n");
3536:
3537: }
3538:
1.127 brouard 3539: 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 3540:
3541: {
3542: /* Covariances of health expectancies eij and of total life expectancies according
3543: to initial status i, ei. .
3544: */
3545: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3546: int nhstepma, nstepma; /* Decreasing with age */
3547: double age, agelim, hf;
3548: double ***p3matp, ***p3matm, ***varhe;
3549: double **dnewm,**doldm;
3550: double *xp, *xm;
3551: double **gp, **gm;
3552: double ***gradg, ***trgradg;
3553: int theta;
3554:
3555: double eip, vip;
3556:
3557: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3558: xp=vector(1,npar);
3559: xm=vector(1,npar);
3560: dnewm=matrix(1,nlstate*nlstate,1,npar);
3561: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3562:
3563: pstamp(ficresstdeij);
3564: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3565: fprintf(ficresstdeij,"# Age");
3566: for(i=1; i<=nlstate;i++){
3567: for(j=1; j<=nlstate;j++)
3568: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3569: fprintf(ficresstdeij," e%1d. ",i);
3570: }
3571: fprintf(ficresstdeij,"\n");
3572:
3573: pstamp(ficrescveij);
3574: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3575: fprintf(ficrescveij,"# Age");
3576: for(i=1; i<=nlstate;i++)
3577: for(j=1; j<=nlstate;j++){
3578: cptj= (j-1)*nlstate+i;
3579: for(i2=1; i2<=nlstate;i2++)
3580: for(j2=1; j2<=nlstate;j2++){
3581: cptj2= (j2-1)*nlstate+i2;
3582: if(cptj2 <= cptj)
3583: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3584: }
3585: }
3586: fprintf(ficrescveij,"\n");
3587:
3588: if(estepm < stepm){
3589: printf ("Problem %d lower than %d\n",estepm, stepm);
3590: }
3591: else hstepm=estepm;
3592: /* We compute the life expectancy from trapezoids spaced every estepm months
3593: * This is mainly to measure the difference between two models: for example
3594: * if stepm=24 months pijx are given only every 2 years and by summing them
3595: * we are calculating an estimate of the Life Expectancy assuming a linear
3596: * progression in between and thus overestimating or underestimating according
3597: * to the curvature of the survival function. If, for the same date, we
3598: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3599: * to compare the new estimate of Life expectancy with the same linear
3600: * hypothesis. A more precise result, taking into account a more precise
3601: * curvature will be obtained if estepm is as small as stepm. */
3602:
3603: /* For example we decided to compute the life expectancy with the smallest unit */
3604: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3605: nhstepm is the number of hstepm from age to agelim
3606: nstepm is the number of stepm from age to agelin.
3607: Look at hpijx to understand the reason of that which relies in memory size
3608: and note for a fixed period like estepm months */
3609: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3610: survival function given by stepm (the optimization length). Unfortunately it
3611: means that if the survival funtion is printed only each two years of age and if
3612: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3613: results. So we changed our mind and took the option of the best precision.
3614: */
3615: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3616:
3617: /* If stepm=6 months */
3618: /* nhstepm age range expressed in number of stepm */
3619: agelim=AGESUP;
3620: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3621: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3622: /* if (stepm >= YEARM) hstepm=1;*/
3623: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3624:
3625: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3626: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3627: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3628: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3629: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3630: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3631:
3632: for (age=bage; age<=fage; age ++){
3633: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3634: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3635: /* if (stepm >= YEARM) hstepm=1;*/
3636: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3637:
3638: /* If stepm=6 months */
3639: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3640: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3641:
3642: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3643:
3644: /* Computing Variances of health expectancies */
3645: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3646: decrease memory allocation */
3647: for(theta=1; theta <=npar; theta++){
3648: for(i=1; i<=npar; i++){
3649: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3650: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3651: }
3652: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3653: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3654:
3655: for(j=1; j<= nlstate; j++){
3656: for(i=1; i<=nlstate; i++){
3657: for(h=0; h<=nhstepm-1; h++){
3658: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3659: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3660: }
3661: }
3662: }
3663:
3664: for(ij=1; ij<= nlstate*nlstate; ij++)
3665: for(h=0; h<=nhstepm-1; h++){
3666: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3667: }
3668: }/* End theta */
3669:
3670:
3671: for(h=0; h<=nhstepm-1; h++)
3672: for(j=1; j<=nlstate*nlstate;j++)
3673: for(theta=1; theta <=npar; theta++)
3674: trgradg[h][j][theta]=gradg[h][theta][j];
3675:
3676:
3677: for(ij=1;ij<=nlstate*nlstate;ij++)
3678: for(ji=1;ji<=nlstate*nlstate;ji++)
3679: varhe[ij][ji][(int)age] =0.;
3680:
3681: printf("%d|",(int)age);fflush(stdout);
3682: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3683: for(h=0;h<=nhstepm-1;h++){
3684: for(k=0;k<=nhstepm-1;k++){
3685: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3686: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3687: for(ij=1;ij<=nlstate*nlstate;ij++)
3688: for(ji=1;ji<=nlstate*nlstate;ji++)
3689: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3690: }
3691: }
3692:
3693: /* Computing expectancies */
3694: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3695: for(i=1; i<=nlstate;i++)
3696: for(j=1; j<=nlstate;j++)
3697: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3698: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3699:
3700: /* 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]);*/
3701:
3702: }
3703:
3704: fprintf(ficresstdeij,"%3.0f",age );
3705: for(i=1; i<=nlstate;i++){
3706: eip=0.;
3707: vip=0.;
3708: for(j=1; j<=nlstate;j++){
3709: eip += eij[i][j][(int)age];
3710: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3711: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3712: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3713: }
3714: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3715: }
3716: fprintf(ficresstdeij,"\n");
3717:
3718: fprintf(ficrescveij,"%3.0f",age );
3719: for(i=1; i<=nlstate;i++)
3720: for(j=1; j<=nlstate;j++){
3721: cptj= (j-1)*nlstate+i;
3722: for(i2=1; i2<=nlstate;i2++)
3723: for(j2=1; j2<=nlstate;j2++){
3724: cptj2= (j2-1)*nlstate+i2;
3725: if(cptj2 <= cptj)
3726: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3727: }
3728: }
3729: fprintf(ficrescveij,"\n");
3730:
3731: }
3732: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3733: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3734: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3735: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3736: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3737: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3738: printf("\n");
3739: fprintf(ficlog,"\n");
3740:
3741: free_vector(xm,1,npar);
3742: free_vector(xp,1,npar);
3743: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3744: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3745: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3746: }
3747:
3748: /************ Variance ******************/
3749: 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[])
3750: {
3751: /* Variance of health expectancies */
3752: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3753: /* double **newm;*/
1.169 brouard 3754: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3755:
3756: int movingaverage();
1.126 brouard 3757: double **dnewm,**doldm;
3758: double **dnewmp,**doldmp;
3759: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3760: int k;
1.126 brouard 3761: double *xp;
3762: double **gp, **gm; /* for var eij */
3763: double ***gradg, ***trgradg; /*for var eij */
3764: double **gradgp, **trgradgp; /* for var p point j */
3765: double *gpp, *gmp; /* for var p point j */
3766: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3767: double ***p3mat;
3768: double age,agelim, hf;
3769: double ***mobaverage;
3770: int theta;
3771: char digit[4];
3772: char digitp[25];
3773:
3774: char fileresprobmorprev[FILENAMELENGTH];
3775:
3776: if(popbased==1){
3777: if(mobilav!=0)
3778: strcpy(digitp,"-populbased-mobilav-");
3779: else strcpy(digitp,"-populbased-nomobil-");
3780: }
3781: else
3782: strcpy(digitp,"-stablbased-");
3783:
3784: if (mobilav!=0) {
3785: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3786: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3787: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3788: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3789: }
3790: }
3791:
3792: strcpy(fileresprobmorprev,"prmorprev");
3793: sprintf(digit,"%-d",ij);
3794: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3795: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3796: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3797: strcat(fileresprobmorprev,fileres);
3798: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3799: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3800: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3801: }
3802: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3803:
3804: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3805: pstamp(ficresprobmorprev);
3806: 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);
3807: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3808: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3809: fprintf(ficresprobmorprev," p.%-d SE",j);
3810: for(i=1; i<=nlstate;i++)
3811: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3812: }
3813: fprintf(ficresprobmorprev,"\n");
3814: fprintf(ficgp,"\n# Routine varevsij");
3815: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3816: 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");
3817: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3818: /* } */
3819: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3820: pstamp(ficresvij);
3821: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3822: if(popbased==1)
1.128 brouard 3823: 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 3824: else
3825: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3826: fprintf(ficresvij,"# Age");
3827: for(i=1; i<=nlstate;i++)
3828: for(j=1; j<=nlstate;j++)
3829: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3830: fprintf(ficresvij,"\n");
3831:
3832: xp=vector(1,npar);
3833: dnewm=matrix(1,nlstate,1,npar);
3834: doldm=matrix(1,nlstate,1,nlstate);
3835: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3836: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3837:
3838: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3839: gpp=vector(nlstate+1,nlstate+ndeath);
3840: gmp=vector(nlstate+1,nlstate+ndeath);
3841: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3842:
3843: if(estepm < stepm){
3844: printf ("Problem %d lower than %d\n",estepm, stepm);
3845: }
3846: else hstepm=estepm;
3847: /* For example we decided to compute the life expectancy with the smallest unit */
3848: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3849: nhstepm is the number of hstepm from age to agelim
3850: nstepm is the number of stepm from age to agelin.
1.128 brouard 3851: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3852: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3853: survival function given by stepm (the optimization length). Unfortunately it
3854: means that if the survival funtion is printed every two years of age and if
3855: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3856: results. So we changed our mind and took the option of the best precision.
3857: */
3858: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3859: agelim = AGESUP;
3860: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3861: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3862: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3863: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3864: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3865: gp=matrix(0,nhstepm,1,nlstate);
3866: gm=matrix(0,nhstepm,1,nlstate);
3867:
3868:
3869: for(theta=1; theta <=npar; theta++){
3870: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3871: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3872: }
3873: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3874: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3875:
3876: if (popbased==1) {
3877: if(mobilav ==0){
3878: for(i=1; i<=nlstate;i++)
3879: prlim[i][i]=probs[(int)age][i][ij];
3880: }else{ /* mobilav */
3881: for(i=1; i<=nlstate;i++)
3882: prlim[i][i]=mobaverage[(int)age][i][ij];
3883: }
3884: }
3885:
3886: for(j=1; j<= nlstate; j++){
3887: for(h=0; h<=nhstepm; h++){
3888: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3889: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3890: }
3891: }
3892: /* This for computing probability of death (h=1 means
3893: computed over hstepm matrices product = hstepm*stepm months)
3894: as a weighted average of prlim.
3895: */
3896: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3897: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3898: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3899: }
3900: /* end probability of death */
3901:
3902: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3903: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3904: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3905: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3906:
3907: if (popbased==1) {
3908: if(mobilav ==0){
3909: for(i=1; i<=nlstate;i++)
3910: prlim[i][i]=probs[(int)age][i][ij];
3911: }else{ /* mobilav */
3912: for(i=1; i<=nlstate;i++)
3913: prlim[i][i]=mobaverage[(int)age][i][ij];
3914: }
3915: }
3916:
1.128 brouard 3917: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3918: for(h=0; h<=nhstepm; h++){
3919: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3920: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3921: }
3922: }
3923: /* This for computing probability of death (h=1 means
3924: computed over hstepm matrices product = hstepm*stepm months)
3925: as a weighted average of prlim.
3926: */
3927: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3928: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3929: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3930: }
3931: /* end probability of death */
3932:
3933: for(j=1; j<= nlstate; j++) /* vareij */
3934: for(h=0; h<=nhstepm; h++){
3935: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3936: }
3937:
3938: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3939: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3940: }
3941:
3942: } /* End theta */
3943:
3944: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3945:
3946: for(h=0; h<=nhstepm; h++) /* veij */
3947: for(j=1; j<=nlstate;j++)
3948: for(theta=1; theta <=npar; theta++)
3949: trgradg[h][j][theta]=gradg[h][theta][j];
3950:
3951: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3952: for(theta=1; theta <=npar; theta++)
3953: trgradgp[j][theta]=gradgp[theta][j];
3954:
3955:
3956: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3957: for(i=1;i<=nlstate;i++)
3958: for(j=1;j<=nlstate;j++)
3959: vareij[i][j][(int)age] =0.;
3960:
3961: for(h=0;h<=nhstepm;h++){
3962: for(k=0;k<=nhstepm;k++){
3963: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3964: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3965: for(i=1;i<=nlstate;i++)
3966: for(j=1;j<=nlstate;j++)
3967: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3968: }
3969: }
3970:
3971: /* pptj */
3972: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3973: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3974: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3975: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3976: varppt[j][i]=doldmp[j][i];
3977: /* end ppptj */
3978: /* x centered again */
3979: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3980: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3981:
3982: if (popbased==1) {
3983: if(mobilav ==0){
3984: for(i=1; i<=nlstate;i++)
3985: prlim[i][i]=probs[(int)age][i][ij];
3986: }else{ /* mobilav */
3987: for(i=1; i<=nlstate;i++)
3988: prlim[i][i]=mobaverage[(int)age][i][ij];
3989: }
3990: }
3991:
3992: /* This for computing probability of death (h=1 means
3993: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3994: as a weighted average of prlim.
3995: */
3996: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3997: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3998: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3999: }
4000: /* end probability of death */
4001:
4002: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4003: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4004: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4005: for(i=1; i<=nlstate;i++){
4006: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4007: }
4008: }
4009: fprintf(ficresprobmorprev,"\n");
4010:
4011: fprintf(ficresvij,"%.0f ",age );
4012: for(i=1; i<=nlstate;i++)
4013: for(j=1; j<=nlstate;j++){
4014: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4015: }
4016: fprintf(ficresvij,"\n");
4017: free_matrix(gp,0,nhstepm,1,nlstate);
4018: free_matrix(gm,0,nhstepm,1,nlstate);
4019: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4020: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4021: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4022: } /* End age */
4023: free_vector(gpp,nlstate+1,nlstate+ndeath);
4024: free_vector(gmp,nlstate+1,nlstate+ndeath);
4025: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4026: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 4027: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 4028: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4029: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 4030: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4031: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4032: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4033: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4034: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4035: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4036: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4037: 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);
4038: /* 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);
4039: */
4040: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4041: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4042:
4043: free_vector(xp,1,npar);
4044: free_matrix(doldm,1,nlstate,1,nlstate);
4045: free_matrix(dnewm,1,nlstate,1,npar);
4046: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4047: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4048: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4049: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4050: fclose(ficresprobmorprev);
4051: fflush(ficgp);
4052: fflush(fichtm);
4053: } /* end varevsij */
4054:
4055: /************ Variance of prevlim ******************/
4056: 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[])
4057: {
4058: /* Variance of prevalence limit */
4059: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4060:
1.126 brouard 4061: double **dnewm,**doldm;
4062: int i, j, nhstepm, hstepm;
4063: double *xp;
4064: double *gp, *gm;
4065: double **gradg, **trgradg;
4066: double age,agelim;
4067: int theta;
4068:
4069: pstamp(ficresvpl);
4070: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4071: fprintf(ficresvpl,"# Age");
4072: for(i=1; i<=nlstate;i++)
4073: fprintf(ficresvpl," %1d-%1d",i,i);
4074: fprintf(ficresvpl,"\n");
4075:
4076: xp=vector(1,npar);
4077: dnewm=matrix(1,nlstate,1,npar);
4078: doldm=matrix(1,nlstate,1,nlstate);
4079:
4080: hstepm=1*YEARM; /* Every year of age */
4081: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4082: agelim = AGESUP;
4083: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4084: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4085: if (stepm >= YEARM) hstepm=1;
4086: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4087: gradg=matrix(1,npar,1,nlstate);
4088: gp=vector(1,nlstate);
4089: gm=vector(1,nlstate);
4090:
4091: for(theta=1; theta <=npar; theta++){
4092: for(i=1; i<=npar; i++){ /* Computes gradient */
4093: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4094: }
4095: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4096: for(i=1;i<=nlstate;i++)
4097: gp[i] = prlim[i][i];
4098:
4099: for(i=1; i<=npar; i++) /* Computes gradient */
4100: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4101: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4102: for(i=1;i<=nlstate;i++)
4103: gm[i] = prlim[i][i];
4104:
4105: for(i=1;i<=nlstate;i++)
4106: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4107: } /* End theta */
4108:
4109: trgradg =matrix(1,nlstate,1,npar);
4110:
4111: for(j=1; j<=nlstate;j++)
4112: for(theta=1; theta <=npar; theta++)
4113: trgradg[j][theta]=gradg[theta][j];
4114:
4115: for(i=1;i<=nlstate;i++)
4116: varpl[i][(int)age] =0.;
4117: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4118: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4119: for(i=1;i<=nlstate;i++)
4120: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4121:
4122: fprintf(ficresvpl,"%.0f ",age );
4123: for(i=1; i<=nlstate;i++)
4124: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4125: fprintf(ficresvpl,"\n");
4126: free_vector(gp,1,nlstate);
4127: free_vector(gm,1,nlstate);
4128: free_matrix(gradg,1,npar,1,nlstate);
4129: free_matrix(trgradg,1,nlstate,1,npar);
4130: } /* End age */
4131:
4132: free_vector(xp,1,npar);
4133: free_matrix(doldm,1,nlstate,1,npar);
4134: free_matrix(dnewm,1,nlstate,1,nlstate);
4135:
4136: }
4137:
4138: /************ Variance of one-step probabilities ******************/
4139: 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[])
4140: {
1.164 brouard 4141: int i, j=0, k1, l1, tj;
1.126 brouard 4142: int k2, l2, j1, z1;
1.164 brouard 4143: int k=0, l;
1.145 brouard 4144: int first=1, first1, first2;
1.126 brouard 4145: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4146: double **dnewm,**doldm;
4147: double *xp;
4148: double *gp, *gm;
4149: double **gradg, **trgradg;
4150: double **mu;
1.164 brouard 4151: double age, cov[NCOVMAX+1];
1.126 brouard 4152: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4153: int theta;
4154: char fileresprob[FILENAMELENGTH];
4155: char fileresprobcov[FILENAMELENGTH];
4156: char fileresprobcor[FILENAMELENGTH];
4157: double ***varpij;
4158:
4159: strcpy(fileresprob,"prob");
4160: strcat(fileresprob,fileres);
4161: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4162: printf("Problem with resultfile: %s\n", fileresprob);
4163: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4164: }
4165: strcpy(fileresprobcov,"probcov");
4166: strcat(fileresprobcov,fileres);
4167: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4168: printf("Problem with resultfile: %s\n", fileresprobcov);
4169: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4170: }
4171: strcpy(fileresprobcor,"probcor");
4172: strcat(fileresprobcor,fileres);
4173: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4174: printf("Problem with resultfile: %s\n", fileresprobcor);
4175: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4176: }
4177: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4178: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4179: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4180: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4181: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4182: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4183: pstamp(ficresprob);
4184: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4185: fprintf(ficresprob,"# Age");
4186: pstamp(ficresprobcov);
4187: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4188: fprintf(ficresprobcov,"# Age");
4189: pstamp(ficresprobcor);
4190: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4191: fprintf(ficresprobcor,"# Age");
4192:
4193:
4194: for(i=1; i<=nlstate;i++)
4195: for(j=1; j<=(nlstate+ndeath);j++){
4196: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4197: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4198: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4199: }
4200: /* fprintf(ficresprob,"\n");
4201: fprintf(ficresprobcov,"\n");
4202: fprintf(ficresprobcor,"\n");
4203: */
1.131 brouard 4204: xp=vector(1,npar);
1.126 brouard 4205: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4206: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4207: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4208: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4209: first=1;
4210: fprintf(ficgp,"\n# Routine varprob");
4211: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4212: fprintf(fichtm,"\n");
4213:
4214: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4215: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4216: file %s<br>\n",optionfilehtmcov);
4217: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4218: and drawn. It helps understanding how is the covariance between two incidences.\
4219: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4220: 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. \
4221: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4222: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4223: standard deviations wide on each axis. <br>\
4224: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4225: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4226: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4227:
4228: cov[1]=1;
1.145 brouard 4229: /* tj=cptcoveff; */
4230: tj = (int) pow(2,cptcoveff);
1.126 brouard 4231: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4232: j1=0;
1.145 brouard 4233: for(j1=1; j1<=tj;j1++){
4234: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4235: /*j1++;*/
1.126 brouard 4236: if (cptcovn>0) {
4237: fprintf(ficresprob, "\n#********** Variable ");
4238: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4239: fprintf(ficresprob, "**********\n#\n");
4240: fprintf(ficresprobcov, "\n#********** Variable ");
4241: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4242: fprintf(ficresprobcov, "**********\n#\n");
4243:
4244: fprintf(ficgp, "\n#********** Variable ");
4245: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4246: fprintf(ficgp, "**********\n#\n");
4247:
4248:
4249: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4250: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4251: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4252:
4253: fprintf(ficresprobcor, "\n#********** Variable ");
4254: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4255: fprintf(ficresprobcor, "**********\n#");
4256: }
4257:
1.145 brouard 4258: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4259: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4260: gp=vector(1,(nlstate)*(nlstate+ndeath));
4261: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4262: for (age=bage; age<=fage; age ++){
4263: cov[2]=age;
1.187 brouard 4264: if(nagesqr==1)
4265: cov[3]= age*age;
1.126 brouard 4266: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4267: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4268: * 1 1 1 1 1
4269: * 2 2 1 1 1
4270: * 3 1 2 1 1
4271: */
4272: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4273: }
1.186 brouard 4274: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4275: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4276: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4277: 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 4278:
4279:
4280: for(theta=1; theta <=npar; theta++){
4281: for(i=1; i<=npar; i++)
4282: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4283:
4284: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4285:
4286: k=0;
4287: for(i=1; i<= (nlstate); i++){
4288: for(j=1; j<=(nlstate+ndeath);j++){
4289: k=k+1;
4290: gp[k]=pmmij[i][j];
4291: }
4292: }
4293:
4294: for(i=1; i<=npar; i++)
4295: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4296:
4297: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4298: k=0;
4299: for(i=1; i<=(nlstate); i++){
4300: for(j=1; j<=(nlstate+ndeath);j++){
4301: k=k+1;
4302: gm[k]=pmmij[i][j];
4303: }
4304: }
4305:
4306: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4307: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4308: }
4309:
4310: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4311: for(theta=1; theta <=npar; theta++)
4312: trgradg[j][theta]=gradg[theta][j];
4313:
4314: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4315: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4316:
4317: pmij(pmmij,cov,ncovmodel,x,nlstate);
4318:
4319: k=0;
4320: for(i=1; i<=(nlstate); i++){
4321: for(j=1; j<=(nlstate+ndeath);j++){
4322: k=k+1;
4323: mu[k][(int) age]=pmmij[i][j];
4324: }
4325: }
4326: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4327: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4328: varpij[i][j][(int)age] = doldm[i][j];
4329:
4330: /*printf("\n%d ",(int)age);
4331: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4332: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4333: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4334: }*/
4335:
4336: fprintf(ficresprob,"\n%d ",(int)age);
4337: fprintf(ficresprobcov,"\n%d ",(int)age);
4338: fprintf(ficresprobcor,"\n%d ",(int)age);
4339:
4340: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4341: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4342: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4343: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4344: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4345: }
4346: i=0;
4347: for (k=1; k<=(nlstate);k++){
4348: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4349: i++;
1.126 brouard 4350: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4351: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4352: for (j=1; j<=i;j++){
1.145 brouard 4353: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4354: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4355: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4356: }
4357: }
4358: }/* end of loop for state */
4359: } /* end of loop for age */
1.145 brouard 4360: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4361: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4362: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4363: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4364:
1.126 brouard 4365: /* Confidence intervalle of pij */
4366: /*
1.131 brouard 4367: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4368: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4369: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4370: 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);
4371: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4372: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4373: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4374: */
4375:
4376: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4377: first1=1;first2=2;
1.126 brouard 4378: for (k2=1; k2<=(nlstate);k2++){
4379: for (l2=1; l2<=(nlstate+ndeath);l2++){
4380: if(l2==k2) continue;
4381: j=(k2-1)*(nlstate+ndeath)+l2;
4382: for (k1=1; k1<=(nlstate);k1++){
4383: for (l1=1; l1<=(nlstate+ndeath);l1++){
4384: if(l1==k1) continue;
4385: i=(k1-1)*(nlstate+ndeath)+l1;
4386: if(i<=j) continue;
4387: for (age=bage; age<=fage; age ++){
4388: if ((int)age %5==0){
4389: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4390: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4391: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4392: mu1=mu[i][(int) age]/stepm*YEARM ;
4393: mu2=mu[j][(int) age]/stepm*YEARM;
4394: c12=cv12/sqrt(v1*v2);
4395: /* Computing eigen value of matrix of covariance */
4396: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4397: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4398: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4399: if(first2==1){
4400: first1=0;
4401: 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);
4402: }
4403: 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);
4404: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4405: /* lc2=fabs(lc2); */
1.135 brouard 4406: }
4407:
1.126 brouard 4408: /* Eigen vectors */
4409: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4410: /*v21=sqrt(1.-v11*v11); *//* error */
4411: v21=(lc1-v1)/cv12*v11;
4412: v12=-v21;
4413: v22=v11;
4414: tnalp=v21/v11;
4415: if(first1==1){
4416: first1=0;
4417: 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);
4418: }
4419: 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);
4420: /*printf(fignu*/
4421: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4422: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4423: if(first==1){
4424: first=0;
4425: fprintf(ficgp,"\nset parametric;unset label");
4426: 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 4427: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4428: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4429: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4430: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4431: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4432: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4433: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4434: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4435: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4436: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4437: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4438: 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",\
4439: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4440: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4441: }else{
4442: first=0;
4443: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4444: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4445: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4446: 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",\
4447: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4448: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4449: }/* if first */
4450: } /* age mod 5 */
4451: } /* end loop age */
4452: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4453: first=1;
4454: } /*l12 */
4455: } /* k12 */
4456: } /*l1 */
4457: }/* k1 */
1.169 brouard 4458: /* } */ /* loop covariates */
1.126 brouard 4459: }
4460: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4461: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4462: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4463: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4464: free_vector(xp,1,npar);
4465: fclose(ficresprob);
4466: fclose(ficresprobcov);
4467: fclose(ficresprobcor);
4468: fflush(ficgp);
4469: fflush(fichtmcov);
4470: }
4471:
4472:
4473: /******************* Printing html file ***********/
4474: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4475: int lastpass, int stepm, int weightopt, char model[],\
4476: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4477: int popforecast, int estepm ,\
4478: double jprev1, double mprev1,double anprev1, \
4479: double jprev2, double mprev2,double anprev2){
4480: int jj1, k1, i1, cpt;
4481:
4482: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4483: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4484: </ul>");
4485: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4486: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4487: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4488: fprintf(fichtm,"\
4489: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4490: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4491: fprintf(fichtm,"\
4492: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4493: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4494: fprintf(fichtm,"\
1.128 brouard 4495: - (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 4496: <a href=\"%s\">%s</a> <br>\n",
4497: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4498: fprintf(fichtm,"\
4499: - Population projections by age and states: \
4500: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4501:
4502: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4503:
1.145 brouard 4504: m=pow(2,cptcoveff);
1.126 brouard 4505: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4506:
4507: jj1=0;
4508: for(k1=1; k1<=m;k1++){
1.192 brouard 4509: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4510: jj1++;
4511: if (cptcovn > 0) {
4512: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4513: for (cpt=1; cpt<=cptcoveff;cpt++){
1.126 brouard 4514: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
1.192 brouard 4515: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
4516: }
1.126 brouard 4517: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4518: }
4519: /* Pij */
1.145 brouard 4520: 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> \
4521: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4522: /* Quasi-incidences */
4523: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4524: 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> \
4525: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4526: /* Period (stable) prevalence in each health state */
1.154 brouard 4527: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4528: 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> \
4529: <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 4530: }
4531: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4532: 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> \
4533: <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 4534: }
1.192 brouard 4535: /* } /\* end i1 *\/ */
1.126 brouard 4536: }/* End k1 */
4537: fprintf(fichtm,"</ul>");
4538:
4539: fprintf(fichtm,"\
4540: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 ! brouard 4541: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
! 4542: - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
1.126 brouard 4543:
1.193 ! brouard 4544: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.126 brouard 4545: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4546: fprintf(fichtm,"\
4547: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4548: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4549:
4550: fprintf(fichtm,"\
4551: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4552: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4553: fprintf(fichtm,"\
4554: - 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): \
4555: <a href=\"%s\">%s</a> <br>\n</li>",
4556: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4557: fprintf(fichtm,"\
4558: - (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): \
4559: <a href=\"%s\">%s</a> <br>\n</li>",
4560: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4561: fprintf(fichtm,"\
1.128 brouard 4562: - 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 4563: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4564: fprintf(fichtm,"\
1.128 brouard 4565: - 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",
4566: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4567: fprintf(fichtm,"\
4568: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4569: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4570:
4571: /* if(popforecast==1) fprintf(fichtm,"\n */
4572: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4573: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4574: /* <br>",fileres,fileres,fileres,fileres); */
4575: /* else */
4576: /* 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); */
4577: fflush(fichtm);
4578: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4579:
1.145 brouard 4580: m=pow(2,cptcoveff);
1.126 brouard 4581: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4582:
4583: jj1=0;
4584: for(k1=1; k1<=m;k1++){
1.192 brouard 4585: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4586: jj1++;
4587: if (cptcovn > 0) {
4588: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4589: for (cpt=1; cpt<=cptcoveff;cpt++)
4590: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4591: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4592: }
4593: for(cpt=1; cpt<=nlstate;cpt++) {
4594: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4595: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4596: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4597: }
4598: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4599: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4600: true period expectancies (those weighted with period prevalences are also\
4601: drawn in addition to the population based expectancies computed using\
4602: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4603: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.192 brouard 4604: /* } /\* end i1 *\/ */
1.126 brouard 4605: }/* End k1 */
4606: fprintf(fichtm,"</ul>");
4607: fflush(fichtm);
4608: }
4609:
4610: /******************* Gnuplot file **************/
4611: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4612:
4613: char dirfileres[132],optfileres[132];
1.164 brouard 4614: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4615: int ng=0;
1.126 brouard 4616: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4617: /* printf("Problem with file %s",optionfilegnuplot); */
4618: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4619: /* } */
4620:
4621: /*#ifdef windows */
4622: fprintf(ficgp,"cd \"%s\" \n",pathc);
4623: /*#endif */
4624: m=pow(2,cptcoveff);
4625:
4626: strcpy(dirfileres,optionfilefiname);
4627: strcpy(optfileres,"vpl");
4628: /* 1eme*/
1.153 brouard 4629: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4630: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4631: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4632: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4633: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4634: fprintf(ficgp,"set xlabel \"Age\" \n\
4635: set ylabel \"Probability\" \n\
1.145 brouard 4636: set ter png small size 320, 240\n\
1.170 brouard 4637: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4638:
4639: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4640: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4641: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4642: }
1.170 brouard 4643: 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 4644: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4645: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4646: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4647: }
1.170 brouard 4648: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4649: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4650: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4651: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4652: }
1.145 brouard 4653: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4654: }
4655: }
4656: /*2 eme*/
1.153 brouard 4657: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4658: for (k1=1; k1<= m ; k1 ++) {
4659: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4660: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4661:
4662: for (i=1; i<= nlstate+1 ; i ++) {
4663: k=2*i;
1.170 brouard 4664: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4665: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4666: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4667: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4668: }
4669: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4670: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4671: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4672: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4673: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4674: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4675: }
1.145 brouard 4676: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4677: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4678: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4679: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4680: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4681: }
1.145 brouard 4682: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4683: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4684: }
4685: }
4686:
4687: /*3eme*/
4688:
4689: for (k1=1; k1<= m ; k1 ++) {
4690: for (cpt=1; cpt<= nlstate ; cpt ++) {
4691: /* k=2+nlstate*(2*cpt-2); */
4692: k=2+(nlstate+1)*(cpt-1);
4693: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4694: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4695: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4696: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4697: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4698: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4699: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4700: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4701: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4702:
4703: */
4704: for (i=1; i< nlstate ; i ++) {
4705: 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);
4706: /* 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);*/
4707:
4708: }
4709: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4710: }
4711: }
4712:
4713: /* CV preval stable (period) */
1.153 brouard 4714: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4715: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4716: k=3;
1.153 brouard 4717: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4718: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4719: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4720: set ter png small size 320, 240\n\
1.126 brouard 4721: unset log y\n\
1.153 brouard 4722: plot [%.f:%.f] ", ageminpar, agemaxpar);
4723: for (i=1; i<= nlstate ; i ++){
4724: if(i==1)
4725: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4726: else
4727: fprintf(ficgp,", '' ");
1.154 brouard 4728: l=(nlstate+ndeath)*(i-1)+1;
4729: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4730: for (j=1; j<= (nlstate-1) ; j ++)
4731: fprintf(ficgp,"+$%d",k+l+j);
4732: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4733: } /* nlstate */
4734: fprintf(ficgp,"\n");
4735: } /* end cpt state*/
4736: } /* end covariate */
1.126 brouard 4737:
4738: /* proba elementaires */
1.187 brouard 4739: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4740: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4741: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4742: for(k=1; k <=(nlstate+ndeath); k++){
4743: if (k != i) {
1.187 brouard 4744: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4745: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4746: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4747: jk++;
4748: }
1.187 brouard 4749: fprintf(ficgp,"\n");
1.126 brouard 4750: }
4751: }
4752: }
1.187 brouard 4753: fprintf(ficgp,"##############\n#\n");
4754:
1.145 brouard 4755: /*goto avoid;*/
1.187 brouard 4756: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4757: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4758: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4759: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4760: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4761: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4762: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4763: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4764: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4765: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4766: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4767: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4768: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4769: fprintf(ficgp,"#\n");
1.126 brouard 4770: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4771: fprintf(ficgp,"# ng=%d\n",ng);
4772: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4773: for(jk=1; jk <=m; jk++) {
1.187 brouard 4774: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4775: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4776: if (ng==2)
4777: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4778: else
4779: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4780: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4781: i=1;
4782: for(k2=1; k2<=nlstate; k2++) {
4783: k3=i;
4784: for(k=1; k<=(nlstate+ndeath); k++) {
4785: if (k != k2){
4786: if(ng==2)
1.187 brouard 4787: if(nagesqr==0)
4788: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4789: else /* nagesqr =1 */
4790: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4791: else
1.187 brouard 4792: if(nagesqr==0)
4793: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4794: else /* nagesqr =1 */
4795: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4796: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4797: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.186 brouard 4798: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.187 brouard 4799: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
1.186 brouard 4800: ij++;
4801: }
4802: else
1.187 brouard 4803: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4804: }
4805: fprintf(ficgp,")/(1");
4806:
1.187 brouard 4807: for(k1=1; k1 <=nlstate; k1++){
4808: if(nagesqr==0)
4809: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4810: else /* nagesqr =1 */
4811: 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);
4812:
1.126 brouard 4813: ij=1;
1.187 brouard 4814: for(j=3; j <=ncovmodel-nagesqr; j++){
1.186 brouard 4815: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
1.187 brouard 4816: 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 4817: ij++;
4818: }
4819: else
1.187 brouard 4820: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4821: }
4822: fprintf(ficgp,")");
4823: }
4824: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4825: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4826: i=i+ncovmodel;
4827: }
4828: } /* end k */
4829: } /* end k2 */
4830: } /* end jk */
4831: } /* end ng */
1.164 brouard 4832: /* avoid: */
1.126 brouard 4833: fflush(ficgp);
4834: } /* end gnuplot */
4835:
4836:
4837: /*************** Moving average **************/
4838: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4839:
4840: int i, cpt, cptcod;
4841: int modcovmax =1;
4842: int mobilavrange, mob;
4843: double age;
4844:
4845: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4846: a covariate has 2 modalities */
4847: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4848:
4849: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4850: if(mobilav==1) mobilavrange=5; /* default */
4851: else mobilavrange=mobilav;
4852: for (age=bage; age<=fage; age++)
4853: for (i=1; i<=nlstate;i++)
4854: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4855: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4856: /* We keep the original values on the extreme ages bage, fage and for
4857: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4858: we use a 5 terms etc. until the borders are no more concerned.
4859: */
4860: for (mob=3;mob <=mobilavrange;mob=mob+2){
4861: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4862: for (i=1; i<=nlstate;i++){
4863: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4864: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4865: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4866: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4867: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4868: }
4869: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4870: }
4871: }
4872: }/* end age */
4873: }/* end mob */
4874: }else return -1;
4875: return 0;
4876: }/* End movingaverage */
4877:
4878:
4879: /************** Forecasting ******************/
1.169 brouard 4880: 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 4881: /* proj1, year, month, day of starting projection
4882: agemin, agemax range of age
4883: dateprev1 dateprev2 range of dates during which prevalence is computed
4884: anproj2 year of en of projection (same day and month as proj1).
4885: */
1.164 brouard 4886: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4887: double agec; /* generic age */
4888: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4889: double *popeffectif,*popcount;
4890: double ***p3mat;
4891: double ***mobaverage;
4892: char fileresf[FILENAMELENGTH];
4893:
4894: agelim=AGESUP;
4895: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4896:
4897: strcpy(fileresf,"f");
4898: strcat(fileresf,fileres);
4899: if((ficresf=fopen(fileresf,"w"))==NULL) {
4900: printf("Problem with forecast resultfile: %s\n", fileresf);
4901: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4902: }
4903: printf("Computing forecasting: result on file '%s' \n", fileresf);
4904: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4905:
4906: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4907:
4908: if (mobilav!=0) {
4909: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4910: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4911: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4912: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4913: }
4914: }
4915:
4916: stepsize=(int) (stepm+YEARM-1)/YEARM;
4917: if (stepm<=12) stepsize=1;
4918: if(estepm < stepm){
4919: printf ("Problem %d lower than %d\n",estepm, stepm);
4920: }
4921: else hstepm=estepm;
4922:
4923: hstepm=hstepm/stepm;
4924: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4925: fractional in yp1 */
4926: anprojmean=yp;
4927: yp2=modf((yp1*12),&yp);
4928: mprojmean=yp;
4929: yp1=modf((yp2*30.5),&yp);
4930: jprojmean=yp;
4931: if(jprojmean==0) jprojmean=1;
4932: if(mprojmean==0) jprojmean=1;
4933:
4934: i1=cptcoveff;
4935: if (cptcovn < 1){i1=1;}
4936:
4937: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4938:
4939: fprintf(ficresf,"#****** Routine prevforecast **\n");
4940:
4941: /* if (h==(int)(YEARM*yearp)){ */
4942: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4943: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4944: k=k+1;
4945: fprintf(ficresf,"\n#******");
4946: for(j=1;j<=cptcoveff;j++) {
4947: 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]]);
4948: }
4949: fprintf(ficresf,"******\n");
4950: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4951: for(j=1; j<=nlstate+ndeath;j++){
4952: for(i=1; i<=nlstate;i++)
4953: fprintf(ficresf," p%d%d",i,j);
4954: fprintf(ficresf," p.%d",j);
4955: }
4956: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4957: fprintf(ficresf,"\n");
4958: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4959:
4960: for (agec=fage; agec>=(ageminpar-1); agec--){
4961: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4962: nhstepm = nhstepm/hstepm;
4963: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4964: oldm=oldms;savm=savms;
4965: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4966:
4967: for (h=0; h<=nhstepm; h++){
4968: if (h*hstepm/YEARM*stepm ==yearp) {
4969: fprintf(ficresf,"\n");
4970: for(j=1;j<=cptcoveff;j++)
4971: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4972: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4973: }
4974: for(j=1; j<=nlstate+ndeath;j++) {
4975: ppij=0.;
4976: for(i=1; i<=nlstate;i++) {
4977: if (mobilav==1)
4978: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4979: else {
4980: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4981: }
4982: if (h*hstepm/YEARM*stepm== yearp) {
4983: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4984: }
4985: } /* end i */
4986: if (h*hstepm/YEARM*stepm==yearp) {
4987: fprintf(ficresf," %.3f", ppij);
4988: }
4989: }/* end j */
4990: } /* end h */
4991: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4992: } /* end agec */
4993: } /* end yearp */
4994: } /* end cptcod */
4995: } /* end cptcov */
4996:
4997: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4998:
4999: fclose(ficresf);
5000: }
5001:
5002: /************** Forecasting *****not tested NB*************/
1.169 brouard 5003: 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 5004:
5005: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5006: int *popage;
5007: double calagedatem, agelim, kk1, kk2;
5008: double *popeffectif,*popcount;
5009: double ***p3mat,***tabpop,***tabpopprev;
5010: double ***mobaverage;
5011: char filerespop[FILENAMELENGTH];
5012:
5013: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5014: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5015: agelim=AGESUP;
5016: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5017:
5018: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5019:
5020:
5021: strcpy(filerespop,"pop");
5022: strcat(filerespop,fileres);
5023: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5024: printf("Problem with forecast resultfile: %s\n", filerespop);
5025: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5026: }
5027: printf("Computing forecasting: result on file '%s' \n", filerespop);
5028: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5029:
5030: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5031:
5032: if (mobilav!=0) {
5033: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5034: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5035: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5036: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5037: }
5038: }
5039:
5040: stepsize=(int) (stepm+YEARM-1)/YEARM;
5041: if (stepm<=12) stepsize=1;
5042:
5043: agelim=AGESUP;
5044:
5045: hstepm=1;
5046: hstepm=hstepm/stepm;
5047:
5048: if (popforecast==1) {
5049: if((ficpop=fopen(popfile,"r"))==NULL) {
5050: printf("Problem with population file : %s\n",popfile);exit(0);
5051: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5052: }
5053: popage=ivector(0,AGESUP);
5054: popeffectif=vector(0,AGESUP);
5055: popcount=vector(0,AGESUP);
5056:
5057: i=1;
5058: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5059:
5060: imx=i;
5061: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5062: }
5063:
5064: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5065: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5066: k=k+1;
5067: fprintf(ficrespop,"\n#******");
5068: for(j=1;j<=cptcoveff;j++) {
5069: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5070: }
5071: fprintf(ficrespop,"******\n");
5072: fprintf(ficrespop,"# Age");
5073: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5074: if (popforecast==1) fprintf(ficrespop," [Population]");
5075:
5076: for (cpt=0; cpt<=0;cpt++) {
5077: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5078:
5079: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5080: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5081: nhstepm = nhstepm/hstepm;
5082:
5083: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5084: oldm=oldms;savm=savms;
5085: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5086:
5087: for (h=0; h<=nhstepm; h++){
5088: if (h==(int) (calagedatem+YEARM*cpt)) {
5089: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5090: }
5091: for(j=1; j<=nlstate+ndeath;j++) {
5092: kk1=0.;kk2=0;
5093: for(i=1; i<=nlstate;i++) {
5094: if (mobilav==1)
5095: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5096: else {
5097: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5098: }
5099: }
5100: if (h==(int)(calagedatem+12*cpt)){
5101: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5102: /*fprintf(ficrespop," %.3f", kk1);
5103: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5104: }
5105: }
5106: for(i=1; i<=nlstate;i++){
5107: kk1=0.;
5108: for(j=1; j<=nlstate;j++){
5109: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5110: }
5111: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5112: }
5113:
5114: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5115: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5116: }
5117: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5118: }
5119: }
5120:
5121: /******/
5122:
5123: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5124: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5125: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5126: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5127: nhstepm = nhstepm/hstepm;
5128:
5129: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5130: oldm=oldms;savm=savms;
5131: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5132: for (h=0; h<=nhstepm; h++){
5133: if (h==(int) (calagedatem+YEARM*cpt)) {
5134: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5135: }
5136: for(j=1; j<=nlstate+ndeath;j++) {
5137: kk1=0.;kk2=0;
5138: for(i=1; i<=nlstate;i++) {
5139: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5140: }
5141: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5142: }
5143: }
5144: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5145: }
5146: }
5147: }
5148: }
5149:
5150: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5151:
5152: if (popforecast==1) {
5153: free_ivector(popage,0,AGESUP);
5154: free_vector(popeffectif,0,AGESUP);
5155: free_vector(popcount,0,AGESUP);
5156: }
5157: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5158: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5159: fclose(ficrespop);
5160: } /* End of popforecast */
5161:
5162: int fileappend(FILE *fichier, char *optionfich)
5163: {
5164: if((fichier=fopen(optionfich,"a"))==NULL) {
5165: printf("Problem with file: %s\n", optionfich);
5166: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5167: return (0);
5168: }
5169: fflush(fichier);
5170: return (1);
5171: }
5172:
5173:
5174: /**************** function prwizard **********************/
5175: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5176: {
5177:
5178: /* Wizard to print covariance matrix template */
5179:
1.164 brouard 5180: char ca[32], cb[32];
5181: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5182: int numlinepar;
5183:
5184: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5185: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5186: for(i=1; i <=nlstate; i++){
5187: jj=0;
5188: for(j=1; j <=nlstate+ndeath; j++){
5189: if(j==i) continue;
5190: jj++;
5191: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5192: printf("%1d%1d",i,j);
5193: fprintf(ficparo,"%1d%1d",i,j);
5194: for(k=1; k<=ncovmodel;k++){
5195: /* printf(" %lf",param[i][j][k]); */
5196: /* fprintf(ficparo," %lf",param[i][j][k]); */
5197: printf(" 0.");
5198: fprintf(ficparo," 0.");
5199: }
5200: printf("\n");
5201: fprintf(ficparo,"\n");
5202: }
5203: }
5204: printf("# Scales (for hessian or gradient estimation)\n");
5205: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5206: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5207: for(i=1; i <=nlstate; i++){
5208: jj=0;
5209: for(j=1; j <=nlstate+ndeath; j++){
5210: if(j==i) continue;
5211: jj++;
5212: fprintf(ficparo,"%1d%1d",i,j);
5213: printf("%1d%1d",i,j);
5214: fflush(stdout);
5215: for(k=1; k<=ncovmodel;k++){
5216: /* printf(" %le",delti3[i][j][k]); */
5217: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5218: printf(" 0.");
5219: fprintf(ficparo," 0.");
5220: }
5221: numlinepar++;
5222: printf("\n");
5223: fprintf(ficparo,"\n");
5224: }
5225: }
5226: printf("# Covariance matrix\n");
5227: /* # 121 Var(a12)\n\ */
5228: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5229: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5230: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5231: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5232: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5233: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5234: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5235: fflush(stdout);
5236: fprintf(ficparo,"# Covariance matrix\n");
5237: /* # 121 Var(a12)\n\ */
5238: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5239: /* # ...\n\ */
5240: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5241:
5242: for(itimes=1;itimes<=2;itimes++){
5243: jj=0;
5244: for(i=1; i <=nlstate; i++){
5245: for(j=1; j <=nlstate+ndeath; j++){
5246: if(j==i) continue;
5247: for(k=1; k<=ncovmodel;k++){
5248: jj++;
5249: ca[0]= k+'a'-1;ca[1]='\0';
5250: if(itimes==1){
5251: printf("#%1d%1d%d",i,j,k);
5252: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5253: }else{
5254: printf("%1d%1d%d",i,j,k);
5255: fprintf(ficparo,"%1d%1d%d",i,j,k);
5256: /* printf(" %.5le",matcov[i][j]); */
5257: }
5258: ll=0;
5259: for(li=1;li <=nlstate; li++){
5260: for(lj=1;lj <=nlstate+ndeath; lj++){
5261: if(lj==li) continue;
5262: for(lk=1;lk<=ncovmodel;lk++){
5263: ll++;
5264: if(ll<=jj){
5265: cb[0]= lk +'a'-1;cb[1]='\0';
5266: if(ll<jj){
5267: if(itimes==1){
5268: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5269: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5270: }else{
5271: printf(" 0.");
5272: fprintf(ficparo," 0.");
5273: }
5274: }else{
5275: if(itimes==1){
5276: printf(" Var(%s%1d%1d)",ca,i,j);
5277: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5278: }else{
5279: printf(" 0.");
5280: fprintf(ficparo," 0.");
5281: }
5282: }
5283: }
5284: } /* end lk */
5285: } /* end lj */
5286: } /* end li */
5287: printf("\n");
5288: fprintf(ficparo,"\n");
5289: numlinepar++;
5290: } /* end k*/
5291: } /*end j */
5292: } /* end i */
5293: } /* end itimes */
5294:
5295: } /* end of prwizard */
5296: /******************* Gompertz Likelihood ******************************/
5297: double gompertz(double x[])
5298: {
5299: double A,B,L=0.0,sump=0.,num=0.;
5300: int i,n=0; /* n is the size of the sample */
5301:
5302: for (i=0;i<=imx-1 ; i++) {
5303: sump=sump+weight[i];
5304: /* sump=sump+1;*/
5305: num=num+1;
5306: }
5307:
5308:
5309: /* for (i=0; i<=imx; i++)
5310: 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]);*/
5311:
5312: for (i=1;i<=imx ; i++)
5313: {
5314: if (cens[i] == 1 && wav[i]>1)
5315: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5316:
5317: if (cens[i] == 0 && wav[i]>1)
5318: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5319: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5320:
5321: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5322: if (wav[i] > 1 ) { /* ??? */
5323: L=L+A*weight[i];
5324: /* 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]);*/
5325: }
5326: }
5327:
5328: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5329:
5330: return -2*L*num/sump;
5331: }
5332:
1.136 brouard 5333: #ifdef GSL
5334: /******************* Gompertz_f Likelihood ******************************/
5335: double gompertz_f(const gsl_vector *v, void *params)
5336: {
5337: double A,B,LL=0.0,sump=0.,num=0.;
5338: double *x= (double *) v->data;
5339: int i,n=0; /* n is the size of the sample */
5340:
5341: for (i=0;i<=imx-1 ; i++) {
5342: sump=sump+weight[i];
5343: /* sump=sump+1;*/
5344: num=num+1;
5345: }
5346:
5347:
5348: /* for (i=0; i<=imx; i++)
5349: 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]);*/
5350: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5351: for (i=1;i<=imx ; i++)
5352: {
5353: if (cens[i] == 1 && wav[i]>1)
5354: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5355:
5356: if (cens[i] == 0 && wav[i]>1)
5357: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5358: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5359:
5360: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5361: if (wav[i] > 1 ) { /* ??? */
5362: LL=LL+A*weight[i];
5363: /* 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]);*/
5364: }
5365: }
5366:
5367: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5368: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5369:
5370: return -2*LL*num/sump;
5371: }
5372: #endif
5373:
1.126 brouard 5374: /******************* Printing html file ***********/
5375: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5376: int lastpass, int stepm, int weightopt, char model[],\
5377: int imx, double p[],double **matcov,double agemortsup){
5378: int i,k;
5379:
5380: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5381: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5382: for (i=1;i<=2;i++)
5383: 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]));
5384: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5385: fprintf(fichtm,"</ul>");
5386:
5387: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5388:
5389: 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>");
5390:
5391: for (k=agegomp;k<(agemortsup-2);k++)
5392: 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]);
5393:
5394:
5395: fflush(fichtm);
5396: }
5397:
5398: /******************* Gnuplot file **************/
5399: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5400:
5401: char dirfileres[132],optfileres[132];
1.164 brouard 5402:
1.126 brouard 5403: int ng;
5404:
5405:
5406: /*#ifdef windows */
5407: fprintf(ficgp,"cd \"%s\" \n",pathc);
5408: /*#endif */
5409:
5410:
5411: strcpy(dirfileres,optionfilefiname);
5412: strcpy(optfileres,"vpl");
5413: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5414: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5415: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5416: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5417: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5418:
5419: }
5420:
1.136 brouard 5421: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5422: {
1.126 brouard 5423:
1.136 brouard 5424: /*-------- data file ----------*/
5425: FILE *fic;
5426: char dummy[]=" ";
1.164 brouard 5427: int i=0, j=0, n=0;
1.136 brouard 5428: int linei, month, year,iout;
5429: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5430: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5431: char *stratrunc;
5432: int lstra;
1.126 brouard 5433:
5434:
1.136 brouard 5435: if((fic=fopen(datafile,"r"))==NULL) {
5436: printf("Problem while opening datafile: %s\n", datafile);return 1;
5437: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5438: }
1.126 brouard 5439:
1.136 brouard 5440: i=1;
5441: linei=0;
5442: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5443: linei=linei+1;
5444: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5445: if(line[j] == '\t')
5446: line[j] = ' ';
5447: }
5448: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5449: ;
5450: };
5451: line[j+1]=0; /* Trims blanks at end of line */
5452: if(line[0]=='#'){
5453: fprintf(ficlog,"Comment line\n%s\n",line);
5454: printf("Comment line\n%s\n",line);
5455: continue;
5456: }
5457: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5458: strcpy(line, linetmp);
1.136 brouard 5459:
1.126 brouard 5460:
1.136 brouard 5461: for (j=maxwav;j>=1;j--){
1.137 brouard 5462: cutv(stra, strb, line, ' ');
1.136 brouard 5463: if(strb[0]=='.') { /* Missing status */
5464: lval=-1;
5465: }else{
5466: errno=0;
5467: lval=strtol(strb,&endptr,10);
5468: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5469: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5470: 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);
5471: 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 5472: return 1;
5473: }
5474: }
5475: s[j][i]=lval;
5476:
5477: strcpy(line,stra);
5478: cutv(stra, strb,line,' ');
1.169 brouard 5479: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5480: }
1.169 brouard 5481: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5482: month=99;
5483: year=9999;
5484: }else{
1.141 brouard 5485: 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);
5486: 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 5487: return 1;
5488: }
5489: anint[j][i]= (double) year;
5490: mint[j][i]= (double)month;
5491: strcpy(line,stra);
5492: } /* ENd Waves */
5493:
5494: cutv(stra, strb,line,' ');
1.169 brouard 5495: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5496: }
1.169 brouard 5497: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5498: month=99;
5499: year=9999;
5500: }else{
1.141 brouard 5501: 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);
5502: 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 5503: return 1;
5504: }
5505: andc[i]=(double) year;
5506: moisdc[i]=(double) month;
5507: strcpy(line,stra);
5508:
5509: cutv(stra, strb,line,' ');
1.169 brouard 5510: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5511: }
1.169 brouard 5512: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5513: month=99;
5514: year=9999;
5515: }else{
1.141 brouard 5516: 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);
5517: 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 5518: return 1;
5519: }
5520: if (year==9999) {
1.141 brouard 5521: 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);
5522: 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 5523: return 1;
1.126 brouard 5524:
1.136 brouard 5525: }
5526: annais[i]=(double)(year);
5527: moisnais[i]=(double)(month);
5528: strcpy(line,stra);
5529:
5530: cutv(stra, strb,line,' ');
5531: errno=0;
5532: dval=strtod(strb,&endptr);
5533: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5534: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5535: 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 5536: fflush(ficlog);
5537: return 1;
5538: }
5539: weight[i]=dval;
5540: strcpy(line,stra);
5541:
5542: for (j=ncovcol;j>=1;j--){
5543: cutv(stra, strb,line,' ');
5544: if(strb[0]=='.') { /* Missing status */
5545: lval=-1;
5546: }else{
5547: errno=0;
5548: lval=strtol(strb,&endptr,10);
5549: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5550: 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);
5551: 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 5552: return 1;
5553: }
5554: }
5555: if(lval <-1 || lval >1){
1.141 brouard 5556: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5557: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5558: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5559: For example, for multinomial values like 1, 2 and 3,\n \
5560: build V1=0 V2=0 for the reference value (1),\n \
5561: V1=1 V2=0 for (2) \n \
5562: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5563: output of IMaCh is often meaningless.\n \
5564: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5565: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5566: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5567: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5568: For example, for multinomial values like 1, 2 and 3,\n \
5569: build V1=0 V2=0 for the reference value (1),\n \
5570: V1=1 V2=0 for (2) \n \
5571: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5572: output of IMaCh is often meaningless.\n \
5573: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5574: return 1;
5575: }
5576: covar[j][i]=(double)(lval);
5577: strcpy(line,stra);
5578: }
5579: lstra=strlen(stra);
5580:
5581: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5582: stratrunc = &(stra[lstra-9]);
5583: num[i]=atol(stratrunc);
5584: }
5585: else
5586: num[i]=atol(stra);
5587: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5588: 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;}*/
5589:
5590: i=i+1;
5591: } /* End loop reading data */
1.126 brouard 5592:
1.136 brouard 5593: *imax=i-1; /* Number of individuals */
5594: fclose(fic);
5595:
5596: return (0);
1.164 brouard 5597: /* endread: */
1.136 brouard 5598: printf("Exiting readdata: ");
5599: fclose(fic);
5600: return (1);
1.126 brouard 5601:
5602:
5603:
1.136 brouard 5604: }
1.145 brouard 5605: void removespace(char *str) {
5606: char *p1 = str, *p2 = str;
5607: do
5608: while (*p2 == ' ')
5609: p2++;
1.169 brouard 5610: while (*p1++ == *p2++);
1.145 brouard 5611: }
5612:
5613: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5614: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5615: * - nagesqr = 1 if age*age in the model, otherwise 0.
5616: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5617: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5618: * - cptcovage number of covariates with age*products =2
5619: * - cptcovs number of simple covariates
5620: * - 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
5621: * which is a new column after the 9 (ncovcol) variables.
5622: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5623: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5624: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5625: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5626: */
1.136 brouard 5627: {
1.145 brouard 5628: int i, j, k, ks;
1.164 brouard 5629: int j1, k1, k2;
1.136 brouard 5630: char modelsav[80];
1.145 brouard 5631: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5632: char *strpt;
1.136 brouard 5633:
1.145 brouard 5634: /*removespace(model);*/
1.136 brouard 5635: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5636: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5637: if (strstr(model,"AGE") !=0){
1.192 brouard 5638: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5639: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5640: return 1;
5641: }
1.141 brouard 5642: if (strstr(model,"v") !=0){
5643: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5644: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5645: return 1;
5646: }
1.187 brouard 5647: strcpy(modelsav,model);
5648: if ((strpt=strstr(model,"age*age")) !=0){
5649: printf(" strpt=%s, model=%s\n",strpt, model);
5650: if(strpt != model){
5651: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5652: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5653: corresponding column of parameters.\n",model);
5654: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5655: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5656: corresponding column of parameters.\n",model); fflush(ficlog);
5657: return 1;
5658: }
5659:
5660: nagesqr=1;
5661: if (strstr(model,"+age*age") !=0)
5662: substrchaine(modelsav, model, "+age*age");
5663: else if (strstr(model,"age*age+") !=0)
5664: substrchaine(modelsav, model, "age*age+");
5665: else
5666: substrchaine(modelsav, model, "age*age");
5667: }else
5668: nagesqr=0;
5669: if (strlen(modelsav) >1){
5670: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5671: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5672: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5673: cptcovt= j+1; /* Number of total covariates in the model, not including
5674: * cst, age and age*age
5675: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5676: /* including age products which are counted in cptcovage.
5677: * but the covariates which are products must be treated
5678: * separately: ncovn=4- 2=2 (V1+V3). */
5679: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5680: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5681:
5682:
5683: /* Design
5684: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5685: * < ncovcol=8 >
5686: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5687: * k= 1 2 3 4 5 6 7 8
5688: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5689: * covar[k,i], value of kth covariate if not including age for individual i:
5690: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5691: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5692: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5693: * Tage[++cptcovage]=k
5694: * if products, new covar are created after ncovcol with k1
5695: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5696: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5697: * 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
5698: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5699: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5700: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5701: * < ncovcol=8 >
5702: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5703: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5704: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5705: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5706: * p Tprod[1]@2={ 6, 5}
5707: *p Tvard[1][1]@4= {7, 8, 5, 6}
5708: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5709: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5710: *How to reorganize?
5711: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5712: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5713: * {2, 1, 4, 8, 5, 6, 3, 7}
5714: * Struct []
5715: */
1.145 brouard 5716:
1.187 brouard 5717: /* This loop fills the array Tvar from the string 'model'.*/
5718: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5719: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5720: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5721: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5722: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5723: /* k=1 Tvar[1]=2 (from V2) */
5724: /* k=5 Tvar[5] */
5725: /* for (k=1; k<=cptcovn;k++) { */
5726: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5727: /* } */
5728: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5729: /*
5730: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5731: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5732: Tvar[k]=0;
1.187 brouard 5733: cptcovage=0;
5734: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5735: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5736: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5737: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5738: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5739: /*scanf("%d",i);*/
5740: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5741: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5742: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5743: /* covar is not filled and then is empty */
5744: cptcovprod--;
5745: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5746: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5747: cptcovage++; /* Sums the number of covariates which include age as a product */
5748: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5749: /*printf("stre=%s ", stre);*/
5750: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5751: cptcovprod--;
5752: cutl(stre,strb,strc,'V');
5753: Tvar[k]=atoi(stre);
5754: cptcovage++;
5755: Tage[cptcovage]=k;
5756: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5757: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5758: cptcovn++;
5759: cptcovprodnoage++;k1++;
5760: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5761: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5762: because this model-covariate is a construction we invent a new column
5763: ncovcol + k1
5764: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5765: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5766: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5767: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5768: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5769: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5770: k2=k2+2;
5771: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5772: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5773: for (i=1; i<=lastobs;i++){
5774: /* Computes the new covariate which is a product of
5775: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5776: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5777: }
5778: } /* End age is not in the model */
5779: } /* End if model includes a product */
5780: else { /* no more sum */
5781: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5782: /* scanf("%d",i);*/
5783: cutl(strd,strc,strb,'V');
5784: ks++; /**< Number of simple covariates */
1.145 brouard 5785: cptcovn++;
1.187 brouard 5786: Tvar[k]=atoi(strd);
5787: }
5788: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5789: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5790: scanf("%d",i);*/
5791: } /* end of loop + on total covariates */
5792: } /* end if strlen(modelsave == 0) age*age might exist */
5793: } /* end if strlen(model == 0) */
1.136 brouard 5794:
5795: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5796: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5797:
5798: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5799: printf("cptcovprod=%d ", cptcovprod);
5800: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5801:
5802: scanf("%d ",i);*/
5803:
5804:
1.137 brouard 5805: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5806: /*endread:*/
1.136 brouard 5807: printf("Exiting decodemodel: ");
5808: return (1);
5809: }
5810:
1.169 brouard 5811: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5812: {
5813: int i, m;
5814:
5815: for (i=1; i<=imx; i++) {
5816: for(m=2; (m<= maxwav); m++) {
5817: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5818: anint[m][i]=9999;
5819: s[m][i]=-1;
5820: }
5821: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5822: *nberr = *nberr + 1;
5823: 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);
5824: 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 5825: s[m][i]=-1;
5826: }
5827: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5828: (*nberr)++;
1.136 brouard 5829: 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]);
5830: 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]);
5831: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5832: }
5833: }
5834: }
5835:
5836: for (i=1; i<=imx; i++) {
5837: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5838: for(m=firstpass; (m<= lastpass); m++){
5839: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5840: if (s[m][i] >= nlstate+1) {
1.169 brouard 5841: if(agedc[i]>0){
5842: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5843: agev[m][i]=agedc[i];
5844: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5845: }else {
1.136 brouard 5846: if ((int)andc[i]!=9999){
5847: nbwarn++;
5848: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5849: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5850: agev[m][i]=-1;
5851: }
5852: }
1.169 brouard 5853: } /* agedc > 0 */
1.136 brouard 5854: }
5855: else if(s[m][i] !=9){ /* Standard case, age in fractional
5856: years but with the precision of a month */
5857: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5858: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5859: agev[m][i]=1;
5860: else if(agev[m][i] < *agemin){
5861: *agemin=agev[m][i];
5862: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5863: }
5864: else if(agev[m][i] >*agemax){
5865: *agemax=agev[m][i];
1.156 brouard 5866: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5867: }
5868: /*agev[m][i]=anint[m][i]-annais[i];*/
5869: /* agev[m][i] = age[i]+2*m;*/
5870: }
5871: else { /* =9 */
5872: agev[m][i]=1;
5873: s[m][i]=-1;
5874: }
5875: }
5876: else /*= 0 Unknown */
5877: agev[m][i]=1;
5878: }
5879:
5880: }
5881: for (i=1; i<=imx; i++) {
5882: for(m=firstpass; (m<=lastpass); m++){
5883: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5884: (*nberr)++;
1.136 brouard 5885: 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);
5886: 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);
5887: return 1;
5888: }
5889: }
5890: }
5891:
5892: /*for (i=1; i<=imx; i++){
5893: for (m=firstpass; (m<lastpass); m++){
5894: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5895: }
5896:
5897: }*/
5898:
5899:
1.139 brouard 5900: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5901: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5902:
5903: return (0);
1.164 brouard 5904: /* endread:*/
1.136 brouard 5905: printf("Exiting calandcheckages: ");
5906: return (1);
5907: }
5908:
1.172 brouard 5909: #if defined(_MSC_VER)
5910: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5911: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5912: //#include "stdafx.h"
5913: //#include <stdio.h>
5914: //#include <tchar.h>
5915: //#include <windows.h>
5916: //#include <iostream>
5917: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5918:
5919: LPFN_ISWOW64PROCESS fnIsWow64Process;
5920:
5921: BOOL IsWow64()
5922: {
5923: BOOL bIsWow64 = FALSE;
5924:
5925: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5926: // (HANDLE, PBOOL);
5927:
5928: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5929:
5930: HMODULE module = GetModuleHandle(_T("kernel32"));
5931: const char funcName[] = "IsWow64Process";
5932: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5933: GetProcAddress(module, funcName);
5934:
5935: if (NULL != fnIsWow64Process)
5936: {
5937: if (!fnIsWow64Process(GetCurrentProcess(),
5938: &bIsWow64))
5939: //throw std::exception("Unknown error");
5940: printf("Unknown error\n");
5941: }
5942: return bIsWow64 != FALSE;
5943: }
5944: #endif
1.177 brouard 5945:
1.191 brouard 5946: void syscompilerinfo(int logged)
1.167 brouard 5947: {
5948: /* #include "syscompilerinfo.h"*/
1.185 brouard 5949: /* command line Intel compiler 32bit windows, XP compatible:*/
5950: /* /GS /W3 /Gy
5951: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5952: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5953: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5954: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5955: */
5956: /* 64 bits */
1.185 brouard 5957: /*
5958: /GS /W3 /Gy
5959: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5960: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5961: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5962: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5963: /* Optimization are useless and O3 is slower than O2 */
5964: /*
5965: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5966: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5967: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5968: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5969: */
1.186 brouard 5970: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5971: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5972: /PDB:"visual studio
5973: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5974: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5975: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5976: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5977: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5978: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5979: uiAccess='false'"
5980: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5981: /NOLOGO /TLBID:1
5982: */
1.177 brouard 5983: #if defined __INTEL_COMPILER
1.178 brouard 5984: #if defined(__GNUC__)
5985: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5986: #endif
1.177 brouard 5987: #elif defined(__GNUC__)
1.179 brouard 5988: #ifndef __APPLE__
1.174 brouard 5989: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5990: #endif
1.177 brouard 5991: struct utsname sysInfo;
1.178 brouard 5992: int cross = CROSS;
5993: if (cross){
5994: printf("Cross-");
1.191 brouard 5995: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 5996: }
1.174 brouard 5997: #endif
5998:
1.171 brouard 5999: #include <stdint.h>
1.178 brouard 6000:
1.191 brouard 6001: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6002: #if defined(__clang__)
1.191 brouard 6003: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6004: #endif
6005: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6006: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6007: #endif
6008: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6009: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6010: #endif
6011: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6012: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6013: #endif
6014: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6015: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6016: #endif
6017: #if defined(_MSC_VER)
1.191 brouard 6018: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6019: #endif
6020: #if defined(__PGI)
1.191 brouard 6021: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6022: #endif
6023: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6024: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6025: #endif
1.191 brouard 6026: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6027:
1.167 brouard 6028: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6029: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6030: // Windows (x64 and x86)
1.191 brouard 6031: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6032: #elif __unix__ // all unices, not all compilers
6033: // Unix
1.191 brouard 6034: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6035: #elif __linux__
6036: // linux
1.191 brouard 6037: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6038: #elif __APPLE__
1.174 brouard 6039: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6040: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6041: #endif
6042:
6043: /* __MINGW32__ */
6044: /* __CYGWIN__ */
6045: /* __MINGW64__ */
6046: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6047: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6048: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6049: /* _WIN64 // Defined for applications for Win64. */
6050: /* _M_X64 // Defined for compilations that target x64 processors. */
6051: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6052:
1.167 brouard 6053: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6054: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6055: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6056: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6057: #else
1.191 brouard 6058: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6059: #endif
6060:
1.169 brouard 6061: #if defined(__GNUC__)
6062: # if defined(__GNUC_PATCHLEVEL__)
6063: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6064: + __GNUC_MINOR__ * 100 \
6065: + __GNUC_PATCHLEVEL__)
6066: # else
6067: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6068: + __GNUC_MINOR__ * 100)
6069: # endif
1.174 brouard 6070: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6071: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6072:
6073: if (uname(&sysInfo) != -1) {
6074: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6075: 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 6076: }
6077: else
6078: perror("uname() error");
1.179 brouard 6079: //#ifndef __INTEL_COMPILER
6080: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6081: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6082: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6083: #endif
1.169 brouard 6084: #endif
1.172 brouard 6085:
6086: // void main()
6087: // {
1.169 brouard 6088: #if defined(_MSC_VER)
1.174 brouard 6089: if (IsWow64()){
1.191 brouard 6090: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6091: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6092: }
6093: else{
1.191 brouard 6094: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6095: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6096: }
1.172 brouard 6097: // printf("\nPress Enter to continue...");
6098: // getchar();
6099: // }
6100:
1.169 brouard 6101: #endif
6102:
1.167 brouard 6103:
6104: }
1.136 brouard 6105:
1.180 brouard 6106: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6107: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6108: int i, j, k, i1 ;
6109: double ftolpl = 1.e-10;
6110: double age, agebase, agelim;
6111:
6112: strcpy(filerespl,"pl");
6113: strcat(filerespl,fileres);
6114: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6115: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6116: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6117: }
6118: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6119: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6120: pstamp(ficrespl);
6121: fprintf(ficrespl,"# Period (stable) prevalence \n");
6122: fprintf(ficrespl,"#Age ");
6123: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6124: fprintf(ficrespl,"\n");
6125:
6126: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6127:
6128: agebase=ageminpar;
6129: agelim=agemaxpar;
6130:
6131: i1=pow(2,cptcoveff);
6132: if (cptcovn < 1){i1=1;}
6133:
6134: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6135: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6136: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6137: k=k+1;
6138: /* to clean */
6139: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6140: fprintf(ficrespl,"\n#******");
6141: printf("\n#******");
6142: fprintf(ficlog,"\n#******");
6143: for(j=1;j<=cptcoveff;j++) {
6144: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6145: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6146: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6147: }
6148: fprintf(ficrespl,"******\n");
6149: printf("******\n");
6150: fprintf(ficlog,"******\n");
6151:
6152: fprintf(ficrespl,"#Age ");
6153: for(j=1;j<=cptcoveff;j++) {
6154: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6155: }
6156: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6157: fprintf(ficrespl,"\n");
6158:
6159: for (age=agebase; age<=agelim; age++){
6160: /* for (age=agebase; age<=agebase; age++){ */
6161: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6162: fprintf(ficrespl,"%.0f ",age );
6163: for(j=1;j<=cptcoveff;j++)
6164: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6165: for(i=1; i<=nlstate;i++)
6166: fprintf(ficrespl," %.5f", prlim[i][i]);
6167: fprintf(ficrespl,"\n");
6168: } /* Age */
6169: /* was end of cptcod */
6170: } /* cptcov */
1.184 brouard 6171: return 0;
1.180 brouard 6172: }
6173:
6174: int hPijx(double *p, int bage, int fage){
6175: /*------------- h Pij x at various ages ------------*/
6176:
6177: int stepsize;
6178: int agelim;
6179: int hstepm;
6180: int nhstepm;
6181: int h, i, i1, j, k;
6182:
6183: double agedeb;
6184: double ***p3mat;
6185:
6186: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6187: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6188: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6189: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6190: }
6191: printf("Computing pij: result on file '%s' \n", filerespij);
6192: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6193:
6194: stepsize=(int) (stepm+YEARM-1)/YEARM;
6195: /*if (stepm<=24) stepsize=2;*/
6196:
6197: agelim=AGESUP;
6198: hstepm=stepsize*YEARM; /* Every year of age */
6199: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6200:
6201: /* hstepm=1; aff par mois*/
6202: pstamp(ficrespij);
6203: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6204: i1= pow(2,cptcoveff);
1.183 brouard 6205: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6206: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6207: /* k=k+1; */
6208: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6209: fprintf(ficrespij,"\n#****** ");
6210: for(j=1;j<=cptcoveff;j++)
6211: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6212: fprintf(ficrespij,"******\n");
6213:
6214: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6215: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6216: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6217:
6218: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6219:
1.183 brouard 6220: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6221: oldm=oldms;savm=savms;
6222: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6223: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6224: for(i=1; i<=nlstate;i++)
6225: for(j=1; j<=nlstate+ndeath;j++)
6226: fprintf(ficrespij," %1d-%1d",i,j);
6227: fprintf(ficrespij,"\n");
6228: for (h=0; h<=nhstepm; h++){
6229: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6230: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6231: for(i=1; i<=nlstate;i++)
6232: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6233: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6234: fprintf(ficrespij,"\n");
6235: }
1.183 brouard 6236: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6237: fprintf(ficrespij,"\n");
6238: }
1.180 brouard 6239: /*}*/
6240: }
1.184 brouard 6241: return 0;
1.180 brouard 6242: }
6243:
6244:
1.136 brouard 6245: /***********************************************/
6246: /**************** Main Program *****************/
6247: /***********************************************/
6248:
6249: int main(int argc, char *argv[])
6250: {
6251: #ifdef GSL
6252: const gsl_multimin_fminimizer_type *T;
6253: size_t iteri = 0, it;
6254: int rval = GSL_CONTINUE;
6255: int status = GSL_SUCCESS;
6256: double ssval;
6257: #endif
6258: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6259: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6260:
6261: int jj, ll, li, lj, lk;
1.136 brouard 6262: int numlinepar=0; /* Current linenumber of parameter file */
6263: int itimes;
6264: int NDIM=2;
6265: int vpopbased=0;
6266:
1.164 brouard 6267: char ca[32], cb[32];
1.136 brouard 6268: /* FILE *fichtm; *//* Html File */
6269: /* FILE *ficgp;*/ /*Gnuplot File */
6270: struct stat info;
1.191 brouard 6271: double agedeb=0.;
1.136 brouard 6272: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
6273:
1.165 brouard 6274: double fret;
1.191 brouard 6275: double dum=0.; /* Dummy variable */
1.136 brouard 6276: double ***p3mat;
6277: double ***mobaverage;
1.164 brouard 6278:
6279: char line[MAXLINE];
1.136 brouard 6280: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6281: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6282: char *tok, *val; /* pathtot */
1.136 brouard 6283: int firstobs=1, lastobs=10;
1.164 brouard 6284: int c, h , cpt;
1.191 brouard 6285: int jl=0;
6286: int i1, j1, jk, stepsize=0;
1.164 brouard 6287: int *tab;
1.136 brouard 6288: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6289: int mobilav=0,popforecast=0;
1.191 brouard 6290: int hstepm=0, nhstepm=0;
1.136 brouard 6291: int agemortsup;
6292: float sumlpop=0.;
6293: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6294: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6295:
1.191 brouard 6296: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6297: double ftolpl=FTOL;
6298: double **prlim;
6299: double ***param; /* Matrix of parameters */
6300: double *p;
6301: double **matcov; /* Matrix of covariance */
6302: double ***delti3; /* Scale */
6303: double *delti; /* Scale */
6304: double ***eij, ***vareij;
6305: double **varpl; /* Variances of prevalence limits by age */
6306: double *epj, vepp;
1.164 brouard 6307:
1.136 brouard 6308: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6309: double **ximort;
1.145 brouard 6310: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6311: int *dcwave;
6312:
1.164 brouard 6313: char z[1]="c";
1.136 brouard 6314:
6315: /*char *strt;*/
6316: char strtend[80];
1.126 brouard 6317:
1.164 brouard 6318:
1.126 brouard 6319: /* setlocale (LC_ALL, ""); */
6320: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6321: /* textdomain (PACKAGE); */
6322: /* setlocale (LC_CTYPE, ""); */
6323: /* setlocale (LC_MESSAGES, ""); */
6324:
6325: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6326: rstart_time = time(NULL);
6327: /* (void) gettimeofday(&start_time,&tzp);*/
6328: start_time = *localtime(&rstart_time);
1.126 brouard 6329: curr_time=start_time;
1.157 brouard 6330: /*tml = *localtime(&start_time.tm_sec);*/
6331: /* strcpy(strstart,asctime(&tml)); */
6332: strcpy(strstart,asctime(&start_time));
1.126 brouard 6333:
6334: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6335: /* tp.tm_sec = tp.tm_sec +86400; */
6336: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6337: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6338: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6339: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6340: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6341: /* strt=asctime(&tmg); */
6342: /* printf("Time(after) =%s",strstart); */
6343: /* (void) time (&time_value);
6344: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6345: * tm = *localtime(&time_value);
6346: * strstart=asctime(&tm);
6347: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6348: */
6349:
6350: nberr=0; /* Number of errors and warnings */
6351: nbwarn=0;
1.184 brouard 6352: #ifdef WIN32
6353: _getcwd(pathcd, size);
6354: #else
1.126 brouard 6355: getcwd(pathcd, size);
1.184 brouard 6356: #endif
1.191 brouard 6357: syscompilerinfo(0);
1.126 brouard 6358: printf("\n%s\n%s",version,fullversion);
6359: if(argc <=1){
6360: printf("\nEnter the parameter file name: ");
6361: fgets(pathr,FILENAMELENGTH,stdin);
6362: i=strlen(pathr);
6363: if(pathr[i-1]=='\n')
6364: pathr[i-1]='\0';
1.156 brouard 6365: i=strlen(pathr);
6366: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6367: pathr[i-1]='\0';
1.126 brouard 6368: for (tok = pathr; tok != NULL; ){
6369: printf("Pathr |%s|\n",pathr);
6370: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6371: printf("val= |%s| pathr=%s\n",val,pathr);
6372: strcpy (pathtot, val);
6373: if(pathr[0] == '\0') break; /* Dirty */
6374: }
6375: }
6376: else{
6377: strcpy(pathtot,argv[1]);
6378: }
6379: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6380: /*cygwin_split_path(pathtot,path,optionfile);
6381: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6382: /* cutv(path,optionfile,pathtot,'\\');*/
6383:
6384: /* Split argv[0], imach program to get pathimach */
6385: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6386: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6387: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6388: /* strcpy(pathimach,argv[0]); */
6389: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6390: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6391: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6392: #ifdef WIN32
6393: _chdir(path); /* Can be a relative path */
6394: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6395: #else
1.126 brouard 6396: chdir(path); /* Can be a relative path */
1.184 brouard 6397: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6398: #endif
6399: printf("Current directory %s!\n",pathcd);
1.126 brouard 6400: strcpy(command,"mkdir ");
6401: strcat(command,optionfilefiname);
6402: if((outcmd=system(command)) != 0){
1.169 brouard 6403: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6404: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6405: /* fclose(ficlog); */
6406: /* exit(1); */
6407: }
6408: /* if((imk=mkdir(optionfilefiname))<0){ */
6409: /* perror("mkdir"); */
6410: /* } */
6411:
6412: /*-------- arguments in the command line --------*/
6413:
1.186 brouard 6414: /* Main Log file */
1.126 brouard 6415: strcat(filelog, optionfilefiname);
6416: strcat(filelog,".log"); /* */
6417: if((ficlog=fopen(filelog,"w"))==NULL) {
6418: printf("Problem with logfile %s\n",filelog);
6419: goto end;
6420: }
6421: fprintf(ficlog,"Log filename:%s\n",filelog);
6422: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6423: fprintf(ficlog,"\nEnter the parameter file name: \n");
6424: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6425: path=%s \n\
6426: optionfile=%s\n\
6427: optionfilext=%s\n\
1.156 brouard 6428: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6429:
1.191 brouard 6430: syscompilerinfo(0);
1.167 brouard 6431:
1.126 brouard 6432: printf("Local time (at start):%s",strstart);
6433: fprintf(ficlog,"Local time (at start): %s",strstart);
6434: fflush(ficlog);
6435: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6436: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6437:
6438: /* */
6439: strcpy(fileres,"r");
6440: strcat(fileres, optionfilefiname);
6441: strcat(fileres,".txt"); /* Other files have txt extension */
6442:
1.186 brouard 6443: /* Main ---------arguments file --------*/
1.126 brouard 6444:
6445: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6446: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6447: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6448: fflush(ficlog);
1.149 brouard 6449: /* goto end; */
6450: exit(70);
1.126 brouard 6451: }
6452:
6453:
6454:
6455: strcpy(filereso,"o");
6456: strcat(filereso,fileres);
6457: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6458: printf("Problem with Output resultfile: %s\n", filereso);
6459: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6460: fflush(ficlog);
6461: goto end;
6462: }
6463:
6464: /* Reads comments: lines beginning with '#' */
6465: numlinepar=0;
6466: while((c=getc(ficpar))=='#' && c!= EOF){
6467: ungetc(c,ficpar);
6468: fgets(line, MAXLINE, ficpar);
6469: numlinepar++;
1.141 brouard 6470: fputs(line,stdout);
1.126 brouard 6471: fputs(line,ficparo);
6472: fputs(line,ficlog);
6473: }
6474: ungetc(c,ficpar);
6475:
1.187 brouard 6476: 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 6477: numlinepar++;
1.187 brouard 6478: 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);
6479: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6480: model[strlen(model)-1]='\0';
6481: 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);
6482: 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 6483: fflush(ficlog);
1.190 brouard 6484: /* if(model[0]=='#'|| model[0]== '\0'){ */
6485: if(model[0]=='#'){
1.187 brouard 6486: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6487: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6488: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6489: if(mle != -1){
6490: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6491: exit(1);
6492: }
6493: }
1.126 brouard 6494: while((c=getc(ficpar))=='#' && c!= EOF){
6495: ungetc(c,ficpar);
6496: fgets(line, MAXLINE, ficpar);
6497: numlinepar++;
1.141 brouard 6498: fputs(line, stdout);
6499: //puts(line);
1.126 brouard 6500: fputs(line,ficparo);
6501: fputs(line,ficlog);
6502: }
6503: ungetc(c,ficpar);
6504:
6505:
1.145 brouard 6506: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6507: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6508: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6509: v1+v2*age+v2*v3 makes cptcovn = 3
6510: */
6511: if (strlen(model)>1)
1.187 brouard 6512: 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 6513: else
1.187 brouard 6514: ncovmodel=2; /* Constant and age */
1.133 brouard 6515: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6516: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6517: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6518: 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);
6519: 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);
6520: fflush(stdout);
6521: fclose (ficlog);
6522: goto end;
6523: }
1.126 brouard 6524: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6525: delti=delti3[1][1];
6526: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6527: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6528: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6529: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6530: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6531: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6532: fclose (ficparo);
6533: fclose (ficlog);
6534: goto end;
6535: exit(0);
6536: }
1.186 brouard 6537: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6538: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6539: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6540: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6541: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6542: matcov=matrix(1,npar,1,npar);
6543: }
6544: else{
1.145 brouard 6545: /* Read guessed parameters */
1.126 brouard 6546: /* Reads comments: lines beginning with '#' */
6547: while((c=getc(ficpar))=='#' && c!= EOF){
6548: ungetc(c,ficpar);
6549: fgets(line, MAXLINE, ficpar);
6550: numlinepar++;
1.141 brouard 6551: fputs(line,stdout);
1.126 brouard 6552: fputs(line,ficparo);
6553: fputs(line,ficlog);
6554: }
6555: ungetc(c,ficpar);
6556:
6557: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6558: for(i=1; i <=nlstate; i++){
6559: j=0;
6560: for(jj=1; jj <=nlstate+ndeath; jj++){
6561: if(jj==i) continue;
6562: j++;
6563: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 ! brouard 6564: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6565: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6566: It might be a problem of design; if ncovcol and the model are correct\n \
6567: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6568: exit(1);
6569: }
6570: fprintf(ficparo,"%1d%1d",i1,j1);
6571: if(mle==1)
1.193 ! brouard 6572: printf("%1d%1d",i,jj);
! 6573: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6574: for(k=1; k<=ncovmodel;k++){
6575: fscanf(ficpar," %lf",¶m[i][j][k]);
6576: if(mle==1){
6577: printf(" %lf",param[i][j][k]);
6578: fprintf(ficlog," %lf",param[i][j][k]);
6579: }
6580: else
6581: fprintf(ficlog," %lf",param[i][j][k]);
6582: fprintf(ficparo," %lf",param[i][j][k]);
6583: }
6584: fscanf(ficpar,"\n");
6585: numlinepar++;
6586: if(mle==1)
6587: printf("\n");
6588: fprintf(ficlog,"\n");
6589: fprintf(ficparo,"\n");
6590: }
6591: }
6592: fflush(ficlog);
6593:
1.145 brouard 6594: /* Reads scales values */
1.126 brouard 6595: p=param[1][1];
6596:
6597: /* Reads comments: lines beginning with '#' */
6598: while((c=getc(ficpar))=='#' && c!= EOF){
6599: ungetc(c,ficpar);
6600: fgets(line, MAXLINE, ficpar);
6601: numlinepar++;
1.141 brouard 6602: fputs(line,stdout);
1.126 brouard 6603: fputs(line,ficparo);
6604: fputs(line,ficlog);
6605: }
6606: ungetc(c,ficpar);
6607:
6608: for(i=1; i <=nlstate; i++){
6609: for(j=1; j <=nlstate+ndeath-1; j++){
6610: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6611: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6612: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6613: exit(1);
6614: }
6615: printf("%1d%1d",i,j);
6616: fprintf(ficparo,"%1d%1d",i1,j1);
6617: fprintf(ficlog,"%1d%1d",i1,j1);
6618: for(k=1; k<=ncovmodel;k++){
6619: fscanf(ficpar,"%le",&delti3[i][j][k]);
6620: printf(" %le",delti3[i][j][k]);
6621: fprintf(ficparo," %le",delti3[i][j][k]);
6622: fprintf(ficlog," %le",delti3[i][j][k]);
6623: }
6624: fscanf(ficpar,"\n");
6625: numlinepar++;
6626: printf("\n");
6627: fprintf(ficparo,"\n");
6628: fprintf(ficlog,"\n");
6629: }
6630: }
6631: fflush(ficlog);
6632:
1.145 brouard 6633: /* Reads covariance matrix */
1.126 brouard 6634: delti=delti3[1][1];
6635:
6636:
6637: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6638:
6639: /* Reads comments: lines beginning with '#' */
6640: while((c=getc(ficpar))=='#' && c!= EOF){
6641: ungetc(c,ficpar);
6642: fgets(line, MAXLINE, ficpar);
6643: numlinepar++;
1.141 brouard 6644: fputs(line,stdout);
1.126 brouard 6645: fputs(line,ficparo);
6646: fputs(line,ficlog);
6647: }
6648: ungetc(c,ficpar);
6649:
6650: matcov=matrix(1,npar,1,npar);
1.131 brouard 6651: for(i=1; i <=npar; i++)
6652: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6653:
1.126 brouard 6654: for(i=1; i <=npar; i++){
1.145 brouard 6655: fscanf(ficpar,"%s",str);
1.126 brouard 6656: if(mle==1)
6657: printf("%s",str);
6658: fprintf(ficlog,"%s",str);
6659: fprintf(ficparo,"%s",str);
6660: for(j=1; j <=i; j++){
6661: fscanf(ficpar," %le",&matcov[i][j]);
6662: if(mle==1){
6663: printf(" %.5le",matcov[i][j]);
6664: }
6665: fprintf(ficlog," %.5le",matcov[i][j]);
6666: fprintf(ficparo," %.5le",matcov[i][j]);
6667: }
6668: fscanf(ficpar,"\n");
6669: numlinepar++;
6670: if(mle==1)
6671: printf("\n");
6672: fprintf(ficlog,"\n");
6673: fprintf(ficparo,"\n");
6674: }
6675: for(i=1; i <=npar; i++)
6676: for(j=i+1;j<=npar;j++)
6677: matcov[i][j]=matcov[j][i];
6678:
6679: if(mle==1)
6680: printf("\n");
6681: fprintf(ficlog,"\n");
6682:
6683: fflush(ficlog);
6684:
6685: /*-------- Rewriting parameter file ----------*/
6686: strcpy(rfileres,"r"); /* "Rparameterfile */
6687: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6688: strcat(rfileres,"."); /* */
6689: strcat(rfileres,optionfilext); /* Other files have txt extension */
6690: if((ficres =fopen(rfileres,"w"))==NULL) {
6691: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6692: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6693: }
6694: fprintf(ficres,"#%s\n",version);
6695: } /* End of mle != -3 */
6696:
1.186 brouard 6697: /* Main data
6698: */
1.126 brouard 6699: n= lastobs;
6700: num=lvector(1,n);
6701: moisnais=vector(1,n);
6702: annais=vector(1,n);
6703: moisdc=vector(1,n);
6704: andc=vector(1,n);
6705: agedc=vector(1,n);
6706: cod=ivector(1,n);
6707: weight=vector(1,n);
6708: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6709: mint=matrix(1,maxwav,1,n);
6710: anint=matrix(1,maxwav,1,n);
1.131 brouard 6711: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6712: tab=ivector(1,NCOVMAX);
1.144 brouard 6713: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 6714: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6715:
1.136 brouard 6716: /* Reads data from file datafile */
6717: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6718: goto end;
6719:
6720: /* Calculation of the number of parameters from char model */
1.137 brouard 6721: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6722: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6723: k=3 V4 Tvar[k=3]= 4 (from V4)
6724: k=2 V1 Tvar[k=2]= 1 (from V1)
6725: k=1 Tvar[1]=2 (from V2)
6726: */
6727: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6728: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6729: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6730: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6731: */
6732: /* For model-covariate k tells which data-covariate to use but
6733: because this model-covariate is a construction we invent a new column
6734: ncovcol + k1
6735: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6736: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6737: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6738: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6739: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6740: */
1.145 brouard 6741: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6742: 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 6743: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6744: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6745: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6746: 4 covariates (3 plus signs)
6747: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6748: */
1.136 brouard 6749:
1.186 brouard 6750: /* Main decodemodel */
6751:
1.187 brouard 6752:
1.136 brouard 6753: if(decodemodel(model, lastobs) == 1)
6754: goto end;
6755:
1.137 brouard 6756: if((double)(lastobs-imx)/(double)imx > 1.10){
6757: nbwarn++;
6758: 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);
6759: 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);
6760: }
1.136 brouard 6761: /* if(mle==1){*/
1.137 brouard 6762: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6763: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6764: }
6765:
6766: /*-calculation of age at interview from date of interview and age at death -*/
6767: agev=matrix(1,maxwav,1,imx);
6768:
6769: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6770: goto end;
6771:
1.126 brouard 6772:
1.136 brouard 6773: agegomp=(int)agemin;
6774: free_vector(moisnais,1,n);
6775: free_vector(annais,1,n);
1.126 brouard 6776: /* free_matrix(mint,1,maxwav,1,n);
6777: free_matrix(anint,1,maxwav,1,n);*/
6778: free_vector(moisdc,1,n);
6779: free_vector(andc,1,n);
1.145 brouard 6780: /* */
6781:
1.126 brouard 6782: wav=ivector(1,imx);
6783: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6784: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6785: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6786:
6787: /* Concatenates waves */
6788: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6789: /* */
6790:
1.126 brouard 6791: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6792:
6793: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6794: ncodemax[1]=1;
1.145 brouard 6795: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6796: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6797: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6798: /* Nbcode gives the value of the lth modality of jth covariate, in
6799: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6800: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6801:
6802: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6803: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6804: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6805: h=0;
6806:
6807:
6808: /*if (cptcovn > 0) */
1.126 brouard 6809:
1.145 brouard 6810:
1.126 brouard 6811: m=pow(2,cptcoveff);
6812:
1.131 brouard 6813: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6814: 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 */
6815: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6816: 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 6817: h++;
1.141 brouard 6818: if (h>m)
1.136 brouard 6819: h=1;
1.144 brouard 6820: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6821: * For k=4 covariates, h goes from 1 to 2**k
6822: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6823: * h\k 1 2 3 4
1.143 brouard 6824: *______________________________
6825: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6826: * 2 2 1 1 1
6827: * 3 i=2 1 2 1 1
6828: * 4 2 2 1 1
6829: * 5 i=3 1 i=2 1 2 1
6830: * 6 2 1 2 1
6831: * 7 i=4 1 2 2 1
6832: * 8 2 2 2 1
6833: * 9 i=5 1 i=3 1 i=2 1 1
6834: * 10 2 1 1 1
6835: * 11 i=6 1 2 1 1
6836: * 12 2 2 1 1
6837: * 13 i=7 1 i=4 1 2 1
6838: * 14 2 1 2 1
6839: * 15 i=8 1 2 2 1
6840: * 16 2 2 2 1
6841: */
1.141 brouard 6842: codtab[h][k]=j;
1.186 brouard 6843: /* codtab[12][3]=1; */
1.145 brouard 6844: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6845: 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 6846: }
6847: }
6848: }
6849: }
6850: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6851: codtab[1][2]=1;codtab[2][2]=2; */
6852: /* for(i=1; i <=m ;i++){
6853: for(k=1; k <=cptcovn; k++){
1.131 brouard 6854: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6855: }
6856: printf("\n");
6857: }
6858: scanf("%d",i);*/
1.145 brouard 6859:
6860: free_ivector(Ndum,-1,NCOVMAX);
6861:
6862:
1.126 brouard 6863:
1.186 brouard 6864: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6865: strcpy(optionfilegnuplot,optionfilefiname);
6866: if(mle==-3)
6867: strcat(optionfilegnuplot,"-mort");
6868: strcat(optionfilegnuplot,".gp");
6869:
6870: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6871: printf("Problem with file %s",optionfilegnuplot);
6872: }
6873: else{
6874: fprintf(ficgp,"\n# %s\n", version);
6875: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6876: //fprintf(ficgp,"set missing 'NaNq'\n");
6877: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6878: }
6879: /* fclose(ficgp);*/
1.186 brouard 6880:
6881:
6882: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6883:
6884: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6885: if(mle==-3)
6886: strcat(optionfilehtm,"-mort");
6887: strcat(optionfilehtm,".htm");
6888: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6889: printf("Problem with %s \n",optionfilehtm);
6890: exit(0);
1.126 brouard 6891: }
6892:
6893: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6894: strcat(optionfilehtmcov,"-cov.htm");
6895: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6896: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6897: }
6898: else{
6899: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6900: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6901: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6902: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6903: }
6904:
6905: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6906: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6907: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6908: \n\
6909: <hr size=\"2\" color=\"#EC5E5E\">\
6910: <ul><li><h4>Parameter files</h4>\n\
6911: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6912: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6913: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6914: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6915: - Date and time at start: %s</ul>\n",\
6916: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6917: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6918: fileres,fileres,\
6919: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6920: fflush(fichtm);
6921:
6922: strcpy(pathr,path);
6923: strcat(pathr,optionfilefiname);
1.184 brouard 6924: #ifdef WIN32
6925: _chdir(optionfilefiname); /* Move to directory named optionfile */
6926: #else
1.126 brouard 6927: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6928: #endif
6929:
1.126 brouard 6930:
6931: /* Calculates basic frequencies. Computes observed prevalence at single age
6932: and prints on file fileres'p'. */
6933: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6934:
6935: fprintf(fichtm,"\n");
6936: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6937: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6938: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6939: imx,agemin,agemax,jmin,jmax,jmean);
6940: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6941: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6942: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6943: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6944: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6945:
6946:
6947: /* For Powell, parameters are in a vector p[] starting at p[1]
6948: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6949: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6950:
6951: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 6952: /* For mortality only */
1.126 brouard 6953: if (mle==-3){
1.136 brouard 6954: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 6955: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6956: cens=ivector(1,n);
6957: ageexmed=vector(1,n);
6958: agecens=vector(1,n);
6959: dcwave=ivector(1,n);
6960:
6961: for (i=1; i<=imx; i++){
6962: dcwave[i]=-1;
6963: for (m=firstpass; m<=lastpass; m++)
6964: if (s[m][i]>nlstate) {
6965: dcwave[i]=m;
6966: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6967: break;
6968: }
6969: }
6970:
6971: for (i=1; i<=imx; i++) {
6972: if (wav[i]>0){
6973: ageexmed[i]=agev[mw[1][i]][i];
6974: j=wav[i];
6975: agecens[i]=1.;
6976:
6977: if (ageexmed[i]> 1 && wav[i] > 0){
6978: agecens[i]=agev[mw[j][i]][i];
6979: cens[i]= 1;
6980: }else if (ageexmed[i]< 1)
6981: cens[i]= -1;
6982: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6983: cens[i]=0 ;
6984: }
6985: else cens[i]=-1;
6986: }
6987:
6988: for (i=1;i<=NDIM;i++) {
6989: for (j=1;j<=NDIM;j++)
6990: ximort[i][j]=(i == j ? 1.0 : 0.0);
6991: }
6992:
1.145 brouard 6993: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6994: /*printf("%lf %lf", p[1], p[2]);*/
6995:
6996:
1.136 brouard 6997: #ifdef GSL
6998: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6999: #else
1.126 brouard 7000: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7001: #endif
1.126 brouard 7002: strcpy(filerespow,"pow-mort");
7003: strcat(filerespow,fileres);
7004: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7005: printf("Problem with resultfile: %s\n", filerespow);
7006: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7007: }
1.136 brouard 7008: #ifdef GSL
7009: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7010: #else
1.126 brouard 7011: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7012: #endif
1.126 brouard 7013: /* for (i=1;i<=nlstate;i++)
7014: for(j=1;j<=nlstate+ndeath;j++)
7015: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7016: */
7017: fprintf(ficrespow,"\n");
1.136 brouard 7018: #ifdef GSL
7019: /* gsl starts here */
7020: T = gsl_multimin_fminimizer_nmsimplex;
7021: gsl_multimin_fminimizer *sfm = NULL;
7022: gsl_vector *ss, *x;
7023: gsl_multimin_function minex_func;
7024:
7025: /* Initial vertex size vector */
7026: ss = gsl_vector_alloc (NDIM);
7027:
7028: if (ss == NULL){
7029: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7030: }
7031: /* Set all step sizes to 1 */
7032: gsl_vector_set_all (ss, 0.001);
7033:
7034: /* Starting point */
1.126 brouard 7035:
1.136 brouard 7036: x = gsl_vector_alloc (NDIM);
7037:
7038: if (x == NULL){
7039: gsl_vector_free(ss);
7040: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7041: }
7042:
7043: /* Initialize method and iterate */
7044: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7045: /* gsl_vector_set(x, 0, 0.0268); */
7046: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7047: gsl_vector_set(x, 0, p[1]);
7048: gsl_vector_set(x, 1, p[2]);
7049:
7050: minex_func.f = &gompertz_f;
7051: minex_func.n = NDIM;
7052: minex_func.params = (void *)&p; /* ??? */
7053:
7054: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7055: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7056:
7057: printf("Iterations beginning .....\n\n");
7058: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7059:
7060: iteri=0;
7061: while (rval == GSL_CONTINUE){
7062: iteri++;
7063: status = gsl_multimin_fminimizer_iterate(sfm);
7064:
7065: if (status) printf("error: %s\n", gsl_strerror (status));
7066: fflush(0);
7067:
7068: if (status)
7069: break;
7070:
7071: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7072: ssval = gsl_multimin_fminimizer_size (sfm);
7073:
7074: if (rval == GSL_SUCCESS)
7075: printf ("converged to a local maximum at\n");
7076:
7077: printf("%5d ", iteri);
7078: for (it = 0; it < NDIM; it++){
7079: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7080: }
7081: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7082: }
7083:
7084: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7085:
7086: gsl_vector_free(x); /* initial values */
7087: gsl_vector_free(ss); /* inital step size */
7088: for (it=0; it<NDIM; it++){
7089: p[it+1]=gsl_vector_get(sfm->x,it);
7090: fprintf(ficrespow," %.12lf", p[it]);
7091: }
7092: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7093: #endif
7094: #ifdef POWELL
7095: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7096: #endif
1.126 brouard 7097: fclose(ficrespow);
7098:
7099: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7100:
7101: for(i=1; i <=NDIM; i++)
7102: for(j=i+1;j<=NDIM;j++)
7103: matcov[i][j]=matcov[j][i];
7104:
7105: printf("\nCovariance matrix\n ");
7106: for(i=1; i <=NDIM; i++) {
7107: for(j=1;j<=NDIM;j++){
7108: printf("%f ",matcov[i][j]);
7109: }
7110: printf("\n ");
7111: }
7112:
7113: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 ! brouard 7114: for (i=1;i<=NDIM;i++) {
1.126 brouard 7115: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 ! brouard 7116: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
! 7117: }
1.126 brouard 7118: lsurv=vector(1,AGESUP);
7119: lpop=vector(1,AGESUP);
7120: tpop=vector(1,AGESUP);
7121: lsurv[agegomp]=100000;
7122:
7123: for (k=agegomp;k<=AGESUP;k++) {
7124: agemortsup=k;
7125: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7126: }
7127:
7128: for (k=agegomp;k<agemortsup;k++)
7129: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7130:
7131: for (k=agegomp;k<agemortsup;k++){
7132: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7133: sumlpop=sumlpop+lpop[k];
7134: }
7135:
7136: tpop[agegomp]=sumlpop;
7137: for (k=agegomp;k<(agemortsup-3);k++){
7138: /* tpop[k+1]=2;*/
7139: tpop[k+1]=tpop[k]-lpop[k];
7140: }
7141:
7142:
7143: printf("\nAge lx qx dx Lx Tx e(x)\n");
7144: for (k=agegomp;k<(agemortsup-2);k++)
7145: 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]);
7146:
7147:
7148: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7149: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7150:
7151: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7152: stepm, weightopt,\
7153: model,imx,p,matcov,agemortsup);
7154:
7155: free_vector(lsurv,1,AGESUP);
7156: free_vector(lpop,1,AGESUP);
7157: free_vector(tpop,1,AGESUP);
1.136 brouard 7158: #ifdef GSL
7159: free_ivector(cens,1,n);
7160: free_vector(agecens,1,n);
7161: free_ivector(dcwave,1,n);
7162: free_matrix(ximort,1,NDIM,1,NDIM);
7163: #endif
1.186 brouard 7164: } /* Endof if mle==-3 mortality only */
7165: /* Standard maximisation */
1.126 brouard 7166: else{ /* For mle >=1 */
1.132 brouard 7167: globpr=0;/* debug */
1.186 brouard 7168: /* Computes likelihood for initial parameters */
1.132 brouard 7169: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7170: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7171: for (k=1; k<=npar;k++)
7172: printf(" %d %8.5f",k,p[k]);
7173: printf("\n");
1.186 brouard 7174: globpr=1; /* again, to print the contributions */
1.126 brouard 7175: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7176: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7177: for (k=1; k<=npar;k++)
7178: printf(" %d %8.5f",k,p[k]);
7179: printf("\n");
1.186 brouard 7180: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7181: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7182: }
7183:
7184: /*--------- results files --------------*/
1.192 brouard 7185: 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 7186:
7187:
7188: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7189: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7190: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7191: for(i=1,jk=1; i <=nlstate; i++){
7192: for(k=1; k <=(nlstate+ndeath); k++){
7193: if (k != i) {
7194: printf("%d%d ",i,k);
7195: fprintf(ficlog,"%d%d ",i,k);
7196: fprintf(ficres,"%1d%1d ",i,k);
7197: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7198: printf("%12.7f ",p[jk]);
7199: fprintf(ficlog,"%12.7f ",p[jk]);
7200: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7201: jk++;
7202: }
7203: printf("\n");
7204: fprintf(ficlog,"\n");
7205: fprintf(ficres,"\n");
7206: }
7207: }
7208: }
7209: if(mle!=0){
7210: /* Computing hessian and covariance matrix */
7211: ftolhess=ftol; /* Usually correct */
7212: hesscov(matcov, p, npar, delti, ftolhess, func);
7213: }
1.193 ! brouard 7214: printf("Parameters and 95%% confidence intervals\n");
! 7215: fprintf(ficlog, "Parameters, T and confidence intervals\n");
! 7216: for(i=1,jk=1; i <=nlstate; i++){
! 7217: for(k=1; k <=(nlstate+ndeath); k++){
! 7218: if (k != i) {
! 7219: printf("%d%d ",i,k);
! 7220: fprintf(ficlog,"%d%d ",i,k);
! 7221: for(j=1; j <=ncovmodel; j++){
! 7222: printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
! 7223: fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
! 7224: jk++;
! 7225: }
! 7226: printf("\n");
! 7227: fprintf(ficlog,"\n");
! 7228: }
! 7229: }
! 7230: }
! 7231:
1.126 brouard 7232: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7233: printf("# Scales (for hessian or gradient estimation)\n");
7234: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7235: for(i=1,jk=1; i <=nlstate; i++){
7236: for(j=1; j <=nlstate+ndeath; j++){
7237: if (j!=i) {
7238: fprintf(ficres,"%1d%1d",i,j);
7239: printf("%1d%1d",i,j);
7240: fprintf(ficlog,"%1d%1d",i,j);
7241: for(k=1; k<=ncovmodel;k++){
7242: printf(" %.5e",delti[jk]);
7243: fprintf(ficlog," %.5e",delti[jk]);
7244: fprintf(ficres," %.5e",delti[jk]);
7245: jk++;
7246: }
7247: printf("\n");
7248: fprintf(ficlog,"\n");
7249: fprintf(ficres,"\n");
7250: }
7251: }
7252: }
7253:
7254: 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");
7255: if(mle>=1)
7256: 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");
7257: 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");
7258: /* # 121 Var(a12)\n\ */
7259: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7260: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7261: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7262: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7263: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7264: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7265: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7266:
7267:
7268: /* Just to have a covariance matrix which will be more understandable
7269: even is we still don't want to manage dictionary of variables
7270: */
7271: for(itimes=1;itimes<=2;itimes++){
7272: jj=0;
7273: for(i=1; i <=nlstate; i++){
7274: for(j=1; j <=nlstate+ndeath; j++){
7275: if(j==i) continue;
7276: for(k=1; k<=ncovmodel;k++){
7277: jj++;
7278: ca[0]= k+'a'-1;ca[1]='\0';
7279: if(itimes==1){
7280: if(mle>=1)
7281: printf("#%1d%1d%d",i,j,k);
7282: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7283: fprintf(ficres,"#%1d%1d%d",i,j,k);
7284: }else{
7285: if(mle>=1)
7286: printf("%1d%1d%d",i,j,k);
7287: fprintf(ficlog,"%1d%1d%d",i,j,k);
7288: fprintf(ficres,"%1d%1d%d",i,j,k);
7289: }
7290: ll=0;
7291: for(li=1;li <=nlstate; li++){
7292: for(lj=1;lj <=nlstate+ndeath; lj++){
7293: if(lj==li) continue;
7294: for(lk=1;lk<=ncovmodel;lk++){
7295: ll++;
7296: if(ll<=jj){
7297: cb[0]= lk +'a'-1;cb[1]='\0';
7298: if(ll<jj){
7299: if(itimes==1){
7300: if(mle>=1)
7301: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7302: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7303: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7304: }else{
7305: if(mle>=1)
7306: printf(" %.5e",matcov[jj][ll]);
7307: fprintf(ficlog," %.5e",matcov[jj][ll]);
7308: fprintf(ficres," %.5e",matcov[jj][ll]);
7309: }
7310: }else{
7311: if(itimes==1){
7312: if(mle>=1)
7313: printf(" Var(%s%1d%1d)",ca,i,j);
7314: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7315: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7316: }else{
7317: if(mle>=1)
7318: printf(" %.5e",matcov[jj][ll]);
7319: fprintf(ficlog," %.5e",matcov[jj][ll]);
7320: fprintf(ficres," %.5e",matcov[jj][ll]);
7321: }
7322: }
7323: }
7324: } /* end lk */
7325: } /* end lj */
7326: } /* end li */
7327: if(mle>=1)
7328: printf("\n");
7329: fprintf(ficlog,"\n");
7330: fprintf(ficres,"\n");
7331: numlinepar++;
7332: } /* end k*/
7333: } /*end j */
7334: } /* end i */
7335: } /* end itimes */
7336:
7337: fflush(ficlog);
7338: fflush(ficres);
7339:
7340: while((c=getc(ficpar))=='#' && c!= EOF){
7341: ungetc(c,ficpar);
7342: fgets(line, MAXLINE, ficpar);
1.141 brouard 7343: fputs(line,stdout);
1.126 brouard 7344: fputs(line,ficparo);
7345: }
7346: ungetc(c,ficpar);
7347:
7348: estepm=0;
7349: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7350: if (estepm==0 || estepm < stepm) estepm=stepm;
7351: if (fage <= 2) {
7352: bage = ageminpar;
7353: fage = agemaxpar;
7354: }
7355:
7356: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7357: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7358: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7359:
7360: /* Other stuffs, more or less useful */
1.126 brouard 7361: while((c=getc(ficpar))=='#' && c!= EOF){
7362: ungetc(c,ficpar);
7363: fgets(line, MAXLINE, ficpar);
1.141 brouard 7364: fputs(line,stdout);
1.126 brouard 7365: fputs(line,ficparo);
7366: }
7367: ungetc(c,ficpar);
7368:
7369: 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);
7370: 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);
7371: 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);
7372: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7373: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7374:
7375: while((c=getc(ficpar))=='#' && c!= EOF){
7376: ungetc(c,ficpar);
7377: fgets(line, MAXLINE, ficpar);
1.141 brouard 7378: fputs(line,stdout);
1.126 brouard 7379: fputs(line,ficparo);
7380: }
7381: ungetc(c,ficpar);
7382:
7383:
7384: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7385: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7386:
7387: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 ! brouard 7388: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7389: fprintf(ficparo,"pop_based=%d\n",popbased);
7390: fprintf(ficres,"pop_based=%d\n",popbased);
7391:
7392: while((c=getc(ficpar))=='#' && c!= EOF){
7393: ungetc(c,ficpar);
7394: fgets(line, MAXLINE, ficpar);
1.141 brouard 7395: fputs(line,stdout);
1.126 brouard 7396: fputs(line,ficparo);
7397: }
7398: ungetc(c,ficpar);
7399:
7400: 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);
7401: 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);
7402: 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);
7403: 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);
7404: 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);
7405: /* day and month of proj2 are not used but only year anproj2.*/
7406:
7407:
7408:
1.145 brouard 7409: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7410: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7411:
7412: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7413: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7414:
7415: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7416: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7417: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7418:
7419: /*------------ free_vector -------------*/
7420: /* chdir(path); */
7421:
7422: free_ivector(wav,1,imx);
7423: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7424: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7425: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7426: free_lvector(num,1,n);
7427: free_vector(agedc,1,n);
7428: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7429: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7430: fclose(ficparo);
7431: fclose(ficres);
7432:
7433:
1.186 brouard 7434: /* Other results (useful)*/
7435:
7436:
1.126 brouard 7437: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7438: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7439: prlim=matrix(1,nlstate,1,nlstate);
7440: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7441: fclose(ficrespl);
7442:
1.145 brouard 7443: #ifdef FREEEXIT2
7444: #include "freeexit2.h"
7445: #endif
7446:
1.126 brouard 7447: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7448: /*#include "hpijx.h"*/
7449: hPijx(p, bage, fage);
1.145 brouard 7450: fclose(ficrespij);
1.126 brouard 7451:
1.145 brouard 7452: /*-------------- Variance of one-step probabilities---*/
7453: k=1;
1.126 brouard 7454: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7455:
7456:
7457: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7458: for(i=1;i<=AGESUP;i++)
7459: for(j=1;j<=NCOVMAX;j++)
7460: for(k=1;k<=NCOVMAX;k++)
7461: probs[i][j][k]=0.;
7462:
7463: /*---------- Forecasting ------------------*/
7464: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7465: if(prevfcast==1){
7466: /* if(stepm ==1){*/
7467: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7468: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7469: /* } */
7470: /* else{ */
7471: /* erreur=108; */
7472: /* 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); */
7473: /* 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); */
7474: /* } */
7475: }
1.186 brouard 7476:
7477: /* ------ Other prevalence ratios------------ */
1.126 brouard 7478:
1.127 brouard 7479: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7480:
7481: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7482: /* 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",\
7483: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7484: */
1.126 brouard 7485:
1.127 brouard 7486: if (mobilav!=0) {
7487: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7488: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7489: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7490: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7491: }
1.126 brouard 7492: }
7493:
7494:
1.127 brouard 7495: /*---------- Health expectancies, no variances ------------*/
7496:
1.126 brouard 7497: strcpy(filerese,"e");
7498: strcat(filerese,fileres);
7499: if((ficreseij=fopen(filerese,"w"))==NULL) {
7500: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7501: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7502: }
7503: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7504: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7505: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7506: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7507:
7508: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7509: fprintf(ficreseij,"\n#****** ");
7510: for(j=1;j<=cptcoveff;j++) {
7511: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7512: }
7513: fprintf(ficreseij,"******\n");
7514:
7515: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7516: oldm=oldms;savm=savms;
7517: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7518:
7519: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7520: /*}*/
1.127 brouard 7521: }
7522: fclose(ficreseij);
7523:
7524:
7525: /*---------- Health expectancies and variances ------------*/
7526:
7527:
7528: strcpy(filerest,"t");
7529: strcat(filerest,fileres);
7530: if((ficrest=fopen(filerest,"w"))==NULL) {
7531: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7532: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7533: }
7534: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7535: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7536:
1.126 brouard 7537:
7538: strcpy(fileresstde,"stde");
7539: strcat(fileresstde,fileres);
7540: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7541: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7542: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7543: }
7544: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7545: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7546:
7547: strcpy(filerescve,"cve");
7548: strcat(filerescve,fileres);
7549: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7550: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7551: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7552: }
7553: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7554: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7555:
7556: strcpy(fileresv,"v");
7557: strcat(fileresv,fileres);
7558: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7559: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7560: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7561: }
7562: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7563: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7564:
1.145 brouard 7565: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7566: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7567:
7568: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7569: fprintf(ficrest,"\n#****** ");
1.126 brouard 7570: for(j=1;j<=cptcoveff;j++)
7571: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7572: fprintf(ficrest,"******\n");
7573:
7574: fprintf(ficresstdeij,"\n#****** ");
7575: fprintf(ficrescveij,"\n#****** ");
7576: for(j=1;j<=cptcoveff;j++) {
7577: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7578: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7579: }
7580: fprintf(ficresstdeij,"******\n");
7581: fprintf(ficrescveij,"******\n");
7582:
7583: fprintf(ficresvij,"\n#****** ");
7584: for(j=1;j<=cptcoveff;j++)
7585: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7586: fprintf(ficresvij,"******\n");
7587:
7588: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7589: oldm=oldms;savm=savms;
1.127 brouard 7590: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7591: /*
7592: */
7593: /* goto endfree; */
1.126 brouard 7594:
7595: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7596: pstamp(ficrest);
1.145 brouard 7597:
7598:
1.128 brouard 7599: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7600: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7601: cptcod= 0; /* To be deleted */
7602: 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 7603: 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 7604: if(vpopbased==1)
7605: 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);
7606: else
7607: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7608: fprintf(ficrest,"# Age e.. (std) ");
7609: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7610: fprintf(ficrest,"\n");
1.126 brouard 7611:
1.128 brouard 7612: epj=vector(1,nlstate+1);
7613: for(age=bage; age <=fage ;age++){
7614: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7615: if (vpopbased==1) {
7616: if(mobilav ==0){
7617: for(i=1; i<=nlstate;i++)
7618: prlim[i][i]=probs[(int)age][i][k];
7619: }else{ /* mobilav */
7620: for(i=1; i<=nlstate;i++)
7621: prlim[i][i]=mobaverage[(int)age][i][k];
7622: }
1.126 brouard 7623: }
7624:
1.128 brouard 7625: fprintf(ficrest," %4.0f",age);
7626: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7627: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7628: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7629: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7630: }
7631: epj[nlstate+1] +=epj[j];
1.126 brouard 7632: }
7633:
1.128 brouard 7634: for(i=1, vepp=0.;i <=nlstate;i++)
7635: for(j=1;j <=nlstate;j++)
7636: vepp += vareij[i][j][(int)age];
7637: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7638: for(j=1;j <=nlstate;j++){
7639: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7640: }
7641: fprintf(ficrest,"\n");
1.126 brouard 7642: }
7643: }
7644: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7645: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7646: free_vector(epj,1,nlstate+1);
1.145 brouard 7647: /*}*/
1.126 brouard 7648: }
7649: free_vector(weight,1,n);
1.145 brouard 7650: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7651: free_imatrix(s,1,maxwav+1,1,n);
7652: free_matrix(anint,1,maxwav,1,n);
7653: free_matrix(mint,1,maxwav,1,n);
7654: free_ivector(cod,1,n);
7655: free_ivector(tab,1,NCOVMAX);
7656: fclose(ficresstdeij);
7657: fclose(ficrescveij);
7658: fclose(ficresvij);
7659: fclose(ficrest);
7660: fclose(ficpar);
7661:
7662: /*------- Variance of period (stable) prevalence------*/
7663:
7664: strcpy(fileresvpl,"vpl");
7665: strcat(fileresvpl,fileres);
7666: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7667: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7668: exit(0);
7669: }
7670: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7671:
1.145 brouard 7672: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7673: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7674:
7675: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7676: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7677: for(j=1;j<=cptcoveff;j++)
7678: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7679: fprintf(ficresvpl,"******\n");
7680:
7681: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7682: oldm=oldms;savm=savms;
7683: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7684: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7685: /*}*/
1.126 brouard 7686: }
7687:
7688: fclose(ficresvpl);
7689:
7690: /*---------- End : free ----------------*/
7691: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7692: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7693: } /* mle==-3 arrives here for freeing */
1.164 brouard 7694: /* endfree:*/
1.141 brouard 7695: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7696: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7697: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7698: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7699: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7700: free_matrix(covar,0,NCOVMAX,1,n);
7701: free_matrix(matcov,1,npar,1,npar);
7702: /*free_vector(delti,1,npar);*/
7703: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7704: free_matrix(agev,1,maxwav,1,imx);
7705: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7706:
1.145 brouard 7707: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 7708: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 7709: free_ivector(Tvar,1,NCOVMAX);
7710: free_ivector(Tprod,1,NCOVMAX);
7711: free_ivector(Tvaraff,1,NCOVMAX);
7712: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7713:
7714: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7715: free_imatrix(codtab,1,100,1,10);
7716: fflush(fichtm);
7717: fflush(ficgp);
7718:
7719:
7720: if((nberr >0) || (nbwarn>0)){
7721: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7722: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7723: }else{
7724: printf("End of Imach\n");
7725: fprintf(ficlog,"End of Imach\n");
7726: }
7727: printf("See log file on %s\n",filelog);
7728: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7729: /*(void) gettimeofday(&end_time,&tzp);*/
7730: rend_time = time(NULL);
7731: end_time = *localtime(&rend_time);
7732: /* tml = *localtime(&end_time.tm_sec); */
7733: strcpy(strtend,asctime(&end_time));
1.126 brouard 7734: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7735: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7736: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7737:
1.157 brouard 7738: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7739: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7740: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7741: /* printf("Total time was %d uSec.\n", total_usecs);*/
7742: /* if(fileappend(fichtm,optionfilehtm)){ */
7743: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7744: fclose(fichtm);
7745: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7746: fclose(fichtmcov);
7747: fclose(ficgp);
7748: fclose(ficlog);
7749: /*------ End -----------*/
7750:
7751:
7752: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7753: #ifdef WIN32
7754: if (_chdir(pathcd) != 0)
7755: printf("Can't move to directory %s!\n",path);
7756: if(_getcwd(pathcd,MAXLINE) > 0)
7757: #else
1.126 brouard 7758: if(chdir(pathcd) != 0)
1.184 brouard 7759: printf("Can't move to directory %s!\n", path);
7760: if (getcwd(pathcd, MAXLINE) > 0)
7761: #endif
1.126 brouard 7762: printf("Current directory %s!\n",pathcd);
7763: /*strcat(plotcmd,CHARSEPARATOR);*/
7764: sprintf(plotcmd,"gnuplot");
1.157 brouard 7765: #ifdef _WIN32
1.126 brouard 7766: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7767: #endif
7768: if(!stat(plotcmd,&info)){
1.158 brouard 7769: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7770: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7771: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7772: }else
7773: strcpy(pplotcmd,plotcmd);
1.157 brouard 7774: #ifdef __unix
1.126 brouard 7775: strcpy(plotcmd,GNUPLOTPROGRAM);
7776: if(!stat(plotcmd,&info)){
1.158 brouard 7777: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7778: }else
7779: strcpy(pplotcmd,plotcmd);
7780: #endif
7781: }else
7782: strcpy(pplotcmd,plotcmd);
7783:
7784: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7785: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7786:
7787: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7788: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7789: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7790: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7791: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7792: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7793: }
1.158 brouard 7794: printf(" Successful, please wait...");
1.126 brouard 7795: while (z[0] != 'q') {
7796: /* chdir(path); */
1.154 brouard 7797: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7798: scanf("%s",z);
7799: /* if (z[0] == 'c') system("./imach"); */
7800: if (z[0] == 'e') {
1.158 brouard 7801: #ifdef __APPLE__
1.152 brouard 7802: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7803: #elif __linux
7804: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7805: #else
1.152 brouard 7806: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7807: #endif
7808: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7809: system(pplotcmd);
1.126 brouard 7810: }
7811: else if (z[0] == 'g') system(plotcmd);
7812: else if (z[0] == 'q') exit(0);
7813: }
7814: end:
7815: while (z[0] != 'q') {
7816: printf("\nType q for exiting: ");
7817: scanf("%s",z);
7818: }
7819: }
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