Annotation of imach/src/imach.c, revision 1.186
1.186 ! brouard 1: /* $Id: imach.c,v 1.185 2015/03/11 13:26:42 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.186 ! brouard 4: Revision 1.185 2015/03/11 13:26:42 brouard
! 5: Summary: Inclusion of compile and links command line for Intel Compiler
! 6:
1.185 brouard 7: Revision 1.184 2015/03/11 11:52:39 brouard
8: Summary: Back from Windows 8. Intel Compiler
9:
1.184 brouard 10: Revision 1.183 2015/03/10 20:34:32 brouard
11: Summary: 0.98q0, trying with directest, mnbrak fixed
12:
13: We use directest instead of original Powell test; probably no
14: incidence on the results, but better justifications;
15: We fixed Numerical Recipes mnbrak routine which was wrong and gave
16: wrong results.
17:
1.183 brouard 18: Revision 1.182 2015/02/12 08:19:57 brouard
19: Summary: Trying to keep directest which seems simpler and more general
20: Author: Nicolas Brouard
21:
1.182 brouard 22: Revision 1.181 2015/02/11 23:22:24 brouard
23: Summary: Comments on Powell added
24:
25: Author:
26:
1.181 brouard 27: Revision 1.180 2015/02/11 17:33:45 brouard
28: Summary: Finishing move from main to function (hpijx and prevalence_limit)
29:
1.180 brouard 30: Revision 1.179 2015/01/04 09:57:06 brouard
31: Summary: back to OS/X
32:
1.179 brouard 33: Revision 1.178 2015/01/04 09:35:48 brouard
34: *** empty log message ***
35:
1.178 brouard 36: Revision 1.177 2015/01/03 18:40:56 brouard
37: Summary: Still testing ilc32 on OSX
38:
1.177 brouard 39: Revision 1.176 2015/01/03 16:45:04 brouard
40: *** empty log message ***
41:
1.176 brouard 42: Revision 1.175 2015/01/03 16:33:42 brouard
43: *** empty log message ***
44:
1.175 brouard 45: Revision 1.174 2015/01/03 16:15:49 brouard
46: Summary: Still in cross-compilation
47:
1.174 brouard 48: Revision 1.173 2015/01/03 12:06:26 brouard
49: Summary: trying to detect cross-compilation
50:
1.173 brouard 51: Revision 1.172 2014/12/27 12:07:47 brouard
52: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
53:
1.172 brouard 54: Revision 1.171 2014/12/23 13:26:59 brouard
55: Summary: Back from Visual C
56:
57: Still problem with utsname.h on Windows
58:
1.171 brouard 59: Revision 1.170 2014/12/23 11:17:12 brouard
60: Summary: Cleaning some \%% back to %%
61:
62: The escape was mandatory for a specific compiler (which one?), but too many warnings.
63:
1.170 brouard 64: Revision 1.169 2014/12/22 23:08:31 brouard
65: Summary: 0.98p
66:
67: Outputs some informations on compiler used, OS etc. Testing on different platforms.
68:
1.169 brouard 69: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 70: Summary: update
1.169 brouard 71:
1.168 brouard 72: Revision 1.167 2014/12/22 13:50:56 brouard
73: Summary: Testing uname and compiler version and if compiled 32 or 64
74:
75: Testing on Linux 64
76:
1.167 brouard 77: Revision 1.166 2014/12/22 11:40:47 brouard
78: *** empty log message ***
79:
1.166 brouard 80: Revision 1.165 2014/12/16 11:20:36 brouard
81: Summary: After compiling on Visual C
82:
83: * imach.c (Module): Merging 1.61 to 1.162
84:
1.165 brouard 85: Revision 1.164 2014/12/16 10:52:11 brouard
86: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
87:
88: * imach.c (Module): Merging 1.61 to 1.162
89:
1.164 brouard 90: Revision 1.163 2014/12/16 10:30:11 brouard
91: * imach.c (Module): Merging 1.61 to 1.162
92:
1.163 brouard 93: Revision 1.162 2014/09/25 11:43:39 brouard
94: Summary: temporary backup 0.99!
95:
1.162 brouard 96: Revision 1.1 2014/09/16 11:06:58 brouard
97: Summary: With some code (wrong) for nlopt
98:
99: Author:
100:
101: Revision 1.161 2014/09/15 20:41:41 brouard
102: Summary: Problem with macro SQR on Intel compiler
103:
1.161 brouard 104: Revision 1.160 2014/09/02 09:24:05 brouard
105: *** empty log message ***
106:
1.160 brouard 107: Revision 1.159 2014/09/01 10:34:10 brouard
108: Summary: WIN32
109: Author: Brouard
110:
1.159 brouard 111: Revision 1.158 2014/08/27 17:11:51 brouard
112: *** empty log message ***
113:
1.158 brouard 114: Revision 1.157 2014/08/27 16:26:55 brouard
115: Summary: Preparing windows Visual studio version
116: Author: Brouard
117:
118: In order to compile on Visual studio, time.h is now correct and time_t
119: and tm struct should be used. difftime should be used but sometimes I
120: just make the differences in raw time format (time(&now).
121: Trying to suppress #ifdef LINUX
122: Add xdg-open for __linux in order to open default browser.
123:
1.157 brouard 124: Revision 1.156 2014/08/25 20:10:10 brouard
125: *** empty log message ***
126:
1.156 brouard 127: Revision 1.155 2014/08/25 18:32:34 brouard
128: Summary: New compile, minor changes
129: Author: Brouard
130:
1.155 brouard 131: Revision 1.154 2014/06/20 17:32:08 brouard
132: Summary: Outputs now all graphs of convergence to period prevalence
133:
1.154 brouard 134: Revision 1.153 2014/06/20 16:45:46 brouard
135: Summary: If 3 live state, convergence to period prevalence on same graph
136: Author: Brouard
137:
1.153 brouard 138: Revision 1.152 2014/06/18 17:54:09 brouard
139: Summary: open browser, use gnuplot on same dir than imach if not found in the path
140:
1.152 brouard 141: Revision 1.151 2014/06/18 16:43:30 brouard
142: *** empty log message ***
143:
1.151 brouard 144: Revision 1.150 2014/06/18 16:42:35 brouard
145: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
146: Author: brouard
147:
1.150 brouard 148: Revision 1.149 2014/06/18 15:51:14 brouard
149: Summary: Some fixes in parameter files errors
150: Author: Nicolas Brouard
151:
1.149 brouard 152: Revision 1.148 2014/06/17 17:38:48 brouard
153: Summary: Nothing new
154: Author: Brouard
155:
156: Just a new packaging for OS/X version 0.98nS
157:
1.148 brouard 158: Revision 1.147 2014/06/16 10:33:11 brouard
159: *** empty log message ***
160:
1.147 brouard 161: Revision 1.146 2014/06/16 10:20:28 brouard
162: Summary: Merge
163: Author: Brouard
164:
165: Merge, before building revised version.
166:
1.146 brouard 167: Revision 1.145 2014/06/10 21:23:15 brouard
168: Summary: Debugging with valgrind
169: Author: Nicolas Brouard
170:
171: Lot of changes in order to output the results with some covariates
172: After the Edimburgh REVES conference 2014, it seems mandatory to
173: improve the code.
174: No more memory valgrind error but a lot has to be done in order to
175: continue the work of splitting the code into subroutines.
176: Also, decodemodel has been improved. Tricode is still not
177: optimal. nbcode should be improved. Documentation has been added in
178: the source code.
179:
1.144 brouard 180: Revision 1.143 2014/01/26 09:45:38 brouard
181: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
182:
183: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
184: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
185:
1.143 brouard 186: Revision 1.142 2014/01/26 03:57:36 brouard
187: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
188:
189: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
190:
1.142 brouard 191: Revision 1.141 2014/01/26 02:42:01 brouard
192: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
193:
1.141 brouard 194: Revision 1.140 2011/09/02 10:37:54 brouard
195: Summary: times.h is ok with mingw32 now.
196:
1.140 brouard 197: Revision 1.139 2010/06/14 07:50:17 brouard
198: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
199: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
200:
1.139 brouard 201: Revision 1.138 2010/04/30 18:19:40 brouard
202: *** empty log message ***
203:
1.138 brouard 204: Revision 1.137 2010/04/29 18:11:38 brouard
205: (Module): Checking covariates for more complex models
206: than V1+V2. A lot of change to be done. Unstable.
207:
1.137 brouard 208: Revision 1.136 2010/04/26 20:30:53 brouard
209: (Module): merging some libgsl code. Fixing computation
210: of likelione (using inter/intrapolation if mle = 0) in order to
211: get same likelihood as if mle=1.
212: Some cleaning of code and comments added.
213:
1.136 brouard 214: Revision 1.135 2009/10/29 15:33:14 brouard
215: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
216:
1.135 brouard 217: Revision 1.134 2009/10/29 13:18:53 brouard
218: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
219:
1.134 brouard 220: Revision 1.133 2009/07/06 10:21:25 brouard
221: just nforces
222:
1.133 brouard 223: Revision 1.132 2009/07/06 08:22:05 brouard
224: Many tings
225:
1.132 brouard 226: Revision 1.131 2009/06/20 16:22:47 brouard
227: Some dimensions resccaled
228:
1.131 brouard 229: Revision 1.130 2009/05/26 06:44:34 brouard
230: (Module): Max Covariate is now set to 20 instead of 8. A
231: lot of cleaning with variables initialized to 0. Trying to make
232: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
233:
1.130 brouard 234: Revision 1.129 2007/08/31 13:49:27 lievre
235: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
236:
1.129 lievre 237: Revision 1.128 2006/06/30 13:02:05 brouard
238: (Module): Clarifications on computing e.j
239:
1.128 brouard 240: Revision 1.127 2006/04/28 18:11:50 brouard
241: (Module): Yes the sum of survivors was wrong since
242: imach-114 because nhstepm was no more computed in the age
243: loop. Now we define nhstepma in the age loop.
244: (Module): In order to speed up (in case of numerous covariates) we
245: compute health expectancies (without variances) in a first step
246: and then all the health expectancies with variances or standard
247: deviation (needs data from the Hessian matrices) which slows the
248: computation.
249: In the future we should be able to stop the program is only health
250: expectancies and graph are needed without standard deviations.
251:
1.127 brouard 252: Revision 1.126 2006/04/28 17:23:28 brouard
253: (Module): Yes the sum of survivors was wrong since
254: imach-114 because nhstepm was no more computed in the age
255: loop. Now we define nhstepma in the age loop.
256: Version 0.98h
257:
1.126 brouard 258: Revision 1.125 2006/04/04 15:20:31 lievre
259: Errors in calculation of health expectancies. Age was not initialized.
260: Forecasting file added.
261:
262: Revision 1.124 2006/03/22 17:13:53 lievre
263: Parameters are printed with %lf instead of %f (more numbers after the comma).
264: The log-likelihood is printed in the log file
265:
266: Revision 1.123 2006/03/20 10:52:43 brouard
267: * imach.c (Module): <title> changed, corresponds to .htm file
268: name. <head> headers where missing.
269:
270: * imach.c (Module): Weights can have a decimal point as for
271: English (a comma might work with a correct LC_NUMERIC environment,
272: otherwise the weight is truncated).
273: Modification of warning when the covariates values are not 0 or
274: 1.
275: Version 0.98g
276:
277: Revision 1.122 2006/03/20 09:45:41 brouard
278: (Module): Weights can have a decimal point as for
279: English (a comma might work with a correct LC_NUMERIC environment,
280: otherwise the weight is truncated).
281: Modification of warning when the covariates values are not 0 or
282: 1.
283: Version 0.98g
284:
285: Revision 1.121 2006/03/16 17:45:01 lievre
286: * imach.c (Module): Comments concerning covariates added
287:
288: * imach.c (Module): refinements in the computation of lli if
289: status=-2 in order to have more reliable computation if stepm is
290: not 1 month. Version 0.98f
291:
292: Revision 1.120 2006/03/16 15:10:38 lievre
293: (Module): refinements in the computation of lli if
294: status=-2 in order to have more reliable computation if stepm is
295: not 1 month. Version 0.98f
296:
297: Revision 1.119 2006/03/15 17:42:26 brouard
298: (Module): Bug if status = -2, the loglikelihood was
299: computed as likelihood omitting the logarithm. Version O.98e
300:
301: Revision 1.118 2006/03/14 18:20:07 brouard
302: (Module): varevsij Comments added explaining the second
303: table of variances if popbased=1 .
304: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
305: (Module): Function pstamp added
306: (Module): Version 0.98d
307:
308: Revision 1.117 2006/03/14 17:16:22 brouard
309: (Module): varevsij Comments added explaining the second
310: table of variances if popbased=1 .
311: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
312: (Module): Function pstamp added
313: (Module): Version 0.98d
314:
315: Revision 1.116 2006/03/06 10:29:27 brouard
316: (Module): Variance-covariance wrong links and
317: varian-covariance of ej. is needed (Saito).
318:
319: Revision 1.115 2006/02/27 12:17:45 brouard
320: (Module): One freematrix added in mlikeli! 0.98c
321:
322: Revision 1.114 2006/02/26 12:57:58 brouard
323: (Module): Some improvements in processing parameter
324: filename with strsep.
325:
326: Revision 1.113 2006/02/24 14:20:24 brouard
327: (Module): Memory leaks checks with valgrind and:
328: datafile was not closed, some imatrix were not freed and on matrix
329: allocation too.
330:
331: Revision 1.112 2006/01/30 09:55:26 brouard
332: (Module): Back to gnuplot.exe instead of wgnuplot.exe
333:
334: Revision 1.111 2006/01/25 20:38:18 brouard
335: (Module): Lots of cleaning and bugs added (Gompertz)
336: (Module): Comments can be added in data file. Missing date values
337: can be a simple dot '.'.
338:
339: Revision 1.110 2006/01/25 00:51:50 brouard
340: (Module): Lots of cleaning and bugs added (Gompertz)
341:
342: Revision 1.109 2006/01/24 19:37:15 brouard
343: (Module): Comments (lines starting with a #) are allowed in data.
344:
345: Revision 1.108 2006/01/19 18:05:42 lievre
346: Gnuplot problem appeared...
347: To be fixed
348:
349: Revision 1.107 2006/01/19 16:20:37 brouard
350: Test existence of gnuplot in imach path
351:
352: Revision 1.106 2006/01/19 13:24:36 brouard
353: Some cleaning and links added in html output
354:
355: Revision 1.105 2006/01/05 20:23:19 lievre
356: *** empty log message ***
357:
358: Revision 1.104 2005/09/30 16:11:43 lievre
359: (Module): sump fixed, loop imx fixed, and simplifications.
360: (Module): If the status is missing at the last wave but we know
361: that the person is alive, then we can code his/her status as -2
362: (instead of missing=-1 in earlier versions) and his/her
363: contributions to the likelihood is 1 - Prob of dying from last
364: health status (= 1-p13= p11+p12 in the easiest case of somebody in
365: the healthy state at last known wave). Version is 0.98
366:
367: Revision 1.103 2005/09/30 15:54:49 lievre
368: (Module): sump fixed, loop imx fixed, and simplifications.
369:
370: Revision 1.102 2004/09/15 17:31:30 brouard
371: Add the possibility to read data file including tab characters.
372:
373: Revision 1.101 2004/09/15 10:38:38 brouard
374: Fix on curr_time
375:
376: Revision 1.100 2004/07/12 18:29:06 brouard
377: Add version for Mac OS X. Just define UNIX in Makefile
378:
379: Revision 1.99 2004/06/05 08:57:40 brouard
380: *** empty log message ***
381:
382: Revision 1.98 2004/05/16 15:05:56 brouard
383: New version 0.97 . First attempt to estimate force of mortality
384: directly from the data i.e. without the need of knowing the health
385: state at each age, but using a Gompertz model: log u =a + b*age .
386: This is the basic analysis of mortality and should be done before any
387: other analysis, in order to test if the mortality estimated from the
388: cross-longitudinal survey is different from the mortality estimated
389: from other sources like vital statistic data.
390:
391: The same imach parameter file can be used but the option for mle should be -3.
392:
1.133 brouard 393: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 394: former routines in order to include the new code within the former code.
395:
396: The output is very simple: only an estimate of the intercept and of
397: the slope with 95% confident intervals.
398:
399: Current limitations:
400: A) Even if you enter covariates, i.e. with the
401: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
402: B) There is no computation of Life Expectancy nor Life Table.
403:
404: Revision 1.97 2004/02/20 13:25:42 lievre
405: Version 0.96d. Population forecasting command line is (temporarily)
406: suppressed.
407:
408: Revision 1.96 2003/07/15 15:38:55 brouard
409: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
410: rewritten within the same printf. Workaround: many printfs.
411:
412: Revision 1.95 2003/07/08 07:54:34 brouard
413: * imach.c (Repository):
414: (Repository): Using imachwizard code to output a more meaningful covariance
415: matrix (cov(a12,c31) instead of numbers.
416:
417: Revision 1.94 2003/06/27 13:00:02 brouard
418: Just cleaning
419:
420: Revision 1.93 2003/06/25 16:33:55 brouard
421: (Module): On windows (cygwin) function asctime_r doesn't
422: exist so I changed back to asctime which exists.
423: (Module): Version 0.96b
424:
425: Revision 1.92 2003/06/25 16:30:45 brouard
426: (Module): On windows (cygwin) function asctime_r doesn't
427: exist so I changed back to asctime which exists.
428:
429: Revision 1.91 2003/06/25 15:30:29 brouard
430: * imach.c (Repository): Duplicated warning errors corrected.
431: (Repository): Elapsed time after each iteration is now output. It
432: helps to forecast when convergence will be reached. Elapsed time
433: is stamped in powell. We created a new html file for the graphs
434: concerning matrix of covariance. It has extension -cov.htm.
435:
436: Revision 1.90 2003/06/24 12:34:15 brouard
437: (Module): Some bugs corrected for windows. Also, when
438: mle=-1 a template is output in file "or"mypar.txt with the design
439: of the covariance matrix to be input.
440:
441: Revision 1.89 2003/06/24 12:30:52 brouard
442: (Module): Some bugs corrected for windows. Also, when
443: mle=-1 a template is output in file "or"mypar.txt with the design
444: of the covariance matrix to be input.
445:
446: Revision 1.88 2003/06/23 17:54:56 brouard
447: * 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.
448:
449: Revision 1.87 2003/06/18 12:26:01 brouard
450: Version 0.96
451:
452: Revision 1.86 2003/06/17 20:04:08 brouard
453: (Module): Change position of html and gnuplot routines and added
454: routine fileappend.
455:
456: Revision 1.85 2003/06/17 13:12:43 brouard
457: * imach.c (Repository): Check when date of death was earlier that
458: current date of interview. It may happen when the death was just
459: prior to the death. In this case, dh was negative and likelihood
460: was wrong (infinity). We still send an "Error" but patch by
461: assuming that the date of death was just one stepm after the
462: interview.
463: (Repository): Because some people have very long ID (first column)
464: we changed int to long in num[] and we added a new lvector for
465: memory allocation. But we also truncated to 8 characters (left
466: truncation)
467: (Repository): No more line truncation errors.
468:
469: Revision 1.84 2003/06/13 21:44:43 brouard
470: * imach.c (Repository): Replace "freqsummary" at a correct
471: place. It differs from routine "prevalence" which may be called
472: many times. Probs is memory consuming and must be used with
473: parcimony.
474: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
475:
476: Revision 1.83 2003/06/10 13:39:11 lievre
477: *** empty log message ***
478:
479: Revision 1.82 2003/06/05 15:57:20 brouard
480: Add log in imach.c and fullversion number is now printed.
481:
482: */
483: /*
484: Interpolated Markov Chain
485:
486: Short summary of the programme:
487:
488: This program computes Healthy Life Expectancies from
489: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
490: first survey ("cross") where individuals from different ages are
491: interviewed on their health status or degree of disability (in the
492: case of a health survey which is our main interest) -2- at least a
493: second wave of interviews ("longitudinal") which measure each change
494: (if any) in individual health status. Health expectancies are
495: computed from the time spent in each health state according to a
496: model. More health states you consider, more time is necessary to reach the
497: Maximum Likelihood of the parameters involved in the model. The
498: simplest model is the multinomial logistic model where pij is the
499: probability to be observed in state j at the second wave
500: conditional to be observed in state i at the first wave. Therefore
501: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
502: 'age' is age and 'sex' is a covariate. If you want to have a more
503: complex model than "constant and age", you should modify the program
504: where the markup *Covariates have to be included here again* invites
505: you to do it. More covariates you add, slower the
506: convergence.
507:
508: The advantage of this computer programme, compared to a simple
509: multinomial logistic model, is clear when the delay between waves is not
510: identical for each individual. Also, if a individual missed an
511: intermediate interview, the information is lost, but taken into
512: account using an interpolation or extrapolation.
513:
514: hPijx is the probability to be observed in state i at age x+h
515: conditional to the observed state i at age x. The delay 'h' can be
516: split into an exact number (nh*stepm) of unobserved intermediate
517: states. This elementary transition (by month, quarter,
518: semester or year) is modelled as a multinomial logistic. The hPx
519: matrix is simply the matrix product of nh*stepm elementary matrices
520: and the contribution of each individual to the likelihood is simply
521: hPijx.
522:
523: Also this programme outputs the covariance matrix of the parameters but also
524: of the life expectancies. It also computes the period (stable) prevalence.
525:
1.133 brouard 526: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
527: Institut national d'études démographiques, Paris.
1.126 brouard 528: This software have been partly granted by Euro-REVES, a concerted action
529: from the European Union.
530: It is copyrighted identically to a GNU software product, ie programme and
531: software can be distributed freely for non commercial use. Latest version
532: can be accessed at http://euroreves.ined.fr/imach .
533:
534: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
535: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
536:
537: **********************************************************************/
538: /*
539: main
540: read parameterfile
541: read datafile
542: concatwav
543: freqsummary
544: if (mle >= 1)
545: mlikeli
546: print results files
547: if mle==1
548: computes hessian
549: read end of parameter file: agemin, agemax, bage, fage, estepm
550: begin-prev-date,...
551: open gnuplot file
552: open html file
1.145 brouard 553: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
554: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
555: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
556: freexexit2 possible for memory heap.
557:
558: h Pij x | pij_nom ficrestpij
559: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
560: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
561: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
562:
563: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
564: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
565: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
566: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
567: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
568:
1.126 brouard 569: forecasting if prevfcast==1 prevforecast call prevalence()
570: health expectancies
571: Variance-covariance of DFLE
572: prevalence()
573: movingaverage()
574: varevsij()
575: if popbased==1 varevsij(,popbased)
576: total life expectancies
577: Variance of period (stable) prevalence
578: end
579: */
580:
1.165 brouard 581: #define POWELL /* Instead of NLOPT */
1.186 ! brouard 582: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
! 583: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 584:
585: #include <math.h>
586: #include <stdio.h>
587: #include <stdlib.h>
588: #include <string.h>
1.159 brouard 589:
590: #ifdef _WIN32
591: #include <io.h>
1.172 brouard 592: #include <windows.h>
593: #include <tchar.h>
1.159 brouard 594: #else
1.126 brouard 595: #include <unistd.h>
1.159 brouard 596: #endif
1.126 brouard 597:
598: #include <limits.h>
599: #include <sys/types.h>
1.171 brouard 600:
601: #if defined(__GNUC__)
602: #include <sys/utsname.h> /* Doesn't work on Windows */
603: #endif
604:
1.126 brouard 605: #include <sys/stat.h>
606: #include <errno.h>
1.159 brouard 607: /* extern int errno; */
1.126 brouard 608:
1.157 brouard 609: /* #ifdef LINUX */
610: /* #include <time.h> */
611: /* #include "timeval.h" */
612: /* #else */
613: /* #include <sys/time.h> */
614: /* #endif */
615:
1.126 brouard 616: #include <time.h>
617:
1.136 brouard 618: #ifdef GSL
619: #include <gsl/gsl_errno.h>
620: #include <gsl/gsl_multimin.h>
621: #endif
622:
1.167 brouard 623:
1.162 brouard 624: #ifdef NLOPT
625: #include <nlopt.h>
626: typedef struct {
627: double (* function)(double [] );
628: } myfunc_data ;
629: #endif
630:
1.126 brouard 631: /* #include <libintl.h> */
632: /* #define _(String) gettext (String) */
633:
1.141 brouard 634: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 635:
636: #define GNUPLOTPROGRAM "gnuplot"
637: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
638: #define FILENAMELENGTH 132
639:
640: #define GLOCK_ERROR_NOPATH -1 /* empty path */
641: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
642:
1.144 brouard 643: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
644: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 645:
646: #define NINTERVMAX 8
1.144 brouard 647: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
648: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
649: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 650: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 651: #define MAXN 20000
1.144 brouard 652: #define YEARM 12. /**< Number of months per year */
1.126 brouard 653: #define AGESUP 130
654: #define AGEBASE 40
1.164 brouard 655: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 656: #ifdef _WIN32
657: #define DIRSEPARATOR '\\'
658: #define CHARSEPARATOR "\\"
659: #define ODIRSEPARATOR '/'
660: #else
1.126 brouard 661: #define DIRSEPARATOR '/'
662: #define CHARSEPARATOR "/"
663: #define ODIRSEPARATOR '\\'
664: #endif
665:
1.186 ! brouard 666: /* $Id: imach.c,v 1.185 2015/03/11 13:26:42 brouard Exp $ */
1.126 brouard 667: /* $State: Exp $ */
668:
1.186 ! brouard 669: char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
! 670: char fullversion[]="$Revision: 1.185 $ $Date: 2015/03/11 13:26:42 $";
1.126 brouard 671: char strstart[80];
672: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 673: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 674: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 675: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
676: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
677: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
678: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
679: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
680: int cptcovprodnoage=0; /**< Number of covariate products without age */
681: int cptcoveff=0; /* Total number of covariates to vary for printing results */
682: int cptcov=0; /* Working variable */
1.126 brouard 683: int npar=NPARMAX;
684: int nlstate=2; /* Number of live states */
685: int ndeath=1; /* Number of dead states */
1.130 brouard 686: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 687: int popbased=0;
688:
689: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 690: int maxwav=0; /* Maxim number of waves */
691: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
692: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
693: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 694: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 695: int mle=1, weightopt=0;
1.126 brouard 696: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
697: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
698: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
699: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 700: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 701: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 702: double **matprod2(); /* test */
1.126 brouard 703: double **oldm, **newm, **savm; /* Working pointers to matrices */
704: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 705: /*FILE *fic ; */ /* Used in readdata only */
706: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 707: FILE *ficlog, *ficrespow;
1.130 brouard 708: int globpr=0; /* Global variable for printing or not */
1.126 brouard 709: double fretone; /* Only one call to likelihood */
1.130 brouard 710: long ipmx=0; /* Number of contributions */
1.126 brouard 711: double sw; /* Sum of weights */
712: char filerespow[FILENAMELENGTH];
713: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
714: FILE *ficresilk;
715: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
716: FILE *ficresprobmorprev;
717: FILE *fichtm, *fichtmcov; /* Html File */
718: FILE *ficreseij;
719: char filerese[FILENAMELENGTH];
720: FILE *ficresstdeij;
721: char fileresstde[FILENAMELENGTH];
722: FILE *ficrescveij;
723: char filerescve[FILENAMELENGTH];
724: FILE *ficresvij;
725: char fileresv[FILENAMELENGTH];
726: FILE *ficresvpl;
727: char fileresvpl[FILENAMELENGTH];
728: char title[MAXLINE];
729: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
730: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
731: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
732: char command[FILENAMELENGTH];
733: int outcmd=0;
734:
735: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
736:
737: char filelog[FILENAMELENGTH]; /* Log file */
738: char filerest[FILENAMELENGTH];
739: char fileregp[FILENAMELENGTH];
740: char popfile[FILENAMELENGTH];
741:
742: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
743:
1.157 brouard 744: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
745: /* struct timezone tzp; */
746: /* extern int gettimeofday(); */
747: struct tm tml, *gmtime(), *localtime();
748:
749: extern time_t time();
750:
751: struct tm start_time, end_time, curr_time, last_time, forecast_time;
752: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
753: struct tm tm;
754:
1.126 brouard 755: char strcurr[80], strfor[80];
756:
757: char *endptr;
758: long lval;
759: double dval;
760:
761: #define NR_END 1
762: #define FREE_ARG char*
763: #define FTOL 1.0e-10
764:
765: #define NRANSI
766: #define ITMAX 200
767:
768: #define TOL 2.0e-4
769:
770: #define CGOLD 0.3819660
771: #define ZEPS 1.0e-10
772: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
773:
774: #define GOLD 1.618034
775: #define GLIMIT 100.0
776: #define TINY 1.0e-20
777:
778: static double maxarg1,maxarg2;
779: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
780: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
781:
782: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
783: #define rint(a) floor(a+0.5)
1.166 brouard 784: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 785: #define mytinydouble 1.0e-16
1.166 brouard 786: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
787: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
788: /* static double dsqrarg; */
789: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 790: static double sqrarg;
791: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
792: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
793: int agegomp= AGEGOMP;
794:
795: int imx;
796: int stepm=1;
797: /* Stepm, step in month: minimum step interpolation*/
798:
799: int estepm;
800: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
801:
802: int m,nb;
803: long *num;
804: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
805: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
806: double **pmmij, ***probs;
807: double *ageexmed,*agecens;
808: double dateintmean=0;
809:
810: double *weight;
811: int **s; /* Status */
1.141 brouard 812: double *agedc;
1.145 brouard 813: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 814: * covar=matrix(0,NCOVMAX,1,n);
815: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
816: double idx;
817: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 818: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 819: int **codtab; /**< codtab=imatrix(1,100,1,10); */
820: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 821: double *lsurv, *lpop, *tpop;
822:
1.143 brouard 823: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
824: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 825:
826: /**************** split *************************/
827: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
828: {
829: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
830: the name of the file (name), its extension only (ext) and its first part of the name (finame)
831: */
832: char *ss; /* pointer */
1.186 ! brouard 833: int l1=0, l2=0; /* length counters */
1.126 brouard 834:
835: l1 = strlen(path ); /* length of path */
836: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
837: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
838: if ( ss == NULL ) { /* no directory, so determine current directory */
839: strcpy( name, path ); /* we got the fullname name because no directory */
840: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
841: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
842: /* get current working directory */
843: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 844: #ifdef WIN32
845: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
846: #else
847: if (getcwd(dirc, FILENAME_MAX) == NULL) {
848: #endif
1.126 brouard 849: return( GLOCK_ERROR_GETCWD );
850: }
851: /* got dirc from getcwd*/
852: printf(" DIRC = %s \n",dirc);
853: } else { /* strip direcotry from path */
854: ss++; /* after this, the filename */
855: l2 = strlen( ss ); /* length of filename */
856: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
857: strcpy( name, ss ); /* save file name */
858: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 ! brouard 859: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 860: printf(" DIRC2 = %s \n",dirc);
861: }
862: /* We add a separator at the end of dirc if not exists */
863: l1 = strlen( dirc ); /* length of directory */
864: if( dirc[l1-1] != DIRSEPARATOR ){
865: dirc[l1] = DIRSEPARATOR;
866: dirc[l1+1] = 0;
867: printf(" DIRC3 = %s \n",dirc);
868: }
869: ss = strrchr( name, '.' ); /* find last / */
870: if (ss >0){
871: ss++;
872: strcpy(ext,ss); /* save extension */
873: l1= strlen( name);
874: l2= strlen(ss)+1;
875: strncpy( finame, name, l1-l2);
876: finame[l1-l2]= 0;
877: }
878:
879: return( 0 ); /* we're done */
880: }
881:
882:
883: /******************************************/
884:
885: void replace_back_to_slash(char *s, char*t)
886: {
887: int i;
888: int lg=0;
889: i=0;
890: lg=strlen(t);
891: for(i=0; i<= lg; i++) {
892: (s[i] = t[i]);
893: if (t[i]== '\\') s[i]='/';
894: }
895: }
896:
1.132 brouard 897: char *trimbb(char *out, char *in)
1.137 brouard 898: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 899: char *s;
900: s=out;
901: while (*in != '\0'){
1.137 brouard 902: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 903: in++;
904: }
905: *out++ = *in++;
906: }
907: *out='\0';
908: return s;
909: }
910:
1.145 brouard 911: char *cutl(char *blocc, char *alocc, char *in, char occ)
912: {
913: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
914: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
915: gives blocc="abcdef2ghi" and alocc="j".
916: If occ is not found blocc is null and alocc is equal to in. Returns blocc
917: */
1.160 brouard 918: char *s, *t;
1.145 brouard 919: t=in;s=in;
920: while ((*in != occ) && (*in != '\0')){
921: *alocc++ = *in++;
922: }
923: if( *in == occ){
924: *(alocc)='\0';
925: s=++in;
926: }
927:
928: if (s == t) {/* occ not found */
929: *(alocc-(in-s))='\0';
930: in=s;
931: }
932: while ( *in != '\0'){
933: *blocc++ = *in++;
934: }
935:
936: *blocc='\0';
937: return t;
938: }
1.137 brouard 939: char *cutv(char *blocc, char *alocc, char *in, char occ)
940: {
941: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
942: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
943: gives blocc="abcdef2ghi" and alocc="j".
944: If occ is not found blocc is null and alocc is equal to in. Returns alocc
945: */
946: char *s, *t;
947: t=in;s=in;
948: while (*in != '\0'){
949: while( *in == occ){
950: *blocc++ = *in++;
951: s=in;
952: }
953: *blocc++ = *in++;
954: }
955: if (s == t) /* occ not found */
956: *(blocc-(in-s))='\0';
957: else
958: *(blocc-(in-s)-1)='\0';
959: in=s;
960: while ( *in != '\0'){
961: *alocc++ = *in++;
962: }
963:
964: *alocc='\0';
965: return s;
966: }
967:
1.126 brouard 968: int nbocc(char *s, char occ)
969: {
970: int i,j=0;
971: int lg=20;
972: i=0;
973: lg=strlen(s);
974: for(i=0; i<= lg; i++) {
975: if (s[i] == occ ) j++;
976: }
977: return j;
978: }
979:
1.137 brouard 980: /* void cutv(char *u,char *v, char*t, char occ) */
981: /* { */
982: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
983: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
984: /* gives u="abcdef2ghi" and v="j" *\/ */
985: /* int i,lg,j,p=0; */
986: /* i=0; */
987: /* lg=strlen(t); */
988: /* for(j=0; j<=lg-1; j++) { */
989: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
990: /* } */
1.126 brouard 991:
1.137 brouard 992: /* for(j=0; j<p; j++) { */
993: /* (u[j] = t[j]); */
994: /* } */
995: /* u[p]='\0'; */
1.126 brouard 996:
1.137 brouard 997: /* for(j=0; j<= lg; j++) { */
998: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
999: /* } */
1000: /* } */
1.126 brouard 1001:
1.160 brouard 1002: #ifdef _WIN32
1003: char * strsep(char **pp, const char *delim)
1004: {
1005: char *p, *q;
1006:
1007: if ((p = *pp) == NULL)
1008: return 0;
1009: if ((q = strpbrk (p, delim)) != NULL)
1010: {
1011: *pp = q + 1;
1012: *q = '\0';
1013: }
1014: else
1015: *pp = 0;
1016: return p;
1017: }
1018: #endif
1019:
1.126 brouard 1020: /********************** nrerror ********************/
1021:
1022: void nrerror(char error_text[])
1023: {
1024: fprintf(stderr,"ERREUR ...\n");
1025: fprintf(stderr,"%s\n",error_text);
1026: exit(EXIT_FAILURE);
1027: }
1028: /*********************** vector *******************/
1029: double *vector(int nl, int nh)
1030: {
1031: double *v;
1032: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1033: if (!v) nrerror("allocation failure in vector");
1034: return v-nl+NR_END;
1035: }
1036:
1037: /************************ free vector ******************/
1038: void free_vector(double*v, int nl, int nh)
1039: {
1040: free((FREE_ARG)(v+nl-NR_END));
1041: }
1042:
1043: /************************ivector *******************************/
1044: int *ivector(long nl,long nh)
1045: {
1046: int *v;
1047: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1048: if (!v) nrerror("allocation failure in ivector");
1049: return v-nl+NR_END;
1050: }
1051:
1052: /******************free ivector **************************/
1053: void free_ivector(int *v, long nl, long nh)
1054: {
1055: free((FREE_ARG)(v+nl-NR_END));
1056: }
1057:
1058: /************************lvector *******************************/
1059: long *lvector(long nl,long nh)
1060: {
1061: long *v;
1062: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1063: if (!v) nrerror("allocation failure in ivector");
1064: return v-nl+NR_END;
1065: }
1066:
1067: /******************free lvector **************************/
1068: void free_lvector(long *v, long nl, long nh)
1069: {
1070: free((FREE_ARG)(v+nl-NR_END));
1071: }
1072:
1073: /******************* imatrix *******************************/
1074: int **imatrix(long nrl, long nrh, long ncl, long nch)
1075: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1076: {
1077: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1078: int **m;
1079:
1080: /* allocate pointers to rows */
1081: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1082: if (!m) nrerror("allocation failure 1 in matrix()");
1083: m += NR_END;
1084: m -= nrl;
1085:
1086:
1087: /* allocate rows and set pointers to them */
1088: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1089: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1090: m[nrl] += NR_END;
1091: m[nrl] -= ncl;
1092:
1093: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1094:
1095: /* return pointer to array of pointers to rows */
1096: return m;
1097: }
1098:
1099: /****************** free_imatrix *************************/
1100: void free_imatrix(m,nrl,nrh,ncl,nch)
1101: int **m;
1102: long nch,ncl,nrh,nrl;
1103: /* free an int matrix allocated by imatrix() */
1104: {
1105: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1106: free((FREE_ARG) (m+nrl-NR_END));
1107: }
1108:
1109: /******************* matrix *******************************/
1110: double **matrix(long nrl, long nrh, long ncl, long nch)
1111: {
1112: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1113: double **m;
1114:
1115: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1116: if (!m) nrerror("allocation failure 1 in matrix()");
1117: m += NR_END;
1118: m -= nrl;
1119:
1120: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1121: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1122: m[nrl] += NR_END;
1123: m[nrl] -= ncl;
1124:
1125: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1126: return m;
1.145 brouard 1127: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1128: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1129: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1130: */
1131: }
1132:
1133: /*************************free matrix ************************/
1134: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1135: {
1136: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1137: free((FREE_ARG)(m+nrl-NR_END));
1138: }
1139:
1140: /******************* ma3x *******************************/
1141: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1142: {
1143: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1144: double ***m;
1145:
1146: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1147: if (!m) nrerror("allocation failure 1 in matrix()");
1148: m += NR_END;
1149: m -= nrl;
1150:
1151: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1152: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1153: m[nrl] += NR_END;
1154: m[nrl] -= ncl;
1155:
1156: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1157:
1158: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1159: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1160: m[nrl][ncl] += NR_END;
1161: m[nrl][ncl] -= nll;
1162: for (j=ncl+1; j<=nch; j++)
1163: m[nrl][j]=m[nrl][j-1]+nlay;
1164:
1165: for (i=nrl+1; i<=nrh; i++) {
1166: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1167: for (j=ncl+1; j<=nch; j++)
1168: m[i][j]=m[i][j-1]+nlay;
1169: }
1170: return m;
1171: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1172: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1173: */
1174: }
1175:
1176: /*************************free ma3x ************************/
1177: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1178: {
1179: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1180: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1181: free((FREE_ARG)(m+nrl-NR_END));
1182: }
1183:
1184: /*************** function subdirf ***********/
1185: char *subdirf(char fileres[])
1186: {
1187: /* Caution optionfilefiname is hidden */
1188: strcpy(tmpout,optionfilefiname);
1189: strcat(tmpout,"/"); /* Add to the right */
1190: strcat(tmpout,fileres);
1191: return tmpout;
1192: }
1193:
1194: /*************** function subdirf2 ***********/
1195: char *subdirf2(char fileres[], char *preop)
1196: {
1197:
1198: /* Caution optionfilefiname is hidden */
1199: strcpy(tmpout,optionfilefiname);
1200: strcat(tmpout,"/");
1201: strcat(tmpout,preop);
1202: strcat(tmpout,fileres);
1203: return tmpout;
1204: }
1205:
1206: /*************** function subdirf3 ***********/
1207: char *subdirf3(char fileres[], char *preop, char *preop2)
1208: {
1209:
1210: /* Caution optionfilefiname is hidden */
1211: strcpy(tmpout,optionfilefiname);
1212: strcat(tmpout,"/");
1213: strcat(tmpout,preop);
1214: strcat(tmpout,preop2);
1215: strcat(tmpout,fileres);
1216: return tmpout;
1217: }
1218:
1.162 brouard 1219: char *asc_diff_time(long time_sec, char ascdiff[])
1220: {
1221: long sec_left, days, hours, minutes;
1222: days = (time_sec) / (60*60*24);
1223: sec_left = (time_sec) % (60*60*24);
1224: hours = (sec_left) / (60*60) ;
1225: sec_left = (sec_left) %(60*60);
1226: minutes = (sec_left) /60;
1227: sec_left = (sec_left) % (60);
1228: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1229: return ascdiff;
1230: }
1231:
1.126 brouard 1232: /***************** f1dim *************************/
1233: extern int ncom;
1234: extern double *pcom,*xicom;
1235: extern double (*nrfunc)(double []);
1236:
1237: double f1dim(double x)
1238: {
1239: int j;
1240: double f;
1241: double *xt;
1242:
1243: xt=vector(1,ncom);
1244: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1245: f=(*nrfunc)(xt);
1246: free_vector(xt,1,ncom);
1247: return f;
1248: }
1249:
1250: /*****************brent *************************/
1251: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1252: {
1253: int iter;
1254: double a,b,d,etemp;
1.159 brouard 1255: double fu=0,fv,fw,fx;
1.164 brouard 1256: double ftemp=0.;
1.126 brouard 1257: double p,q,r,tol1,tol2,u,v,w,x,xm;
1258: double e=0.0;
1259:
1260: a=(ax < cx ? ax : cx);
1261: b=(ax > cx ? ax : cx);
1262: x=w=v=bx;
1263: fw=fv=fx=(*f)(x);
1264: for (iter=1;iter<=ITMAX;iter++) {
1265: xm=0.5*(a+b);
1266: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1267: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1268: printf(".");fflush(stdout);
1269: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1270: #ifdef DEBUGBRENT
1.126 brouard 1271: 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);
1272: 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);
1273: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1274: #endif
1275: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1276: *xmin=x;
1277: return fx;
1278: }
1279: ftemp=fu;
1280: if (fabs(e) > tol1) {
1281: r=(x-w)*(fx-fv);
1282: q=(x-v)*(fx-fw);
1283: p=(x-v)*q-(x-w)*r;
1284: q=2.0*(q-r);
1285: if (q > 0.0) p = -p;
1286: q=fabs(q);
1287: etemp=e;
1288: e=d;
1289: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1290: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1291: else {
1292: d=p/q;
1293: u=x+d;
1294: if (u-a < tol2 || b-u < tol2)
1295: d=SIGN(tol1,xm-x);
1296: }
1297: } else {
1298: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1299: }
1300: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1301: fu=(*f)(u);
1302: if (fu <= fx) {
1303: if (u >= x) a=x; else b=x;
1304: SHFT(v,w,x,u)
1.183 brouard 1305: SHFT(fv,fw,fx,fu)
1306: } else {
1307: if (u < x) a=u; else b=u;
1308: if (fu <= fw || w == x) {
1309: v=w;
1310: w=u;
1311: fv=fw;
1312: fw=fu;
1313: } else if (fu <= fv || v == x || v == w) {
1314: v=u;
1315: fv=fu;
1316: }
1317: }
1.126 brouard 1318: }
1319: nrerror("Too many iterations in brent");
1320: *xmin=x;
1321: return fx;
1322: }
1323:
1324: /****************** mnbrak ***********************/
1325:
1326: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1327: double (*func)(double))
1.183 brouard 1328: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1329: the downhill direction (defined by the function as evaluated at the initial points) and returns
1330: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1331: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1332: */
1.126 brouard 1333: double ulim,u,r,q, dum;
1334: double fu;
1335:
1336: *fa=(*func)(*ax);
1337: *fb=(*func)(*bx);
1338: if (*fb > *fa) {
1339: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1340: SHFT(dum,*fb,*fa,dum)
1341: }
1.126 brouard 1342: *cx=(*bx)+GOLD*(*bx-*ax);
1343: *fc=(*func)(*cx);
1.183 brouard 1344: #ifdef DEBUG
1345: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1346: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1347: #endif
1348: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1349: r=(*bx-*ax)*(*fb-*fc);
1350: q=(*bx-*cx)*(*fb-*fa);
1351: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1352: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1353: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1354: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1355: fu=(*func)(u);
1.163 brouard 1356: #ifdef DEBUG
1357: /* f(x)=A(x-u)**2+f(u) */
1358: double A, fparabu;
1359: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1360: fparabu= *fa - A*(*ax-u)*(*ax-u);
1361: 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);
1362: 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 1363: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1364: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1365: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1366: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1367: #endif
1.184 brouard 1368: #ifdef MNBRAKORIGINAL
1.183 brouard 1369: #else
1370: if (fu > *fc) {
1371: #ifdef DEBUG
1372: printf("mnbrak4 fu > fc \n");
1373: fprintf(ficlog, "mnbrak4 fu > fc\n");
1374: #endif
1375: /* 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 *\/ */
1376: /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */
1377: dum=u; /* Shifting c and u */
1378: u = *cx;
1379: *cx = dum;
1380: dum = fu;
1381: fu = *fc;
1382: *fc =dum;
1383: } else { /* end */
1384: #ifdef DEBUG
1385: printf("mnbrak3 fu < fc \n");
1386: fprintf(ficlog, "mnbrak3 fu < fc\n");
1387: #endif
1388: dum=u; /* Shifting c and u */
1389: u = *cx;
1390: *cx = dum;
1391: dum = fu;
1392: fu = *fc;
1393: *fc =dum;
1394: }
1395: #endif
1.162 brouard 1396: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1397: #ifdef DEBUG
1398: printf("mnbrak2 u after c but before ulim\n");
1399: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1400: #endif
1.126 brouard 1401: fu=(*func)(u);
1402: if (fu < *fc) {
1.183 brouard 1403: #ifdef DEBUG
1404: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1405: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1406: #endif
1.126 brouard 1407: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1408: SHFT(*fb,*fc,fu,(*func)(u))
1409: }
1.162 brouard 1410: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1411: #ifdef DEBUG
1412: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1413: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1414: #endif
1.126 brouard 1415: u=ulim;
1416: fu=(*func)(u);
1.183 brouard 1417: } else { /* u could be left to b (if r > q parabola has a maximum) */
1418: #ifdef DEBUG
1419: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1420: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1421: #endif
1.126 brouard 1422: u=(*cx)+GOLD*(*cx-*bx);
1423: fu=(*func)(u);
1.183 brouard 1424: } /* end tests */
1.126 brouard 1425: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1426: SHFT(*fa,*fb,*fc,fu)
1427: #ifdef DEBUG
1428: 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);
1429: 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);
1430: #endif
1431: } /* 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 1432: }
1433:
1434: /*************** linmin ************************/
1.162 brouard 1435: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1436: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1437: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1438: the value of func at the returned location p . This is actually all accomplished by calling the
1439: routines mnbrak and brent .*/
1.126 brouard 1440: int ncom;
1441: double *pcom,*xicom;
1442: double (*nrfunc)(double []);
1443:
1444: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1445: {
1446: double brent(double ax, double bx, double cx,
1447: double (*f)(double), double tol, double *xmin);
1448: double f1dim(double x);
1449: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1450: double *fc, double (*func)(double));
1451: int j;
1452: double xx,xmin,bx,ax;
1453: double fx,fb,fa;
1454:
1455: ncom=n;
1456: pcom=vector(1,n);
1457: xicom=vector(1,n);
1458: nrfunc=func;
1459: for (j=1;j<=n;j++) {
1460: pcom[j]=p[j];
1461: xicom[j]=xi[j];
1462: }
1463: ax=0.0;
1464: xx=1.0;
1.162 brouard 1465: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1466: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1.126 brouard 1467: #ifdef DEBUG
1468: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1469: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1470: #endif
1471: for (j=1;j<=n;j++) {
1472: xi[j] *= xmin;
1473: p[j] += xi[j];
1474: }
1475: free_vector(xicom,1,n);
1476: free_vector(pcom,1,n);
1477: }
1478:
1479:
1480: /*************** powell ************************/
1.162 brouard 1481: /*
1482: Minimization of a function func of n variables. Input consists of an initial starting point
1483: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1484: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1485: such that failure to decrease by more than this amount on one iteration signals doneness. On
1486: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1487: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1488: */
1.126 brouard 1489: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1490: double (*func)(double []))
1491: {
1492: void linmin(double p[], double xi[], int n, double *fret,
1493: double (*func)(double []));
1494: int i,ibig,j;
1495: double del,t,*pt,*ptt,*xit;
1.181 brouard 1496: double directest;
1.126 brouard 1497: double fp,fptt;
1498: double *xits;
1499: int niterf, itmp;
1500:
1501: pt=vector(1,n);
1502: ptt=vector(1,n);
1503: xit=vector(1,n);
1504: xits=vector(1,n);
1505: *fret=(*func)(p);
1506: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1507: rcurr_time = time(NULL);
1.126 brouard 1508: for (*iter=1;;++(*iter)) {
1509: fp=(*fret);
1510: ibig=0;
1511: del=0.0;
1.157 brouard 1512: rlast_time=rcurr_time;
1513: /* (void) gettimeofday(&curr_time,&tzp); */
1514: rcurr_time = time(NULL);
1515: curr_time = *localtime(&rcurr_time);
1516: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1517: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1518: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1519: for (i=1;i<=n;i++) {
1520: printf(" %d %.12f",i, p[i]);
1521: fprintf(ficlog," %d %.12lf",i, p[i]);
1522: fprintf(ficrespow," %.12lf", p[i]);
1523: }
1524: printf("\n");
1525: fprintf(ficlog,"\n");
1526: fprintf(ficrespow,"\n");fflush(ficrespow);
1527: if(*iter <=3){
1.157 brouard 1528: tml = *localtime(&rcurr_time);
1529: strcpy(strcurr,asctime(&tml));
1530: rforecast_time=rcurr_time;
1.126 brouard 1531: itmp = strlen(strcurr);
1532: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1533: strcurr[itmp-1]='\0';
1.162 brouard 1534: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1535: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1536: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1537: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1538: forecast_time = *localtime(&rforecast_time);
1539: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1540: itmp = strlen(strfor);
1541: if(strfor[itmp-1]=='\n')
1542: strfor[itmp-1]='\0';
1.157 brouard 1543: 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);
1544: 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 1545: }
1546: }
1547: for (i=1;i<=n;i++) {
1548: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1549: fptt=(*fret);
1550: #ifdef DEBUG
1.164 brouard 1551: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1552: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1553: #endif
1554: printf("%d",i);fflush(stdout);
1555: fprintf(ficlog,"%d",i);fflush(ficlog);
1.183 brouard 1556: linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
1.181 brouard 1557: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions
1558: because that direction will be replaced unless the gain del is small
1559: in comparison with the 'probable' gain, mu^2, with the last average direction.
1560: Unless the n directions are conjugate some gain in the determinant may be obtained
1561: with the new direction.
1562: */
1.126 brouard 1563: del=fabs(fptt-(*fret));
1564: ibig=i;
1565: }
1566: #ifdef DEBUG
1567: printf("%d %.12e",i,(*fret));
1568: fprintf(ficlog,"%d %.12e",i,(*fret));
1569: for (j=1;j<=n;j++) {
1570: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1571: printf(" x(%d)=%.12e",j,xit[j]);
1572: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1573: }
1574: for(j=1;j<=n;j++) {
1.162 brouard 1575: printf(" p(%d)=%.12e",j,p[j]);
1576: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1577: }
1578: printf("\n");
1579: fprintf(ficlog,"\n");
1580: #endif
1.162 brouard 1581: } /* end i */
1.182 brouard 1582: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.126 brouard 1583: #ifdef DEBUG
1584: int k[2],l;
1585: k[0]=1;
1586: k[1]=-1;
1587: printf("Max: %.12e",(*func)(p));
1588: fprintf(ficlog,"Max: %.12e",(*func)(p));
1589: for (j=1;j<=n;j++) {
1590: printf(" %.12e",p[j]);
1591: fprintf(ficlog," %.12e",p[j]);
1592: }
1593: printf("\n");
1594: fprintf(ficlog,"\n");
1595: for(l=0;l<=1;l++) {
1596: for (j=1;j<=n;j++) {
1597: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1598: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1599: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1600: }
1601: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1602: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1603: }
1604: #endif
1605:
1606:
1607: free_vector(xit,1,n);
1608: free_vector(xits,1,n);
1609: free_vector(ptt,1,n);
1610: free_vector(pt,1,n);
1611: return;
1612: }
1613: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1614: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1615: ptt[j]=2.0*p[j]-pt[j];
1616: xit[j]=p[j]-pt[j];
1617: pt[j]=p[j];
1618: }
1.181 brouard 1619: fptt=(*func)(ptt); /* f_3 */
1.161 brouard 1620: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1621: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1622: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1623: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1624: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1625: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1626: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1627: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1628: #ifdef NRCORIGINAL
1629: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1630: #else
1631: 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 1632: t= t- del*SQR(fp-fptt);
1.183 brouard 1633: #endif
1.182 brouard 1634: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1635: #ifdef DEBUG
1.181 brouard 1636: 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);
1637: 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 1638: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1639: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1640: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1641: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1642: 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);
1643: 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);
1644: #endif
1.183 brouard 1645: #ifdef POWELLORIGINAL
1646: if (t < 0.0) { /* Then we use it for new direction */
1647: #else
1.182 brouard 1648: if (directest*t < 0.0) { /* Contradiction between both tests */
1.184 brouard 1649: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182 brouard 1650: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.184 brouard 1651: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182 brouard 1652: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1653: }
1.181 brouard 1654: if (directest < 0.0) { /* Then we use it for new direction */
1655: #endif
1656: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
1.126 brouard 1657: for (j=1;j<=n;j++) {
1.181 brouard 1658: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1659: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1660: }
1.181 brouard 1661: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1662: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1663:
1.126 brouard 1664: #ifdef DEBUG
1.164 brouard 1665: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1666: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1667: for(j=1;j<=n;j++){
1668: printf(" %.12e",xit[j]);
1669: fprintf(ficlog," %.12e",xit[j]);
1670: }
1671: printf("\n");
1672: fprintf(ficlog,"\n");
1673: #endif
1.162 brouard 1674: } /* end of t negative */
1675: } /* end if (fptt < fp) */
1.126 brouard 1676: }
1677: }
1678:
1679: /**** Prevalence limit (stable or period prevalence) ****************/
1680:
1681: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1682: {
1683: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1684: matrix by transitions matrix until convergence is reached */
1.169 brouard 1685:
1.126 brouard 1686: int i, ii,j,k;
1687: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1688: /* double **matprod2(); */ /* test */
1.131 brouard 1689: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1690: double **newm;
1691: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1692:
1.126 brouard 1693: for (ii=1;ii<=nlstate+ndeath;ii++)
1694: for (j=1;j<=nlstate+ndeath;j++){
1695: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1696: }
1.169 brouard 1697:
1698: cov[1]=1.;
1699:
1700: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1701: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1702: newm=savm;
1703: /* Covariates have to be included here again */
1.138 brouard 1704: cov[2]=agefin;
1705:
1706: for (k=1; k<=cptcovn;k++) {
1707: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1708: /*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 1709: }
1.186 ! brouard 1710: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 1711: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
! 1712: for (k=1; k<=cptcovprod;k++) /* Useless */
! 1713: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1714:
1715: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1716: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1717: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1718: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1719: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1720: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1721:
1.126 brouard 1722: savm=oldm;
1723: oldm=newm;
1724: maxmax=0.;
1725: for(j=1;j<=nlstate;j++){
1726: min=1.;
1727: max=0.;
1728: for(i=1; i<=nlstate; i++) {
1729: sumnew=0;
1730: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1731: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1732: /*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 1733: max=FMAX(max,prlim[i][j]);
1734: min=FMIN(min,prlim[i][j]);
1735: }
1736: maxmin=max-min;
1737: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1738: } /* j loop */
1.126 brouard 1739: if(maxmax < ftolpl){
1740: return prlim;
1741: }
1.169 brouard 1742: } /* age loop */
1743: return prlim; /* should not reach here */
1.126 brouard 1744: }
1745:
1746: /*************** transition probabilities ***************/
1747:
1748: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1749: {
1.138 brouard 1750: /* According to parameters values stored in x and the covariate's values stored in cov,
1751: computes the probability to be observed in state j being in state i by appying the
1752: model to the ncovmodel covariates (including constant and age).
1753: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1754: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1755: ncth covariate in the global vector x is given by the formula:
1756: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1757: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1758: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1759: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1760: Outputs ps[i][j] the probability to be observed in j being in j according to
1761: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1762: */
1763: double s1, lnpijopii;
1.126 brouard 1764: /*double t34;*/
1.164 brouard 1765: int i,j, nc, ii, jj;
1.126 brouard 1766:
1767: for(i=1; i<= nlstate; i++){
1768: for(j=1; j<i;j++){
1.138 brouard 1769: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1770: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1771: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1772: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1773: }
1.138 brouard 1774: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1775: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1776: }
1777: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1778: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1779: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1780: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1781: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1782: }
1.138 brouard 1783: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1784: }
1785: }
1786:
1787: for(i=1; i<= nlstate; i++){
1788: s1=0;
1.131 brouard 1789: for(j=1; j<i; j++){
1.138 brouard 1790: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1791: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1792: }
1793: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1794: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1795: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1796: }
1.138 brouard 1797: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1798: ps[i][i]=1./(s1+1.);
1.138 brouard 1799: /* Computing other pijs */
1.126 brouard 1800: for(j=1; j<i; j++)
1801: ps[i][j]= exp(ps[i][j])*ps[i][i];
1802: for(j=i+1; j<=nlstate+ndeath; j++)
1803: ps[i][j]= exp(ps[i][j])*ps[i][i];
1804: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1805: } /* end i */
1806:
1807: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1808: for(jj=1; jj<= nlstate+ndeath; jj++){
1809: ps[ii][jj]=0;
1810: ps[ii][ii]=1;
1811: }
1812: }
1813:
1.145 brouard 1814:
1815: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1816: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1817: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1818: /* } */
1819: /* printf("\n "); */
1820: /* } */
1821: /* printf("\n ");printf("%lf ",cov[2]);*/
1822: /*
1.126 brouard 1823: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1824: goto end;*/
1825: return ps;
1826: }
1827:
1828: /**************** Product of 2 matrices ******************/
1829:
1.145 brouard 1830: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1831: {
1832: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1833: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1834: /* in, b, out are matrice of pointers which should have been initialized
1835: before: only the contents of out is modified. The function returns
1836: a pointer to pointers identical to out */
1.145 brouard 1837: int i, j, k;
1.126 brouard 1838: for(i=nrl; i<= nrh; i++)
1.145 brouard 1839: for(k=ncolol; k<=ncoloh; k++){
1840: out[i][k]=0.;
1841: for(j=ncl; j<=nch; j++)
1842: out[i][k] +=in[i][j]*b[j][k];
1843: }
1.126 brouard 1844: return out;
1845: }
1846:
1847:
1848: /************* Higher Matrix Product ***************/
1849:
1850: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1851: {
1852: /* Computes the transition matrix starting at age 'age' over
1853: 'nhstepm*hstepm*stepm' months (i.e. until
1854: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1855: nhstepm*hstepm matrices.
1856: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1857: (typically every 2 years instead of every month which is too big
1858: for the memory).
1859: Model is determined by parameters x and covariates have to be
1860: included manually here.
1861:
1862: */
1863:
1864: int i, j, d, h, k;
1.131 brouard 1865: double **out, cov[NCOVMAX+1];
1.126 brouard 1866: double **newm;
1867:
1868: /* Hstepm could be zero and should return the unit matrix */
1869: for (i=1;i<=nlstate+ndeath;i++)
1870: for (j=1;j<=nlstate+ndeath;j++){
1871: oldm[i][j]=(i==j ? 1.0 : 0.0);
1872: po[i][j][0]=(i==j ? 1.0 : 0.0);
1873: }
1874: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1875: for(h=1; h <=nhstepm; h++){
1876: for(d=1; d <=hstepm; d++){
1877: newm=savm;
1878: /* Covariates have to be included here again */
1879: cov[1]=1.;
1880: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1881: for (k=1; k<=cptcovn;k++)
1882: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 ! brouard 1883: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
! 1884: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 1885: cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 1886: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1887: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1888:
1889:
1890: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1891: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1892: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1893: pmij(pmmij,cov,ncovmodel,x,nlstate));
1894: savm=oldm;
1895: oldm=newm;
1896: }
1897: for(i=1; i<=nlstate+ndeath; i++)
1898: for(j=1;j<=nlstate+ndeath;j++) {
1899: po[i][j][h]=newm[i][j];
1.128 brouard 1900: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1901: }
1.128 brouard 1902: /*printf("h=%d ",h);*/
1.126 brouard 1903: } /* end h */
1.128 brouard 1904: /* printf("\n H=%d \n",h); */
1.126 brouard 1905: return po;
1906: }
1907:
1.162 brouard 1908: #ifdef NLOPT
1909: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1910: double fret;
1911: double *xt;
1912: int j;
1913: myfunc_data *d2 = (myfunc_data *) pd;
1914: /* xt = (p1-1); */
1915: xt=vector(1,n);
1916: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1917:
1918: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1919: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1920: printf("Function = %.12lf ",fret);
1921: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1922: printf("\n");
1923: free_vector(xt,1,n);
1924: return fret;
1925: }
1926: #endif
1.126 brouard 1927:
1928: /*************** log-likelihood *************/
1929: double func( double *x)
1930: {
1931: int i, ii, j, k, mi, d, kk;
1.131 brouard 1932: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1933: double **out;
1934: double sw; /* Sum of weights */
1935: double lli; /* Individual log likelihood */
1936: int s1, s2;
1937: double bbh, survp;
1938: long ipmx;
1939: /*extern weight */
1940: /* We are differentiating ll according to initial status */
1941: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1942: /*for(i=1;i<imx;i++)
1943: printf(" %d\n",s[4][i]);
1944: */
1.162 brouard 1945:
1946: ++countcallfunc;
1947:
1.126 brouard 1948: cov[1]=1.;
1949:
1950: for(k=1; k<=nlstate; k++) ll[k]=0.;
1951:
1952: if(mle==1){
1953: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1954: /* Computes the values of the ncovmodel covariates of the model
1955: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1956: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1957: to be observed in j being in i according to the model.
1958: */
1.145 brouard 1959: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1960: cov[2+k]=covar[Tvar[k]][i];
1961: }
1.137 brouard 1962: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1963: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1964: has been calculated etc */
1.126 brouard 1965: for(mi=1; mi<= wav[i]-1; mi++){
1966: for (ii=1;ii<=nlstate+ndeath;ii++)
1967: for (j=1;j<=nlstate+ndeath;j++){
1968: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1969: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1970: }
1971: for(d=0; d<dh[mi][i]; d++){
1972: newm=savm;
1973: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1974: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1975: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1976: }
1977: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1978: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1979: savm=oldm;
1980: oldm=newm;
1981: } /* end mult */
1982:
1983: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1984: /* But now since version 0.9 we anticipate for bias at large stepm.
1985: * If stepm is larger than one month (smallest stepm) and if the exact delay
1986: * (in months) between two waves is not a multiple of stepm, we rounded to
1987: * the nearest (and in case of equal distance, to the lowest) interval but now
1988: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1989: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1990: * probability in order to take into account the bias as a fraction of the way
1991: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1992: * -stepm/2 to stepm/2 .
1993: * For stepm=1 the results are the same as for previous versions of Imach.
1994: * For stepm > 1 the results are less biased than in previous versions.
1995: */
1996: s1=s[mw[mi][i]][i];
1997: s2=s[mw[mi+1][i]][i];
1998: bbh=(double)bh[mi][i]/(double)stepm;
1999: /* bias bh is positive if real duration
2000: * is higher than the multiple of stepm and negative otherwise.
2001: */
2002: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2003: if( s2 > nlstate){
2004: /* i.e. if s2 is a death state and if the date of death is known
2005: then the contribution to the likelihood is the probability to
2006: die between last step unit time and current step unit time,
2007: which is also equal to probability to die before dh
2008: minus probability to die before dh-stepm .
2009: In version up to 0.92 likelihood was computed
2010: as if date of death was unknown. Death was treated as any other
2011: health state: the date of the interview describes the actual state
2012: and not the date of a change in health state. The former idea was
2013: to consider that at each interview the state was recorded
2014: (healthy, disable or death) and IMaCh was corrected; but when we
2015: introduced the exact date of death then we should have modified
2016: the contribution of an exact death to the likelihood. This new
2017: contribution is smaller and very dependent of the step unit
2018: stepm. It is no more the probability to die between last interview
2019: and month of death but the probability to survive from last
2020: interview up to one month before death multiplied by the
2021: probability to die within a month. Thanks to Chris
2022: Jackson for correcting this bug. Former versions increased
2023: mortality artificially. The bad side is that we add another loop
2024: which slows down the processing. The difference can be up to 10%
2025: lower mortality.
2026: */
1.183 brouard 2027: /* If, at the beginning of the maximization mostly, the
2028: cumulative probability or probability to be dead is
2029: constant (ie = 1) over time d, the difference is equal to
2030: 0. out[s1][3] = savm[s1][3]: probability, being at state
2031: s1 at precedent wave, to be dead a month before current
2032: wave is equal to probability, being at state s1 at
2033: precedent wave, to be dead at mont of the current
2034: wave. Then the observed probability (that this person died)
2035: is null according to current estimated parameter. In fact,
2036: it should be very low but not zero otherwise the log go to
2037: infinity.
2038: */
2039: /* #ifdef INFINITYORIGINAL */
2040: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2041: /* #else */
2042: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2043: /* lli=log(mytinydouble); */
2044: /* else */
2045: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2046: /* #endif */
2047: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2048:
2049: } else if (s2==-2) {
2050: for (j=1,survp=0. ; j<=nlstate; j++)
2051: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2052: /*survp += out[s1][j]; */
2053: lli= log(survp);
2054: }
2055:
2056: else if (s2==-4) {
2057: for (j=3,survp=0. ; j<=nlstate; j++)
2058: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2059: lli= log(survp);
2060: }
2061:
2062: else if (s2==-5) {
2063: for (j=1,survp=0. ; j<=2; j++)
2064: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2065: lli= log(survp);
2066: }
2067:
2068: else{
2069: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2070: /* 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 */
2071: }
2072: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2073: /*if(lli ==000.0)*/
2074: /*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); */
2075: ipmx +=1;
2076: sw += weight[i];
2077: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2078: /* if (lli < log(mytinydouble)){ */
2079: /* 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); */
2080: /* 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]); */
2081: /* } */
1.126 brouard 2082: } /* end of wave */
2083: } /* end of individual */
2084: } else if(mle==2){
2085: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2086: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2087: for(mi=1; mi<= wav[i]-1; mi++){
2088: for (ii=1;ii<=nlstate+ndeath;ii++)
2089: for (j=1;j<=nlstate+ndeath;j++){
2090: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2091: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2092: }
2093: for(d=0; d<=dh[mi][i]; d++){
2094: newm=savm;
2095: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2096: for (kk=1; kk<=cptcovage;kk++) {
2097: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2098: }
2099: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2100: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2101: savm=oldm;
2102: oldm=newm;
2103: } /* end mult */
2104:
2105: s1=s[mw[mi][i]][i];
2106: s2=s[mw[mi+1][i]][i];
2107: bbh=(double)bh[mi][i]/(double)stepm;
2108: 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 */
2109: ipmx +=1;
2110: sw += weight[i];
2111: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2112: } /* end of wave */
2113: } /* end of individual */
2114: } else if(mle==3){ /* exponential inter-extrapolation */
2115: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2116: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2117: for(mi=1; mi<= wav[i]-1; mi++){
2118: for (ii=1;ii<=nlstate+ndeath;ii++)
2119: for (j=1;j<=nlstate+ndeath;j++){
2120: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2121: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2122: }
2123: for(d=0; d<dh[mi][i]; d++){
2124: newm=savm;
2125: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2126: for (kk=1; kk<=cptcovage;kk++) {
2127: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2128: }
2129: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2130: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2131: savm=oldm;
2132: oldm=newm;
2133: } /* end mult */
2134:
2135: s1=s[mw[mi][i]][i];
2136: s2=s[mw[mi+1][i]][i];
2137: bbh=(double)bh[mi][i]/(double)stepm;
2138: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
2139: ipmx +=1;
2140: sw += weight[i];
2141: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2142: } /* end of wave */
2143: } /* end of individual */
2144: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2145: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2146: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2147: for(mi=1; mi<= wav[i]-1; mi++){
2148: for (ii=1;ii<=nlstate+ndeath;ii++)
2149: for (j=1;j<=nlstate+ndeath;j++){
2150: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2151: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2152: }
2153: for(d=0; d<dh[mi][i]; d++){
2154: newm=savm;
2155: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2156: for (kk=1; kk<=cptcovage;kk++) {
2157: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2158: }
2159:
2160: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2161: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2162: savm=oldm;
2163: oldm=newm;
2164: } /* end mult */
2165:
2166: s1=s[mw[mi][i]][i];
2167: s2=s[mw[mi+1][i]][i];
2168: if( s2 > nlstate){
2169: lli=log(out[s1][s2] - savm[s1][s2]);
2170: }else{
2171: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2172: }
2173: ipmx +=1;
2174: sw += weight[i];
2175: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2176: /* 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]); */
2177: } /* end of wave */
2178: } /* end of individual */
2179: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2180: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2181: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2182: for(mi=1; mi<= wav[i]-1; mi++){
2183: for (ii=1;ii<=nlstate+ndeath;ii++)
2184: for (j=1;j<=nlstate+ndeath;j++){
2185: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2186: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2187: }
2188: for(d=0; d<dh[mi][i]; d++){
2189: newm=savm;
2190: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2191: for (kk=1; kk<=cptcovage;kk++) {
2192: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2193: }
2194:
2195: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2196: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2197: savm=oldm;
2198: oldm=newm;
2199: } /* end mult */
2200:
2201: s1=s[mw[mi][i]][i];
2202: s2=s[mw[mi+1][i]][i];
2203: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2204: ipmx +=1;
2205: sw += weight[i];
2206: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2207: /*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]);*/
2208: } /* end of wave */
2209: } /* end of individual */
2210: } /* End of if */
2211: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2212: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2213: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2214: return -l;
2215: }
2216:
2217: /*************** log-likelihood *************/
2218: double funcone( double *x)
2219: {
2220: /* Same as likeli but slower because of a lot of printf and if */
2221: int i, ii, j, k, mi, d, kk;
1.131 brouard 2222: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2223: double **out;
2224: double lli; /* Individual log likelihood */
2225: double llt;
2226: int s1, s2;
2227: double bbh, survp;
2228: /*extern weight */
2229: /* We are differentiating ll according to initial status */
2230: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2231: /*for(i=1;i<imx;i++)
2232: printf(" %d\n",s[4][i]);
2233: */
2234: cov[1]=1.;
2235:
2236: for(k=1; k<=nlstate; k++) ll[k]=0.;
2237:
2238: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2239: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2240: for(mi=1; mi<= wav[i]-1; mi++){
2241: for (ii=1;ii<=nlstate+ndeath;ii++)
2242: for (j=1;j<=nlstate+ndeath;j++){
2243: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2244: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2245: }
2246: for(d=0; d<dh[mi][i]; d++){
2247: newm=savm;
2248: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2249: for (kk=1; kk<=cptcovage;kk++) {
2250: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2251: }
1.145 brouard 2252: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2253: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2254: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2255: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2256: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2257: savm=oldm;
2258: oldm=newm;
2259: } /* end mult */
2260:
2261: s1=s[mw[mi][i]][i];
2262: s2=s[mw[mi+1][i]][i];
2263: bbh=(double)bh[mi][i]/(double)stepm;
2264: /* bias is positive if real duration
2265: * is higher than the multiple of stepm and negative otherwise.
2266: */
2267: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2268: lli=log(out[s1][s2] - savm[s1][s2]);
2269: } else if (s2==-2) {
2270: for (j=1,survp=0. ; j<=nlstate; j++)
2271: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2272: lli= log(survp);
2273: }else if (mle==1){
2274: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2275: } else if(mle==2){
2276: 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 */
2277: } else if(mle==3){ /* exponential inter-extrapolation */
2278: 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 */
2279: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2280: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2281: } else{ /* mle=0 back to 1 */
2282: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2283: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2284: } /* End of if */
2285: ipmx +=1;
2286: sw += weight[i];
2287: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2288: /*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 2289: if(globpr){
1.141 brouard 2290: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2291: %11.6f %11.6f %11.6f ", \
2292: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2293: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2294: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2295: llt +=ll[k]*gipmx/gsw;
2296: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2297: }
2298: fprintf(ficresilk," %10.6f\n", -llt);
2299: }
2300: } /* end of wave */
2301: } /* end of individual */
2302: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2303: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2304: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2305: if(globpr==0){ /* First time we count the contributions and weights */
2306: gipmx=ipmx;
2307: gsw=sw;
2308: }
2309: return -l;
2310: }
2311:
2312:
2313: /*************** function likelione ***********/
2314: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2315: {
2316: /* This routine should help understanding what is done with
2317: the selection of individuals/waves and
2318: to check the exact contribution to the likelihood.
2319: Plotting could be done.
2320: */
2321: int k;
2322:
2323: if(*globpri !=0){ /* Just counts and sums, no printings */
2324: strcpy(fileresilk,"ilk");
2325: strcat(fileresilk,fileres);
2326: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2327: printf("Problem with resultfile: %s\n", fileresilk);
2328: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2329: }
2330: 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");
2331: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2332: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2333: for(k=1; k<=nlstate; k++)
2334: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2335: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2336: }
2337:
2338: *fretone=(*funcone)(p);
2339: if(*globpri !=0){
2340: fclose(ficresilk);
2341: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2342: fflush(fichtm);
2343: }
2344: return;
2345: }
2346:
2347:
2348: /*********** Maximum Likelihood Estimation ***************/
2349:
2350: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2351: {
1.165 brouard 2352: int i,j, iter=0;
1.126 brouard 2353: double **xi;
2354: double fret;
2355: double fretone; /* Only one call to likelihood */
2356: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2357:
2358: #ifdef NLOPT
2359: int creturn;
2360: nlopt_opt opt;
2361: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2362: double *lb;
2363: double minf; /* the minimum objective value, upon return */
2364: double * p1; /* Shifted parameters from 0 instead of 1 */
2365: myfunc_data dinst, *d = &dinst;
2366: #endif
2367:
2368:
1.126 brouard 2369: xi=matrix(1,npar,1,npar);
2370: for (i=1;i<=npar;i++)
2371: for (j=1;j<=npar;j++)
2372: xi[i][j]=(i==j ? 1.0 : 0.0);
2373: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2374: strcpy(filerespow,"pow");
2375: strcat(filerespow,fileres);
2376: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2377: printf("Problem with resultfile: %s\n", filerespow);
2378: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2379: }
2380: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2381: for (i=1;i<=nlstate;i++)
2382: for(j=1;j<=nlstate+ndeath;j++)
2383: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2384: fprintf(ficrespow,"\n");
1.162 brouard 2385: #ifdef POWELL
1.126 brouard 2386: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2387: #endif
1.126 brouard 2388:
1.162 brouard 2389: #ifdef NLOPT
2390: #ifdef NEWUOA
2391: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2392: #else
2393: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2394: #endif
2395: lb=vector(0,npar-1);
2396: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2397: nlopt_set_lower_bounds(opt, lb);
2398: nlopt_set_initial_step1(opt, 0.1);
2399:
2400: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2401: d->function = func;
2402: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2403: nlopt_set_min_objective(opt, myfunc, d);
2404: nlopt_set_xtol_rel(opt, ftol);
2405: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2406: printf("nlopt failed! %d\n",creturn);
2407: }
2408: else {
2409: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2410: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2411: iter=1; /* not equal */
2412: }
2413: nlopt_destroy(opt);
2414: #endif
1.126 brouard 2415: free_matrix(xi,1,npar,1,npar);
2416: fclose(ficrespow);
1.180 brouard 2417: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2418: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2419: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2420:
2421: }
2422:
2423: /**** Computes Hessian and covariance matrix ***/
2424: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2425: {
2426: double **a,**y,*x,pd;
2427: double **hess;
1.164 brouard 2428: int i, j;
1.126 brouard 2429: int *indx;
2430:
2431: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2432: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2433: void lubksb(double **a, int npar, int *indx, double b[]) ;
2434: void ludcmp(double **a, int npar, int *indx, double *d) ;
2435: double gompertz(double p[]);
2436: hess=matrix(1,npar,1,npar);
2437:
2438: printf("\nCalculation of the hessian matrix. Wait...\n");
2439: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2440: for (i=1;i<=npar;i++){
2441: printf("%d",i);fflush(stdout);
2442: fprintf(ficlog,"%d",i);fflush(ficlog);
2443:
2444: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2445:
2446: /* printf(" %f ",p[i]);
2447: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2448: }
2449:
2450: for (i=1;i<=npar;i++) {
2451: for (j=1;j<=npar;j++) {
2452: if (j>i) {
2453: printf(".%d%d",i,j);fflush(stdout);
2454: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2455: hess[i][j]=hessij(p,delti,i,j,func,npar);
2456:
2457: hess[j][i]=hess[i][j];
2458: /*printf(" %lf ",hess[i][j]);*/
2459: }
2460: }
2461: }
2462: printf("\n");
2463: fprintf(ficlog,"\n");
2464:
2465: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2466: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2467:
2468: a=matrix(1,npar,1,npar);
2469: y=matrix(1,npar,1,npar);
2470: x=vector(1,npar);
2471: indx=ivector(1,npar);
2472: for (i=1;i<=npar;i++)
2473: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2474: ludcmp(a,npar,indx,&pd);
2475:
2476: for (j=1;j<=npar;j++) {
2477: for (i=1;i<=npar;i++) x[i]=0;
2478: x[j]=1;
2479: lubksb(a,npar,indx,x);
2480: for (i=1;i<=npar;i++){
2481: matcov[i][j]=x[i];
2482: }
2483: }
2484:
2485: printf("\n#Hessian matrix#\n");
2486: fprintf(ficlog,"\n#Hessian matrix#\n");
2487: for (i=1;i<=npar;i++) {
2488: for (j=1;j<=npar;j++) {
2489: printf("%.3e ",hess[i][j]);
2490: fprintf(ficlog,"%.3e ",hess[i][j]);
2491: }
2492: printf("\n");
2493: fprintf(ficlog,"\n");
2494: }
2495:
2496: /* Recompute Inverse */
2497: for (i=1;i<=npar;i++)
2498: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2499: ludcmp(a,npar,indx,&pd);
2500:
2501: /* printf("\n#Hessian matrix recomputed#\n");
2502:
2503: for (j=1;j<=npar;j++) {
2504: for (i=1;i<=npar;i++) x[i]=0;
2505: x[j]=1;
2506: lubksb(a,npar,indx,x);
2507: for (i=1;i<=npar;i++){
2508: y[i][j]=x[i];
2509: printf("%.3e ",y[i][j]);
2510: fprintf(ficlog,"%.3e ",y[i][j]);
2511: }
2512: printf("\n");
2513: fprintf(ficlog,"\n");
2514: }
2515: */
2516:
2517: free_matrix(a,1,npar,1,npar);
2518: free_matrix(y,1,npar,1,npar);
2519: free_vector(x,1,npar);
2520: free_ivector(indx,1,npar);
2521: free_matrix(hess,1,npar,1,npar);
2522:
2523:
2524: }
2525:
2526: /*************** hessian matrix ****************/
2527: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2528: {
2529: int i;
2530: int l=1, lmax=20;
2531: double k1,k2;
1.132 brouard 2532: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2533: double res;
2534: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2535: double fx;
2536: int k=0,kmax=10;
2537: double l1;
2538:
2539: fx=func(x);
2540: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2541: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2542: l1=pow(10,l);
2543: delts=delt;
2544: for(k=1 ; k <kmax; k=k+1){
2545: delt = delta*(l1*k);
2546: p2[theta]=x[theta] +delt;
1.145 brouard 2547: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2548: p2[theta]=x[theta]-delt;
2549: k2=func(p2)-fx;
2550: /*res= (k1-2.0*fx+k2)/delt/delt; */
2551: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2552:
1.132 brouard 2553: #ifdef DEBUGHESS
1.126 brouard 2554: 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);
2555: 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);
2556: #endif
2557: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2558: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2559: k=kmax;
2560: }
2561: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2562: k=kmax; l=lmax*10;
1.126 brouard 2563: }
2564: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2565: delts=delt;
2566: }
2567: }
2568: }
2569: delti[theta]=delts;
2570: return res;
2571:
2572: }
2573:
2574: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2575: {
2576: int i;
1.164 brouard 2577: int l=1, lmax=20;
1.126 brouard 2578: double k1,k2,k3,k4,res,fx;
1.132 brouard 2579: double p2[MAXPARM+1];
1.126 brouard 2580: int k;
2581:
2582: fx=func(x);
2583: for (k=1; k<=2; k++) {
2584: for (i=1;i<=npar;i++) p2[i]=x[i];
2585: p2[thetai]=x[thetai]+delti[thetai]/k;
2586: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2587: k1=func(p2)-fx;
2588:
2589: p2[thetai]=x[thetai]+delti[thetai]/k;
2590: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2591: k2=func(p2)-fx;
2592:
2593: p2[thetai]=x[thetai]-delti[thetai]/k;
2594: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2595: k3=func(p2)-fx;
2596:
2597: p2[thetai]=x[thetai]-delti[thetai]/k;
2598: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2599: k4=func(p2)-fx;
2600: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2601: #ifdef DEBUG
2602: 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);
2603: 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);
2604: #endif
2605: }
2606: return res;
2607: }
2608:
2609: /************** Inverse of matrix **************/
2610: void ludcmp(double **a, int n, int *indx, double *d)
2611: {
2612: int i,imax,j,k;
2613: double big,dum,sum,temp;
2614: double *vv;
2615:
2616: vv=vector(1,n);
2617: *d=1.0;
2618: for (i=1;i<=n;i++) {
2619: big=0.0;
2620: for (j=1;j<=n;j++)
2621: if ((temp=fabs(a[i][j])) > big) big=temp;
2622: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2623: vv[i]=1.0/big;
2624: }
2625: for (j=1;j<=n;j++) {
2626: for (i=1;i<j;i++) {
2627: sum=a[i][j];
2628: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2629: a[i][j]=sum;
2630: }
2631: big=0.0;
2632: for (i=j;i<=n;i++) {
2633: sum=a[i][j];
2634: for (k=1;k<j;k++)
2635: sum -= a[i][k]*a[k][j];
2636: a[i][j]=sum;
2637: if ( (dum=vv[i]*fabs(sum)) >= big) {
2638: big=dum;
2639: imax=i;
2640: }
2641: }
2642: if (j != imax) {
2643: for (k=1;k<=n;k++) {
2644: dum=a[imax][k];
2645: a[imax][k]=a[j][k];
2646: a[j][k]=dum;
2647: }
2648: *d = -(*d);
2649: vv[imax]=vv[j];
2650: }
2651: indx[j]=imax;
2652: if (a[j][j] == 0.0) a[j][j]=TINY;
2653: if (j != n) {
2654: dum=1.0/(a[j][j]);
2655: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2656: }
2657: }
2658: free_vector(vv,1,n); /* Doesn't work */
2659: ;
2660: }
2661:
2662: void lubksb(double **a, int n, int *indx, double b[])
2663: {
2664: int i,ii=0,ip,j;
2665: double sum;
2666:
2667: for (i=1;i<=n;i++) {
2668: ip=indx[i];
2669: sum=b[ip];
2670: b[ip]=b[i];
2671: if (ii)
2672: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2673: else if (sum) ii=i;
2674: b[i]=sum;
2675: }
2676: for (i=n;i>=1;i--) {
2677: sum=b[i];
2678: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2679: b[i]=sum/a[i][i];
2680: }
2681: }
2682:
2683: void pstamp(FILE *fichier)
2684: {
2685: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2686: }
2687:
2688: /************ Frequencies ********************/
2689: 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[])
2690: { /* Some frequencies */
2691:
1.164 brouard 2692: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2693: int first;
2694: double ***freq; /* Frequencies */
2695: double *pp, **prop;
2696: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2697: char fileresp[FILENAMELENGTH];
2698:
2699: pp=vector(1,nlstate);
2700: prop=matrix(1,nlstate,iagemin,iagemax+3);
2701: strcpy(fileresp,"p");
2702: strcat(fileresp,fileres);
2703: if((ficresp=fopen(fileresp,"w"))==NULL) {
2704: printf("Problem with prevalence resultfile: %s\n", fileresp);
2705: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2706: exit(0);
2707: }
2708: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2709: j1=0;
2710:
2711: j=cptcoveff;
2712: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2713:
2714: first=1;
2715:
1.169 brouard 2716: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2717: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2718: /* j1++; */
1.145 brouard 2719: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2720: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2721: scanf("%d", i);*/
2722: for (i=-5; i<=nlstate+ndeath; i++)
2723: for (jk=-5; jk<=nlstate+ndeath; jk++)
2724: for(m=iagemin; m <= iagemax+3; m++)
2725: freq[i][jk][m]=0;
1.143 brouard 2726:
2727: for (i=1; i<=nlstate; i++)
2728: for(m=iagemin; m <= iagemax+3; m++)
2729: prop[i][m]=0;
1.126 brouard 2730:
2731: dateintsum=0;
2732: k2cpt=0;
2733: for (i=1; i<=imx; i++) {
2734: bool=1;
1.144 brouard 2735: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2736: for (z1=1; z1<=cptcoveff; z1++)
2737: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2738: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2739: bool=0;
1.145 brouard 2740: /* 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",
2741: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2742: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2743: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2744: }
1.126 brouard 2745: }
1.144 brouard 2746:
1.126 brouard 2747: if (bool==1){
2748: for(m=firstpass; m<=lastpass; m++){
2749: k2=anint[m][i]+(mint[m][i]/12.);
2750: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2751: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2752: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2753: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2754: if (m<lastpass) {
2755: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2756: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2757: }
2758:
2759: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2760: dateintsum=dateintsum+k2;
2761: k2cpt++;
2762: }
2763: /*}*/
2764: }
2765: }
1.145 brouard 2766: } /* end i */
1.126 brouard 2767:
2768: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2769: pstamp(ficresp);
2770: if (cptcovn>0) {
2771: fprintf(ficresp, "\n#********** Variable ");
2772: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2773: fprintf(ficresp, "**********\n#");
1.143 brouard 2774: fprintf(ficlog, "\n#********** Variable ");
2775: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2776: fprintf(ficlog, "**********\n#");
1.126 brouard 2777: }
2778: for(i=1; i<=nlstate;i++)
2779: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2780: fprintf(ficresp, "\n");
2781:
2782: for(i=iagemin; i <= iagemax+3; i++){
2783: if(i==iagemax+3){
2784: fprintf(ficlog,"Total");
2785: }else{
2786: if(first==1){
2787: first=0;
2788: printf("See log file for details...\n");
2789: }
2790: fprintf(ficlog,"Age %d", i);
2791: }
2792: for(jk=1; jk <=nlstate ; jk++){
2793: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2794: pp[jk] += freq[jk][m][i];
2795: }
2796: for(jk=1; jk <=nlstate ; jk++){
2797: for(m=-1, pos=0; m <=0 ; m++)
2798: pos += freq[jk][m][i];
2799: if(pp[jk]>=1.e-10){
2800: if(first==1){
1.132 brouard 2801: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2802: }
2803: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2804: }else{
2805: if(first==1)
2806: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2807: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2808: }
2809: }
2810:
2811: for(jk=1; jk <=nlstate ; jk++){
2812: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2813: pp[jk] += freq[jk][m][i];
2814: }
2815: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2816: pos += pp[jk];
2817: posprop += prop[jk][i];
2818: }
2819: for(jk=1; jk <=nlstate ; jk++){
2820: if(pos>=1.e-5){
2821: if(first==1)
2822: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2823: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2824: }else{
2825: if(first==1)
2826: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2827: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2828: }
2829: if( i <= iagemax){
2830: if(pos>=1.e-5){
2831: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2832: /*probs[i][jk][j1]= pp[jk]/pos;*/
2833: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2834: }
2835: else
2836: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2837: }
2838: }
2839:
2840: for(jk=-1; jk <=nlstate+ndeath; jk++)
2841: for(m=-1; m <=nlstate+ndeath; m++)
2842: if(freq[jk][m][i] !=0 ) {
2843: if(first==1)
2844: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2845: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2846: }
2847: if(i <= iagemax)
2848: fprintf(ficresp,"\n");
2849: if(first==1)
2850: printf("Others in log...\n");
2851: fprintf(ficlog,"\n");
2852: }
1.145 brouard 2853: /*}*/
1.126 brouard 2854: }
2855: dateintmean=dateintsum/k2cpt;
2856:
2857: fclose(ficresp);
2858: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2859: free_vector(pp,1,nlstate);
2860: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2861: /* End of Freq */
2862: }
2863:
2864: /************ Prevalence ********************/
2865: 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)
2866: {
2867: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2868: in each health status at the date of interview (if between dateprev1 and dateprev2).
2869: We still use firstpass and lastpass as another selection.
2870: */
2871:
1.164 brouard 2872: int i, m, jk, j1, bool, z1,j;
2873:
2874: double **prop;
2875: double posprop;
1.126 brouard 2876: double y2; /* in fractional years */
2877: int iagemin, iagemax;
1.145 brouard 2878: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2879:
2880: iagemin= (int) agemin;
2881: iagemax= (int) agemax;
2882: /*pp=vector(1,nlstate);*/
2883: prop=matrix(1,nlstate,iagemin,iagemax+3);
2884: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2885: j1=0;
2886:
1.145 brouard 2887: /*j=cptcoveff;*/
1.126 brouard 2888: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2889:
1.145 brouard 2890: first=1;
2891: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2892: /*for(i1=1; i1<=ncodemax[k1];i1++){
2893: j1++;*/
1.126 brouard 2894:
2895: for (i=1; i<=nlstate; i++)
2896: for(m=iagemin; m <= iagemax+3; m++)
2897: prop[i][m]=0.0;
2898:
2899: for (i=1; i<=imx; i++) { /* Each individual */
2900: bool=1;
2901: if (cptcovn>0) {
2902: for (z1=1; z1<=cptcoveff; z1++)
2903: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2904: bool=0;
2905: }
2906: if (bool==1) {
2907: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2908: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2909: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2910: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2911: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2912: 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);
2913: if (s[m][i]>0 && s[m][i]<=nlstate) {
2914: /*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]]);*/
2915: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2916: prop[s[m][i]][iagemax+3] += weight[i];
2917: }
2918: }
2919: } /* end selection of waves */
2920: }
2921: }
2922: for(i=iagemin; i <= iagemax+3; i++){
2923: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2924: posprop += prop[jk][i];
2925: }
1.145 brouard 2926:
1.126 brouard 2927: for(jk=1; jk <=nlstate ; jk++){
2928: if( i <= iagemax){
2929: if(posprop>=1.e-5){
2930: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2931: } else{
2932: if(first==1){
2933: first=0;
2934: 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]);
2935: }
2936: }
1.126 brouard 2937: }
2938: }/* end jk */
2939: }/* end i */
1.145 brouard 2940: /*} *//* end i1 */
2941: } /* end j1 */
1.126 brouard 2942:
2943: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2944: /*free_vector(pp,1,nlstate);*/
2945: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2946: } /* End of prevalence */
2947:
2948: /************* Waves Concatenation ***************/
2949:
2950: 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)
2951: {
2952: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2953: Death is a valid wave (if date is known).
2954: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2955: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2956: and mw[mi+1][i]. dh depends on stepm.
2957: */
2958:
2959: int i, mi, m;
2960: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2961: double sum=0., jmean=0.;*/
2962: int first;
2963: int j, k=0,jk, ju, jl;
2964: double sum=0.;
2965: first=0;
1.164 brouard 2966: jmin=100000;
1.126 brouard 2967: jmax=-1;
2968: jmean=0.;
2969: for(i=1; i<=imx; i++){
2970: mi=0;
2971: m=firstpass;
2972: while(s[m][i] <= nlstate){
2973: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2974: mw[++mi][i]=m;
2975: if(m >=lastpass)
2976: break;
2977: else
2978: m++;
2979: }/* end while */
2980: if (s[m][i] > nlstate){
2981: mi++; /* Death is another wave */
2982: /* if(mi==0) never been interviewed correctly before death */
2983: /* Only death is a correct wave */
2984: mw[mi][i]=m;
2985: }
2986:
2987: wav[i]=mi;
2988: if(mi==0){
2989: nbwarn++;
2990: if(first==0){
2991: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2992: first=1;
2993: }
2994: if(first==1){
2995: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2996: }
2997: } /* end mi==0 */
2998: } /* End individuals */
2999:
3000: for(i=1; i<=imx; i++){
3001: for(mi=1; mi<wav[i];mi++){
3002: if (stepm <=0)
3003: dh[mi][i]=1;
3004: else{
3005: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3006: if (agedc[i] < 2*AGESUP) {
3007: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3008: if(j==0) j=1; /* Survives at least one month after exam */
3009: else if(j<0){
3010: nberr++;
3011: 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]);
3012: j=1; /* Temporary Dangerous patch */
3013: 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);
3014: 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]);
3015: 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);
3016: }
3017: k=k+1;
3018: if (j >= jmax){
3019: jmax=j;
3020: ijmax=i;
3021: }
3022: if (j <= jmin){
3023: jmin=j;
3024: ijmin=i;
3025: }
3026: sum=sum+j;
3027: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3028: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3029: }
3030: }
3031: else{
3032: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3033: /* 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]); */
3034:
3035: k=k+1;
3036: if (j >= jmax) {
3037: jmax=j;
3038: ijmax=i;
3039: }
3040: else if (j <= jmin){
3041: jmin=j;
3042: ijmin=i;
3043: }
3044: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3045: /*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]);*/
3046: if(j<0){
3047: nberr++;
3048: 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]);
3049: 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]);
3050: }
3051: sum=sum+j;
3052: }
3053: jk= j/stepm;
3054: jl= j -jk*stepm;
3055: ju= j -(jk+1)*stepm;
3056: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3057: if(jl==0){
3058: dh[mi][i]=jk;
3059: bh[mi][i]=0;
3060: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3061: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3062: dh[mi][i]=jk+1;
3063: bh[mi][i]=ju;
3064: }
3065: }else{
3066: if(jl <= -ju){
3067: dh[mi][i]=jk;
3068: bh[mi][i]=jl; /* bias is positive if real duration
3069: * is higher than the multiple of stepm and negative otherwise.
3070: */
3071: }
3072: else{
3073: dh[mi][i]=jk+1;
3074: bh[mi][i]=ju;
3075: }
3076: if(dh[mi][i]==0){
3077: dh[mi][i]=1; /* At least one step */
3078: bh[mi][i]=ju; /* At least one step */
3079: /* 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);*/
3080: }
3081: } /* end if mle */
3082: }
3083: } /* end wave */
3084: }
3085: jmean=sum/k;
3086: 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 3087: 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 3088: }
3089:
3090: /*********** Tricode ****************************/
1.145 brouard 3091: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3092: {
1.144 brouard 3093: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3094: /* 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 3095: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3096: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3097: * nbcode[Tvar[j]][1]=
1.144 brouard 3098: */
1.130 brouard 3099:
1.145 brouard 3100: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3101: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3102: int cptcode=0; /* Modality max of covariates j */
3103: int modmincovj=0; /* Modality min of covariates j */
3104:
3105:
1.126 brouard 3106: cptcoveff=0;
3107:
1.145 brouard 3108: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 3109: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3110:
1.145 brouard 3111: /* Loop on covariates without age and products */
1.186 ! brouard 3112: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
! 3113: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3114: modality of this covariate Vj*/
1.145 brouard 3115: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3116: * If product of Vn*Vm, still boolean *:
3117: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3118: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3119: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3120: modality of the nth covariate of individual i. */
1.145 brouard 3121: if (ij > modmaxcovj)
3122: modmaxcovj=ij;
3123: else if (ij < modmincovj)
3124: modmincovj=ij;
3125: if ((ij < -1) && (ij > NCOVMAX)){
3126: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3127: exit(1);
3128: }else
1.136 brouard 3129: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3130: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3131: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3132: /* getting the maximum value of the modality of the covariate
3133: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3134: female is 1, then modmaxcovj=1.*/
1.126 brouard 3135: }
1.145 brouard 3136: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3137: cptcode=modmaxcovj;
1.137 brouard 3138: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3139: /*for (i=0; i<=cptcode; i++) {*/
3140: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3141: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3142: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3143: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3144: }
3145: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3146: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3147: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3148:
1.136 brouard 3149: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 ! brouard 3150: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
! 3151: 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 3152: modmincovj=3; modmaxcovj = 7;
1.186 ! brouard 3153: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
! 3154: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
! 3155: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3156: nbcode[Tvar[j]][ij]=k;
3157: nbcode[Tvar[j]][1]=0;
3158: nbcode[Tvar[j]][2]=1;
3159: nbcode[Tvar[j]][3]=2;
3160: */
3161: ij=1; /* ij is similar to i but can jumps over null modalities */
3162: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3163: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3164: /*recode from 0 */
1.131 brouard 3165: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
1.186 ! brouard 3166: nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
1.131 brouard 3167: k is a modality. If we have model=V1+V1*sex
3168: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3169: ij++;
3170: }
3171: if (ij > ncodemax[j]) break;
1.137 brouard 3172: } /* end of loop on */
3173: } /* end of loop on modality */
3174: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3175:
1.145 brouard 3176: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3177:
1.145 brouard 3178: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3179: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3180: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3181: Ndum[ij]++;
3182: }
1.126 brouard 3183:
3184: ij=1;
1.145 brouard 3185: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3186: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3187: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3188: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3189: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3190: ij++;
1.145 brouard 3191: }else
3192: Tvaraff[ij]=0;
1.126 brouard 3193: }
1.131 brouard 3194: ij--;
1.144 brouard 3195: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3196:
1.126 brouard 3197: }
3198:
1.145 brouard 3199:
1.126 brouard 3200: /*********** Health Expectancies ****************/
3201:
1.127 brouard 3202: 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 3203:
3204: {
3205: /* Health expectancies, no variances */
1.164 brouard 3206: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3207: int nhstepma, nstepma; /* Decreasing with age */
3208: double age, agelim, hf;
3209: double ***p3mat;
3210: double eip;
3211:
3212: pstamp(ficreseij);
3213: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3214: fprintf(ficreseij,"# Age");
3215: for(i=1; i<=nlstate;i++){
3216: for(j=1; j<=nlstate;j++){
3217: fprintf(ficreseij," e%1d%1d ",i,j);
3218: }
3219: fprintf(ficreseij," e%1d. ",i);
3220: }
3221: fprintf(ficreseij,"\n");
3222:
3223:
3224: if(estepm < stepm){
3225: printf ("Problem %d lower than %d\n",estepm, stepm);
3226: }
3227: else hstepm=estepm;
3228: /* We compute the life expectancy from trapezoids spaced every estepm months
3229: * This is mainly to measure the difference between two models: for example
3230: * if stepm=24 months pijx are given only every 2 years and by summing them
3231: * we are calculating an estimate of the Life Expectancy assuming a linear
3232: * progression in between and thus overestimating or underestimating according
3233: * to the curvature of the survival function. If, for the same date, we
3234: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3235: * to compare the new estimate of Life expectancy with the same linear
3236: * hypothesis. A more precise result, taking into account a more precise
3237: * curvature will be obtained if estepm is as small as stepm. */
3238:
3239: /* For example we decided to compute the life expectancy with the smallest unit */
3240: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3241: nhstepm is the number of hstepm from age to agelim
3242: nstepm is the number of stepm from age to agelin.
3243: Look at hpijx to understand the reason of that which relies in memory size
3244: and note for a fixed period like estepm months */
3245: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3246: survival function given by stepm (the optimization length). Unfortunately it
3247: means that if the survival funtion is printed only each two years of age and if
3248: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3249: results. So we changed our mind and took the option of the best precision.
3250: */
3251: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3252:
3253: agelim=AGESUP;
3254: /* If stepm=6 months */
3255: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3256: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3257:
3258: /* nhstepm age range expressed in number of stepm */
3259: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3260: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3261: /* if (stepm >= YEARM) hstepm=1;*/
3262: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3263: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3264:
3265: for (age=bage; age<=fage; age ++){
3266: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3267: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3268: /* if (stepm >= YEARM) hstepm=1;*/
3269: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3270:
3271: /* If stepm=6 months */
3272: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3273: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3274:
3275: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3276:
3277: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3278:
3279: printf("%d|",(int)age);fflush(stdout);
3280: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3281:
3282: /* Computing expectancies */
3283: for(i=1; i<=nlstate;i++)
3284: for(j=1; j<=nlstate;j++)
3285: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3286: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3287:
3288: /* 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]);*/
3289:
3290: }
3291:
3292: fprintf(ficreseij,"%3.0f",age );
3293: for(i=1; i<=nlstate;i++){
3294: eip=0;
3295: for(j=1; j<=nlstate;j++){
3296: eip +=eij[i][j][(int)age];
3297: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3298: }
3299: fprintf(ficreseij,"%9.4f", eip );
3300: }
3301: fprintf(ficreseij,"\n");
3302:
3303: }
3304: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3305: printf("\n");
3306: fprintf(ficlog,"\n");
3307:
3308: }
3309:
1.127 brouard 3310: 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 3311:
3312: {
3313: /* Covariances of health expectancies eij and of total life expectancies according
3314: to initial status i, ei. .
3315: */
3316: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3317: int nhstepma, nstepma; /* Decreasing with age */
3318: double age, agelim, hf;
3319: double ***p3matp, ***p3matm, ***varhe;
3320: double **dnewm,**doldm;
3321: double *xp, *xm;
3322: double **gp, **gm;
3323: double ***gradg, ***trgradg;
3324: int theta;
3325:
3326: double eip, vip;
3327:
3328: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3329: xp=vector(1,npar);
3330: xm=vector(1,npar);
3331: dnewm=matrix(1,nlstate*nlstate,1,npar);
3332: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3333:
3334: pstamp(ficresstdeij);
3335: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3336: fprintf(ficresstdeij,"# Age");
3337: for(i=1; i<=nlstate;i++){
3338: for(j=1; j<=nlstate;j++)
3339: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3340: fprintf(ficresstdeij," e%1d. ",i);
3341: }
3342: fprintf(ficresstdeij,"\n");
3343:
3344: pstamp(ficrescveij);
3345: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3346: fprintf(ficrescveij,"# Age");
3347: for(i=1; i<=nlstate;i++)
3348: for(j=1; j<=nlstate;j++){
3349: cptj= (j-1)*nlstate+i;
3350: for(i2=1; i2<=nlstate;i2++)
3351: for(j2=1; j2<=nlstate;j2++){
3352: cptj2= (j2-1)*nlstate+i2;
3353: if(cptj2 <= cptj)
3354: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3355: }
3356: }
3357: fprintf(ficrescveij,"\n");
3358:
3359: if(estepm < stepm){
3360: printf ("Problem %d lower than %d\n",estepm, stepm);
3361: }
3362: else hstepm=estepm;
3363: /* We compute the life expectancy from trapezoids spaced every estepm months
3364: * This is mainly to measure the difference between two models: for example
3365: * if stepm=24 months pijx are given only every 2 years and by summing them
3366: * we are calculating an estimate of the Life Expectancy assuming a linear
3367: * progression in between and thus overestimating or underestimating according
3368: * to the curvature of the survival function. If, for the same date, we
3369: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3370: * to compare the new estimate of Life expectancy with the same linear
3371: * hypothesis. A more precise result, taking into account a more precise
3372: * curvature will be obtained if estepm is as small as stepm. */
3373:
3374: /* For example we decided to compute the life expectancy with the smallest unit */
3375: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3376: nhstepm is the number of hstepm from age to agelim
3377: nstepm is the number of stepm from age to agelin.
3378: Look at hpijx to understand the reason of that which relies in memory size
3379: and note for a fixed period like estepm months */
3380: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3381: survival function given by stepm (the optimization length). Unfortunately it
3382: means that if the survival funtion is printed only each two years of age and if
3383: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3384: results. So we changed our mind and took the option of the best precision.
3385: */
3386: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3387:
3388: /* If stepm=6 months */
3389: /* nhstepm age range expressed in number of stepm */
3390: agelim=AGESUP;
3391: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3392: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3393: /* if (stepm >= YEARM) hstepm=1;*/
3394: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3395:
3396: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3397: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3398: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3399: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3400: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3401: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3402:
3403: for (age=bage; age<=fage; age ++){
3404: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3405: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3406: /* if (stepm >= YEARM) hstepm=1;*/
3407: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3408:
3409: /* If stepm=6 months */
3410: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3411: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3412:
3413: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3414:
3415: /* Computing Variances of health expectancies */
3416: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3417: decrease memory allocation */
3418: for(theta=1; theta <=npar; theta++){
3419: for(i=1; i<=npar; i++){
3420: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3421: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3422: }
3423: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3424: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3425:
3426: for(j=1; j<= nlstate; j++){
3427: for(i=1; i<=nlstate; i++){
3428: for(h=0; h<=nhstepm-1; h++){
3429: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3430: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3431: }
3432: }
3433: }
3434:
3435: for(ij=1; ij<= nlstate*nlstate; ij++)
3436: for(h=0; h<=nhstepm-1; h++){
3437: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3438: }
3439: }/* End theta */
3440:
3441:
3442: for(h=0; h<=nhstepm-1; h++)
3443: for(j=1; j<=nlstate*nlstate;j++)
3444: for(theta=1; theta <=npar; theta++)
3445: trgradg[h][j][theta]=gradg[h][theta][j];
3446:
3447:
3448: for(ij=1;ij<=nlstate*nlstate;ij++)
3449: for(ji=1;ji<=nlstate*nlstate;ji++)
3450: varhe[ij][ji][(int)age] =0.;
3451:
3452: printf("%d|",(int)age);fflush(stdout);
3453: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3454: for(h=0;h<=nhstepm-1;h++){
3455: for(k=0;k<=nhstepm-1;k++){
3456: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3457: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3458: for(ij=1;ij<=nlstate*nlstate;ij++)
3459: for(ji=1;ji<=nlstate*nlstate;ji++)
3460: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3461: }
3462: }
3463:
3464: /* Computing expectancies */
3465: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3466: for(i=1; i<=nlstate;i++)
3467: for(j=1; j<=nlstate;j++)
3468: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3469: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3470:
3471: /* 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]);*/
3472:
3473: }
3474:
3475: fprintf(ficresstdeij,"%3.0f",age );
3476: for(i=1; i<=nlstate;i++){
3477: eip=0.;
3478: vip=0.;
3479: for(j=1; j<=nlstate;j++){
3480: eip += eij[i][j][(int)age];
3481: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3482: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3483: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3484: }
3485: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3486: }
3487: fprintf(ficresstdeij,"\n");
3488:
3489: fprintf(ficrescveij,"%3.0f",age );
3490: for(i=1; i<=nlstate;i++)
3491: for(j=1; j<=nlstate;j++){
3492: cptj= (j-1)*nlstate+i;
3493: for(i2=1; i2<=nlstate;i2++)
3494: for(j2=1; j2<=nlstate;j2++){
3495: cptj2= (j2-1)*nlstate+i2;
3496: if(cptj2 <= cptj)
3497: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3498: }
3499: }
3500: fprintf(ficrescveij,"\n");
3501:
3502: }
3503: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3504: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3505: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3506: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3507: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3508: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3509: printf("\n");
3510: fprintf(ficlog,"\n");
3511:
3512: free_vector(xm,1,npar);
3513: free_vector(xp,1,npar);
3514: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3515: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3516: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3517: }
3518:
3519: /************ Variance ******************/
3520: 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[])
3521: {
3522: /* Variance of health expectancies */
3523: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3524: /* double **newm;*/
1.169 brouard 3525: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3526:
3527: int movingaverage();
1.126 brouard 3528: double **dnewm,**doldm;
3529: double **dnewmp,**doldmp;
3530: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3531: int k;
1.126 brouard 3532: double *xp;
3533: double **gp, **gm; /* for var eij */
3534: double ***gradg, ***trgradg; /*for var eij */
3535: double **gradgp, **trgradgp; /* for var p point j */
3536: double *gpp, *gmp; /* for var p point j */
3537: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3538: double ***p3mat;
3539: double age,agelim, hf;
3540: double ***mobaverage;
3541: int theta;
3542: char digit[4];
3543: char digitp[25];
3544:
3545: char fileresprobmorprev[FILENAMELENGTH];
3546:
3547: if(popbased==1){
3548: if(mobilav!=0)
3549: strcpy(digitp,"-populbased-mobilav-");
3550: else strcpy(digitp,"-populbased-nomobil-");
3551: }
3552: else
3553: strcpy(digitp,"-stablbased-");
3554:
3555: if (mobilav!=0) {
3556: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3557: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3558: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3559: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3560: }
3561: }
3562:
3563: strcpy(fileresprobmorprev,"prmorprev");
3564: sprintf(digit,"%-d",ij);
3565: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3566: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3567: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3568: strcat(fileresprobmorprev,fileres);
3569: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3570: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3571: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3572: }
3573: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3574:
3575: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3576: pstamp(ficresprobmorprev);
3577: 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);
3578: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3579: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3580: fprintf(ficresprobmorprev," p.%-d SE",j);
3581: for(i=1; i<=nlstate;i++)
3582: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3583: }
3584: fprintf(ficresprobmorprev,"\n");
3585: fprintf(ficgp,"\n# Routine varevsij");
3586: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3587: 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");
3588: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3589: /* } */
3590: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3591: pstamp(ficresvij);
3592: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3593: if(popbased==1)
1.128 brouard 3594: 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 3595: else
3596: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3597: fprintf(ficresvij,"# Age");
3598: for(i=1; i<=nlstate;i++)
3599: for(j=1; j<=nlstate;j++)
3600: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3601: fprintf(ficresvij,"\n");
3602:
3603: xp=vector(1,npar);
3604: dnewm=matrix(1,nlstate,1,npar);
3605: doldm=matrix(1,nlstate,1,nlstate);
3606: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3607: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3608:
3609: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3610: gpp=vector(nlstate+1,nlstate+ndeath);
3611: gmp=vector(nlstate+1,nlstate+ndeath);
3612: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3613:
3614: if(estepm < stepm){
3615: printf ("Problem %d lower than %d\n",estepm, stepm);
3616: }
3617: else hstepm=estepm;
3618: /* For example we decided to compute the life expectancy with the smallest unit */
3619: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3620: nhstepm is the number of hstepm from age to agelim
3621: nstepm is the number of stepm from age to agelin.
1.128 brouard 3622: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3623: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3624: survival function given by stepm (the optimization length). Unfortunately it
3625: means that if the survival funtion is printed every two years of age and if
3626: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3627: results. So we changed our mind and took the option of the best precision.
3628: */
3629: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3630: agelim = AGESUP;
3631: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3632: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3633: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3634: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3635: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3636: gp=matrix(0,nhstepm,1,nlstate);
3637: gm=matrix(0,nhstepm,1,nlstate);
3638:
3639:
3640: for(theta=1; theta <=npar; theta++){
3641: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3642: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3643: }
3644: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3645: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3646:
3647: if (popbased==1) {
3648: if(mobilav ==0){
3649: for(i=1; i<=nlstate;i++)
3650: prlim[i][i]=probs[(int)age][i][ij];
3651: }else{ /* mobilav */
3652: for(i=1; i<=nlstate;i++)
3653: prlim[i][i]=mobaverage[(int)age][i][ij];
3654: }
3655: }
3656:
3657: for(j=1; j<= nlstate; j++){
3658: for(h=0; h<=nhstepm; h++){
3659: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3660: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3661: }
3662: }
3663: /* This for computing probability of death (h=1 means
3664: computed over hstepm matrices product = hstepm*stepm months)
3665: as a weighted average of prlim.
3666: */
3667: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3668: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3669: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3670: }
3671: /* end probability of death */
3672:
3673: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3674: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3675: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3676: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3677:
3678: if (popbased==1) {
3679: if(mobilav ==0){
3680: for(i=1; i<=nlstate;i++)
3681: prlim[i][i]=probs[(int)age][i][ij];
3682: }else{ /* mobilav */
3683: for(i=1; i<=nlstate;i++)
3684: prlim[i][i]=mobaverage[(int)age][i][ij];
3685: }
3686: }
3687:
1.128 brouard 3688: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3689: for(h=0; h<=nhstepm; h++){
3690: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3691: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3692: }
3693: }
3694: /* This for computing probability of death (h=1 means
3695: computed over hstepm matrices product = hstepm*stepm months)
3696: as a weighted average of prlim.
3697: */
3698: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3699: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3700: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3701: }
3702: /* end probability of death */
3703:
3704: for(j=1; j<= nlstate; j++) /* vareij */
3705: for(h=0; h<=nhstepm; h++){
3706: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3707: }
3708:
3709: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3710: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3711: }
3712:
3713: } /* End theta */
3714:
3715: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3716:
3717: for(h=0; h<=nhstepm; h++) /* veij */
3718: for(j=1; j<=nlstate;j++)
3719: for(theta=1; theta <=npar; theta++)
3720: trgradg[h][j][theta]=gradg[h][theta][j];
3721:
3722: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3723: for(theta=1; theta <=npar; theta++)
3724: trgradgp[j][theta]=gradgp[theta][j];
3725:
3726:
3727: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3728: for(i=1;i<=nlstate;i++)
3729: for(j=1;j<=nlstate;j++)
3730: vareij[i][j][(int)age] =0.;
3731:
3732: for(h=0;h<=nhstepm;h++){
3733: for(k=0;k<=nhstepm;k++){
3734: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3735: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3736: for(i=1;i<=nlstate;i++)
3737: for(j=1;j<=nlstate;j++)
3738: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3739: }
3740: }
3741:
3742: /* pptj */
3743: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3744: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3745: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3746: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3747: varppt[j][i]=doldmp[j][i];
3748: /* end ppptj */
3749: /* x centered again */
3750: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3751: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3752:
3753: if (popbased==1) {
3754: if(mobilav ==0){
3755: for(i=1; i<=nlstate;i++)
3756: prlim[i][i]=probs[(int)age][i][ij];
3757: }else{ /* mobilav */
3758: for(i=1; i<=nlstate;i++)
3759: prlim[i][i]=mobaverage[(int)age][i][ij];
3760: }
3761: }
3762:
3763: /* This for computing probability of death (h=1 means
3764: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3765: as a weighted average of prlim.
3766: */
3767: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3768: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3769: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3770: }
3771: /* end probability of death */
3772:
3773: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3774: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3775: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3776: for(i=1; i<=nlstate;i++){
3777: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3778: }
3779: }
3780: fprintf(ficresprobmorprev,"\n");
3781:
3782: fprintf(ficresvij,"%.0f ",age );
3783: for(i=1; i<=nlstate;i++)
3784: for(j=1; j<=nlstate;j++){
3785: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3786: }
3787: fprintf(ficresvij,"\n");
3788: free_matrix(gp,0,nhstepm,1,nlstate);
3789: free_matrix(gm,0,nhstepm,1,nlstate);
3790: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3791: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3792: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3793: } /* End age */
3794: free_vector(gpp,nlstate+1,nlstate+ndeath);
3795: free_vector(gmp,nlstate+1,nlstate+ndeath);
3796: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3797: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3798: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3799: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3800: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3801: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3802: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3803: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3804: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3805: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3806: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3807: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3808: 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);
3809: /* 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);
3810: */
3811: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3812: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3813:
3814: free_vector(xp,1,npar);
3815: free_matrix(doldm,1,nlstate,1,nlstate);
3816: free_matrix(dnewm,1,nlstate,1,npar);
3817: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3818: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3819: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3820: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3821: fclose(ficresprobmorprev);
3822: fflush(ficgp);
3823: fflush(fichtm);
3824: } /* end varevsij */
3825:
3826: /************ Variance of prevlim ******************/
3827: 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[])
3828: {
3829: /* Variance of prevalence limit */
3830: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3831:
1.126 brouard 3832: double **dnewm,**doldm;
3833: int i, j, nhstepm, hstepm;
3834: double *xp;
3835: double *gp, *gm;
3836: double **gradg, **trgradg;
3837: double age,agelim;
3838: int theta;
3839:
3840: pstamp(ficresvpl);
3841: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3842: fprintf(ficresvpl,"# Age");
3843: for(i=1; i<=nlstate;i++)
3844: fprintf(ficresvpl," %1d-%1d",i,i);
3845: fprintf(ficresvpl,"\n");
3846:
3847: xp=vector(1,npar);
3848: dnewm=matrix(1,nlstate,1,npar);
3849: doldm=matrix(1,nlstate,1,nlstate);
3850:
3851: hstepm=1*YEARM; /* Every year of age */
3852: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3853: agelim = AGESUP;
3854: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3855: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3856: if (stepm >= YEARM) hstepm=1;
3857: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3858: gradg=matrix(1,npar,1,nlstate);
3859: gp=vector(1,nlstate);
3860: gm=vector(1,nlstate);
3861:
3862: for(theta=1; theta <=npar; theta++){
3863: for(i=1; i<=npar; i++){ /* Computes gradient */
3864: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3865: }
3866: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3867: for(i=1;i<=nlstate;i++)
3868: gp[i] = prlim[i][i];
3869:
3870: for(i=1; i<=npar; i++) /* Computes gradient */
3871: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3872: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3873: for(i=1;i<=nlstate;i++)
3874: gm[i] = prlim[i][i];
3875:
3876: for(i=1;i<=nlstate;i++)
3877: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3878: } /* End theta */
3879:
3880: trgradg =matrix(1,nlstate,1,npar);
3881:
3882: for(j=1; j<=nlstate;j++)
3883: for(theta=1; theta <=npar; theta++)
3884: trgradg[j][theta]=gradg[theta][j];
3885:
3886: for(i=1;i<=nlstate;i++)
3887: varpl[i][(int)age] =0.;
3888: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3889: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3890: for(i=1;i<=nlstate;i++)
3891: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3892:
3893: fprintf(ficresvpl,"%.0f ",age );
3894: for(i=1; i<=nlstate;i++)
3895: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3896: fprintf(ficresvpl,"\n");
3897: free_vector(gp,1,nlstate);
3898: free_vector(gm,1,nlstate);
3899: free_matrix(gradg,1,npar,1,nlstate);
3900: free_matrix(trgradg,1,nlstate,1,npar);
3901: } /* End age */
3902:
3903: free_vector(xp,1,npar);
3904: free_matrix(doldm,1,nlstate,1,npar);
3905: free_matrix(dnewm,1,nlstate,1,nlstate);
3906:
3907: }
3908:
3909: /************ Variance of one-step probabilities ******************/
3910: 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[])
3911: {
1.164 brouard 3912: int i, j=0, k1, l1, tj;
1.126 brouard 3913: int k2, l2, j1, z1;
1.164 brouard 3914: int k=0, l;
1.145 brouard 3915: int first=1, first1, first2;
1.126 brouard 3916: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3917: double **dnewm,**doldm;
3918: double *xp;
3919: double *gp, *gm;
3920: double **gradg, **trgradg;
3921: double **mu;
1.164 brouard 3922: double age, cov[NCOVMAX+1];
1.126 brouard 3923: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3924: int theta;
3925: char fileresprob[FILENAMELENGTH];
3926: char fileresprobcov[FILENAMELENGTH];
3927: char fileresprobcor[FILENAMELENGTH];
3928: double ***varpij;
3929:
3930: strcpy(fileresprob,"prob");
3931: strcat(fileresprob,fileres);
3932: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3933: printf("Problem with resultfile: %s\n", fileresprob);
3934: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3935: }
3936: strcpy(fileresprobcov,"probcov");
3937: strcat(fileresprobcov,fileres);
3938: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3939: printf("Problem with resultfile: %s\n", fileresprobcov);
3940: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3941: }
3942: strcpy(fileresprobcor,"probcor");
3943: strcat(fileresprobcor,fileres);
3944: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3945: printf("Problem with resultfile: %s\n", fileresprobcor);
3946: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3947: }
3948: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3949: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3950: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3951: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3952: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3953: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3954: pstamp(ficresprob);
3955: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3956: fprintf(ficresprob,"# Age");
3957: pstamp(ficresprobcov);
3958: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3959: fprintf(ficresprobcov,"# Age");
3960: pstamp(ficresprobcor);
3961: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3962: fprintf(ficresprobcor,"# Age");
3963:
3964:
3965: for(i=1; i<=nlstate;i++)
3966: for(j=1; j<=(nlstate+ndeath);j++){
3967: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3968: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3969: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3970: }
3971: /* fprintf(ficresprob,"\n");
3972: fprintf(ficresprobcov,"\n");
3973: fprintf(ficresprobcor,"\n");
3974: */
1.131 brouard 3975: xp=vector(1,npar);
1.126 brouard 3976: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3977: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3978: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3979: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3980: first=1;
3981: fprintf(ficgp,"\n# Routine varprob");
3982: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3983: fprintf(fichtm,"\n");
3984:
3985: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3986: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3987: file %s<br>\n",optionfilehtmcov);
3988: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3989: and drawn. It helps understanding how is the covariance between two incidences.\
3990: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3991: 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. \
3992: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3993: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3994: standard deviations wide on each axis. <br>\
3995: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3996: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3997: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3998:
3999: cov[1]=1;
1.145 brouard 4000: /* tj=cptcoveff; */
4001: tj = (int) pow(2,cptcoveff);
1.126 brouard 4002: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4003: j1=0;
1.145 brouard 4004: for(j1=1; j1<=tj;j1++){
4005: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4006: /*j1++;*/
1.126 brouard 4007: if (cptcovn>0) {
4008: fprintf(ficresprob, "\n#********** Variable ");
4009: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4010: fprintf(ficresprob, "**********\n#\n");
4011: fprintf(ficresprobcov, "\n#********** Variable ");
4012: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4013: fprintf(ficresprobcov, "**********\n#\n");
4014:
4015: fprintf(ficgp, "\n#********** Variable ");
4016: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4017: fprintf(ficgp, "**********\n#\n");
4018:
4019:
4020: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4021: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4022: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4023:
4024: fprintf(ficresprobcor, "\n#********** Variable ");
4025: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4026: fprintf(ficresprobcor, "**********\n#");
4027: }
4028:
1.145 brouard 4029: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4030: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4031: gp=vector(1,(nlstate)*(nlstate+ndeath));
4032: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4033: for (age=bage; age<=fage; age ++){
4034: cov[2]=age;
4035: for (k=1; k<=cptcovn;k++) {
1.145 brouard 4036: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4037: * 1 1 1 1 1
4038: * 2 2 1 1 1
4039: * 3 1 2 1 1
4040: */
4041: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4042: }
1.186 ! brouard 4043: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 4044: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4045: for (k=1; k<=cptcovprod;k++)
4046: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4047:
4048:
4049: for(theta=1; theta <=npar; theta++){
4050: for(i=1; i<=npar; i++)
4051: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4052:
4053: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4054:
4055: k=0;
4056: for(i=1; i<= (nlstate); i++){
4057: for(j=1; j<=(nlstate+ndeath);j++){
4058: k=k+1;
4059: gp[k]=pmmij[i][j];
4060: }
4061: }
4062:
4063: for(i=1; i<=npar; i++)
4064: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4065:
4066: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4067: k=0;
4068: for(i=1; i<=(nlstate); i++){
4069: for(j=1; j<=(nlstate+ndeath);j++){
4070: k=k+1;
4071: gm[k]=pmmij[i][j];
4072: }
4073: }
4074:
4075: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4076: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4077: }
4078:
4079: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4080: for(theta=1; theta <=npar; theta++)
4081: trgradg[j][theta]=gradg[theta][j];
4082:
4083: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4084: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4085:
4086: pmij(pmmij,cov,ncovmodel,x,nlstate);
4087:
4088: k=0;
4089: for(i=1; i<=(nlstate); i++){
4090: for(j=1; j<=(nlstate+ndeath);j++){
4091: k=k+1;
4092: mu[k][(int) age]=pmmij[i][j];
4093: }
4094: }
4095: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4096: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4097: varpij[i][j][(int)age] = doldm[i][j];
4098:
4099: /*printf("\n%d ",(int)age);
4100: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4101: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4102: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4103: }*/
4104:
4105: fprintf(ficresprob,"\n%d ",(int)age);
4106: fprintf(ficresprobcov,"\n%d ",(int)age);
4107: fprintf(ficresprobcor,"\n%d ",(int)age);
4108:
4109: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4110: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4111: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4112: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4113: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4114: }
4115: i=0;
4116: for (k=1; k<=(nlstate);k++){
4117: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4118: i++;
1.126 brouard 4119: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4120: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4121: for (j=1; j<=i;j++){
1.145 brouard 4122: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4123: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4124: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4125: }
4126: }
4127: }/* end of loop for state */
4128: } /* end of loop for age */
1.145 brouard 4129: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4130: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4131: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4132: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4133:
1.126 brouard 4134: /* Confidence intervalle of pij */
4135: /*
1.131 brouard 4136: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4137: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4138: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4139: 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);
4140: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4141: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4142: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4143: */
4144:
4145: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4146: first1=1;first2=2;
1.126 brouard 4147: for (k2=1; k2<=(nlstate);k2++){
4148: for (l2=1; l2<=(nlstate+ndeath);l2++){
4149: if(l2==k2) continue;
4150: j=(k2-1)*(nlstate+ndeath)+l2;
4151: for (k1=1; k1<=(nlstate);k1++){
4152: for (l1=1; l1<=(nlstate+ndeath);l1++){
4153: if(l1==k1) continue;
4154: i=(k1-1)*(nlstate+ndeath)+l1;
4155: if(i<=j) continue;
4156: for (age=bage; age<=fage; age ++){
4157: if ((int)age %5==0){
4158: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4159: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4160: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4161: mu1=mu[i][(int) age]/stepm*YEARM ;
4162: mu2=mu[j][(int) age]/stepm*YEARM;
4163: c12=cv12/sqrt(v1*v2);
4164: /* Computing eigen value of matrix of covariance */
4165: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4166: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4167: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4168: if(first2==1){
4169: first1=0;
4170: 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);
4171: }
4172: 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);
4173: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4174: /* lc2=fabs(lc2); */
1.135 brouard 4175: }
4176:
1.126 brouard 4177: /* Eigen vectors */
4178: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4179: /*v21=sqrt(1.-v11*v11); *//* error */
4180: v21=(lc1-v1)/cv12*v11;
4181: v12=-v21;
4182: v22=v11;
4183: tnalp=v21/v11;
4184: if(first1==1){
4185: first1=0;
4186: 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);
4187: }
4188: 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);
4189: /*printf(fignu*/
4190: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4191: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4192: if(first==1){
4193: first=0;
4194: fprintf(ficgp,"\nset parametric;unset label");
4195: 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 4196: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4197: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4198: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4199: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4200: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4201: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4202: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4203: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4204: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4205: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4206: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4207: 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",\
4208: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4209: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4210: }else{
4211: first=0;
4212: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4213: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4214: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4215: 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",\
4216: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4217: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4218: }/* if first */
4219: } /* age mod 5 */
4220: } /* end loop age */
4221: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4222: first=1;
4223: } /*l12 */
4224: } /* k12 */
4225: } /*l1 */
4226: }/* k1 */
1.169 brouard 4227: /* } */ /* loop covariates */
1.126 brouard 4228: }
4229: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4230: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4231: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4232: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4233: free_vector(xp,1,npar);
4234: fclose(ficresprob);
4235: fclose(ficresprobcov);
4236: fclose(ficresprobcor);
4237: fflush(ficgp);
4238: fflush(fichtmcov);
4239: }
4240:
4241:
4242: /******************* Printing html file ***********/
4243: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4244: int lastpass, int stepm, int weightopt, char model[],\
4245: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4246: int popforecast, int estepm ,\
4247: double jprev1, double mprev1,double anprev1, \
4248: double jprev2, double mprev2,double anprev2){
4249: int jj1, k1, i1, cpt;
4250:
4251: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4252: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4253: </ul>");
4254: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4255: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4256: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4257: fprintf(fichtm,"\
4258: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4259: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4260: fprintf(fichtm,"\
4261: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4262: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4263: fprintf(fichtm,"\
1.128 brouard 4264: - (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 4265: <a href=\"%s\">%s</a> <br>\n",
4266: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4267: fprintf(fichtm,"\
4268: - Population projections by age and states: \
4269: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4270:
4271: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4272:
1.145 brouard 4273: m=pow(2,cptcoveff);
1.126 brouard 4274: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4275:
4276: jj1=0;
4277: for(k1=1; k1<=m;k1++){
4278: for(i1=1; i1<=ncodemax[k1];i1++){
4279: jj1++;
4280: if (cptcovn > 0) {
4281: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4282: for (cpt=1; cpt<=cptcoveff;cpt++)
4283: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4284: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4285: }
4286: /* Pij */
1.145 brouard 4287: 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> \
4288: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4289: /* Quasi-incidences */
4290: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4291: 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> \
4292: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4293: /* Period (stable) prevalence in each health state */
1.154 brouard 4294: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4295: 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> \
4296: <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 4297: }
4298: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4299: 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> \
4300: <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 4301: }
4302: } /* end i1 */
4303: }/* End k1 */
4304: fprintf(fichtm,"</ul>");
4305:
4306:
4307: fprintf(fichtm,"\
4308: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4309: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4310:
4311: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4312: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4313: fprintf(fichtm,"\
4314: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4315: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4316:
4317: fprintf(fichtm,"\
4318: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4319: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4320: fprintf(fichtm,"\
4321: - 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): \
4322: <a href=\"%s\">%s</a> <br>\n</li>",
4323: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4324: fprintf(fichtm,"\
4325: - (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): \
4326: <a href=\"%s\">%s</a> <br>\n</li>",
4327: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4328: fprintf(fichtm,"\
1.128 brouard 4329: - 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 4330: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4331: fprintf(fichtm,"\
1.128 brouard 4332: - 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",
4333: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4334: fprintf(fichtm,"\
4335: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4336: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4337:
4338: /* if(popforecast==1) fprintf(fichtm,"\n */
4339: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4340: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4341: /* <br>",fileres,fileres,fileres,fileres); */
4342: /* else */
4343: /* 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); */
4344: fflush(fichtm);
4345: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4346:
1.145 brouard 4347: m=pow(2,cptcoveff);
1.126 brouard 4348: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4349:
4350: jj1=0;
4351: for(k1=1; k1<=m;k1++){
4352: for(i1=1; i1<=ncodemax[k1];i1++){
4353: jj1++;
4354: if (cptcovn > 0) {
4355: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4356: for (cpt=1; cpt<=cptcoveff;cpt++)
4357: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4358: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4359: }
4360: for(cpt=1; cpt<=nlstate;cpt++) {
4361: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4362: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4363: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4364: }
4365: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4366: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4367: true period expectancies (those weighted with period prevalences are also\
4368: drawn in addition to the population based expectancies computed using\
4369: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4370: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4371: } /* end i1 */
4372: }/* End k1 */
4373: fprintf(fichtm,"</ul>");
4374: fflush(fichtm);
4375: }
4376:
4377: /******************* Gnuplot file **************/
4378: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4379:
4380: char dirfileres[132],optfileres[132];
1.164 brouard 4381: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4382: int ng=0;
1.126 brouard 4383: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4384: /* printf("Problem with file %s",optionfilegnuplot); */
4385: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4386: /* } */
4387:
4388: /*#ifdef windows */
4389: fprintf(ficgp,"cd \"%s\" \n",pathc);
4390: /*#endif */
4391: m=pow(2,cptcoveff);
4392:
4393: strcpy(dirfileres,optionfilefiname);
4394: strcpy(optfileres,"vpl");
4395: /* 1eme*/
1.153 brouard 4396: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4397: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4398: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4399: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4400: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4401: fprintf(ficgp,"set xlabel \"Age\" \n\
4402: set ylabel \"Probability\" \n\
1.145 brouard 4403: set ter png small size 320, 240\n\
1.170 brouard 4404: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4405:
4406: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4407: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4408: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4409: }
1.170 brouard 4410: 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 4411: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4412: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4413: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4414: }
1.170 brouard 4415: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4416: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4417: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4418: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4419: }
1.145 brouard 4420: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4421: }
4422: }
4423: /*2 eme*/
1.153 brouard 4424: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4425: for (k1=1; k1<= m ; k1 ++) {
4426: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4427: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4428:
4429: for (i=1; i<= nlstate+1 ; i ++) {
4430: k=2*i;
1.170 brouard 4431: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4432: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4433: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4434: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4435: }
4436: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4437: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4438: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4439: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4440: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4441: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4442: }
1.145 brouard 4443: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4444: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4445: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4446: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4447: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4448: }
1.145 brouard 4449: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4450: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4451: }
4452: }
4453:
4454: /*3eme*/
4455:
4456: for (k1=1; k1<= m ; k1 ++) {
4457: for (cpt=1; cpt<= nlstate ; cpt ++) {
4458: /* k=2+nlstate*(2*cpt-2); */
4459: k=2+(nlstate+1)*(cpt-1);
4460: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4461: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4462: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4463: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4464: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4465: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4466: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4467: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4468: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4469:
4470: */
4471: for (i=1; i< nlstate ; i ++) {
4472: 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);
4473: /* 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);*/
4474:
4475: }
4476: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4477: }
4478: }
4479:
4480: /* CV preval stable (period) */
1.153 brouard 4481: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4482: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4483: k=3;
1.153 brouard 4484: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4485: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4486: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4487: set ter png small size 320, 240\n\
1.126 brouard 4488: unset log y\n\
1.153 brouard 4489: plot [%.f:%.f] ", ageminpar, agemaxpar);
4490: for (i=1; i<= nlstate ; i ++){
4491: if(i==1)
4492: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4493: else
4494: fprintf(ficgp,", '' ");
1.154 brouard 4495: l=(nlstate+ndeath)*(i-1)+1;
4496: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4497: for (j=1; j<= (nlstate-1) ; j ++)
4498: fprintf(ficgp,"+$%d",k+l+j);
4499: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4500: } /* nlstate */
4501: fprintf(ficgp,"\n");
4502: } /* end cpt state*/
4503: } /* end covariate */
1.126 brouard 4504:
4505: /* proba elementaires */
4506: for(i=1,jk=1; i <=nlstate; i++){
4507: for(k=1; k <=(nlstate+ndeath); k++){
4508: if (k != i) {
4509: for(j=1; j <=ncovmodel; j++){
4510: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4511: jk++;
4512: fprintf(ficgp,"\n");
4513: }
4514: }
4515: }
4516: }
1.145 brouard 4517: /*goto avoid;*/
1.126 brouard 4518: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4519: for(jk=1; jk <=m; jk++) {
1.145 brouard 4520: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4521: if (ng==2)
4522: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4523: else
4524: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4525: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4526: i=1;
4527: for(k2=1; k2<=nlstate; k2++) {
4528: k3=i;
4529: for(k=1; k<=(nlstate+ndeath); k++) {
4530: if (k != k2){
4531: if(ng==2)
4532: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4533: else
4534: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4535: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4536: for(j=3; j <=ncovmodel; j++) {
1.186 ! brouard 4537: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
! 4538: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 4539: ij++;
! 4540: }
! 4541: else
1.126 brouard 4542: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4543: }
4544: fprintf(ficgp,")/(1");
4545:
4546: for(k1=1; k1 <=nlstate; k1++){
4547: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4548: ij=1;
4549: for(j=3; j <=ncovmodel; j++){
1.186 ! brouard 4550: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
! 4551: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 4552: ij++;
! 4553: }
! 4554: else
1.126 brouard 4555: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4556: }
4557: fprintf(ficgp,")");
4558: }
4559: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4560: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4561: i=i+ncovmodel;
4562: }
4563: } /* end k */
4564: } /* end k2 */
4565: } /* end jk */
4566: } /* end ng */
1.164 brouard 4567: /* avoid: */
1.126 brouard 4568: fflush(ficgp);
4569: } /* end gnuplot */
4570:
4571:
4572: /*************** Moving average **************/
4573: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4574:
4575: int i, cpt, cptcod;
4576: int modcovmax =1;
4577: int mobilavrange, mob;
4578: double age;
4579:
4580: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4581: a covariate has 2 modalities */
4582: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4583:
4584: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4585: if(mobilav==1) mobilavrange=5; /* default */
4586: else mobilavrange=mobilav;
4587: for (age=bage; age<=fage; age++)
4588: for (i=1; i<=nlstate;i++)
4589: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4590: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4591: /* We keep the original values on the extreme ages bage, fage and for
4592: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4593: we use a 5 terms etc. until the borders are no more concerned.
4594: */
4595: for (mob=3;mob <=mobilavrange;mob=mob+2){
4596: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4597: for (i=1; i<=nlstate;i++){
4598: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4599: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4600: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4601: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4602: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4603: }
4604: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4605: }
4606: }
4607: }/* end age */
4608: }/* end mob */
4609: }else return -1;
4610: return 0;
4611: }/* End movingaverage */
4612:
4613:
4614: /************** Forecasting ******************/
1.169 brouard 4615: 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 4616: /* proj1, year, month, day of starting projection
4617: agemin, agemax range of age
4618: dateprev1 dateprev2 range of dates during which prevalence is computed
4619: anproj2 year of en of projection (same day and month as proj1).
4620: */
1.164 brouard 4621: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4622: double agec; /* generic age */
4623: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4624: double *popeffectif,*popcount;
4625: double ***p3mat;
4626: double ***mobaverage;
4627: char fileresf[FILENAMELENGTH];
4628:
4629: agelim=AGESUP;
4630: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4631:
4632: strcpy(fileresf,"f");
4633: strcat(fileresf,fileres);
4634: if((ficresf=fopen(fileresf,"w"))==NULL) {
4635: printf("Problem with forecast resultfile: %s\n", fileresf);
4636: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4637: }
4638: printf("Computing forecasting: result on file '%s' \n", fileresf);
4639: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4640:
4641: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4642:
4643: if (mobilav!=0) {
4644: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4645: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4646: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4647: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4648: }
4649: }
4650:
4651: stepsize=(int) (stepm+YEARM-1)/YEARM;
4652: if (stepm<=12) stepsize=1;
4653: if(estepm < stepm){
4654: printf ("Problem %d lower than %d\n",estepm, stepm);
4655: }
4656: else hstepm=estepm;
4657:
4658: hstepm=hstepm/stepm;
4659: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4660: fractional in yp1 */
4661: anprojmean=yp;
4662: yp2=modf((yp1*12),&yp);
4663: mprojmean=yp;
4664: yp1=modf((yp2*30.5),&yp);
4665: jprojmean=yp;
4666: if(jprojmean==0) jprojmean=1;
4667: if(mprojmean==0) jprojmean=1;
4668:
4669: i1=cptcoveff;
4670: if (cptcovn < 1){i1=1;}
4671:
4672: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4673:
4674: fprintf(ficresf,"#****** Routine prevforecast **\n");
4675:
4676: /* if (h==(int)(YEARM*yearp)){ */
4677: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4678: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4679: k=k+1;
4680: fprintf(ficresf,"\n#******");
4681: for(j=1;j<=cptcoveff;j++) {
4682: 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]]);
4683: }
4684: fprintf(ficresf,"******\n");
4685: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4686: for(j=1; j<=nlstate+ndeath;j++){
4687: for(i=1; i<=nlstate;i++)
4688: fprintf(ficresf," p%d%d",i,j);
4689: fprintf(ficresf," p.%d",j);
4690: }
4691: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4692: fprintf(ficresf,"\n");
4693: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4694:
4695: for (agec=fage; agec>=(ageminpar-1); agec--){
4696: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4697: nhstepm = nhstepm/hstepm;
4698: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4699: oldm=oldms;savm=savms;
4700: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4701:
4702: for (h=0; h<=nhstepm; h++){
4703: if (h*hstepm/YEARM*stepm ==yearp) {
4704: fprintf(ficresf,"\n");
4705: for(j=1;j<=cptcoveff;j++)
4706: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4707: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4708: }
4709: for(j=1; j<=nlstate+ndeath;j++) {
4710: ppij=0.;
4711: for(i=1; i<=nlstate;i++) {
4712: if (mobilav==1)
4713: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4714: else {
4715: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4716: }
4717: if (h*hstepm/YEARM*stepm== yearp) {
4718: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4719: }
4720: } /* end i */
4721: if (h*hstepm/YEARM*stepm==yearp) {
4722: fprintf(ficresf," %.3f", ppij);
4723: }
4724: }/* end j */
4725: } /* end h */
4726: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4727: } /* end agec */
4728: } /* end yearp */
4729: } /* end cptcod */
4730: } /* end cptcov */
4731:
4732: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4733:
4734: fclose(ficresf);
4735: }
4736:
4737: /************** Forecasting *****not tested NB*************/
1.169 brouard 4738: 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 4739:
4740: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4741: int *popage;
4742: double calagedatem, agelim, kk1, kk2;
4743: double *popeffectif,*popcount;
4744: double ***p3mat,***tabpop,***tabpopprev;
4745: double ***mobaverage;
4746: char filerespop[FILENAMELENGTH];
4747:
4748: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4749: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4750: agelim=AGESUP;
4751: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4752:
4753: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4754:
4755:
4756: strcpy(filerespop,"pop");
4757: strcat(filerespop,fileres);
4758: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4759: printf("Problem with forecast resultfile: %s\n", filerespop);
4760: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4761: }
4762: printf("Computing forecasting: result on file '%s' \n", filerespop);
4763: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4764:
4765: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4766:
4767: if (mobilav!=0) {
4768: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4769: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4770: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4771: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4772: }
4773: }
4774:
4775: stepsize=(int) (stepm+YEARM-1)/YEARM;
4776: if (stepm<=12) stepsize=1;
4777:
4778: agelim=AGESUP;
4779:
4780: hstepm=1;
4781: hstepm=hstepm/stepm;
4782:
4783: if (popforecast==1) {
4784: if((ficpop=fopen(popfile,"r"))==NULL) {
4785: printf("Problem with population file : %s\n",popfile);exit(0);
4786: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4787: }
4788: popage=ivector(0,AGESUP);
4789: popeffectif=vector(0,AGESUP);
4790: popcount=vector(0,AGESUP);
4791:
4792: i=1;
4793: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4794:
4795: imx=i;
4796: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4797: }
4798:
4799: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4800: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4801: k=k+1;
4802: fprintf(ficrespop,"\n#******");
4803: for(j=1;j<=cptcoveff;j++) {
4804: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4805: }
4806: fprintf(ficrespop,"******\n");
4807: fprintf(ficrespop,"# Age");
4808: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4809: if (popforecast==1) fprintf(ficrespop," [Population]");
4810:
4811: for (cpt=0; cpt<=0;cpt++) {
4812: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4813:
4814: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4815: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4816: nhstepm = nhstepm/hstepm;
4817:
4818: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4819: oldm=oldms;savm=savms;
4820: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4821:
4822: for (h=0; h<=nhstepm; h++){
4823: if (h==(int) (calagedatem+YEARM*cpt)) {
4824: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4825: }
4826: for(j=1; j<=nlstate+ndeath;j++) {
4827: kk1=0.;kk2=0;
4828: for(i=1; i<=nlstate;i++) {
4829: if (mobilav==1)
4830: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4831: else {
4832: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4833: }
4834: }
4835: if (h==(int)(calagedatem+12*cpt)){
4836: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4837: /*fprintf(ficrespop," %.3f", kk1);
4838: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4839: }
4840: }
4841: for(i=1; i<=nlstate;i++){
4842: kk1=0.;
4843: for(j=1; j<=nlstate;j++){
4844: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4845: }
4846: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4847: }
4848:
4849: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4850: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4851: }
4852: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4853: }
4854: }
4855:
4856: /******/
4857:
4858: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4859: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4860: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4861: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4862: nhstepm = nhstepm/hstepm;
4863:
4864: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4865: oldm=oldms;savm=savms;
4866: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4867: for (h=0; h<=nhstepm; h++){
4868: if (h==(int) (calagedatem+YEARM*cpt)) {
4869: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4870: }
4871: for(j=1; j<=nlstate+ndeath;j++) {
4872: kk1=0.;kk2=0;
4873: for(i=1; i<=nlstate;i++) {
4874: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4875: }
4876: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4877: }
4878: }
4879: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4880: }
4881: }
4882: }
4883: }
4884:
4885: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4886:
4887: if (popforecast==1) {
4888: free_ivector(popage,0,AGESUP);
4889: free_vector(popeffectif,0,AGESUP);
4890: free_vector(popcount,0,AGESUP);
4891: }
4892: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4893: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4894: fclose(ficrespop);
4895: } /* End of popforecast */
4896:
4897: int fileappend(FILE *fichier, char *optionfich)
4898: {
4899: if((fichier=fopen(optionfich,"a"))==NULL) {
4900: printf("Problem with file: %s\n", optionfich);
4901: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4902: return (0);
4903: }
4904: fflush(fichier);
4905: return (1);
4906: }
4907:
4908:
4909: /**************** function prwizard **********************/
4910: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4911: {
4912:
4913: /* Wizard to print covariance matrix template */
4914:
1.164 brouard 4915: char ca[32], cb[32];
4916: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 4917: int numlinepar;
4918:
4919: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4920: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4921: for(i=1; i <=nlstate; i++){
4922: jj=0;
4923: for(j=1; j <=nlstate+ndeath; j++){
4924: if(j==i) continue;
4925: jj++;
4926: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4927: printf("%1d%1d",i,j);
4928: fprintf(ficparo,"%1d%1d",i,j);
4929: for(k=1; k<=ncovmodel;k++){
4930: /* printf(" %lf",param[i][j][k]); */
4931: /* fprintf(ficparo," %lf",param[i][j][k]); */
4932: printf(" 0.");
4933: fprintf(ficparo," 0.");
4934: }
4935: printf("\n");
4936: fprintf(ficparo,"\n");
4937: }
4938: }
4939: printf("# Scales (for hessian or gradient estimation)\n");
4940: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4941: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4942: for(i=1; i <=nlstate; i++){
4943: jj=0;
4944: for(j=1; j <=nlstate+ndeath; j++){
4945: if(j==i) continue;
4946: jj++;
4947: fprintf(ficparo,"%1d%1d",i,j);
4948: printf("%1d%1d",i,j);
4949: fflush(stdout);
4950: for(k=1; k<=ncovmodel;k++){
4951: /* printf(" %le",delti3[i][j][k]); */
4952: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4953: printf(" 0.");
4954: fprintf(ficparo," 0.");
4955: }
4956: numlinepar++;
4957: printf("\n");
4958: fprintf(ficparo,"\n");
4959: }
4960: }
4961: printf("# Covariance matrix\n");
4962: /* # 121 Var(a12)\n\ */
4963: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4964: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4965: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4966: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4967: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4968: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4969: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4970: fflush(stdout);
4971: fprintf(ficparo,"# Covariance matrix\n");
4972: /* # 121 Var(a12)\n\ */
4973: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4974: /* # ...\n\ */
4975: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4976:
4977: for(itimes=1;itimes<=2;itimes++){
4978: jj=0;
4979: for(i=1; i <=nlstate; i++){
4980: for(j=1; j <=nlstate+ndeath; j++){
4981: if(j==i) continue;
4982: for(k=1; k<=ncovmodel;k++){
4983: jj++;
4984: ca[0]= k+'a'-1;ca[1]='\0';
4985: if(itimes==1){
4986: printf("#%1d%1d%d",i,j,k);
4987: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4988: }else{
4989: printf("%1d%1d%d",i,j,k);
4990: fprintf(ficparo,"%1d%1d%d",i,j,k);
4991: /* printf(" %.5le",matcov[i][j]); */
4992: }
4993: ll=0;
4994: for(li=1;li <=nlstate; li++){
4995: for(lj=1;lj <=nlstate+ndeath; lj++){
4996: if(lj==li) continue;
4997: for(lk=1;lk<=ncovmodel;lk++){
4998: ll++;
4999: if(ll<=jj){
5000: cb[0]= lk +'a'-1;cb[1]='\0';
5001: if(ll<jj){
5002: if(itimes==1){
5003: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5004: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5005: }else{
5006: printf(" 0.");
5007: fprintf(ficparo," 0.");
5008: }
5009: }else{
5010: if(itimes==1){
5011: printf(" Var(%s%1d%1d)",ca,i,j);
5012: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5013: }else{
5014: printf(" 0.");
5015: fprintf(ficparo," 0.");
5016: }
5017: }
5018: }
5019: } /* end lk */
5020: } /* end lj */
5021: } /* end li */
5022: printf("\n");
5023: fprintf(ficparo,"\n");
5024: numlinepar++;
5025: } /* end k*/
5026: } /*end j */
5027: } /* end i */
5028: } /* end itimes */
5029:
5030: } /* end of prwizard */
5031: /******************* Gompertz Likelihood ******************************/
5032: double gompertz(double x[])
5033: {
5034: double A,B,L=0.0,sump=0.,num=0.;
5035: int i,n=0; /* n is the size of the sample */
5036:
5037: for (i=0;i<=imx-1 ; i++) {
5038: sump=sump+weight[i];
5039: /* sump=sump+1;*/
5040: num=num+1;
5041: }
5042:
5043:
5044: /* for (i=0; i<=imx; i++)
5045: 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]);*/
5046:
5047: for (i=1;i<=imx ; i++)
5048: {
5049: if (cens[i] == 1 && wav[i]>1)
5050: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5051:
5052: if (cens[i] == 0 && wav[i]>1)
5053: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5054: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5055:
5056: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5057: if (wav[i] > 1 ) { /* ??? */
5058: L=L+A*weight[i];
5059: /* 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]);*/
5060: }
5061: }
5062:
5063: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5064:
5065: return -2*L*num/sump;
5066: }
5067:
1.136 brouard 5068: #ifdef GSL
5069: /******************* Gompertz_f Likelihood ******************************/
5070: double gompertz_f(const gsl_vector *v, void *params)
5071: {
5072: double A,B,LL=0.0,sump=0.,num=0.;
5073: double *x= (double *) v->data;
5074: int i,n=0; /* n is the size of the sample */
5075:
5076: for (i=0;i<=imx-1 ; i++) {
5077: sump=sump+weight[i];
5078: /* sump=sump+1;*/
5079: num=num+1;
5080: }
5081:
5082:
5083: /* for (i=0; i<=imx; i++)
5084: 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]);*/
5085: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5086: for (i=1;i<=imx ; i++)
5087: {
5088: if (cens[i] == 1 && wav[i]>1)
5089: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5090:
5091: if (cens[i] == 0 && wav[i]>1)
5092: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5093: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5094:
5095: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5096: if (wav[i] > 1 ) { /* ??? */
5097: LL=LL+A*weight[i];
5098: /* 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]);*/
5099: }
5100: }
5101:
5102: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5103: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5104:
5105: return -2*LL*num/sump;
5106: }
5107: #endif
5108:
1.126 brouard 5109: /******************* Printing html file ***********/
5110: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5111: int lastpass, int stepm, int weightopt, char model[],\
5112: int imx, double p[],double **matcov,double agemortsup){
5113: int i,k;
5114:
5115: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5116: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5117: for (i=1;i<=2;i++)
5118: 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]));
5119: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5120: fprintf(fichtm,"</ul>");
5121:
5122: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5123:
5124: 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>");
5125:
5126: for (k=agegomp;k<(agemortsup-2);k++)
5127: 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]);
5128:
5129:
5130: fflush(fichtm);
5131: }
5132:
5133: /******************* Gnuplot file **************/
5134: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5135:
5136: char dirfileres[132],optfileres[132];
1.164 brouard 5137:
1.126 brouard 5138: int ng;
5139:
5140:
5141: /*#ifdef windows */
5142: fprintf(ficgp,"cd \"%s\" \n",pathc);
5143: /*#endif */
5144:
5145:
5146: strcpy(dirfileres,optionfilefiname);
5147: strcpy(optfileres,"vpl");
5148: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5149: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5150: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5151: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5152: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5153:
5154: }
5155:
1.136 brouard 5156: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5157: {
1.126 brouard 5158:
1.136 brouard 5159: /*-------- data file ----------*/
5160: FILE *fic;
5161: char dummy[]=" ";
1.164 brouard 5162: int i=0, j=0, n=0;
1.136 brouard 5163: int linei, month, year,iout;
5164: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5165: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5166: char *stratrunc;
5167: int lstra;
1.126 brouard 5168:
5169:
1.136 brouard 5170: if((fic=fopen(datafile,"r"))==NULL) {
5171: printf("Problem while opening datafile: %s\n", datafile);return 1;
5172: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5173: }
1.126 brouard 5174:
1.136 brouard 5175: i=1;
5176: linei=0;
5177: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5178: linei=linei+1;
5179: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5180: if(line[j] == '\t')
5181: line[j] = ' ';
5182: }
5183: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5184: ;
5185: };
5186: line[j+1]=0; /* Trims blanks at end of line */
5187: if(line[0]=='#'){
5188: fprintf(ficlog,"Comment line\n%s\n",line);
5189: printf("Comment line\n%s\n",line);
5190: continue;
5191: }
5192: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5193: strcpy(line, linetmp);
1.136 brouard 5194:
1.126 brouard 5195:
1.136 brouard 5196: for (j=maxwav;j>=1;j--){
1.137 brouard 5197: cutv(stra, strb, line, ' ');
1.136 brouard 5198: if(strb[0]=='.') { /* Missing status */
5199: lval=-1;
5200: }else{
5201: errno=0;
5202: lval=strtol(strb,&endptr,10);
5203: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5204: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5205: 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);
5206: 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 5207: return 1;
5208: }
5209: }
5210: s[j][i]=lval;
5211:
5212: strcpy(line,stra);
5213: cutv(stra, strb,line,' ');
1.169 brouard 5214: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5215: }
1.169 brouard 5216: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5217: month=99;
5218: year=9999;
5219: }else{
1.141 brouard 5220: 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);
5221: 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 5222: return 1;
5223: }
5224: anint[j][i]= (double) year;
5225: mint[j][i]= (double)month;
5226: strcpy(line,stra);
5227: } /* ENd Waves */
5228:
5229: cutv(stra, strb,line,' ');
1.169 brouard 5230: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5231: }
1.169 brouard 5232: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5233: month=99;
5234: year=9999;
5235: }else{
1.141 brouard 5236: 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);
5237: 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 5238: return 1;
5239: }
5240: andc[i]=(double) year;
5241: moisdc[i]=(double) month;
5242: strcpy(line,stra);
5243:
5244: cutv(stra, strb,line,' ');
1.169 brouard 5245: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5246: }
1.169 brouard 5247: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5248: month=99;
5249: year=9999;
5250: }else{
1.141 brouard 5251: 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);
5252: 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 5253: return 1;
5254: }
5255: if (year==9999) {
1.141 brouard 5256: 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);
5257: 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 5258: return 1;
1.126 brouard 5259:
1.136 brouard 5260: }
5261: annais[i]=(double)(year);
5262: moisnais[i]=(double)(month);
5263: strcpy(line,stra);
5264:
5265: cutv(stra, strb,line,' ');
5266: errno=0;
5267: dval=strtod(strb,&endptr);
5268: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5269: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5270: 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 5271: fflush(ficlog);
5272: return 1;
5273: }
5274: weight[i]=dval;
5275: strcpy(line,stra);
5276:
5277: for (j=ncovcol;j>=1;j--){
5278: cutv(stra, strb,line,' ');
5279: if(strb[0]=='.') { /* Missing status */
5280: lval=-1;
5281: }else{
5282: errno=0;
5283: lval=strtol(strb,&endptr,10);
5284: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5285: 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);
5286: 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 5287: return 1;
5288: }
5289: }
5290: if(lval <-1 || lval >1){
1.141 brouard 5291: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5292: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5293: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5294: For example, for multinomial values like 1, 2 and 3,\n \
5295: build V1=0 V2=0 for the reference value (1),\n \
5296: V1=1 V2=0 for (2) \n \
5297: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5298: output of IMaCh is often meaningless.\n \
5299: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5300: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5301: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5302: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5303: For example, for multinomial values like 1, 2 and 3,\n \
5304: build V1=0 V2=0 for the reference value (1),\n \
5305: V1=1 V2=0 for (2) \n \
5306: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5307: output of IMaCh is often meaningless.\n \
5308: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5309: return 1;
5310: }
5311: covar[j][i]=(double)(lval);
5312: strcpy(line,stra);
5313: }
5314: lstra=strlen(stra);
5315:
5316: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5317: stratrunc = &(stra[lstra-9]);
5318: num[i]=atol(stratrunc);
5319: }
5320: else
5321: num[i]=atol(stra);
5322: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5323: 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;}*/
5324:
5325: i=i+1;
5326: } /* End loop reading data */
1.126 brouard 5327:
1.136 brouard 5328: *imax=i-1; /* Number of individuals */
5329: fclose(fic);
5330:
5331: return (0);
1.164 brouard 5332: /* endread: */
1.136 brouard 5333: printf("Exiting readdata: ");
5334: fclose(fic);
5335: return (1);
1.126 brouard 5336:
5337:
5338:
1.136 brouard 5339: }
1.145 brouard 5340: void removespace(char *str) {
5341: char *p1 = str, *p2 = str;
5342: do
5343: while (*p2 == ' ')
5344: p2++;
1.169 brouard 5345: while (*p1++ == *p2++);
1.145 brouard 5346: }
5347:
5348: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5349: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5350: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5351: * - cptcovn or number of covariates k of the models excluding age*products =6
5352: * - cptcovage number of covariates with age*products =2
5353: * - cptcovs number of simple covariates
5354: * - 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
5355: * which is a new column after the 9 (ncovcol) variables.
5356: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5357: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5358: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5359: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5360: */
1.136 brouard 5361: {
1.145 brouard 5362: int i, j, k, ks;
1.164 brouard 5363: int j1, k1, k2;
1.136 brouard 5364: char modelsav[80];
1.145 brouard 5365: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5366:
1.145 brouard 5367: /*removespace(model);*/
1.136 brouard 5368: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5369: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5370: j=nbocc(model,'+'); /**< j=Number of '+' */
5371: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5372: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5373: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5374: /* including age products which are counted in cptcovage.
1.169 brouard 5375: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145 brouard 5376: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5377: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5378: strcpy(modelsav,model);
1.137 brouard 5379: if (strstr(model,"AGE") !=0){
5380: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5381: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5382: return 1;
5383: }
1.141 brouard 5384: if (strstr(model,"v") !=0){
5385: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5386: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5387: return 1;
5388: }
1.136 brouard 5389:
1.145 brouard 5390: /* Design
5391: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5392: * < ncovcol=8 >
5393: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5394: * k= 1 2 3 4 5 6 7 8
5395: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5396: * covar[k,i], value of kth covariate if not including age for individual i:
5397: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5398: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5399: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5400: * Tage[++cptcovage]=k
5401: * if products, new covar are created after ncovcol with k1
5402: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5403: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5404: * 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
5405: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5406: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5407: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5408: * < ncovcol=8 >
5409: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5410: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5411: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5412: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5413: * p Tprod[1]@2={ 6, 5}
5414: *p Tvard[1][1]@4= {7, 8, 5, 6}
5415: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5416: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5417: *How to reorganize?
5418: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5419: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5420: * {2, 1, 4, 8, 5, 6, 3, 7}
5421: * Struct []
5422: */
5423:
1.136 brouard 5424: /* This loop fills the array Tvar from the string 'model'.*/
5425: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5426: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5427: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5428: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5429: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5430: /* k=1 Tvar[1]=2 (from V2) */
5431: /* k=5 Tvar[5] */
5432: /* for (k=1; k<=cptcovn;k++) { */
5433: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5434: /* } */
1.186 ! brouard 5435: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
1.145 brouard 5436: /*
5437: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5438: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5439: Tvar[k]=0;
5440: cptcovage=0;
5441: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5442: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5443: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5444: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5445: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5446: /*scanf("%d",i);*/
1.145 brouard 5447: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5448: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5449: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5450: /* covar is not filled and then is empty */
1.136 brouard 5451: cptcovprod--;
1.145 brouard 5452: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5453: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5454: cptcovage++; /* Sums the number of covariates which include age as a product */
1.186 ! brouard 5455: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
1.136 brouard 5456: /*printf("stre=%s ", stre);*/
1.137 brouard 5457: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5458: cptcovprod--;
1.145 brouard 5459: cutl(stre,strb,strc,'V');
1.136 brouard 5460: Tvar[k]=atoi(stre);
5461: cptcovage++;
5462: Tage[cptcovage]=k;
1.137 brouard 5463: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5464: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5465: cptcovn++;
5466: cptcovprodnoage++;k1++;
5467: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5468: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5469: because this model-covariate is a construction we invent a new column
5470: ncovcol + k1
5471: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5472: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5473: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5474: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5475: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5476: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5477: k2=k2+2;
5478: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5479: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5480: for (i=1; i<=lastobs;i++){
5481: /* Computes the new covariate which is a product of
1.145 brouard 5482: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5483: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5484: }
5485: } /* End age is not in the model */
5486: } /* End if model includes a product */
1.136 brouard 5487: else { /* no more sum */
5488: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5489: /* scanf("%d",i);*/
1.145 brouard 5490: cutl(strd,strc,strb,'V');
5491: ks++; /**< Number of simple covariates */
5492: cptcovn++;
5493: Tvar[k]=atoi(strd);
1.136 brouard 5494: }
1.137 brouard 5495: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5496: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5497: scanf("%d",i);*/
5498: } /* end of loop + */
5499: } /* end model */
5500:
5501: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5502: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5503:
5504: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5505: printf("cptcovprod=%d ", cptcovprod);
5506: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5507:
5508: scanf("%d ",i);*/
5509:
5510:
1.137 brouard 5511: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5512: /*endread:*/
1.136 brouard 5513: printf("Exiting decodemodel: ");
5514: return (1);
5515: }
5516:
1.169 brouard 5517: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5518: {
5519: int i, m;
5520:
5521: for (i=1; i<=imx; i++) {
5522: for(m=2; (m<= maxwav); m++) {
5523: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5524: anint[m][i]=9999;
5525: s[m][i]=-1;
5526: }
5527: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5528: *nberr = *nberr + 1;
5529: 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);
5530: 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 5531: s[m][i]=-1;
5532: }
5533: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5534: (*nberr)++;
1.136 brouard 5535: 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]);
5536: 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]);
5537: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5538: }
5539: }
5540: }
5541:
5542: for (i=1; i<=imx; i++) {
5543: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5544: for(m=firstpass; (m<= lastpass); m++){
5545: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5546: if (s[m][i] >= nlstate+1) {
1.169 brouard 5547: if(agedc[i]>0){
5548: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5549: agev[m][i]=agedc[i];
5550: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5551: }else {
1.136 brouard 5552: if ((int)andc[i]!=9999){
5553: nbwarn++;
5554: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5555: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5556: agev[m][i]=-1;
5557: }
5558: }
1.169 brouard 5559: } /* agedc > 0 */
1.136 brouard 5560: }
5561: else if(s[m][i] !=9){ /* Standard case, age in fractional
5562: years but with the precision of a month */
5563: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5564: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5565: agev[m][i]=1;
5566: else if(agev[m][i] < *agemin){
5567: *agemin=agev[m][i];
5568: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5569: }
5570: else if(agev[m][i] >*agemax){
5571: *agemax=agev[m][i];
1.156 brouard 5572: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5573: }
5574: /*agev[m][i]=anint[m][i]-annais[i];*/
5575: /* agev[m][i] = age[i]+2*m;*/
5576: }
5577: else { /* =9 */
5578: agev[m][i]=1;
5579: s[m][i]=-1;
5580: }
5581: }
5582: else /*= 0 Unknown */
5583: agev[m][i]=1;
5584: }
5585:
5586: }
5587: for (i=1; i<=imx; i++) {
5588: for(m=firstpass; (m<=lastpass); m++){
5589: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5590: (*nberr)++;
1.136 brouard 5591: 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);
5592: 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);
5593: return 1;
5594: }
5595: }
5596: }
5597:
5598: /*for (i=1; i<=imx; i++){
5599: for (m=firstpass; (m<lastpass); m++){
5600: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5601: }
5602:
5603: }*/
5604:
5605:
1.139 brouard 5606: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5607: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5608:
5609: return (0);
1.164 brouard 5610: /* endread:*/
1.136 brouard 5611: printf("Exiting calandcheckages: ");
5612: return (1);
5613: }
5614:
1.172 brouard 5615: #if defined(_MSC_VER)
5616: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5617: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5618: //#include "stdafx.h"
5619: //#include <stdio.h>
5620: //#include <tchar.h>
5621: //#include <windows.h>
5622: //#include <iostream>
5623: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5624:
5625: LPFN_ISWOW64PROCESS fnIsWow64Process;
5626:
5627: BOOL IsWow64()
5628: {
5629: BOOL bIsWow64 = FALSE;
5630:
5631: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5632: // (HANDLE, PBOOL);
5633:
5634: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5635:
5636: HMODULE module = GetModuleHandle(_T("kernel32"));
5637: const char funcName[] = "IsWow64Process";
5638: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5639: GetProcAddress(module, funcName);
5640:
5641: if (NULL != fnIsWow64Process)
5642: {
5643: if (!fnIsWow64Process(GetCurrentProcess(),
5644: &bIsWow64))
5645: //throw std::exception("Unknown error");
5646: printf("Unknown error\n");
5647: }
5648: return bIsWow64 != FALSE;
5649: }
5650: #endif
1.177 brouard 5651:
1.169 brouard 5652: void syscompilerinfo()
1.167 brouard 5653: {
5654: /* #include "syscompilerinfo.h"*/
1.185 brouard 5655: /* command line Intel compiler 32bit windows, XP compatible:*/
5656: /* /GS /W3 /Gy
5657: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5658: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5659: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 ! brouard 5660: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
! 5661: */
! 5662: /* 64 bits */
1.185 brouard 5663: /*
5664: /GS /W3 /Gy
5665: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5666: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5667: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5668: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5669: /* Optimization are useless and O3 is slower than O2 */
5670: /*
5671: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5672: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5673: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5674: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5675: */
1.186 ! brouard 5676: /* Link is */ /* /OUT:"visual studio
1.185 brouard 5677: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5678: /PDB:"visual studio
5679: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5680: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5681: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5682: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5683: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5684: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5685: uiAccess='false'"
5686: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5687: /NOLOGO /TLBID:1
5688: */
1.177 brouard 5689: #if defined __INTEL_COMPILER
1.178 brouard 5690: #if defined(__GNUC__)
5691: struct utsname sysInfo; /* For Intel on Linux and OS/X */
5692: #endif
1.177 brouard 5693: #elif defined(__GNUC__)
1.179 brouard 5694: #ifndef __APPLE__
1.174 brouard 5695: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 5696: #endif
1.177 brouard 5697: struct utsname sysInfo;
1.178 brouard 5698: int cross = CROSS;
5699: if (cross){
5700: printf("Cross-");
5701: fprintf(ficlog, "Cross-");
5702: }
1.174 brouard 5703: #endif
5704:
1.171 brouard 5705: #include <stdint.h>
1.178 brouard 5706:
1.169 brouard 5707: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5708: #if defined(__clang__)
5709: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5710: #endif
5711: #if defined(__ICC) || defined(__INTEL_COMPILER)
5712: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5713: #endif
5714: #if defined(__GNUC__) || defined(__GNUG__)
5715: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5716: #endif
5717: #if defined(__HP_cc) || defined(__HP_aCC)
5718: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5719: #endif
5720: #if defined(__IBMC__) || defined(__IBMCPP__)
5721: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5722: #endif
5723: #if defined(_MSC_VER)
5724: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5725: #endif
5726: #if defined(__PGI)
5727: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5728: #endif
5729: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5730: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5731: #endif
1.174 brouard 5732: printf(" for ");fprintf(ficlog," for ");
1.169 brouard 5733:
1.167 brouard 5734: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5735: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5736: // Windows (x64 and x86)
1.174 brouard 5737: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 5738: #elif __unix__ // all unices, not all compilers
5739: // Unix
1.174 brouard 5740: printf("Unix ");fprintf(ficlog,"Unix ");
1.167 brouard 5741: #elif __linux__
5742: // linux
1.174 brouard 5743: printf("linux ");fprintf(ficlog,"linux ");
1.167 brouard 5744: #elif __APPLE__
1.174 brouard 5745: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5746: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167 brouard 5747: #endif
5748:
5749: /* __MINGW32__ */
5750: /* __CYGWIN__ */
5751: /* __MINGW64__ */
5752: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5753: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5754: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5755: /* _WIN64 // Defined for applications for Win64. */
5756: /* _M_X64 // Defined for compilations that target x64 processors. */
5757: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 5758:
1.167 brouard 5759: #if UINTPTR_MAX == 0xffffffff
1.174 brouard 5760: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 5761: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174 brouard 5762: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 5763: #else
1.174 brouard 5764: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 5765: #endif
5766:
1.169 brouard 5767: #if defined(__GNUC__)
5768: # if defined(__GNUC_PATCHLEVEL__)
5769: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5770: + __GNUC_MINOR__ * 100 \
5771: + __GNUC_PATCHLEVEL__)
5772: # else
5773: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5774: + __GNUC_MINOR__ * 100)
5775: # endif
1.174 brouard 5776: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5777: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 5778:
5779: if (uname(&sysInfo) != -1) {
5780: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5781: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5782: }
5783: else
5784: perror("uname() error");
1.179 brouard 5785: //#ifndef __INTEL_COMPILER
5786: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 5787: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.179 brouard 5788: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 5789: #endif
1.169 brouard 5790: #endif
1.172 brouard 5791:
5792: // void main()
5793: // {
1.169 brouard 5794: #if defined(_MSC_VER)
1.174 brouard 5795: if (IsWow64()){
1.176 brouard 5796: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5797: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 5798: }
5799: else{
1.176 brouard 5800: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178 brouard 5801: fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 5802: }
1.172 brouard 5803: // printf("\nPress Enter to continue...");
5804: // getchar();
5805: // }
5806:
1.169 brouard 5807: #endif
5808:
1.167 brouard 5809:
5810: }
1.136 brouard 5811:
1.180 brouard 5812: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
5813: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5814: int i, j, k, i1 ;
5815: double ftolpl = 1.e-10;
5816: double age, agebase, agelim;
5817:
5818: strcpy(filerespl,"pl");
5819: strcat(filerespl,fileres);
5820: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5821: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5822: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
5823: }
5824: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5825: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5826: pstamp(ficrespl);
5827: fprintf(ficrespl,"# Period (stable) prevalence \n");
5828: fprintf(ficrespl,"#Age ");
5829: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5830: fprintf(ficrespl,"\n");
5831:
5832: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
5833:
5834: agebase=ageminpar;
5835: agelim=agemaxpar;
5836:
5837: i1=pow(2,cptcoveff);
5838: if (cptcovn < 1){i1=1;}
5839:
5840: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5841: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
5842: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5843: k=k+1;
5844: /* to clean */
5845: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
5846: fprintf(ficrespl,"\n#******");
5847: printf("\n#******");
5848: fprintf(ficlog,"\n#******");
5849: for(j=1;j<=cptcoveff;j++) {
5850: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5851: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5852: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5853: }
5854: fprintf(ficrespl,"******\n");
5855: printf("******\n");
5856: fprintf(ficlog,"******\n");
5857:
5858: fprintf(ficrespl,"#Age ");
5859: for(j=1;j<=cptcoveff;j++) {
5860: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5861: }
5862: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5863: fprintf(ficrespl,"\n");
5864:
5865: for (age=agebase; age<=agelim; age++){
5866: /* for (age=agebase; age<=agebase; age++){ */
5867: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5868: fprintf(ficrespl,"%.0f ",age );
5869: for(j=1;j<=cptcoveff;j++)
5870: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5871: for(i=1; i<=nlstate;i++)
5872: fprintf(ficrespl," %.5f", prlim[i][i]);
5873: fprintf(ficrespl,"\n");
5874: } /* Age */
5875: /* was end of cptcod */
5876: } /* cptcov */
1.184 brouard 5877: return 0;
1.180 brouard 5878: }
5879:
5880: int hPijx(double *p, int bage, int fage){
5881: /*------------- h Pij x at various ages ------------*/
5882:
5883: int stepsize;
5884: int agelim;
5885: int hstepm;
5886: int nhstepm;
5887: int h, i, i1, j, k;
5888:
5889: double agedeb;
5890: double ***p3mat;
5891:
5892: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5893: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5894: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
5895: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
5896: }
5897: printf("Computing pij: result on file '%s' \n", filerespij);
5898: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5899:
5900: stepsize=(int) (stepm+YEARM-1)/YEARM;
5901: /*if (stepm<=24) stepsize=2;*/
5902:
5903: agelim=AGESUP;
5904: hstepm=stepsize*YEARM; /* Every year of age */
5905: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5906:
5907: /* hstepm=1; aff par mois*/
5908: pstamp(ficrespij);
5909: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5910: i1= pow(2,cptcoveff);
1.183 brouard 5911: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
5912: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
5913: /* k=k+1; */
5914: for (k=1; k <= (int) pow(2,cptcoveff); k++){
5915: fprintf(ficrespij,"\n#****** ");
5916: for(j=1;j<=cptcoveff;j++)
5917: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5918: fprintf(ficrespij,"******\n");
5919:
5920: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5921: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5922: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5923:
5924: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 5925:
1.183 brouard 5926: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5927: oldm=oldms;savm=savms;
5928: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5929: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5930: for(i=1; i<=nlstate;i++)
5931: for(j=1; j<=nlstate+ndeath;j++)
5932: fprintf(ficrespij," %1d-%1d",i,j);
5933: fprintf(ficrespij,"\n");
5934: for (h=0; h<=nhstepm; h++){
5935: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
5936: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 5937: for(i=1; i<=nlstate;i++)
5938: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 5939: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 5940: fprintf(ficrespij,"\n");
5941: }
1.183 brouard 5942: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5943: fprintf(ficrespij,"\n");
5944: }
1.180 brouard 5945: /*}*/
5946: }
1.184 brouard 5947: return 0;
1.180 brouard 5948: }
5949:
5950:
1.136 brouard 5951: /***********************************************/
5952: /**************** Main Program *****************/
5953: /***********************************************/
5954:
5955: int main(int argc, char *argv[])
5956: {
5957: #ifdef GSL
5958: const gsl_multimin_fminimizer_type *T;
5959: size_t iteri = 0, it;
5960: int rval = GSL_CONTINUE;
5961: int status = GSL_SUCCESS;
5962: double ssval;
5963: #endif
5964: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 5965: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5966:
5967: int jj, ll, li, lj, lk;
1.136 brouard 5968: int numlinepar=0; /* Current linenumber of parameter file */
5969: int itimes;
5970: int NDIM=2;
5971: int vpopbased=0;
5972:
1.164 brouard 5973: char ca[32], cb[32];
1.136 brouard 5974: /* FILE *fichtm; *//* Html File */
5975: /* FILE *ficgp;*/ /*Gnuplot File */
5976: struct stat info;
1.164 brouard 5977: double agedeb;
1.136 brouard 5978: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5979:
1.165 brouard 5980: double fret;
1.136 brouard 5981: double dum; /* Dummy variable */
5982: double ***p3mat;
5983: double ***mobaverage;
1.164 brouard 5984:
5985: char line[MAXLINE];
1.136 brouard 5986: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5987: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 5988: char *tok, *val; /* pathtot */
1.136 brouard 5989: int firstobs=1, lastobs=10;
1.164 brouard 5990: int c, h , cpt;
5991: int jl;
5992: int i1, j1, jk, stepsize;
5993: int *tab;
1.136 brouard 5994: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5995: int mobilav=0,popforecast=0;
5996: int hstepm, nhstepm;
5997: int agemortsup;
5998: float sumlpop=0.;
5999: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6000: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6001:
1.164 brouard 6002: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 6003: double ftolpl=FTOL;
6004: double **prlim;
6005: double ***param; /* Matrix of parameters */
6006: double *p;
6007: double **matcov; /* Matrix of covariance */
6008: double ***delti3; /* Scale */
6009: double *delti; /* Scale */
6010: double ***eij, ***vareij;
6011: double **varpl; /* Variances of prevalence limits by age */
6012: double *epj, vepp;
1.164 brouard 6013:
1.136 brouard 6014: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6015: double **ximort;
1.145 brouard 6016: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6017: int *dcwave;
6018:
1.164 brouard 6019: char z[1]="c";
1.136 brouard 6020:
6021: /*char *strt;*/
6022: char strtend[80];
1.126 brouard 6023:
1.164 brouard 6024:
1.126 brouard 6025: /* setlocale (LC_ALL, ""); */
6026: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6027: /* textdomain (PACKAGE); */
6028: /* setlocale (LC_CTYPE, ""); */
6029: /* setlocale (LC_MESSAGES, ""); */
6030:
6031: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6032: rstart_time = time(NULL);
6033: /* (void) gettimeofday(&start_time,&tzp);*/
6034: start_time = *localtime(&rstart_time);
1.126 brouard 6035: curr_time=start_time;
1.157 brouard 6036: /*tml = *localtime(&start_time.tm_sec);*/
6037: /* strcpy(strstart,asctime(&tml)); */
6038: strcpy(strstart,asctime(&start_time));
1.126 brouard 6039:
6040: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6041: /* tp.tm_sec = tp.tm_sec +86400; */
6042: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6043: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6044: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6045: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6046: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6047: /* strt=asctime(&tmg); */
6048: /* printf("Time(after) =%s",strstart); */
6049: /* (void) time (&time_value);
6050: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6051: * tm = *localtime(&time_value);
6052: * strstart=asctime(&tm);
6053: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6054: */
6055:
6056: nberr=0; /* Number of errors and warnings */
6057: nbwarn=0;
1.184 brouard 6058: #ifdef WIN32
6059: _getcwd(pathcd, size);
6060: #else
1.126 brouard 6061: getcwd(pathcd, size);
1.184 brouard 6062: #endif
1.126 brouard 6063:
6064: printf("\n%s\n%s",version,fullversion);
6065: if(argc <=1){
6066: printf("\nEnter the parameter file name: ");
6067: fgets(pathr,FILENAMELENGTH,stdin);
6068: i=strlen(pathr);
6069: if(pathr[i-1]=='\n')
6070: pathr[i-1]='\0';
1.156 brouard 6071: i=strlen(pathr);
6072: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6073: pathr[i-1]='\0';
1.126 brouard 6074: for (tok = pathr; tok != NULL; ){
6075: printf("Pathr |%s|\n",pathr);
6076: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6077: printf("val= |%s| pathr=%s\n",val,pathr);
6078: strcpy (pathtot, val);
6079: if(pathr[0] == '\0') break; /* Dirty */
6080: }
6081: }
6082: else{
6083: strcpy(pathtot,argv[1]);
6084: }
6085: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6086: /*cygwin_split_path(pathtot,path,optionfile);
6087: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6088: /* cutv(path,optionfile,pathtot,'\\');*/
6089:
6090: /* Split argv[0], imach program to get pathimach */
6091: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6092: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6093: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6094: /* strcpy(pathimach,argv[0]); */
6095: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6096: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6097: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6098: #ifdef WIN32
6099: _chdir(path); /* Can be a relative path */
6100: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6101: #else
1.126 brouard 6102: chdir(path); /* Can be a relative path */
1.184 brouard 6103: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6104: #endif
6105: printf("Current directory %s!\n",pathcd);
1.126 brouard 6106: strcpy(command,"mkdir ");
6107: strcat(command,optionfilefiname);
6108: if((outcmd=system(command)) != 0){
1.169 brouard 6109: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6110: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6111: /* fclose(ficlog); */
6112: /* exit(1); */
6113: }
6114: /* if((imk=mkdir(optionfilefiname))<0){ */
6115: /* perror("mkdir"); */
6116: /* } */
6117:
6118: /*-------- arguments in the command line --------*/
6119:
1.186 ! brouard 6120: /* Main Log file */
1.126 brouard 6121: strcat(filelog, optionfilefiname);
6122: strcat(filelog,".log"); /* */
6123: if((ficlog=fopen(filelog,"w"))==NULL) {
6124: printf("Problem with logfile %s\n",filelog);
6125: goto end;
6126: }
6127: fprintf(ficlog,"Log filename:%s\n",filelog);
6128: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6129: fprintf(ficlog,"\nEnter the parameter file name: \n");
6130: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6131: path=%s \n\
6132: optionfile=%s\n\
6133: optionfilext=%s\n\
1.156 brouard 6134: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6135:
1.167 brouard 6136: syscompilerinfo();
6137:
1.126 brouard 6138: printf("Local time (at start):%s",strstart);
6139: fprintf(ficlog,"Local time (at start): %s",strstart);
6140: fflush(ficlog);
6141: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6142: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6143:
6144: /* */
6145: strcpy(fileres,"r");
6146: strcat(fileres, optionfilefiname);
6147: strcat(fileres,".txt"); /* Other files have txt extension */
6148:
1.186 ! brouard 6149: /* Main ---------arguments file --------*/
1.126 brouard 6150:
6151: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6152: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6153: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6154: fflush(ficlog);
1.149 brouard 6155: /* goto end; */
6156: exit(70);
1.126 brouard 6157: }
6158:
6159:
6160:
6161: strcpy(filereso,"o");
6162: strcat(filereso,fileres);
6163: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6164: printf("Problem with Output resultfile: %s\n", filereso);
6165: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6166: fflush(ficlog);
6167: goto end;
6168: }
6169:
6170: /* Reads comments: lines beginning with '#' */
6171: numlinepar=0;
6172: while((c=getc(ficpar))=='#' && c!= EOF){
6173: ungetc(c,ficpar);
6174: fgets(line, MAXLINE, ficpar);
6175: numlinepar++;
1.141 brouard 6176: fputs(line,stdout);
1.126 brouard 6177: fputs(line,ficparo);
6178: fputs(line,ficlog);
6179: }
6180: ungetc(c,ficpar);
6181:
6182: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6183: numlinepar++;
1.186 ! brouard 6184: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
! 6185: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass);
! 6186: /*
! 6187:
! 6188:
! 6189:
! 6190: */
! 6191: printf("\nftol=%e \n", ftol);
! 6192: printf("stepm=%d \n", stepm);
! 6193: printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate);
! 6194: printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt);
! 6195: printf("model=%s\n",model);
1.126 brouard 6196: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6197: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6198: fflush(ficlog);
6199: while((c=getc(ficpar))=='#' && c!= EOF){
6200: ungetc(c,ficpar);
6201: fgets(line, MAXLINE, ficpar);
6202: numlinepar++;
1.141 brouard 6203: fputs(line, stdout);
6204: //puts(line);
1.126 brouard 6205: fputs(line,ficparo);
6206: fputs(line,ficlog);
6207: }
6208: ungetc(c,ficpar);
6209:
6210:
1.145 brouard 6211: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6212: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6213: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6214: v1+v2*age+v2*v3 makes cptcovn = 3
6215: */
6216: if (strlen(model)>1)
1.145 brouard 6217: 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*/
6218: else
6219: ncovmodel=2;
1.126 brouard 6220: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 6221: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6222: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6223: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6224: 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);
6225: 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);
6226: fflush(stdout);
6227: fclose (ficlog);
6228: goto end;
6229: }
1.126 brouard 6230: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6231: delti=delti3[1][1];
6232: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6233: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6234: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6235: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6236: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6237: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6238: fclose (ficparo);
6239: fclose (ficlog);
6240: goto end;
6241: exit(0);
6242: }
1.186 ! brouard 6243: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6244: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6245: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6246: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6247: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6248: matcov=matrix(1,npar,1,npar);
6249: }
6250: else{
1.145 brouard 6251: /* Read guessed parameters */
1.126 brouard 6252: /* Reads comments: lines beginning with '#' */
6253: while((c=getc(ficpar))=='#' && c!= EOF){
6254: ungetc(c,ficpar);
6255: fgets(line, MAXLINE, ficpar);
6256: numlinepar++;
1.141 brouard 6257: fputs(line,stdout);
1.126 brouard 6258: fputs(line,ficparo);
6259: fputs(line,ficlog);
6260: }
6261: ungetc(c,ficpar);
6262:
6263: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6264: for(i=1; i <=nlstate; i++){
6265: j=0;
6266: for(jj=1; jj <=nlstate+ndeath; jj++){
6267: if(jj==i) continue;
6268: j++;
6269: fscanf(ficpar,"%1d%1d",&i1,&j1);
6270: if ((i1 != i) && (j1 != j)){
6271: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6272: It might be a problem of design; if ncovcol and the model are correct\n \
6273: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6274: exit(1);
6275: }
6276: fprintf(ficparo,"%1d%1d",i1,j1);
6277: if(mle==1)
6278: printf("%1d%1d",i,j);
6279: fprintf(ficlog,"%1d%1d",i,j);
6280: for(k=1; k<=ncovmodel;k++){
6281: fscanf(ficpar," %lf",¶m[i][j][k]);
6282: if(mle==1){
6283: printf(" %lf",param[i][j][k]);
6284: fprintf(ficlog," %lf",param[i][j][k]);
6285: }
6286: else
6287: fprintf(ficlog," %lf",param[i][j][k]);
6288: fprintf(ficparo," %lf",param[i][j][k]);
6289: }
6290: fscanf(ficpar,"\n");
6291: numlinepar++;
6292: if(mle==1)
6293: printf("\n");
6294: fprintf(ficlog,"\n");
6295: fprintf(ficparo,"\n");
6296: }
6297: }
6298: fflush(ficlog);
6299:
1.145 brouard 6300: /* Reads scales values */
1.126 brouard 6301: p=param[1][1];
6302:
6303: /* Reads comments: lines beginning with '#' */
6304: while((c=getc(ficpar))=='#' && c!= EOF){
6305: ungetc(c,ficpar);
6306: fgets(line, MAXLINE, ficpar);
6307: numlinepar++;
1.141 brouard 6308: fputs(line,stdout);
1.126 brouard 6309: fputs(line,ficparo);
6310: fputs(line,ficlog);
6311: }
6312: ungetc(c,ficpar);
6313:
6314: for(i=1; i <=nlstate; i++){
6315: for(j=1; j <=nlstate+ndeath-1; j++){
6316: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6317: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6318: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6319: exit(1);
6320: }
6321: printf("%1d%1d",i,j);
6322: fprintf(ficparo,"%1d%1d",i1,j1);
6323: fprintf(ficlog,"%1d%1d",i1,j1);
6324: for(k=1; k<=ncovmodel;k++){
6325: fscanf(ficpar,"%le",&delti3[i][j][k]);
6326: printf(" %le",delti3[i][j][k]);
6327: fprintf(ficparo," %le",delti3[i][j][k]);
6328: fprintf(ficlog," %le",delti3[i][j][k]);
6329: }
6330: fscanf(ficpar,"\n");
6331: numlinepar++;
6332: printf("\n");
6333: fprintf(ficparo,"\n");
6334: fprintf(ficlog,"\n");
6335: }
6336: }
6337: fflush(ficlog);
6338:
1.145 brouard 6339: /* Reads covariance matrix */
1.126 brouard 6340: delti=delti3[1][1];
6341:
6342:
6343: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6344:
6345: /* Reads comments: lines beginning with '#' */
6346: while((c=getc(ficpar))=='#' && c!= EOF){
6347: ungetc(c,ficpar);
6348: fgets(line, MAXLINE, ficpar);
6349: numlinepar++;
1.141 brouard 6350: fputs(line,stdout);
1.126 brouard 6351: fputs(line,ficparo);
6352: fputs(line,ficlog);
6353: }
6354: ungetc(c,ficpar);
6355:
6356: matcov=matrix(1,npar,1,npar);
1.131 brouard 6357: for(i=1; i <=npar; i++)
6358: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6359:
1.126 brouard 6360: for(i=1; i <=npar; i++){
1.145 brouard 6361: fscanf(ficpar,"%s",str);
1.126 brouard 6362: if(mle==1)
6363: printf("%s",str);
6364: fprintf(ficlog,"%s",str);
6365: fprintf(ficparo,"%s",str);
6366: for(j=1; j <=i; j++){
6367: fscanf(ficpar," %le",&matcov[i][j]);
6368: if(mle==1){
6369: printf(" %.5le",matcov[i][j]);
6370: }
6371: fprintf(ficlog," %.5le",matcov[i][j]);
6372: fprintf(ficparo," %.5le",matcov[i][j]);
6373: }
6374: fscanf(ficpar,"\n");
6375: numlinepar++;
6376: if(mle==1)
6377: printf("\n");
6378: fprintf(ficlog,"\n");
6379: fprintf(ficparo,"\n");
6380: }
6381: for(i=1; i <=npar; i++)
6382: for(j=i+1;j<=npar;j++)
6383: matcov[i][j]=matcov[j][i];
6384:
6385: if(mle==1)
6386: printf("\n");
6387: fprintf(ficlog,"\n");
6388:
6389: fflush(ficlog);
6390:
6391: /*-------- Rewriting parameter file ----------*/
6392: strcpy(rfileres,"r"); /* "Rparameterfile */
6393: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6394: strcat(rfileres,"."); /* */
6395: strcat(rfileres,optionfilext); /* Other files have txt extension */
6396: if((ficres =fopen(rfileres,"w"))==NULL) {
6397: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6398: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6399: }
6400: fprintf(ficres,"#%s\n",version);
6401: } /* End of mle != -3 */
6402:
1.186 ! brouard 6403: /* Main data
! 6404: */
1.126 brouard 6405: n= lastobs;
6406: num=lvector(1,n);
6407: moisnais=vector(1,n);
6408: annais=vector(1,n);
6409: moisdc=vector(1,n);
6410: andc=vector(1,n);
6411: agedc=vector(1,n);
6412: cod=ivector(1,n);
6413: weight=vector(1,n);
6414: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6415: mint=matrix(1,maxwav,1,n);
6416: anint=matrix(1,maxwav,1,n);
1.131 brouard 6417: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6418: tab=ivector(1,NCOVMAX);
1.144 brouard 6419: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6420:
1.136 brouard 6421: /* Reads data from file datafile */
6422: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6423: goto end;
6424:
6425: /* Calculation of the number of parameters from char model */
1.137 brouard 6426: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6427: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6428: k=3 V4 Tvar[k=3]= 4 (from V4)
6429: k=2 V1 Tvar[k=2]= 1 (from V1)
6430: k=1 Tvar[1]=2 (from V2)
6431: */
6432: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6433: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6434: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6435: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6436: */
6437: /* For model-covariate k tells which data-covariate to use but
6438: because this model-covariate is a construction we invent a new column
6439: ncovcol + k1
6440: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6441: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6442: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6443: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6444: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6445: */
1.145 brouard 6446: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6447: 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 6448: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6449: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6450: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6451: 4 covariates (3 plus signs)
6452: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6453: */
1.136 brouard 6454:
1.186 ! brouard 6455: /* Main decodemodel */
! 6456:
1.136 brouard 6457: if(decodemodel(model, lastobs) == 1)
6458: goto end;
6459:
1.137 brouard 6460: if((double)(lastobs-imx)/(double)imx > 1.10){
6461: nbwarn++;
6462: 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);
6463: 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);
6464: }
1.136 brouard 6465: /* if(mle==1){*/
1.137 brouard 6466: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6467: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6468: }
6469:
6470: /*-calculation of age at interview from date of interview and age at death -*/
6471: agev=matrix(1,maxwav,1,imx);
6472:
6473: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6474: goto end;
6475:
1.126 brouard 6476:
1.136 brouard 6477: agegomp=(int)agemin;
6478: free_vector(moisnais,1,n);
6479: free_vector(annais,1,n);
1.126 brouard 6480: /* free_matrix(mint,1,maxwav,1,n);
6481: free_matrix(anint,1,maxwav,1,n);*/
6482: free_vector(moisdc,1,n);
6483: free_vector(andc,1,n);
1.145 brouard 6484: /* */
6485:
1.126 brouard 6486: wav=ivector(1,imx);
6487: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6488: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6489: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6490:
6491: /* Concatenates waves */
6492: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6493: /* */
6494:
1.126 brouard 6495: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6496:
6497: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6498: ncodemax[1]=1;
1.145 brouard 6499: Ndum =ivector(-1,NCOVMAX);
6500: if (ncovmodel > 2)
6501: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 ! brouard 6502: /* Nbcode gives the value of the lth modality of jth covariate, in
! 6503: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
! 6504: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6505:
6506: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6507: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 ! brouard 6508: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6509: h=0;
6510:
6511:
6512: /*if (cptcovn > 0) */
1.126 brouard 6513:
1.145 brouard 6514:
1.126 brouard 6515: m=pow(2,cptcoveff);
6516:
1.131 brouard 6517: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6518: 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 */
6519: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6520: 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 6521: h++;
1.141 brouard 6522: if (h>m)
1.136 brouard 6523: h=1;
1.144 brouard 6524: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 ! brouard 6525: * For k=4 covariates, h goes from 1 to 2**k
! 6526: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
! 6527: * h\k 1 2 3 4
1.143 brouard 6528: *______________________________
6529: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6530: * 2 2 1 1 1
6531: * 3 i=2 1 2 1 1
6532: * 4 2 2 1 1
6533: * 5 i=3 1 i=2 1 2 1
6534: * 6 2 1 2 1
6535: * 7 i=4 1 2 2 1
6536: * 8 2 2 2 1
6537: * 9 i=5 1 i=3 1 i=2 1 1
6538: * 10 2 1 1 1
6539: * 11 i=6 1 2 1 1
6540: * 12 2 2 1 1
6541: * 13 i=7 1 i=4 1 2 1
6542: * 14 2 1 2 1
6543: * 15 i=8 1 2 2 1
6544: * 16 2 2 2 1
6545: */
1.141 brouard 6546: codtab[h][k]=j;
1.186 ! brouard 6547: /* codtab[12][3]=1; */
1.145 brouard 6548: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6549: 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 6550: }
6551: }
6552: }
6553: }
6554: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6555: codtab[1][2]=1;codtab[2][2]=2; */
6556: /* for(i=1; i <=m ;i++){
6557: for(k=1; k <=cptcovn; k++){
1.131 brouard 6558: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6559: }
6560: printf("\n");
6561: }
6562: scanf("%d",i);*/
1.145 brouard 6563:
6564: free_ivector(Ndum,-1,NCOVMAX);
6565:
6566:
1.126 brouard 6567:
1.186 ! brouard 6568: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6569: strcpy(optionfilegnuplot,optionfilefiname);
6570: if(mle==-3)
6571: strcat(optionfilegnuplot,"-mort");
6572: strcat(optionfilegnuplot,".gp");
6573:
6574: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6575: printf("Problem with file %s",optionfilegnuplot);
6576: }
6577: else{
6578: fprintf(ficgp,"\n# %s\n", version);
6579: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6580: //fprintf(ficgp,"set missing 'NaNq'\n");
6581: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6582: }
6583: /* fclose(ficgp);*/
1.186 ! brouard 6584:
! 6585:
! 6586: /* Initialisation of --------- index.htm --------*/
1.126 brouard 6587:
6588: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6589: if(mle==-3)
6590: strcat(optionfilehtm,"-mort");
6591: strcat(optionfilehtm,".htm");
6592: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6593: printf("Problem with %s \n",optionfilehtm);
6594: exit(0);
1.126 brouard 6595: }
6596:
6597: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6598: strcat(optionfilehtmcov,"-cov.htm");
6599: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6600: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6601: }
6602: else{
6603: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6604: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6605: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6606: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6607: }
6608:
6609: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6610: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6611: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6612: \n\
6613: <hr size=\"2\" color=\"#EC5E5E\">\
6614: <ul><li><h4>Parameter files</h4>\n\
6615: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6616: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6617: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6618: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6619: - Date and time at start: %s</ul>\n",\
6620: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6621: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6622: fileres,fileres,\
6623: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6624: fflush(fichtm);
6625:
6626: strcpy(pathr,path);
6627: strcat(pathr,optionfilefiname);
1.184 brouard 6628: #ifdef WIN32
6629: _chdir(optionfilefiname); /* Move to directory named optionfile */
6630: #else
1.126 brouard 6631: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 6632: #endif
6633:
1.126 brouard 6634:
6635: /* Calculates basic frequencies. Computes observed prevalence at single age
6636: and prints on file fileres'p'. */
6637: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6638:
6639: fprintf(fichtm,"\n");
6640: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6641: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6642: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6643: imx,agemin,agemax,jmin,jmax,jmean);
6644: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6645: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6646: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6647: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6648: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6649:
6650:
6651: /* For Powell, parameters are in a vector p[] starting at p[1]
6652: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6653: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6654:
6655: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 ! brouard 6656: /* For mortality only */
1.126 brouard 6657: if (mle==-3){
1.136 brouard 6658: ximort=matrix(1,NDIM,1,NDIM);
1.186 ! brouard 6659: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6660: cens=ivector(1,n);
6661: ageexmed=vector(1,n);
6662: agecens=vector(1,n);
6663: dcwave=ivector(1,n);
6664:
6665: for (i=1; i<=imx; i++){
6666: dcwave[i]=-1;
6667: for (m=firstpass; m<=lastpass; m++)
6668: if (s[m][i]>nlstate) {
6669: dcwave[i]=m;
6670: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6671: break;
6672: }
6673: }
6674:
6675: for (i=1; i<=imx; i++) {
6676: if (wav[i]>0){
6677: ageexmed[i]=agev[mw[1][i]][i];
6678: j=wav[i];
6679: agecens[i]=1.;
6680:
6681: if (ageexmed[i]> 1 && wav[i] > 0){
6682: agecens[i]=agev[mw[j][i]][i];
6683: cens[i]= 1;
6684: }else if (ageexmed[i]< 1)
6685: cens[i]= -1;
6686: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6687: cens[i]=0 ;
6688: }
6689: else cens[i]=-1;
6690: }
6691:
6692: for (i=1;i<=NDIM;i++) {
6693: for (j=1;j<=NDIM;j++)
6694: ximort[i][j]=(i == j ? 1.0 : 0.0);
6695: }
6696:
1.145 brouard 6697: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6698: /*printf("%lf %lf", p[1], p[2]);*/
6699:
6700:
1.136 brouard 6701: #ifdef GSL
6702: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6703: #else
1.126 brouard 6704: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6705: #endif
1.126 brouard 6706: strcpy(filerespow,"pow-mort");
6707: strcat(filerespow,fileres);
6708: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6709: printf("Problem with resultfile: %s\n", filerespow);
6710: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6711: }
1.136 brouard 6712: #ifdef GSL
6713: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6714: #else
1.126 brouard 6715: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6716: #endif
1.126 brouard 6717: /* for (i=1;i<=nlstate;i++)
6718: for(j=1;j<=nlstate+ndeath;j++)
6719: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6720: */
6721: fprintf(ficrespow,"\n");
1.136 brouard 6722: #ifdef GSL
6723: /* gsl starts here */
6724: T = gsl_multimin_fminimizer_nmsimplex;
6725: gsl_multimin_fminimizer *sfm = NULL;
6726: gsl_vector *ss, *x;
6727: gsl_multimin_function minex_func;
6728:
6729: /* Initial vertex size vector */
6730: ss = gsl_vector_alloc (NDIM);
6731:
6732: if (ss == NULL){
6733: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6734: }
6735: /* Set all step sizes to 1 */
6736: gsl_vector_set_all (ss, 0.001);
6737:
6738: /* Starting point */
1.126 brouard 6739:
1.136 brouard 6740: x = gsl_vector_alloc (NDIM);
6741:
6742: if (x == NULL){
6743: gsl_vector_free(ss);
6744: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6745: }
6746:
6747: /* Initialize method and iterate */
6748: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 ! brouard 6749: /* gsl_vector_set(x, 0, 0.0268); */
! 6750: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 6751: gsl_vector_set(x, 0, p[1]);
6752: gsl_vector_set(x, 1, p[2]);
6753:
6754: minex_func.f = &gompertz_f;
6755: minex_func.n = NDIM;
6756: minex_func.params = (void *)&p; /* ??? */
6757:
6758: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6759: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6760:
6761: printf("Iterations beginning .....\n\n");
6762: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6763:
6764: iteri=0;
6765: while (rval == GSL_CONTINUE){
6766: iteri++;
6767: status = gsl_multimin_fminimizer_iterate(sfm);
6768:
6769: if (status) printf("error: %s\n", gsl_strerror (status));
6770: fflush(0);
6771:
6772: if (status)
6773: break;
6774:
6775: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6776: ssval = gsl_multimin_fminimizer_size (sfm);
6777:
6778: if (rval == GSL_SUCCESS)
6779: printf ("converged to a local maximum at\n");
6780:
6781: printf("%5d ", iteri);
6782: for (it = 0; it < NDIM; it++){
6783: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6784: }
6785: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6786: }
6787:
6788: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6789:
6790: gsl_vector_free(x); /* initial values */
6791: gsl_vector_free(ss); /* inital step size */
6792: for (it=0; it<NDIM; it++){
6793: p[it+1]=gsl_vector_get(sfm->x,it);
6794: fprintf(ficrespow," %.12lf", p[it]);
6795: }
6796: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6797: #endif
6798: #ifdef POWELL
6799: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6800: #endif
1.126 brouard 6801: fclose(ficrespow);
6802:
6803: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6804:
6805: for(i=1; i <=NDIM; i++)
6806: for(j=i+1;j<=NDIM;j++)
6807: matcov[i][j]=matcov[j][i];
6808:
6809: printf("\nCovariance matrix\n ");
6810: for(i=1; i <=NDIM; i++) {
6811: for(j=1;j<=NDIM;j++){
6812: printf("%f ",matcov[i][j]);
6813: }
6814: printf("\n ");
6815: }
6816:
6817: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6818: for (i=1;i<=NDIM;i++)
6819: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6820:
6821: lsurv=vector(1,AGESUP);
6822: lpop=vector(1,AGESUP);
6823: tpop=vector(1,AGESUP);
6824: lsurv[agegomp]=100000;
6825:
6826: for (k=agegomp;k<=AGESUP;k++) {
6827: agemortsup=k;
6828: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6829: }
6830:
6831: for (k=agegomp;k<agemortsup;k++)
6832: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6833:
6834: for (k=agegomp;k<agemortsup;k++){
6835: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6836: sumlpop=sumlpop+lpop[k];
6837: }
6838:
6839: tpop[agegomp]=sumlpop;
6840: for (k=agegomp;k<(agemortsup-3);k++){
6841: /* tpop[k+1]=2;*/
6842: tpop[k+1]=tpop[k]-lpop[k];
6843: }
6844:
6845:
6846: printf("\nAge lx qx dx Lx Tx e(x)\n");
6847: for (k=agegomp;k<(agemortsup-2);k++)
6848: 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]);
6849:
6850:
6851: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6852: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6853:
6854: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6855: stepm, weightopt,\
6856: model,imx,p,matcov,agemortsup);
6857:
6858: free_vector(lsurv,1,AGESUP);
6859: free_vector(lpop,1,AGESUP);
6860: free_vector(tpop,1,AGESUP);
1.136 brouard 6861: #ifdef GSL
6862: free_ivector(cens,1,n);
6863: free_vector(agecens,1,n);
6864: free_ivector(dcwave,1,n);
6865: free_matrix(ximort,1,NDIM,1,NDIM);
6866: #endif
1.186 ! brouard 6867: } /* Endof if mle==-3 mortality only */
! 6868: /* Standard maximisation */
1.126 brouard 6869: else{ /* For mle >=1 */
1.132 brouard 6870: globpr=0;/* debug */
1.186 ! brouard 6871: /* Computes likelihood for initial parameters */
1.132 brouard 6872: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6873: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6874: for (k=1; k<=npar;k++)
6875: printf(" %d %8.5f",k,p[k]);
6876: printf("\n");
1.186 ! brouard 6877: globpr=1; /* again, to print the contributions */
1.126 brouard 6878: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6879: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6880: for (k=1; k<=npar;k++)
6881: printf(" %d %8.5f",k,p[k]);
6882: printf("\n");
1.186 ! brouard 6883: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 6884: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6885: }
6886:
6887: /*--------- results files --------------*/
6888: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6889:
6890:
6891: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6892: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6893: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6894: for(i=1,jk=1; i <=nlstate; i++){
6895: for(k=1; k <=(nlstate+ndeath); k++){
6896: if (k != i) {
6897: printf("%d%d ",i,k);
6898: fprintf(ficlog,"%d%d ",i,k);
6899: fprintf(ficres,"%1d%1d ",i,k);
6900: for(j=1; j <=ncovmodel; j++){
6901: printf("%lf ",p[jk]);
6902: fprintf(ficlog,"%lf ",p[jk]);
6903: fprintf(ficres,"%lf ",p[jk]);
6904: jk++;
6905: }
6906: printf("\n");
6907: fprintf(ficlog,"\n");
6908: fprintf(ficres,"\n");
6909: }
6910: }
6911: }
6912: if(mle!=0){
6913: /* Computing hessian and covariance matrix */
6914: ftolhess=ftol; /* Usually correct */
6915: hesscov(matcov, p, npar, delti, ftolhess, func);
6916: }
6917: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6918: printf("# Scales (for hessian or gradient estimation)\n");
6919: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6920: for(i=1,jk=1; i <=nlstate; i++){
6921: for(j=1; j <=nlstate+ndeath; j++){
6922: if (j!=i) {
6923: fprintf(ficres,"%1d%1d",i,j);
6924: printf("%1d%1d",i,j);
6925: fprintf(ficlog,"%1d%1d",i,j);
6926: for(k=1; k<=ncovmodel;k++){
6927: printf(" %.5e",delti[jk]);
6928: fprintf(ficlog," %.5e",delti[jk]);
6929: fprintf(ficres," %.5e",delti[jk]);
6930: jk++;
6931: }
6932: printf("\n");
6933: fprintf(ficlog,"\n");
6934: fprintf(ficres,"\n");
6935: }
6936: }
6937: }
6938:
6939: 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");
6940: if(mle>=1)
6941: 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");
6942: 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");
6943: /* # 121 Var(a12)\n\ */
6944: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6945: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6946: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6947: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6948: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6949: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6950: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6951:
6952:
6953: /* Just to have a covariance matrix which will be more understandable
6954: even is we still don't want to manage dictionary of variables
6955: */
6956: for(itimes=1;itimes<=2;itimes++){
6957: jj=0;
6958: for(i=1; i <=nlstate; i++){
6959: for(j=1; j <=nlstate+ndeath; j++){
6960: if(j==i) continue;
6961: for(k=1; k<=ncovmodel;k++){
6962: jj++;
6963: ca[0]= k+'a'-1;ca[1]='\0';
6964: if(itimes==1){
6965: if(mle>=1)
6966: printf("#%1d%1d%d",i,j,k);
6967: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6968: fprintf(ficres,"#%1d%1d%d",i,j,k);
6969: }else{
6970: if(mle>=1)
6971: printf("%1d%1d%d",i,j,k);
6972: fprintf(ficlog,"%1d%1d%d",i,j,k);
6973: fprintf(ficres,"%1d%1d%d",i,j,k);
6974: }
6975: ll=0;
6976: for(li=1;li <=nlstate; li++){
6977: for(lj=1;lj <=nlstate+ndeath; lj++){
6978: if(lj==li) continue;
6979: for(lk=1;lk<=ncovmodel;lk++){
6980: ll++;
6981: if(ll<=jj){
6982: cb[0]= lk +'a'-1;cb[1]='\0';
6983: if(ll<jj){
6984: if(itimes==1){
6985: if(mle>=1)
6986: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6987: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6988: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6989: }else{
6990: if(mle>=1)
6991: printf(" %.5e",matcov[jj][ll]);
6992: fprintf(ficlog," %.5e",matcov[jj][ll]);
6993: fprintf(ficres," %.5e",matcov[jj][ll]);
6994: }
6995: }else{
6996: if(itimes==1){
6997: if(mle>=1)
6998: printf(" Var(%s%1d%1d)",ca,i,j);
6999: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7000: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7001: }else{
7002: if(mle>=1)
7003: printf(" %.5e",matcov[jj][ll]);
7004: fprintf(ficlog," %.5e",matcov[jj][ll]);
7005: fprintf(ficres," %.5e",matcov[jj][ll]);
7006: }
7007: }
7008: }
7009: } /* end lk */
7010: } /* end lj */
7011: } /* end li */
7012: if(mle>=1)
7013: printf("\n");
7014: fprintf(ficlog,"\n");
7015: fprintf(ficres,"\n");
7016: numlinepar++;
7017: } /* end k*/
7018: } /*end j */
7019: } /* end i */
7020: } /* end itimes */
7021:
7022: fflush(ficlog);
7023: fflush(ficres);
7024:
7025: while((c=getc(ficpar))=='#' && c!= EOF){
7026: ungetc(c,ficpar);
7027: fgets(line, MAXLINE, ficpar);
1.141 brouard 7028: fputs(line,stdout);
1.126 brouard 7029: fputs(line,ficparo);
7030: }
7031: ungetc(c,ficpar);
7032:
7033: estepm=0;
7034: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7035: if (estepm==0 || estepm < stepm) estepm=stepm;
7036: if (fage <= 2) {
7037: bage = ageminpar;
7038: fage = agemaxpar;
7039: }
7040:
7041: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7042: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7043: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 ! brouard 7044:
! 7045: /* Other stuffs, more or less useful */
1.126 brouard 7046: while((c=getc(ficpar))=='#' && c!= EOF){
7047: ungetc(c,ficpar);
7048: fgets(line, MAXLINE, ficpar);
1.141 brouard 7049: fputs(line,stdout);
1.126 brouard 7050: fputs(line,ficparo);
7051: }
7052: ungetc(c,ficpar);
7053:
7054: 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);
7055: 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);
7056: 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);
7057: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7058: 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);
7059:
7060: while((c=getc(ficpar))=='#' && c!= EOF){
7061: ungetc(c,ficpar);
7062: fgets(line, MAXLINE, ficpar);
1.141 brouard 7063: fputs(line,stdout);
1.126 brouard 7064: fputs(line,ficparo);
7065: }
7066: ungetc(c,ficpar);
7067:
7068:
7069: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7070: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7071:
7072: fscanf(ficpar,"pop_based=%d\n",&popbased);
7073: fprintf(ficparo,"pop_based=%d\n",popbased);
7074: fprintf(ficres,"pop_based=%d\n",popbased);
7075:
7076: while((c=getc(ficpar))=='#' && c!= EOF){
7077: ungetc(c,ficpar);
7078: fgets(line, MAXLINE, ficpar);
1.141 brouard 7079: fputs(line,stdout);
1.126 brouard 7080: fputs(line,ficparo);
7081: }
7082: ungetc(c,ficpar);
7083:
7084: 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);
7085: 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);
7086: 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);
7087: 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);
7088: 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);
7089: /* day and month of proj2 are not used but only year anproj2.*/
7090:
7091:
7092:
1.145 brouard 7093: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7094: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7095:
7096: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7097: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7098:
7099: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7100: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7101: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7102:
7103: /*------------ free_vector -------------*/
7104: /* chdir(path); */
7105:
7106: free_ivector(wav,1,imx);
7107: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7108: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7109: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7110: free_lvector(num,1,n);
7111: free_vector(agedc,1,n);
7112: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7113: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7114: fclose(ficparo);
7115: fclose(ficres);
7116:
7117:
1.186 ! brouard 7118: /* Other results (useful)*/
! 7119:
! 7120:
1.126 brouard 7121: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7122: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7123: prlim=matrix(1,nlstate,1,nlstate);
7124: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7125: fclose(ficrespl);
7126:
1.145 brouard 7127: #ifdef FREEEXIT2
7128: #include "freeexit2.h"
7129: #endif
7130:
1.126 brouard 7131: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7132: /*#include "hpijx.h"*/
7133: hPijx(p, bage, fage);
1.145 brouard 7134: fclose(ficrespij);
1.126 brouard 7135:
1.145 brouard 7136: /*-------------- Variance of one-step probabilities---*/
7137: k=1;
1.126 brouard 7138: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7139:
7140:
7141: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7142: for(i=1;i<=AGESUP;i++)
7143: for(j=1;j<=NCOVMAX;j++)
7144: for(k=1;k<=NCOVMAX;k++)
7145: probs[i][j][k]=0.;
7146:
7147: /*---------- Forecasting ------------------*/
7148: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7149: if(prevfcast==1){
7150: /* if(stepm ==1){*/
7151: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7152: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7153: /* } */
7154: /* else{ */
7155: /* erreur=108; */
7156: /* 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); */
7157: /* 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); */
7158: /* } */
7159: }
1.186 ! brouard 7160:
! 7161: /* ------ Other prevalence ratios------------ */
1.126 brouard 7162:
1.127 brouard 7163: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7164:
7165: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7166: /* 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",\
7167: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7168: */
1.126 brouard 7169:
1.127 brouard 7170: if (mobilav!=0) {
7171: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7172: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7173: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7174: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7175: }
1.126 brouard 7176: }
7177:
7178:
1.127 brouard 7179: /*---------- Health expectancies, no variances ------------*/
7180:
1.126 brouard 7181: strcpy(filerese,"e");
7182: strcat(filerese,fileres);
7183: if((ficreseij=fopen(filerese,"w"))==NULL) {
7184: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7185: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7186: }
7187: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7188: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7189: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7190: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7191:
7192: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7193: fprintf(ficreseij,"\n#****** ");
7194: for(j=1;j<=cptcoveff;j++) {
7195: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7196: }
7197: fprintf(ficreseij,"******\n");
7198:
7199: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7200: oldm=oldms;savm=savms;
7201: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7202:
7203: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7204: /*}*/
1.127 brouard 7205: }
7206: fclose(ficreseij);
7207:
7208:
7209: /*---------- Health expectancies and variances ------------*/
7210:
7211:
7212: strcpy(filerest,"t");
7213: strcat(filerest,fileres);
7214: if((ficrest=fopen(filerest,"w"))==NULL) {
7215: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7216: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7217: }
7218: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7219: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7220:
1.126 brouard 7221:
7222: strcpy(fileresstde,"stde");
7223: strcat(fileresstde,fileres);
7224: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7225: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7226: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7227: }
7228: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7229: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7230:
7231: strcpy(filerescve,"cve");
7232: strcat(filerescve,fileres);
7233: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7234: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7235: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7236: }
7237: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7238: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7239:
7240: strcpy(fileresv,"v");
7241: strcat(fileresv,fileres);
7242: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7243: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7244: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7245: }
7246: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7247: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7248:
1.145 brouard 7249: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7250: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7251:
7252: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7253: fprintf(ficrest,"\n#****** ");
1.126 brouard 7254: for(j=1;j<=cptcoveff;j++)
7255: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7256: fprintf(ficrest,"******\n");
7257:
7258: fprintf(ficresstdeij,"\n#****** ");
7259: fprintf(ficrescveij,"\n#****** ");
7260: for(j=1;j<=cptcoveff;j++) {
7261: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7262: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7263: }
7264: fprintf(ficresstdeij,"******\n");
7265: fprintf(ficrescveij,"******\n");
7266:
7267: fprintf(ficresvij,"\n#****** ");
7268: for(j=1;j<=cptcoveff;j++)
7269: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7270: fprintf(ficresvij,"******\n");
7271:
7272: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7273: oldm=oldms;savm=savms;
1.127 brouard 7274: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7275: /*
7276: */
7277: /* goto endfree; */
1.126 brouard 7278:
7279: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7280: pstamp(ficrest);
1.145 brouard 7281:
7282:
1.128 brouard 7283: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7284: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7285: cptcod= 0; /* To be deleted */
7286: 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 7287: 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 7288: if(vpopbased==1)
7289: 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);
7290: else
7291: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7292: fprintf(ficrest,"# Age e.. (std) ");
7293: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7294: fprintf(ficrest,"\n");
1.126 brouard 7295:
1.128 brouard 7296: epj=vector(1,nlstate+1);
7297: for(age=bage; age <=fage ;age++){
7298: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7299: if (vpopbased==1) {
7300: if(mobilav ==0){
7301: for(i=1; i<=nlstate;i++)
7302: prlim[i][i]=probs[(int)age][i][k];
7303: }else{ /* mobilav */
7304: for(i=1; i<=nlstate;i++)
7305: prlim[i][i]=mobaverage[(int)age][i][k];
7306: }
1.126 brouard 7307: }
7308:
1.128 brouard 7309: fprintf(ficrest," %4.0f",age);
7310: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7311: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7312: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7313: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7314: }
7315: epj[nlstate+1] +=epj[j];
1.126 brouard 7316: }
7317:
1.128 brouard 7318: for(i=1, vepp=0.;i <=nlstate;i++)
7319: for(j=1;j <=nlstate;j++)
7320: vepp += vareij[i][j][(int)age];
7321: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7322: for(j=1;j <=nlstate;j++){
7323: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7324: }
7325: fprintf(ficrest,"\n");
1.126 brouard 7326: }
7327: }
7328: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7329: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7330: free_vector(epj,1,nlstate+1);
1.145 brouard 7331: /*}*/
1.126 brouard 7332: }
7333: free_vector(weight,1,n);
1.145 brouard 7334: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7335: free_imatrix(s,1,maxwav+1,1,n);
7336: free_matrix(anint,1,maxwav,1,n);
7337: free_matrix(mint,1,maxwav,1,n);
7338: free_ivector(cod,1,n);
7339: free_ivector(tab,1,NCOVMAX);
7340: fclose(ficresstdeij);
7341: fclose(ficrescveij);
7342: fclose(ficresvij);
7343: fclose(ficrest);
7344: fclose(ficpar);
7345:
7346: /*------- Variance of period (stable) prevalence------*/
7347:
7348: strcpy(fileresvpl,"vpl");
7349: strcat(fileresvpl,fileres);
7350: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7351: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7352: exit(0);
7353: }
7354: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7355:
1.145 brouard 7356: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7357: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7358:
7359: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7360: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7361: for(j=1;j<=cptcoveff;j++)
7362: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7363: fprintf(ficresvpl,"******\n");
7364:
7365: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7366: oldm=oldms;savm=savms;
7367: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7368: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7369: /*}*/
1.126 brouard 7370: }
7371:
7372: fclose(ficresvpl);
7373:
7374: /*---------- End : free ----------------*/
7375: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7376: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7377: } /* mle==-3 arrives here for freeing */
1.164 brouard 7378: /* endfree:*/
1.141 brouard 7379: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7380: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7381: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7382: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7383: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7384: free_matrix(covar,0,NCOVMAX,1,n);
7385: free_matrix(matcov,1,npar,1,npar);
7386: /*free_vector(delti,1,npar);*/
7387: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7388: free_matrix(agev,1,maxwav,1,imx);
7389: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7390:
1.145 brouard 7391: free_ivector(ncodemax,1,NCOVMAX);
7392: free_ivector(Tvar,1,NCOVMAX);
7393: free_ivector(Tprod,1,NCOVMAX);
7394: free_ivector(Tvaraff,1,NCOVMAX);
7395: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7396:
7397: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7398: free_imatrix(codtab,1,100,1,10);
7399: fflush(fichtm);
7400: fflush(ficgp);
7401:
7402:
7403: if((nberr >0) || (nbwarn>0)){
7404: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7405: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7406: }else{
7407: printf("End of Imach\n");
7408: fprintf(ficlog,"End of Imach\n");
7409: }
7410: printf("See log file on %s\n",filelog);
7411: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7412: /*(void) gettimeofday(&end_time,&tzp);*/
7413: rend_time = time(NULL);
7414: end_time = *localtime(&rend_time);
7415: /* tml = *localtime(&end_time.tm_sec); */
7416: strcpy(strtend,asctime(&end_time));
1.126 brouard 7417: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7418: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7419: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7420:
1.157 brouard 7421: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7422: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7423: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7424: /* printf("Total time was %d uSec.\n", total_usecs);*/
7425: /* if(fileappend(fichtm,optionfilehtm)){ */
7426: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7427: fclose(fichtm);
7428: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7429: fclose(fichtmcov);
7430: fclose(ficgp);
7431: fclose(ficlog);
7432: /*------ End -----------*/
7433:
7434:
7435: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7436: #ifdef WIN32
7437: if (_chdir(pathcd) != 0)
7438: printf("Can't move to directory %s!\n",path);
7439: if(_getcwd(pathcd,MAXLINE) > 0)
7440: #else
1.126 brouard 7441: if(chdir(pathcd) != 0)
1.184 brouard 7442: printf("Can't move to directory %s!\n", path);
7443: if (getcwd(pathcd, MAXLINE) > 0)
7444: #endif
1.126 brouard 7445: printf("Current directory %s!\n",pathcd);
7446: /*strcat(plotcmd,CHARSEPARATOR);*/
7447: sprintf(plotcmd,"gnuplot");
1.157 brouard 7448: #ifdef _WIN32
1.126 brouard 7449: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7450: #endif
7451: if(!stat(plotcmd,&info)){
1.158 brouard 7452: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7453: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7454: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7455: }else
7456: strcpy(pplotcmd,plotcmd);
1.157 brouard 7457: #ifdef __unix
1.126 brouard 7458: strcpy(plotcmd,GNUPLOTPROGRAM);
7459: if(!stat(plotcmd,&info)){
1.158 brouard 7460: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7461: }else
7462: strcpy(pplotcmd,plotcmd);
7463: #endif
7464: }else
7465: strcpy(pplotcmd,plotcmd);
7466:
7467: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7468: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7469:
7470: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7471: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7472: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7473: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7474: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7475: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7476: }
1.158 brouard 7477: printf(" Successful, please wait...");
1.126 brouard 7478: while (z[0] != 'q') {
7479: /* chdir(path); */
1.154 brouard 7480: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7481: scanf("%s",z);
7482: /* if (z[0] == 'c') system("./imach"); */
7483: if (z[0] == 'e') {
1.158 brouard 7484: #ifdef __APPLE__
1.152 brouard 7485: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7486: #elif __linux
7487: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7488: #else
1.152 brouard 7489: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7490: #endif
7491: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7492: system(pplotcmd);
1.126 brouard 7493: }
7494: else if (z[0] == 'g') system(plotcmd);
7495: else if (z[0] == 'q') exit(0);
7496: }
7497: end:
7498: while (z[0] != 'q') {
7499: printf("\nType q for exiting: ");
7500: scanf("%s",z);
7501: }
7502: }
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