Annotation of imach/src/imach.c, revision 1.171
1.171 ! brouard 1: /* $Id: imach.c,v 1.170 2014/12/23 11:17:12 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.171 ! brouard 4: Revision 1.170 2014/12/23 11:17:12 brouard
! 5: Summary: Cleaning some \%% back to %%
! 6:
! 7: The escape was mandatory for a specific compiler (which one?), but too many warnings.
! 8:
1.170 brouard 9: Revision 1.169 2014/12/22 23:08:31 brouard
10: Summary: 0.98p
11:
12: Outputs some informations on compiler used, OS etc. Testing on different platforms.
13:
1.169 brouard 14: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 15: Summary: update
1.169 brouard 16:
1.168 brouard 17: Revision 1.167 2014/12/22 13:50:56 brouard
18: Summary: Testing uname and compiler version and if compiled 32 or 64
19:
20: Testing on Linux 64
21:
1.167 brouard 22: Revision 1.166 2014/12/22 11:40:47 brouard
23: *** empty log message ***
24:
1.166 brouard 25: Revision 1.165 2014/12/16 11:20:36 brouard
26: Summary: After compiling on Visual C
27:
28: * imach.c (Module): Merging 1.61 to 1.162
29:
1.165 brouard 30: Revision 1.164 2014/12/16 10:52:11 brouard
31: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
32:
33: * imach.c (Module): Merging 1.61 to 1.162
34:
1.164 brouard 35: Revision 1.163 2014/12/16 10:30:11 brouard
36: * imach.c (Module): Merging 1.61 to 1.162
37:
1.163 brouard 38: Revision 1.162 2014/09/25 11:43:39 brouard
39: Summary: temporary backup 0.99!
40:
1.162 brouard 41: Revision 1.1 2014/09/16 11:06:58 brouard
42: Summary: With some code (wrong) for nlopt
43:
44: Author:
45:
46: Revision 1.161 2014/09/15 20:41:41 brouard
47: Summary: Problem with macro SQR on Intel compiler
48:
1.161 brouard 49: Revision 1.160 2014/09/02 09:24:05 brouard
50: *** empty log message ***
51:
1.160 brouard 52: Revision 1.159 2014/09/01 10:34:10 brouard
53: Summary: WIN32
54: Author: Brouard
55:
1.159 brouard 56: Revision 1.158 2014/08/27 17:11:51 brouard
57: *** empty log message ***
58:
1.158 brouard 59: Revision 1.157 2014/08/27 16:26:55 brouard
60: Summary: Preparing windows Visual studio version
61: Author: Brouard
62:
63: In order to compile on Visual studio, time.h is now correct and time_t
64: and tm struct should be used. difftime should be used but sometimes I
65: just make the differences in raw time format (time(&now).
66: Trying to suppress #ifdef LINUX
67: Add xdg-open for __linux in order to open default browser.
68:
1.157 brouard 69: Revision 1.156 2014/08/25 20:10:10 brouard
70: *** empty log message ***
71:
1.156 brouard 72: Revision 1.155 2014/08/25 18:32:34 brouard
73: Summary: New compile, minor changes
74: Author: Brouard
75:
1.155 brouard 76: Revision 1.154 2014/06/20 17:32:08 brouard
77: Summary: Outputs now all graphs of convergence to period prevalence
78:
1.154 brouard 79: Revision 1.153 2014/06/20 16:45:46 brouard
80: Summary: If 3 live state, convergence to period prevalence on same graph
81: Author: Brouard
82:
1.153 brouard 83: Revision 1.152 2014/06/18 17:54:09 brouard
84: Summary: open browser, use gnuplot on same dir than imach if not found in the path
85:
1.152 brouard 86: Revision 1.151 2014/06/18 16:43:30 brouard
87: *** empty log message ***
88:
1.151 brouard 89: Revision 1.150 2014/06/18 16:42:35 brouard
90: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
91: Author: brouard
92:
1.150 brouard 93: Revision 1.149 2014/06/18 15:51:14 brouard
94: Summary: Some fixes in parameter files errors
95: Author: Nicolas Brouard
96:
1.149 brouard 97: Revision 1.148 2014/06/17 17:38:48 brouard
98: Summary: Nothing new
99: Author: Brouard
100:
101: Just a new packaging for OS/X version 0.98nS
102:
1.148 brouard 103: Revision 1.147 2014/06/16 10:33:11 brouard
104: *** empty log message ***
105:
1.147 brouard 106: Revision 1.146 2014/06/16 10:20:28 brouard
107: Summary: Merge
108: Author: Brouard
109:
110: Merge, before building revised version.
111:
1.146 brouard 112: Revision 1.145 2014/06/10 21:23:15 brouard
113: Summary: Debugging with valgrind
114: Author: Nicolas Brouard
115:
116: Lot of changes in order to output the results with some covariates
117: After the Edimburgh REVES conference 2014, it seems mandatory to
118: improve the code.
119: No more memory valgrind error but a lot has to be done in order to
120: continue the work of splitting the code into subroutines.
121: Also, decodemodel has been improved. Tricode is still not
122: optimal. nbcode should be improved. Documentation has been added in
123: the source code.
124:
1.144 brouard 125: Revision 1.143 2014/01/26 09:45:38 brouard
126: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
127:
128: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
129: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
130:
1.143 brouard 131: Revision 1.142 2014/01/26 03:57:36 brouard
132: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
133:
134: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
135:
1.142 brouard 136: Revision 1.141 2014/01/26 02:42:01 brouard
137: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
138:
1.141 brouard 139: Revision 1.140 2011/09/02 10:37:54 brouard
140: Summary: times.h is ok with mingw32 now.
141:
1.140 brouard 142: Revision 1.139 2010/06/14 07:50:17 brouard
143: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
144: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
145:
1.139 brouard 146: Revision 1.138 2010/04/30 18:19:40 brouard
147: *** empty log message ***
148:
1.138 brouard 149: Revision 1.137 2010/04/29 18:11:38 brouard
150: (Module): Checking covariates for more complex models
151: than V1+V2. A lot of change to be done. Unstable.
152:
1.137 brouard 153: Revision 1.136 2010/04/26 20:30:53 brouard
154: (Module): merging some libgsl code. Fixing computation
155: of likelione (using inter/intrapolation if mle = 0) in order to
156: get same likelihood as if mle=1.
157: Some cleaning of code and comments added.
158:
1.136 brouard 159: Revision 1.135 2009/10/29 15:33:14 brouard
160: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
161:
1.135 brouard 162: Revision 1.134 2009/10/29 13:18:53 brouard
163: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
164:
1.134 brouard 165: Revision 1.133 2009/07/06 10:21:25 brouard
166: just nforces
167:
1.133 brouard 168: Revision 1.132 2009/07/06 08:22:05 brouard
169: Many tings
170:
1.132 brouard 171: Revision 1.131 2009/06/20 16:22:47 brouard
172: Some dimensions resccaled
173:
1.131 brouard 174: Revision 1.130 2009/05/26 06:44:34 brouard
175: (Module): Max Covariate is now set to 20 instead of 8. A
176: lot of cleaning with variables initialized to 0. Trying to make
177: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
178:
1.130 brouard 179: Revision 1.129 2007/08/31 13:49:27 lievre
180: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
181:
1.129 lievre 182: Revision 1.128 2006/06/30 13:02:05 brouard
183: (Module): Clarifications on computing e.j
184:
1.128 brouard 185: Revision 1.127 2006/04/28 18:11:50 brouard
186: (Module): Yes the sum of survivors was wrong since
187: imach-114 because nhstepm was no more computed in the age
188: loop. Now we define nhstepma in the age loop.
189: (Module): In order to speed up (in case of numerous covariates) we
190: compute health expectancies (without variances) in a first step
191: and then all the health expectancies with variances or standard
192: deviation (needs data from the Hessian matrices) which slows the
193: computation.
194: In the future we should be able to stop the program is only health
195: expectancies and graph are needed without standard deviations.
196:
1.127 brouard 197: Revision 1.126 2006/04/28 17:23:28 brouard
198: (Module): Yes the sum of survivors was wrong since
199: imach-114 because nhstepm was no more computed in the age
200: loop. Now we define nhstepma in the age loop.
201: Version 0.98h
202:
1.126 brouard 203: Revision 1.125 2006/04/04 15:20:31 lievre
204: Errors in calculation of health expectancies. Age was not initialized.
205: Forecasting file added.
206:
207: Revision 1.124 2006/03/22 17:13:53 lievre
208: Parameters are printed with %lf instead of %f (more numbers after the comma).
209: The log-likelihood is printed in the log file
210:
211: Revision 1.123 2006/03/20 10:52:43 brouard
212: * imach.c (Module): <title> changed, corresponds to .htm file
213: name. <head> headers where missing.
214:
215: * imach.c (Module): Weights can have a decimal point as for
216: English (a comma might work with a correct LC_NUMERIC environment,
217: otherwise the weight is truncated).
218: Modification of warning when the covariates values are not 0 or
219: 1.
220: Version 0.98g
221:
222: Revision 1.122 2006/03/20 09:45:41 brouard
223: (Module): Weights can have a decimal point as for
224: English (a comma might work with a correct LC_NUMERIC environment,
225: otherwise the weight is truncated).
226: Modification of warning when the covariates values are not 0 or
227: 1.
228: Version 0.98g
229:
230: Revision 1.121 2006/03/16 17:45:01 lievre
231: * imach.c (Module): Comments concerning covariates added
232:
233: * imach.c (Module): refinements in the computation of lli if
234: status=-2 in order to have more reliable computation if stepm is
235: not 1 month. Version 0.98f
236:
237: Revision 1.120 2006/03/16 15:10:38 lievre
238: (Module): refinements in the computation of lli if
239: status=-2 in order to have more reliable computation if stepm is
240: not 1 month. Version 0.98f
241:
242: Revision 1.119 2006/03/15 17:42:26 brouard
243: (Module): Bug if status = -2, the loglikelihood was
244: computed as likelihood omitting the logarithm. Version O.98e
245:
246: Revision 1.118 2006/03/14 18:20:07 brouard
247: (Module): varevsij Comments added explaining the second
248: table of variances if popbased=1 .
249: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
250: (Module): Function pstamp added
251: (Module): Version 0.98d
252:
253: Revision 1.117 2006/03/14 17:16:22 brouard
254: (Module): varevsij Comments added explaining the second
255: table of variances if popbased=1 .
256: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
257: (Module): Function pstamp added
258: (Module): Version 0.98d
259:
260: Revision 1.116 2006/03/06 10:29:27 brouard
261: (Module): Variance-covariance wrong links and
262: varian-covariance of ej. is needed (Saito).
263:
264: Revision 1.115 2006/02/27 12:17:45 brouard
265: (Module): One freematrix added in mlikeli! 0.98c
266:
267: Revision 1.114 2006/02/26 12:57:58 brouard
268: (Module): Some improvements in processing parameter
269: filename with strsep.
270:
271: Revision 1.113 2006/02/24 14:20:24 brouard
272: (Module): Memory leaks checks with valgrind and:
273: datafile was not closed, some imatrix were not freed and on matrix
274: allocation too.
275:
276: Revision 1.112 2006/01/30 09:55:26 brouard
277: (Module): Back to gnuplot.exe instead of wgnuplot.exe
278:
279: Revision 1.111 2006/01/25 20:38:18 brouard
280: (Module): Lots of cleaning and bugs added (Gompertz)
281: (Module): Comments can be added in data file. Missing date values
282: can be a simple dot '.'.
283:
284: Revision 1.110 2006/01/25 00:51:50 brouard
285: (Module): Lots of cleaning and bugs added (Gompertz)
286:
287: Revision 1.109 2006/01/24 19:37:15 brouard
288: (Module): Comments (lines starting with a #) are allowed in data.
289:
290: Revision 1.108 2006/01/19 18:05:42 lievre
291: Gnuplot problem appeared...
292: To be fixed
293:
294: Revision 1.107 2006/01/19 16:20:37 brouard
295: Test existence of gnuplot in imach path
296:
297: Revision 1.106 2006/01/19 13:24:36 brouard
298: Some cleaning and links added in html output
299:
300: Revision 1.105 2006/01/05 20:23:19 lievre
301: *** empty log message ***
302:
303: Revision 1.104 2005/09/30 16:11:43 lievre
304: (Module): sump fixed, loop imx fixed, and simplifications.
305: (Module): If the status is missing at the last wave but we know
306: that the person is alive, then we can code his/her status as -2
307: (instead of missing=-1 in earlier versions) and his/her
308: contributions to the likelihood is 1 - Prob of dying from last
309: health status (= 1-p13= p11+p12 in the easiest case of somebody in
310: the healthy state at last known wave). Version is 0.98
311:
312: Revision 1.103 2005/09/30 15:54:49 lievre
313: (Module): sump fixed, loop imx fixed, and simplifications.
314:
315: Revision 1.102 2004/09/15 17:31:30 brouard
316: Add the possibility to read data file including tab characters.
317:
318: Revision 1.101 2004/09/15 10:38:38 brouard
319: Fix on curr_time
320:
321: Revision 1.100 2004/07/12 18:29:06 brouard
322: Add version for Mac OS X. Just define UNIX in Makefile
323:
324: Revision 1.99 2004/06/05 08:57:40 brouard
325: *** empty log message ***
326:
327: Revision 1.98 2004/05/16 15:05:56 brouard
328: New version 0.97 . First attempt to estimate force of mortality
329: directly from the data i.e. without the need of knowing the health
330: state at each age, but using a Gompertz model: log u =a + b*age .
331: This is the basic analysis of mortality and should be done before any
332: other analysis, in order to test if the mortality estimated from the
333: cross-longitudinal survey is different from the mortality estimated
334: from other sources like vital statistic data.
335:
336: The same imach parameter file can be used but the option for mle should be -3.
337:
1.133 brouard 338: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 339: former routines in order to include the new code within the former code.
340:
341: The output is very simple: only an estimate of the intercept and of
342: the slope with 95% confident intervals.
343:
344: Current limitations:
345: A) Even if you enter covariates, i.e. with the
346: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
347: B) There is no computation of Life Expectancy nor Life Table.
348:
349: Revision 1.97 2004/02/20 13:25:42 lievre
350: Version 0.96d. Population forecasting command line is (temporarily)
351: suppressed.
352:
353: Revision 1.96 2003/07/15 15:38:55 brouard
354: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
355: rewritten within the same printf. Workaround: many printfs.
356:
357: Revision 1.95 2003/07/08 07:54:34 brouard
358: * imach.c (Repository):
359: (Repository): Using imachwizard code to output a more meaningful covariance
360: matrix (cov(a12,c31) instead of numbers.
361:
362: Revision 1.94 2003/06/27 13:00:02 brouard
363: Just cleaning
364:
365: Revision 1.93 2003/06/25 16:33:55 brouard
366: (Module): On windows (cygwin) function asctime_r doesn't
367: exist so I changed back to asctime which exists.
368: (Module): Version 0.96b
369:
370: Revision 1.92 2003/06/25 16:30:45 brouard
371: (Module): On windows (cygwin) function asctime_r doesn't
372: exist so I changed back to asctime which exists.
373:
374: Revision 1.91 2003/06/25 15:30:29 brouard
375: * imach.c (Repository): Duplicated warning errors corrected.
376: (Repository): Elapsed time after each iteration is now output. It
377: helps to forecast when convergence will be reached. Elapsed time
378: is stamped in powell. We created a new html file for the graphs
379: concerning matrix of covariance. It has extension -cov.htm.
380:
381: Revision 1.90 2003/06/24 12:34:15 brouard
382: (Module): Some bugs corrected for windows. Also, when
383: mle=-1 a template is output in file "or"mypar.txt with the design
384: of the covariance matrix to be input.
385:
386: Revision 1.89 2003/06/24 12:30:52 brouard
387: (Module): Some bugs corrected for windows. Also, when
388: mle=-1 a template is output in file "or"mypar.txt with the design
389: of the covariance matrix to be input.
390:
391: Revision 1.88 2003/06/23 17:54:56 brouard
392: * 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.
393:
394: Revision 1.87 2003/06/18 12:26:01 brouard
395: Version 0.96
396:
397: Revision 1.86 2003/06/17 20:04:08 brouard
398: (Module): Change position of html and gnuplot routines and added
399: routine fileappend.
400:
401: Revision 1.85 2003/06/17 13:12:43 brouard
402: * imach.c (Repository): Check when date of death was earlier that
403: current date of interview. It may happen when the death was just
404: prior to the death. In this case, dh was negative and likelihood
405: was wrong (infinity). We still send an "Error" but patch by
406: assuming that the date of death was just one stepm after the
407: interview.
408: (Repository): Because some people have very long ID (first column)
409: we changed int to long in num[] and we added a new lvector for
410: memory allocation. But we also truncated to 8 characters (left
411: truncation)
412: (Repository): No more line truncation errors.
413:
414: Revision 1.84 2003/06/13 21:44:43 brouard
415: * imach.c (Repository): Replace "freqsummary" at a correct
416: place. It differs from routine "prevalence" which may be called
417: many times. Probs is memory consuming and must be used with
418: parcimony.
419: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
420:
421: Revision 1.83 2003/06/10 13:39:11 lievre
422: *** empty log message ***
423:
424: Revision 1.82 2003/06/05 15:57:20 brouard
425: Add log in imach.c and fullversion number is now printed.
426:
427: */
428: /*
429: Interpolated Markov Chain
430:
431: Short summary of the programme:
432:
433: This program computes Healthy Life Expectancies from
434: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
435: first survey ("cross") where individuals from different ages are
436: interviewed on their health status or degree of disability (in the
437: case of a health survey which is our main interest) -2- at least a
438: second wave of interviews ("longitudinal") which measure each change
439: (if any) in individual health status. Health expectancies are
440: computed from the time spent in each health state according to a
441: model. More health states you consider, more time is necessary to reach the
442: Maximum Likelihood of the parameters involved in the model. The
443: simplest model is the multinomial logistic model where pij is the
444: probability to be observed in state j at the second wave
445: conditional to be observed in state i at the first wave. Therefore
446: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
447: 'age' is age and 'sex' is a covariate. If you want to have a more
448: complex model than "constant and age", you should modify the program
449: where the markup *Covariates have to be included here again* invites
450: you to do it. More covariates you add, slower the
451: convergence.
452:
453: The advantage of this computer programme, compared to a simple
454: multinomial logistic model, is clear when the delay between waves is not
455: identical for each individual. Also, if a individual missed an
456: intermediate interview, the information is lost, but taken into
457: account using an interpolation or extrapolation.
458:
459: hPijx is the probability to be observed in state i at age x+h
460: conditional to the observed state i at age x. The delay 'h' can be
461: split into an exact number (nh*stepm) of unobserved intermediate
462: states. This elementary transition (by month, quarter,
463: semester or year) is modelled as a multinomial logistic. The hPx
464: matrix is simply the matrix product of nh*stepm elementary matrices
465: and the contribution of each individual to the likelihood is simply
466: hPijx.
467:
468: Also this programme outputs the covariance matrix of the parameters but also
469: of the life expectancies. It also computes the period (stable) prevalence.
470:
1.133 brouard 471: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
472: Institut national d'études démographiques, Paris.
1.126 brouard 473: This software have been partly granted by Euro-REVES, a concerted action
474: from the European Union.
475: It is copyrighted identically to a GNU software product, ie programme and
476: software can be distributed freely for non commercial use. Latest version
477: can be accessed at http://euroreves.ined.fr/imach .
478:
479: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
480: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
481:
482: **********************************************************************/
483: /*
484: main
485: read parameterfile
486: read datafile
487: concatwav
488: freqsummary
489: if (mle >= 1)
490: mlikeli
491: print results files
492: if mle==1
493: computes hessian
494: read end of parameter file: agemin, agemax, bage, fage, estepm
495: begin-prev-date,...
496: open gnuplot file
497: open html file
1.145 brouard 498: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
499: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
500: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
501: freexexit2 possible for memory heap.
502:
503: h Pij x | pij_nom ficrestpij
504: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
505: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
506: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
507:
508: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
509: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
510: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
511: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
512: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
513:
1.126 brouard 514: forecasting if prevfcast==1 prevforecast call prevalence()
515: health expectancies
516: Variance-covariance of DFLE
517: prevalence()
518: movingaverage()
519: varevsij()
520: if popbased==1 varevsij(,popbased)
521: total life expectancies
522: Variance of period (stable) prevalence
523: end
524: */
525:
1.165 brouard 526: #define POWELL /* Instead of NLOPT */
1.126 brouard 527:
528: #include <math.h>
529: #include <stdio.h>
530: #include <stdlib.h>
531: #include <string.h>
1.159 brouard 532:
533: #ifdef _WIN32
534: #include <io.h>
535: #else
1.126 brouard 536: #include <unistd.h>
1.159 brouard 537: #endif
1.126 brouard 538:
539: #include <limits.h>
540: #include <sys/types.h>
1.171 ! brouard 541:
! 542: #if defined(__GNUC__)
! 543: #include <sys/utsname.h> /* Doesn't work on Windows */
! 544: #endif
! 545:
1.126 brouard 546: #include <sys/stat.h>
547: #include <errno.h>
1.159 brouard 548: /* extern int errno; */
1.126 brouard 549:
1.157 brouard 550: /* #ifdef LINUX */
551: /* #include <time.h> */
552: /* #include "timeval.h" */
553: /* #else */
554: /* #include <sys/time.h> */
555: /* #endif */
556:
1.126 brouard 557: #include <time.h>
558:
1.136 brouard 559: #ifdef GSL
560: #include <gsl/gsl_errno.h>
561: #include <gsl/gsl_multimin.h>
562: #endif
563:
1.167 brouard 564:
1.162 brouard 565: #ifdef NLOPT
566: #include <nlopt.h>
567: typedef struct {
568: double (* function)(double [] );
569: } myfunc_data ;
570: #endif
571:
1.126 brouard 572: /* #include <libintl.h> */
573: /* #define _(String) gettext (String) */
574:
1.141 brouard 575: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 576:
577: #define GNUPLOTPROGRAM "gnuplot"
578: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
579: #define FILENAMELENGTH 132
580:
581: #define GLOCK_ERROR_NOPATH -1 /* empty path */
582: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
583:
1.144 brouard 584: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
585: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 586:
587: #define NINTERVMAX 8
1.144 brouard 588: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
589: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
590: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 591: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 592: #define MAXN 20000
1.144 brouard 593: #define YEARM 12. /**< Number of months per year */
1.126 brouard 594: #define AGESUP 130
595: #define AGEBASE 40
1.164 brouard 596: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 597: #ifdef _WIN32
598: #define DIRSEPARATOR '\\'
599: #define CHARSEPARATOR "\\"
600: #define ODIRSEPARATOR '/'
601: #else
1.126 brouard 602: #define DIRSEPARATOR '/'
603: #define CHARSEPARATOR "/"
604: #define ODIRSEPARATOR '\\'
605: #endif
606:
1.171 ! brouard 607: /* $Id: imach.c,v 1.170 2014/12/23 11:17:12 brouard Exp $ */
1.126 brouard 608: /* $State: Exp $ */
609:
1.169 brouard 610: char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.171 ! brouard 611: char fullversion[]="$Revision: 1.170 $ $Date: 2014/12/23 11:17:12 $";
1.126 brouard 612: char strstart[80];
613: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 614: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 615: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 616: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
617: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
618: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
619: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
620: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
621: int cptcovprodnoage=0; /**< Number of covariate products without age */
622: int cptcoveff=0; /* Total number of covariates to vary for printing results */
623: int cptcov=0; /* Working variable */
1.126 brouard 624: int npar=NPARMAX;
625: int nlstate=2; /* Number of live states */
626: int ndeath=1; /* Number of dead states */
1.130 brouard 627: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 628: int popbased=0;
629:
630: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 631: int maxwav=0; /* Maxim number of waves */
632: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
633: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
634: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 635: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 636: int mle=1, weightopt=0;
1.126 brouard 637: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
638: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
639: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
640: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 641: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 642: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 643: double **matprod2(); /* test */
1.126 brouard 644: double **oldm, **newm, **savm; /* Working pointers to matrices */
645: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 646: /*FILE *fic ; */ /* Used in readdata only */
647: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 648: FILE *ficlog, *ficrespow;
1.130 brouard 649: int globpr=0; /* Global variable for printing or not */
1.126 brouard 650: double fretone; /* Only one call to likelihood */
1.130 brouard 651: long ipmx=0; /* Number of contributions */
1.126 brouard 652: double sw; /* Sum of weights */
653: char filerespow[FILENAMELENGTH];
654: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
655: FILE *ficresilk;
656: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
657: FILE *ficresprobmorprev;
658: FILE *fichtm, *fichtmcov; /* Html File */
659: FILE *ficreseij;
660: char filerese[FILENAMELENGTH];
661: FILE *ficresstdeij;
662: char fileresstde[FILENAMELENGTH];
663: FILE *ficrescveij;
664: char filerescve[FILENAMELENGTH];
665: FILE *ficresvij;
666: char fileresv[FILENAMELENGTH];
667: FILE *ficresvpl;
668: char fileresvpl[FILENAMELENGTH];
669: char title[MAXLINE];
670: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
671: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
672: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
673: char command[FILENAMELENGTH];
674: int outcmd=0;
675:
676: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
677:
678: char filelog[FILENAMELENGTH]; /* Log file */
679: char filerest[FILENAMELENGTH];
680: char fileregp[FILENAMELENGTH];
681: char popfile[FILENAMELENGTH];
682:
683: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
684:
1.157 brouard 685: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
686: /* struct timezone tzp; */
687: /* extern int gettimeofday(); */
688: struct tm tml, *gmtime(), *localtime();
689:
690: extern time_t time();
691:
692: struct tm start_time, end_time, curr_time, last_time, forecast_time;
693: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
694: struct tm tm;
695:
1.126 brouard 696: char strcurr[80], strfor[80];
697:
698: char *endptr;
699: long lval;
700: double dval;
701:
702: #define NR_END 1
703: #define FREE_ARG char*
704: #define FTOL 1.0e-10
705:
706: #define NRANSI
707: #define ITMAX 200
708:
709: #define TOL 2.0e-4
710:
711: #define CGOLD 0.3819660
712: #define ZEPS 1.0e-10
713: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
714:
715: #define GOLD 1.618034
716: #define GLIMIT 100.0
717: #define TINY 1.0e-20
718:
719: static double maxarg1,maxarg2;
720: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
721: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
722:
723: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
724: #define rint(a) floor(a+0.5)
1.166 brouard 725: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
726: /* #define mytinydouble 1.0e-16 */
727: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
728: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
729: /* static double dsqrarg; */
730: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 731: static double sqrarg;
732: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
733: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
734: int agegomp= AGEGOMP;
735:
736: int imx;
737: int stepm=1;
738: /* Stepm, step in month: minimum step interpolation*/
739:
740: int estepm;
741: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
742:
743: int m,nb;
744: long *num;
745: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
746: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
747: double **pmmij, ***probs;
748: double *ageexmed,*agecens;
749: double dateintmean=0;
750:
751: double *weight;
752: int **s; /* Status */
1.141 brouard 753: double *agedc;
1.145 brouard 754: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 755: * covar=matrix(0,NCOVMAX,1,n);
756: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
757: double idx;
758: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 759: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 760: int **codtab; /**< codtab=imatrix(1,100,1,10); */
761: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 762: double *lsurv, *lpop, *tpop;
763:
1.143 brouard 764: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
765: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 766:
767: /**************** split *************************/
768: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
769: {
770: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
771: the name of the file (name), its extension only (ext) and its first part of the name (finame)
772: */
773: char *ss; /* pointer */
774: int l1, l2; /* length counters */
775:
776: l1 = strlen(path ); /* length of path */
777: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
778: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
779: if ( ss == NULL ) { /* no directory, so determine current directory */
780: strcpy( name, path ); /* we got the fullname name because no directory */
781: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
782: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
783: /* get current working directory */
784: /* extern char* getcwd ( char *buf , int len);*/
785: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
786: return( GLOCK_ERROR_GETCWD );
787: }
788: /* got dirc from getcwd*/
789: printf(" DIRC = %s \n",dirc);
790: } else { /* strip direcotry from path */
791: ss++; /* after this, the filename */
792: l2 = strlen( ss ); /* length of filename */
793: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
794: strcpy( name, ss ); /* save file name */
795: strncpy( dirc, path, l1 - l2 ); /* now the directory */
796: dirc[l1-l2] = 0; /* add zero */
797: printf(" DIRC2 = %s \n",dirc);
798: }
799: /* We add a separator at the end of dirc if not exists */
800: l1 = strlen( dirc ); /* length of directory */
801: if( dirc[l1-1] != DIRSEPARATOR ){
802: dirc[l1] = DIRSEPARATOR;
803: dirc[l1+1] = 0;
804: printf(" DIRC3 = %s \n",dirc);
805: }
806: ss = strrchr( name, '.' ); /* find last / */
807: if (ss >0){
808: ss++;
809: strcpy(ext,ss); /* save extension */
810: l1= strlen( name);
811: l2= strlen(ss)+1;
812: strncpy( finame, name, l1-l2);
813: finame[l1-l2]= 0;
814: }
815:
816: return( 0 ); /* we're done */
817: }
818:
819:
820: /******************************************/
821:
822: void replace_back_to_slash(char *s, char*t)
823: {
824: int i;
825: int lg=0;
826: i=0;
827: lg=strlen(t);
828: for(i=0; i<= lg; i++) {
829: (s[i] = t[i]);
830: if (t[i]== '\\') s[i]='/';
831: }
832: }
833:
1.132 brouard 834: char *trimbb(char *out, char *in)
1.137 brouard 835: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 836: char *s;
837: s=out;
838: while (*in != '\0'){
1.137 brouard 839: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 840: in++;
841: }
842: *out++ = *in++;
843: }
844: *out='\0';
845: return s;
846: }
847:
1.145 brouard 848: char *cutl(char *blocc, char *alocc, char *in, char occ)
849: {
850: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
851: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
852: gives blocc="abcdef2ghi" and alocc="j".
853: If occ is not found blocc is null and alocc is equal to in. Returns blocc
854: */
1.160 brouard 855: char *s, *t;
1.145 brouard 856: t=in;s=in;
857: while ((*in != occ) && (*in != '\0')){
858: *alocc++ = *in++;
859: }
860: if( *in == occ){
861: *(alocc)='\0';
862: s=++in;
863: }
864:
865: if (s == t) {/* occ not found */
866: *(alocc-(in-s))='\0';
867: in=s;
868: }
869: while ( *in != '\0'){
870: *blocc++ = *in++;
871: }
872:
873: *blocc='\0';
874: return t;
875: }
1.137 brouard 876: char *cutv(char *blocc, char *alocc, char *in, char occ)
877: {
878: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
879: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
880: gives blocc="abcdef2ghi" and alocc="j".
881: If occ is not found blocc is null and alocc is equal to in. Returns alocc
882: */
883: char *s, *t;
884: t=in;s=in;
885: while (*in != '\0'){
886: while( *in == occ){
887: *blocc++ = *in++;
888: s=in;
889: }
890: *blocc++ = *in++;
891: }
892: if (s == t) /* occ not found */
893: *(blocc-(in-s))='\0';
894: else
895: *(blocc-(in-s)-1)='\0';
896: in=s;
897: while ( *in != '\0'){
898: *alocc++ = *in++;
899: }
900:
901: *alocc='\0';
902: return s;
903: }
904:
1.126 brouard 905: int nbocc(char *s, char occ)
906: {
907: int i,j=0;
908: int lg=20;
909: i=0;
910: lg=strlen(s);
911: for(i=0; i<= lg; i++) {
912: if (s[i] == occ ) j++;
913: }
914: return j;
915: }
916:
1.137 brouard 917: /* void cutv(char *u,char *v, char*t, char occ) */
918: /* { */
919: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
920: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
921: /* gives u="abcdef2ghi" and v="j" *\/ */
922: /* int i,lg,j,p=0; */
923: /* i=0; */
924: /* lg=strlen(t); */
925: /* for(j=0; j<=lg-1; j++) { */
926: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
927: /* } */
1.126 brouard 928:
1.137 brouard 929: /* for(j=0; j<p; j++) { */
930: /* (u[j] = t[j]); */
931: /* } */
932: /* u[p]='\0'; */
1.126 brouard 933:
1.137 brouard 934: /* for(j=0; j<= lg; j++) { */
935: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
936: /* } */
937: /* } */
1.126 brouard 938:
1.160 brouard 939: #ifdef _WIN32
940: char * strsep(char **pp, const char *delim)
941: {
942: char *p, *q;
943:
944: if ((p = *pp) == NULL)
945: return 0;
946: if ((q = strpbrk (p, delim)) != NULL)
947: {
948: *pp = q + 1;
949: *q = '\0';
950: }
951: else
952: *pp = 0;
953: return p;
954: }
955: #endif
956:
1.126 brouard 957: /********************** nrerror ********************/
958:
959: void nrerror(char error_text[])
960: {
961: fprintf(stderr,"ERREUR ...\n");
962: fprintf(stderr,"%s\n",error_text);
963: exit(EXIT_FAILURE);
964: }
965: /*********************** vector *******************/
966: double *vector(int nl, int nh)
967: {
968: double *v;
969: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
970: if (!v) nrerror("allocation failure in vector");
971: return v-nl+NR_END;
972: }
973:
974: /************************ free vector ******************/
975: void free_vector(double*v, int nl, int nh)
976: {
977: free((FREE_ARG)(v+nl-NR_END));
978: }
979:
980: /************************ivector *******************************/
981: int *ivector(long nl,long nh)
982: {
983: int *v;
984: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
985: if (!v) nrerror("allocation failure in ivector");
986: return v-nl+NR_END;
987: }
988:
989: /******************free ivector **************************/
990: void free_ivector(int *v, long nl, long nh)
991: {
992: free((FREE_ARG)(v+nl-NR_END));
993: }
994:
995: /************************lvector *******************************/
996: long *lvector(long nl,long nh)
997: {
998: long *v;
999: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1000: if (!v) nrerror("allocation failure in ivector");
1001: return v-nl+NR_END;
1002: }
1003:
1004: /******************free lvector **************************/
1005: void free_lvector(long *v, long nl, long nh)
1006: {
1007: free((FREE_ARG)(v+nl-NR_END));
1008: }
1009:
1010: /******************* imatrix *******************************/
1011: int **imatrix(long nrl, long nrh, long ncl, long nch)
1012: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1013: {
1014: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1015: int **m;
1016:
1017: /* allocate pointers to rows */
1018: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1019: if (!m) nrerror("allocation failure 1 in matrix()");
1020: m += NR_END;
1021: m -= nrl;
1022:
1023:
1024: /* allocate rows and set pointers to them */
1025: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1026: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1027: m[nrl] += NR_END;
1028: m[nrl] -= ncl;
1029:
1030: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1031:
1032: /* return pointer to array of pointers to rows */
1033: return m;
1034: }
1035:
1036: /****************** free_imatrix *************************/
1037: void free_imatrix(m,nrl,nrh,ncl,nch)
1038: int **m;
1039: long nch,ncl,nrh,nrl;
1040: /* free an int matrix allocated by imatrix() */
1041: {
1042: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1043: free((FREE_ARG) (m+nrl-NR_END));
1044: }
1045:
1046: /******************* matrix *******************************/
1047: double **matrix(long nrl, long nrh, long ncl, long nch)
1048: {
1049: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1050: double **m;
1051:
1052: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1053: if (!m) nrerror("allocation failure 1 in matrix()");
1054: m += NR_END;
1055: m -= nrl;
1056:
1057: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1058: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1059: m[nrl] += NR_END;
1060: m[nrl] -= ncl;
1061:
1062: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1063: return m;
1.145 brouard 1064: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1065: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1066: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1067: */
1068: }
1069:
1070: /*************************free matrix ************************/
1071: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1072: {
1073: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1074: free((FREE_ARG)(m+nrl-NR_END));
1075: }
1076:
1077: /******************* ma3x *******************************/
1078: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1079: {
1080: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1081: double ***m;
1082:
1083: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1084: if (!m) nrerror("allocation failure 1 in matrix()");
1085: m += NR_END;
1086: m -= nrl;
1087:
1088: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
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: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1096: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1097: m[nrl][ncl] += NR_END;
1098: m[nrl][ncl] -= nll;
1099: for (j=ncl+1; j<=nch; j++)
1100: m[nrl][j]=m[nrl][j-1]+nlay;
1101:
1102: for (i=nrl+1; i<=nrh; i++) {
1103: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1104: for (j=ncl+1; j<=nch; j++)
1105: m[i][j]=m[i][j-1]+nlay;
1106: }
1107: return m;
1108: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1109: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1110: */
1111: }
1112:
1113: /*************************free ma3x ************************/
1114: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1115: {
1116: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1117: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1118: free((FREE_ARG)(m+nrl-NR_END));
1119: }
1120:
1121: /*************** function subdirf ***********/
1122: char *subdirf(char fileres[])
1123: {
1124: /* Caution optionfilefiname is hidden */
1125: strcpy(tmpout,optionfilefiname);
1126: strcat(tmpout,"/"); /* Add to the right */
1127: strcat(tmpout,fileres);
1128: return tmpout;
1129: }
1130:
1131: /*************** function subdirf2 ***********/
1132: char *subdirf2(char fileres[], char *preop)
1133: {
1134:
1135: /* Caution optionfilefiname is hidden */
1136: strcpy(tmpout,optionfilefiname);
1137: strcat(tmpout,"/");
1138: strcat(tmpout,preop);
1139: strcat(tmpout,fileres);
1140: return tmpout;
1141: }
1142:
1143: /*************** function subdirf3 ***********/
1144: char *subdirf3(char fileres[], char *preop, char *preop2)
1145: {
1146:
1147: /* Caution optionfilefiname is hidden */
1148: strcpy(tmpout,optionfilefiname);
1149: strcat(tmpout,"/");
1150: strcat(tmpout,preop);
1151: strcat(tmpout,preop2);
1152: strcat(tmpout,fileres);
1153: return tmpout;
1154: }
1155:
1.162 brouard 1156: char *asc_diff_time(long time_sec, char ascdiff[])
1157: {
1158: long sec_left, days, hours, minutes;
1159: days = (time_sec) / (60*60*24);
1160: sec_left = (time_sec) % (60*60*24);
1161: hours = (sec_left) / (60*60) ;
1162: sec_left = (sec_left) %(60*60);
1163: minutes = (sec_left) /60;
1164: sec_left = (sec_left) % (60);
1165: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1166: return ascdiff;
1167: }
1168:
1.126 brouard 1169: /***************** f1dim *************************/
1170: extern int ncom;
1171: extern double *pcom,*xicom;
1172: extern double (*nrfunc)(double []);
1173:
1174: double f1dim(double x)
1175: {
1176: int j;
1177: double f;
1178: double *xt;
1179:
1180: xt=vector(1,ncom);
1181: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1182: f=(*nrfunc)(xt);
1183: free_vector(xt,1,ncom);
1184: return f;
1185: }
1186:
1187: /*****************brent *************************/
1188: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1189: {
1190: int iter;
1191: double a,b,d,etemp;
1.159 brouard 1192: double fu=0,fv,fw,fx;
1.164 brouard 1193: double ftemp=0.;
1.126 brouard 1194: double p,q,r,tol1,tol2,u,v,w,x,xm;
1195: double e=0.0;
1196:
1197: a=(ax < cx ? ax : cx);
1198: b=(ax > cx ? ax : cx);
1199: x=w=v=bx;
1200: fw=fv=fx=(*f)(x);
1201: for (iter=1;iter<=ITMAX;iter++) {
1202: xm=0.5*(a+b);
1203: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1204: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1205: printf(".");fflush(stdout);
1206: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1207: #ifdef DEBUGBRENT
1.126 brouard 1208: 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);
1209: 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);
1210: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1211: #endif
1212: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1213: *xmin=x;
1214: return fx;
1215: }
1216: ftemp=fu;
1217: if (fabs(e) > tol1) {
1218: r=(x-w)*(fx-fv);
1219: q=(x-v)*(fx-fw);
1220: p=(x-v)*q-(x-w)*r;
1221: q=2.0*(q-r);
1222: if (q > 0.0) p = -p;
1223: q=fabs(q);
1224: etemp=e;
1225: e=d;
1226: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1227: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1228: else {
1229: d=p/q;
1230: u=x+d;
1231: if (u-a < tol2 || b-u < tol2)
1232: d=SIGN(tol1,xm-x);
1233: }
1234: } else {
1235: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1236: }
1237: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1238: fu=(*f)(u);
1239: if (fu <= fx) {
1240: if (u >= x) a=x; else b=x;
1241: SHFT(v,w,x,u)
1242: SHFT(fv,fw,fx,fu)
1243: } else {
1244: if (u < x) a=u; else b=u;
1245: if (fu <= fw || w == x) {
1246: v=w;
1247: w=u;
1248: fv=fw;
1249: fw=fu;
1250: } else if (fu <= fv || v == x || v == w) {
1251: v=u;
1252: fv=fu;
1253: }
1254: }
1255: }
1256: nrerror("Too many iterations in brent");
1257: *xmin=x;
1258: return fx;
1259: }
1260:
1261: /****************** mnbrak ***********************/
1262:
1263: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1264: double (*func)(double))
1265: {
1266: double ulim,u,r,q, dum;
1267: double fu;
1268:
1269: *fa=(*func)(*ax);
1270: *fb=(*func)(*bx);
1271: if (*fb > *fa) {
1272: SHFT(dum,*ax,*bx,dum)
1273: SHFT(dum,*fb,*fa,dum)
1274: }
1275: *cx=(*bx)+GOLD*(*bx-*ax);
1276: *fc=(*func)(*cx);
1.162 brouard 1277: while (*fb > *fc) { /* Declining fa, fb, fc */
1.126 brouard 1278: r=(*bx-*ax)*(*fb-*fc);
1279: q=(*bx-*cx)*(*fb-*fa);
1280: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.162 brouard 1281: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1282: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1283: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1.126 brouard 1284: fu=(*func)(u);
1.163 brouard 1285: #ifdef DEBUG
1286: /* f(x)=A(x-u)**2+f(u) */
1287: double A, fparabu;
1288: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1289: fparabu= *fa - A*(*ax-u)*(*ax-u);
1290: 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);
1291: 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);
1292: #endif
1.162 brouard 1293: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.126 brouard 1294: fu=(*func)(u);
1295: if (fu < *fc) {
1296: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1297: SHFT(*fb,*fc,fu,(*func)(u))
1298: }
1.162 brouard 1299: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.126 brouard 1300: u=ulim;
1301: fu=(*func)(u);
1302: } else {
1303: u=(*cx)+GOLD*(*cx-*bx);
1304: fu=(*func)(u);
1305: }
1306: SHFT(*ax,*bx,*cx,u)
1307: SHFT(*fa,*fb,*fc,fu)
1308: }
1309: }
1310:
1311: /*************** linmin ************************/
1.162 brouard 1312: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1313: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1314: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1315: the value of func at the returned location p . This is actually all accomplished by calling the
1316: routines mnbrak and brent .*/
1.126 brouard 1317: int ncom;
1318: double *pcom,*xicom;
1319: double (*nrfunc)(double []);
1320:
1321: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1322: {
1323: double brent(double ax, double bx, double cx,
1324: double (*f)(double), double tol, double *xmin);
1325: double f1dim(double x);
1326: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1327: double *fc, double (*func)(double));
1328: int j;
1329: double xx,xmin,bx,ax;
1330: double fx,fb,fa;
1331:
1332: ncom=n;
1333: pcom=vector(1,n);
1334: xicom=vector(1,n);
1335: nrfunc=func;
1336: for (j=1;j<=n;j++) {
1337: pcom[j]=p[j];
1338: xicom[j]=xi[j];
1339: }
1340: ax=0.0;
1341: xx=1.0;
1.162 brouard 1342: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1343: *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 1344: #ifdef DEBUG
1345: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1346: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1347: #endif
1348: for (j=1;j<=n;j++) {
1349: xi[j] *= xmin;
1350: p[j] += xi[j];
1351: }
1352: free_vector(xicom,1,n);
1353: free_vector(pcom,1,n);
1354: }
1355:
1356:
1357: /*************** powell ************************/
1.162 brouard 1358: /*
1359: Minimization of a function func of n variables. Input consists of an initial starting point
1360: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1361: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1362: such that failure to decrease by more than this amount on one iteration signals doneness. On
1363: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1364: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1365: */
1.126 brouard 1366: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1367: double (*func)(double []))
1368: {
1369: void linmin(double p[], double xi[], int n, double *fret,
1370: double (*func)(double []));
1371: int i,ibig,j;
1372: double del,t,*pt,*ptt,*xit;
1373: double fp,fptt;
1374: double *xits;
1375: int niterf, itmp;
1376:
1377: pt=vector(1,n);
1378: ptt=vector(1,n);
1379: xit=vector(1,n);
1380: xits=vector(1,n);
1381: *fret=(*func)(p);
1382: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1383: rcurr_time = time(NULL);
1.126 brouard 1384: for (*iter=1;;++(*iter)) {
1385: fp=(*fret);
1386: ibig=0;
1387: del=0.0;
1.157 brouard 1388: rlast_time=rcurr_time;
1389: /* (void) gettimeofday(&curr_time,&tzp); */
1390: rcurr_time = time(NULL);
1391: curr_time = *localtime(&rcurr_time);
1392: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1393: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1394: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1395: for (i=1;i<=n;i++) {
1396: printf(" %d %.12f",i, p[i]);
1397: fprintf(ficlog," %d %.12lf",i, p[i]);
1398: fprintf(ficrespow," %.12lf", p[i]);
1399: }
1400: printf("\n");
1401: fprintf(ficlog,"\n");
1402: fprintf(ficrespow,"\n");fflush(ficrespow);
1403: if(*iter <=3){
1.157 brouard 1404: tml = *localtime(&rcurr_time);
1405: strcpy(strcurr,asctime(&tml));
1406: rforecast_time=rcurr_time;
1.126 brouard 1407: itmp = strlen(strcurr);
1408: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1409: strcurr[itmp-1]='\0';
1.162 brouard 1410: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1411: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1412: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1413: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1414: forecast_time = *localtime(&rforecast_time);
1415: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1416: itmp = strlen(strfor);
1417: if(strfor[itmp-1]=='\n')
1418: strfor[itmp-1]='\0';
1.157 brouard 1419: 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);
1420: 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 1421: }
1422: }
1423: for (i=1;i<=n;i++) {
1424: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1425: fptt=(*fret);
1426: #ifdef DEBUG
1.164 brouard 1427: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1428: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1429: #endif
1430: printf("%d",i);fflush(stdout);
1431: fprintf(ficlog,"%d",i);fflush(ficlog);
1432: linmin(p,xit,n,fret,func);
1433: if (fabs(fptt-(*fret)) > del) {
1434: del=fabs(fptt-(*fret));
1435: ibig=i;
1436: }
1437: #ifdef DEBUG
1438: printf("%d %.12e",i,(*fret));
1439: fprintf(ficlog,"%d %.12e",i,(*fret));
1440: for (j=1;j<=n;j++) {
1441: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1442: printf(" x(%d)=%.12e",j,xit[j]);
1443: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1444: }
1445: for(j=1;j<=n;j++) {
1.162 brouard 1446: printf(" p(%d)=%.12e",j,p[j]);
1447: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1448: }
1449: printf("\n");
1450: fprintf(ficlog,"\n");
1451: #endif
1.162 brouard 1452: } /* end i */
1.126 brouard 1453: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1454: #ifdef DEBUG
1455: int k[2],l;
1456: k[0]=1;
1457: k[1]=-1;
1458: printf("Max: %.12e",(*func)(p));
1459: fprintf(ficlog,"Max: %.12e",(*func)(p));
1460: for (j=1;j<=n;j++) {
1461: printf(" %.12e",p[j]);
1462: fprintf(ficlog," %.12e",p[j]);
1463: }
1464: printf("\n");
1465: fprintf(ficlog,"\n");
1466: for(l=0;l<=1;l++) {
1467: for (j=1;j<=n;j++) {
1468: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1469: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1470: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1471: }
1472: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1473: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1474: }
1475: #endif
1476:
1477:
1478: free_vector(xit,1,n);
1479: free_vector(xits,1,n);
1480: free_vector(ptt,1,n);
1481: free_vector(pt,1,n);
1482: return;
1483: }
1484: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.161 brouard 1485: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1.126 brouard 1486: ptt[j]=2.0*p[j]-pt[j];
1487: xit[j]=p[j]-pt[j];
1488: pt[j]=p[j];
1489: }
1490: fptt=(*func)(ptt);
1.161 brouard 1491: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1492: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1493: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1494: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1495: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1496: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.161 brouard 1497: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1498: /* Thus we compare delta(2h) with observed f1-f3 */
1.162 brouard 1499: /* or best gain on one ancient line 'del' with total */
1500: /* gain f1-f2 = f1 - f2 - 'del' with del */
1.161 brouard 1501: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.162 brouard 1502:
1.161 brouard 1503: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1504: t= t- del*SQR(fp-fptt);
1505: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1506: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1507: #ifdef DEBUG
1508: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1509: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1510: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1511: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1512: 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);
1513: 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);
1514: #endif
1515: if (t < 0.0) { /* Then we use it for last direction */
1516: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1.126 brouard 1517: for (j=1;j<=n;j++) {
1.161 brouard 1518: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1519: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1.126 brouard 1520: }
1.161 brouard 1521: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.169 brouard 1522: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1523:
1.126 brouard 1524: #ifdef DEBUG
1.164 brouard 1525: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1526: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1527: for(j=1;j<=n;j++){
1528: printf(" %.12e",xit[j]);
1529: fprintf(ficlog," %.12e",xit[j]);
1530: }
1531: printf("\n");
1532: fprintf(ficlog,"\n");
1533: #endif
1.162 brouard 1534: } /* end of t negative */
1535: } /* end if (fptt < fp) */
1.126 brouard 1536: }
1537: }
1538:
1539: /**** Prevalence limit (stable or period prevalence) ****************/
1540:
1541: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1542: {
1543: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1544: matrix by transitions matrix until convergence is reached */
1.169 brouard 1545:
1.126 brouard 1546: int i, ii,j,k;
1547: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1548: /* double **matprod2(); */ /* test */
1.131 brouard 1549: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1550: double **newm;
1551: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1552:
1.126 brouard 1553: for (ii=1;ii<=nlstate+ndeath;ii++)
1554: for (j=1;j<=nlstate+ndeath;j++){
1555: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1556: }
1.169 brouard 1557:
1558: cov[1]=1.;
1559:
1560: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1561: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1562: newm=savm;
1563: /* Covariates have to be included here again */
1.138 brouard 1564: cov[2]=agefin;
1565:
1566: for (k=1; k<=cptcovn;k++) {
1567: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1568: /*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 1569: }
1.145 brouard 1570: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1571: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1572: /* 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 1573:
1574: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1575: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1576: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1577: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1578: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1579: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1580:
1.126 brouard 1581: savm=oldm;
1582: oldm=newm;
1583: maxmax=0.;
1584: for(j=1;j<=nlstate;j++){
1585: min=1.;
1586: max=0.;
1587: for(i=1; i<=nlstate; i++) {
1588: sumnew=0;
1589: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1590: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1591: /*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 1592: max=FMAX(max,prlim[i][j]);
1593: min=FMIN(min,prlim[i][j]);
1594: }
1595: maxmin=max-min;
1596: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1597: } /* j loop */
1.126 brouard 1598: if(maxmax < ftolpl){
1599: return prlim;
1600: }
1.169 brouard 1601: } /* age loop */
1602: return prlim; /* should not reach here */
1.126 brouard 1603: }
1604:
1605: /*************** transition probabilities ***************/
1606:
1607: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1608: {
1.138 brouard 1609: /* According to parameters values stored in x and the covariate's values stored in cov,
1610: computes the probability to be observed in state j being in state i by appying the
1611: model to the ncovmodel covariates (including constant and age).
1612: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1613: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1614: ncth covariate in the global vector x is given by the formula:
1615: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1616: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1617: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1618: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1619: Outputs ps[i][j] the probability to be observed in j being in j according to
1620: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1621: */
1622: double s1, lnpijopii;
1.126 brouard 1623: /*double t34;*/
1.164 brouard 1624: int i,j, nc, ii, jj;
1.126 brouard 1625:
1626: for(i=1; i<= nlstate; i++){
1627: for(j=1; j<i;j++){
1.138 brouard 1628: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1629: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1630: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1631: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1632: }
1.138 brouard 1633: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1634: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1635: }
1636: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1637: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1638: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1639: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1640: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1641: }
1.138 brouard 1642: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1643: }
1644: }
1645:
1646: for(i=1; i<= nlstate; i++){
1647: s1=0;
1.131 brouard 1648: for(j=1; j<i; j++){
1.138 brouard 1649: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1650: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1651: }
1652: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1653: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1654: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1655: }
1.138 brouard 1656: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1657: ps[i][i]=1./(s1+1.);
1.138 brouard 1658: /* Computing other pijs */
1.126 brouard 1659: for(j=1; j<i; j++)
1660: ps[i][j]= exp(ps[i][j])*ps[i][i];
1661: for(j=i+1; j<=nlstate+ndeath; j++)
1662: ps[i][j]= exp(ps[i][j])*ps[i][i];
1663: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1664: } /* end i */
1665:
1666: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1667: for(jj=1; jj<= nlstate+ndeath; jj++){
1668: ps[ii][jj]=0;
1669: ps[ii][ii]=1;
1670: }
1671: }
1672:
1.145 brouard 1673:
1674: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1675: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1676: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1677: /* } */
1678: /* printf("\n "); */
1679: /* } */
1680: /* printf("\n ");printf("%lf ",cov[2]);*/
1681: /*
1.126 brouard 1682: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1683: goto end;*/
1684: return ps;
1685: }
1686:
1687: /**************** Product of 2 matrices ******************/
1688:
1.145 brouard 1689: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1690: {
1691: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1692: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1693: /* in, b, out are matrice of pointers which should have been initialized
1694: before: only the contents of out is modified. The function returns
1695: a pointer to pointers identical to out */
1.145 brouard 1696: int i, j, k;
1.126 brouard 1697: for(i=nrl; i<= nrh; i++)
1.145 brouard 1698: for(k=ncolol; k<=ncoloh; k++){
1699: out[i][k]=0.;
1700: for(j=ncl; j<=nch; j++)
1701: out[i][k] +=in[i][j]*b[j][k];
1702: }
1.126 brouard 1703: return out;
1704: }
1705:
1706:
1707: /************* Higher Matrix Product ***************/
1708:
1709: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1710: {
1711: /* Computes the transition matrix starting at age 'age' over
1712: 'nhstepm*hstepm*stepm' months (i.e. until
1713: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1714: nhstepm*hstepm matrices.
1715: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1716: (typically every 2 years instead of every month which is too big
1717: for the memory).
1718: Model is determined by parameters x and covariates have to be
1719: included manually here.
1720:
1721: */
1722:
1723: int i, j, d, h, k;
1.131 brouard 1724: double **out, cov[NCOVMAX+1];
1.126 brouard 1725: double **newm;
1726:
1727: /* Hstepm could be zero and should return the unit matrix */
1728: for (i=1;i<=nlstate+ndeath;i++)
1729: for (j=1;j<=nlstate+ndeath;j++){
1730: oldm[i][j]=(i==j ? 1.0 : 0.0);
1731: po[i][j][0]=(i==j ? 1.0 : 0.0);
1732: }
1733: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1734: for(h=1; h <=nhstepm; h++){
1735: for(d=1; d <=hstepm; d++){
1736: newm=savm;
1737: /* Covariates have to be included here again */
1738: cov[1]=1.;
1739: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1740: for (k=1; k<=cptcovn;k++)
1741: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1742: for (k=1; k<=cptcovage;k++)
1743: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1744: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1745: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1746:
1747:
1748: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1749: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1750: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1751: pmij(pmmij,cov,ncovmodel,x,nlstate));
1752: savm=oldm;
1753: oldm=newm;
1754: }
1755: for(i=1; i<=nlstate+ndeath; i++)
1756: for(j=1;j<=nlstate+ndeath;j++) {
1757: po[i][j][h]=newm[i][j];
1.128 brouard 1758: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1759: }
1.128 brouard 1760: /*printf("h=%d ",h);*/
1.126 brouard 1761: } /* end h */
1.128 brouard 1762: /* printf("\n H=%d \n",h); */
1.126 brouard 1763: return po;
1764: }
1765:
1.162 brouard 1766: #ifdef NLOPT
1767: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1768: double fret;
1769: double *xt;
1770: int j;
1771: myfunc_data *d2 = (myfunc_data *) pd;
1772: /* xt = (p1-1); */
1773: xt=vector(1,n);
1774: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1775:
1776: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1777: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1778: printf("Function = %.12lf ",fret);
1779: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1780: printf("\n");
1781: free_vector(xt,1,n);
1782: return fret;
1783: }
1784: #endif
1.126 brouard 1785:
1786: /*************** log-likelihood *************/
1787: double func( double *x)
1788: {
1789: int i, ii, j, k, mi, d, kk;
1.131 brouard 1790: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1791: double **out;
1792: double sw; /* Sum of weights */
1793: double lli; /* Individual log likelihood */
1794: int s1, s2;
1795: double bbh, survp;
1796: long ipmx;
1797: /*extern weight */
1798: /* We are differentiating ll according to initial status */
1799: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1800: /*for(i=1;i<imx;i++)
1801: printf(" %d\n",s[4][i]);
1802: */
1.162 brouard 1803:
1804: ++countcallfunc;
1805:
1.126 brouard 1806: cov[1]=1.;
1807:
1808: for(k=1; k<=nlstate; k++) ll[k]=0.;
1809:
1810: if(mle==1){
1811: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1812: /* Computes the values of the ncovmodel covariates of the model
1813: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1814: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1815: to be observed in j being in i according to the model.
1816: */
1.145 brouard 1817: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1818: cov[2+k]=covar[Tvar[k]][i];
1819: }
1.137 brouard 1820: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1821: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1822: has been calculated etc */
1.126 brouard 1823: for(mi=1; mi<= wav[i]-1; mi++){
1824: for (ii=1;ii<=nlstate+ndeath;ii++)
1825: for (j=1;j<=nlstate+ndeath;j++){
1826: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1827: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1828: }
1829: for(d=0; d<dh[mi][i]; d++){
1830: newm=savm;
1831: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1832: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1833: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1834: }
1835: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1836: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1837: savm=oldm;
1838: oldm=newm;
1839: } /* end mult */
1840:
1841: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1842: /* But now since version 0.9 we anticipate for bias at large stepm.
1843: * If stepm is larger than one month (smallest stepm) and if the exact delay
1844: * (in months) between two waves is not a multiple of stepm, we rounded to
1845: * the nearest (and in case of equal distance, to the lowest) interval but now
1846: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1847: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1848: * probability in order to take into account the bias as a fraction of the way
1849: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1850: * -stepm/2 to stepm/2 .
1851: * For stepm=1 the results are the same as for previous versions of Imach.
1852: * For stepm > 1 the results are less biased than in previous versions.
1853: */
1854: s1=s[mw[mi][i]][i];
1855: s2=s[mw[mi+1][i]][i];
1856: bbh=(double)bh[mi][i]/(double)stepm;
1857: /* bias bh is positive if real duration
1858: * is higher than the multiple of stepm and negative otherwise.
1859: */
1860: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1861: if( s2 > nlstate){
1862: /* i.e. if s2 is a death state and if the date of death is known
1863: then the contribution to the likelihood is the probability to
1864: die between last step unit time and current step unit time,
1865: which is also equal to probability to die before dh
1866: minus probability to die before dh-stepm .
1867: In version up to 0.92 likelihood was computed
1868: as if date of death was unknown. Death was treated as any other
1869: health state: the date of the interview describes the actual state
1870: and not the date of a change in health state. The former idea was
1871: to consider that at each interview the state was recorded
1872: (healthy, disable or death) and IMaCh was corrected; but when we
1873: introduced the exact date of death then we should have modified
1874: the contribution of an exact death to the likelihood. This new
1875: contribution is smaller and very dependent of the step unit
1876: stepm. It is no more the probability to die between last interview
1877: and month of death but the probability to survive from last
1878: interview up to one month before death multiplied by the
1879: probability to die within a month. Thanks to Chris
1880: Jackson for correcting this bug. Former versions increased
1881: mortality artificially. The bad side is that we add another loop
1882: which slows down the processing. The difference can be up to 10%
1883: lower mortality.
1884: */
1885: lli=log(out[s1][s2] - savm[s1][s2]);
1886:
1887:
1888: } else if (s2==-2) {
1889: for (j=1,survp=0. ; j<=nlstate; j++)
1890: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1891: /*survp += out[s1][j]; */
1892: lli= log(survp);
1893: }
1894:
1895: else if (s2==-4) {
1896: for (j=3,survp=0. ; j<=nlstate; j++)
1897: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1898: lli= log(survp);
1899: }
1900:
1901: else if (s2==-5) {
1902: for (j=1,survp=0. ; j<=2; j++)
1903: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1904: lli= log(survp);
1905: }
1906:
1907: else{
1908: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1909: /* 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 */
1910: }
1911: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1912: /*if(lli ==000.0)*/
1913: /*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); */
1914: ipmx +=1;
1915: sw += weight[i];
1916: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1917: } /* end of wave */
1918: } /* end of individual */
1919: } else if(mle==2){
1920: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1921: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1922: for(mi=1; mi<= wav[i]-1; mi++){
1923: for (ii=1;ii<=nlstate+ndeath;ii++)
1924: for (j=1;j<=nlstate+ndeath;j++){
1925: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1926: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1927: }
1928: for(d=0; d<=dh[mi][i]; d++){
1929: newm=savm;
1930: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1931: for (kk=1; kk<=cptcovage;kk++) {
1932: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1933: }
1934: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1935: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1936: savm=oldm;
1937: oldm=newm;
1938: } /* end mult */
1939:
1940: s1=s[mw[mi][i]][i];
1941: s2=s[mw[mi+1][i]][i];
1942: bbh=(double)bh[mi][i]/(double)stepm;
1943: 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 */
1944: ipmx +=1;
1945: sw += weight[i];
1946: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1947: } /* end of wave */
1948: } /* end of individual */
1949: } else if(mle==3){ /* exponential inter-extrapolation */
1950: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1951: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1952: for(mi=1; mi<= wav[i]-1; mi++){
1953: for (ii=1;ii<=nlstate+ndeath;ii++)
1954: for (j=1;j<=nlstate+ndeath;j++){
1955: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1956: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1957: }
1958: for(d=0; d<dh[mi][i]; d++){
1959: newm=savm;
1960: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1961: for (kk=1; kk<=cptcovage;kk++) {
1962: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1963: }
1964: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1965: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1966: savm=oldm;
1967: oldm=newm;
1968: } /* end mult */
1969:
1970: s1=s[mw[mi][i]][i];
1971: s2=s[mw[mi+1][i]][i];
1972: bbh=(double)bh[mi][i]/(double)stepm;
1973: 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 */
1974: ipmx +=1;
1975: sw += weight[i];
1976: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1977: } /* end of wave */
1978: } /* end of individual */
1979: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1980: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1981: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1982: for(mi=1; mi<= wav[i]-1; mi++){
1983: for (ii=1;ii<=nlstate+ndeath;ii++)
1984: for (j=1;j<=nlstate+ndeath;j++){
1985: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1986: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1987: }
1988: for(d=0; d<dh[mi][i]; d++){
1989: newm=savm;
1990: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1991: for (kk=1; kk<=cptcovage;kk++) {
1992: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1993: }
1994:
1995: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1996: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1997: savm=oldm;
1998: oldm=newm;
1999: } /* end mult */
2000:
2001: s1=s[mw[mi][i]][i];
2002: s2=s[mw[mi+1][i]][i];
2003: if( s2 > nlstate){
2004: lli=log(out[s1][s2] - savm[s1][s2]);
2005: }else{
2006: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2007: }
2008: ipmx +=1;
2009: sw += weight[i];
2010: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2011: /* 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]); */
2012: } /* end of wave */
2013: } /* end of individual */
2014: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2015: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2016: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2017: for(mi=1; mi<= wav[i]-1; mi++){
2018: for (ii=1;ii<=nlstate+ndeath;ii++)
2019: for (j=1;j<=nlstate+ndeath;j++){
2020: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2021: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2022: }
2023: for(d=0; d<dh[mi][i]; d++){
2024: newm=savm;
2025: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2026: for (kk=1; kk<=cptcovage;kk++) {
2027: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2028: }
2029:
2030: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2031: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2032: savm=oldm;
2033: oldm=newm;
2034: } /* end mult */
2035:
2036: s1=s[mw[mi][i]][i];
2037: s2=s[mw[mi+1][i]][i];
2038: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2039: ipmx +=1;
2040: sw += weight[i];
2041: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2042: /*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]);*/
2043: } /* end of wave */
2044: } /* end of individual */
2045: } /* End of if */
2046: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2047: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2048: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2049: return -l;
2050: }
2051:
2052: /*************** log-likelihood *************/
2053: double funcone( double *x)
2054: {
2055: /* Same as likeli but slower because of a lot of printf and if */
2056: int i, ii, j, k, mi, d, kk;
1.131 brouard 2057: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2058: double **out;
2059: double lli; /* Individual log likelihood */
2060: double llt;
2061: int s1, s2;
2062: double bbh, survp;
2063: /*extern weight */
2064: /* We are differentiating ll according to initial status */
2065: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2066: /*for(i=1;i<imx;i++)
2067: printf(" %d\n",s[4][i]);
2068: */
2069: cov[1]=1.;
2070:
2071: for(k=1; k<=nlstate; k++) ll[k]=0.;
2072:
2073: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2074: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2075: for(mi=1; mi<= wav[i]-1; mi++){
2076: for (ii=1;ii<=nlstate+ndeath;ii++)
2077: for (j=1;j<=nlstate+ndeath;j++){
2078: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2079: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2080: }
2081: for(d=0; d<dh[mi][i]; d++){
2082: newm=savm;
2083: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2084: for (kk=1; kk<=cptcovage;kk++) {
2085: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2086: }
1.145 brouard 2087: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2088: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2089: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2090: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2091: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2092: savm=oldm;
2093: oldm=newm;
2094: } /* end mult */
2095:
2096: s1=s[mw[mi][i]][i];
2097: s2=s[mw[mi+1][i]][i];
2098: bbh=(double)bh[mi][i]/(double)stepm;
2099: /* bias is positive if real duration
2100: * is higher than the multiple of stepm and negative otherwise.
2101: */
2102: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2103: lli=log(out[s1][s2] - savm[s1][s2]);
2104: } else if (s2==-2) {
2105: for (j=1,survp=0. ; j<=nlstate; j++)
2106: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2107: lli= log(survp);
2108: }else if (mle==1){
2109: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2110: } else if(mle==2){
2111: 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 */
2112: } else if(mle==3){ /* exponential inter-extrapolation */
2113: 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 */
2114: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2115: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2116: } else{ /* mle=0 back to 1 */
2117: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2118: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2119: } /* End of if */
2120: ipmx +=1;
2121: sw += weight[i];
2122: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2123: /*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 2124: if(globpr){
1.141 brouard 2125: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2126: %11.6f %11.6f %11.6f ", \
2127: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2128: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2129: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2130: llt +=ll[k]*gipmx/gsw;
2131: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2132: }
2133: fprintf(ficresilk," %10.6f\n", -llt);
2134: }
2135: } /* end of wave */
2136: } /* end of individual */
2137: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2138: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2139: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2140: if(globpr==0){ /* First time we count the contributions and weights */
2141: gipmx=ipmx;
2142: gsw=sw;
2143: }
2144: return -l;
2145: }
2146:
2147:
2148: /*************** function likelione ***********/
2149: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2150: {
2151: /* This routine should help understanding what is done with
2152: the selection of individuals/waves and
2153: to check the exact contribution to the likelihood.
2154: Plotting could be done.
2155: */
2156: int k;
2157:
2158: if(*globpri !=0){ /* Just counts and sums, no printings */
2159: strcpy(fileresilk,"ilk");
2160: strcat(fileresilk,fileres);
2161: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2162: printf("Problem with resultfile: %s\n", fileresilk);
2163: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2164: }
2165: 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");
2166: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2167: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2168: for(k=1; k<=nlstate; k++)
2169: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2170: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2171: }
2172:
2173: *fretone=(*funcone)(p);
2174: if(*globpri !=0){
2175: fclose(ficresilk);
2176: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2177: fflush(fichtm);
2178: }
2179: return;
2180: }
2181:
2182:
2183: /*********** Maximum Likelihood Estimation ***************/
2184:
2185: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2186: {
1.165 brouard 2187: int i,j, iter=0;
1.126 brouard 2188: double **xi;
2189: double fret;
2190: double fretone; /* Only one call to likelihood */
2191: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2192:
2193: #ifdef NLOPT
2194: int creturn;
2195: nlopt_opt opt;
2196: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2197: double *lb;
2198: double minf; /* the minimum objective value, upon return */
2199: double * p1; /* Shifted parameters from 0 instead of 1 */
2200: myfunc_data dinst, *d = &dinst;
2201: #endif
2202:
2203:
1.126 brouard 2204: xi=matrix(1,npar,1,npar);
2205: for (i=1;i<=npar;i++)
2206: for (j=1;j<=npar;j++)
2207: xi[i][j]=(i==j ? 1.0 : 0.0);
2208: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2209: strcpy(filerespow,"pow");
2210: strcat(filerespow,fileres);
2211: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2212: printf("Problem with resultfile: %s\n", filerespow);
2213: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2214: }
2215: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2216: for (i=1;i<=nlstate;i++)
2217: for(j=1;j<=nlstate+ndeath;j++)
2218: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2219: fprintf(ficrespow,"\n");
1.162 brouard 2220: #ifdef POWELL
1.126 brouard 2221: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2222: #endif
1.126 brouard 2223:
1.162 brouard 2224: #ifdef NLOPT
2225: #ifdef NEWUOA
2226: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2227: #else
2228: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2229: #endif
2230: lb=vector(0,npar-1);
2231: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2232: nlopt_set_lower_bounds(opt, lb);
2233: nlopt_set_initial_step1(opt, 0.1);
2234:
2235: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2236: d->function = func;
2237: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2238: nlopt_set_min_objective(opt, myfunc, d);
2239: nlopt_set_xtol_rel(opt, ftol);
2240: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2241: printf("nlopt failed! %d\n",creturn);
2242: }
2243: else {
2244: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2245: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2246: iter=1; /* not equal */
2247: }
2248: nlopt_destroy(opt);
2249: #endif
1.126 brouard 2250: free_matrix(xi,1,npar,1,npar);
2251: fclose(ficrespow);
1.162 brouard 2252: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2253: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2254: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2255:
2256: }
2257:
2258: /**** Computes Hessian and covariance matrix ***/
2259: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2260: {
2261: double **a,**y,*x,pd;
2262: double **hess;
1.164 brouard 2263: int i, j;
1.126 brouard 2264: int *indx;
2265:
2266: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2267: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2268: void lubksb(double **a, int npar, int *indx, double b[]) ;
2269: void ludcmp(double **a, int npar, int *indx, double *d) ;
2270: double gompertz(double p[]);
2271: hess=matrix(1,npar,1,npar);
2272:
2273: printf("\nCalculation of the hessian matrix. Wait...\n");
2274: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2275: for (i=1;i<=npar;i++){
2276: printf("%d",i);fflush(stdout);
2277: fprintf(ficlog,"%d",i);fflush(ficlog);
2278:
2279: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2280:
2281: /* printf(" %f ",p[i]);
2282: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2283: }
2284:
2285: for (i=1;i<=npar;i++) {
2286: for (j=1;j<=npar;j++) {
2287: if (j>i) {
2288: printf(".%d%d",i,j);fflush(stdout);
2289: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2290: hess[i][j]=hessij(p,delti,i,j,func,npar);
2291:
2292: hess[j][i]=hess[i][j];
2293: /*printf(" %lf ",hess[i][j]);*/
2294: }
2295: }
2296: }
2297: printf("\n");
2298: fprintf(ficlog,"\n");
2299:
2300: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2301: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2302:
2303: a=matrix(1,npar,1,npar);
2304: y=matrix(1,npar,1,npar);
2305: x=vector(1,npar);
2306: indx=ivector(1,npar);
2307: for (i=1;i<=npar;i++)
2308: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2309: ludcmp(a,npar,indx,&pd);
2310:
2311: for (j=1;j<=npar;j++) {
2312: for (i=1;i<=npar;i++) x[i]=0;
2313: x[j]=1;
2314: lubksb(a,npar,indx,x);
2315: for (i=1;i<=npar;i++){
2316: matcov[i][j]=x[i];
2317: }
2318: }
2319:
2320: printf("\n#Hessian matrix#\n");
2321: fprintf(ficlog,"\n#Hessian matrix#\n");
2322: for (i=1;i<=npar;i++) {
2323: for (j=1;j<=npar;j++) {
2324: printf("%.3e ",hess[i][j]);
2325: fprintf(ficlog,"%.3e ",hess[i][j]);
2326: }
2327: printf("\n");
2328: fprintf(ficlog,"\n");
2329: }
2330:
2331: /* Recompute Inverse */
2332: for (i=1;i<=npar;i++)
2333: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2334: ludcmp(a,npar,indx,&pd);
2335:
2336: /* printf("\n#Hessian matrix recomputed#\n");
2337:
2338: for (j=1;j<=npar;j++) {
2339: for (i=1;i<=npar;i++) x[i]=0;
2340: x[j]=1;
2341: lubksb(a,npar,indx,x);
2342: for (i=1;i<=npar;i++){
2343: y[i][j]=x[i];
2344: printf("%.3e ",y[i][j]);
2345: fprintf(ficlog,"%.3e ",y[i][j]);
2346: }
2347: printf("\n");
2348: fprintf(ficlog,"\n");
2349: }
2350: */
2351:
2352: free_matrix(a,1,npar,1,npar);
2353: free_matrix(y,1,npar,1,npar);
2354: free_vector(x,1,npar);
2355: free_ivector(indx,1,npar);
2356: free_matrix(hess,1,npar,1,npar);
2357:
2358:
2359: }
2360:
2361: /*************** hessian matrix ****************/
2362: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2363: {
2364: int i;
2365: int l=1, lmax=20;
2366: double k1,k2;
1.132 brouard 2367: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2368: double res;
2369: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2370: double fx;
2371: int k=0,kmax=10;
2372: double l1;
2373:
2374: fx=func(x);
2375: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2376: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2377: l1=pow(10,l);
2378: delts=delt;
2379: for(k=1 ; k <kmax; k=k+1){
2380: delt = delta*(l1*k);
2381: p2[theta]=x[theta] +delt;
1.145 brouard 2382: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2383: p2[theta]=x[theta]-delt;
2384: k2=func(p2)-fx;
2385: /*res= (k1-2.0*fx+k2)/delt/delt; */
2386: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2387:
1.132 brouard 2388: #ifdef DEBUGHESS
1.126 brouard 2389: 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);
2390: 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);
2391: #endif
2392: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2393: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2394: k=kmax;
2395: }
2396: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2397: k=kmax; l=lmax*10;
1.126 brouard 2398: }
2399: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2400: delts=delt;
2401: }
2402: }
2403: }
2404: delti[theta]=delts;
2405: return res;
2406:
2407: }
2408:
2409: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2410: {
2411: int i;
1.164 brouard 2412: int l=1, lmax=20;
1.126 brouard 2413: double k1,k2,k3,k4,res,fx;
1.132 brouard 2414: double p2[MAXPARM+1];
1.126 brouard 2415: int k;
2416:
2417: fx=func(x);
2418: for (k=1; k<=2; k++) {
2419: for (i=1;i<=npar;i++) p2[i]=x[i];
2420: p2[thetai]=x[thetai]+delti[thetai]/k;
2421: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2422: k1=func(p2)-fx;
2423:
2424: p2[thetai]=x[thetai]+delti[thetai]/k;
2425: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2426: k2=func(p2)-fx;
2427:
2428: p2[thetai]=x[thetai]-delti[thetai]/k;
2429: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2430: k3=func(p2)-fx;
2431:
2432: p2[thetai]=x[thetai]-delti[thetai]/k;
2433: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2434: k4=func(p2)-fx;
2435: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2436: #ifdef DEBUG
2437: 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);
2438: 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);
2439: #endif
2440: }
2441: return res;
2442: }
2443:
2444: /************** Inverse of matrix **************/
2445: void ludcmp(double **a, int n, int *indx, double *d)
2446: {
2447: int i,imax,j,k;
2448: double big,dum,sum,temp;
2449: double *vv;
2450:
2451: vv=vector(1,n);
2452: *d=1.0;
2453: for (i=1;i<=n;i++) {
2454: big=0.0;
2455: for (j=1;j<=n;j++)
2456: if ((temp=fabs(a[i][j])) > big) big=temp;
2457: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2458: vv[i]=1.0/big;
2459: }
2460: for (j=1;j<=n;j++) {
2461: for (i=1;i<j;i++) {
2462: sum=a[i][j];
2463: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2464: a[i][j]=sum;
2465: }
2466: big=0.0;
2467: for (i=j;i<=n;i++) {
2468: sum=a[i][j];
2469: for (k=1;k<j;k++)
2470: sum -= a[i][k]*a[k][j];
2471: a[i][j]=sum;
2472: if ( (dum=vv[i]*fabs(sum)) >= big) {
2473: big=dum;
2474: imax=i;
2475: }
2476: }
2477: if (j != imax) {
2478: for (k=1;k<=n;k++) {
2479: dum=a[imax][k];
2480: a[imax][k]=a[j][k];
2481: a[j][k]=dum;
2482: }
2483: *d = -(*d);
2484: vv[imax]=vv[j];
2485: }
2486: indx[j]=imax;
2487: if (a[j][j] == 0.0) a[j][j]=TINY;
2488: if (j != n) {
2489: dum=1.0/(a[j][j]);
2490: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2491: }
2492: }
2493: free_vector(vv,1,n); /* Doesn't work */
2494: ;
2495: }
2496:
2497: void lubksb(double **a, int n, int *indx, double b[])
2498: {
2499: int i,ii=0,ip,j;
2500: double sum;
2501:
2502: for (i=1;i<=n;i++) {
2503: ip=indx[i];
2504: sum=b[ip];
2505: b[ip]=b[i];
2506: if (ii)
2507: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2508: else if (sum) ii=i;
2509: b[i]=sum;
2510: }
2511: for (i=n;i>=1;i--) {
2512: sum=b[i];
2513: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2514: b[i]=sum/a[i][i];
2515: }
2516: }
2517:
2518: void pstamp(FILE *fichier)
2519: {
2520: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2521: }
2522:
2523: /************ Frequencies ********************/
2524: 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[])
2525: { /* Some frequencies */
2526:
1.164 brouard 2527: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2528: int first;
2529: double ***freq; /* Frequencies */
2530: double *pp, **prop;
2531: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2532: char fileresp[FILENAMELENGTH];
2533:
2534: pp=vector(1,nlstate);
2535: prop=matrix(1,nlstate,iagemin,iagemax+3);
2536: strcpy(fileresp,"p");
2537: strcat(fileresp,fileres);
2538: if((ficresp=fopen(fileresp,"w"))==NULL) {
2539: printf("Problem with prevalence resultfile: %s\n", fileresp);
2540: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2541: exit(0);
2542: }
2543: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2544: j1=0;
2545:
2546: j=cptcoveff;
2547: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2548:
2549: first=1;
2550:
1.169 brouard 2551: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2552: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2553: /* j1++; */
1.145 brouard 2554: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2555: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2556: scanf("%d", i);*/
2557: for (i=-5; i<=nlstate+ndeath; i++)
2558: for (jk=-5; jk<=nlstate+ndeath; jk++)
2559: for(m=iagemin; m <= iagemax+3; m++)
2560: freq[i][jk][m]=0;
1.143 brouard 2561:
2562: for (i=1; i<=nlstate; i++)
2563: for(m=iagemin; m <= iagemax+3; m++)
2564: prop[i][m]=0;
1.126 brouard 2565:
2566: dateintsum=0;
2567: k2cpt=0;
2568: for (i=1; i<=imx; i++) {
2569: bool=1;
1.144 brouard 2570: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2571: for (z1=1; z1<=cptcoveff; z1++)
2572: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2573: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2574: bool=0;
1.145 brouard 2575: /* 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",
2576: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2577: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2578: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2579: }
1.126 brouard 2580: }
1.144 brouard 2581:
1.126 brouard 2582: if (bool==1){
2583: for(m=firstpass; m<=lastpass; m++){
2584: k2=anint[m][i]+(mint[m][i]/12.);
2585: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2586: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2587: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2588: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2589: if (m<lastpass) {
2590: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2591: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2592: }
2593:
2594: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2595: dateintsum=dateintsum+k2;
2596: k2cpt++;
2597: }
2598: /*}*/
2599: }
2600: }
1.145 brouard 2601: } /* end i */
1.126 brouard 2602:
2603: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2604: pstamp(ficresp);
2605: if (cptcovn>0) {
2606: fprintf(ficresp, "\n#********** Variable ");
2607: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2608: fprintf(ficresp, "**********\n#");
1.143 brouard 2609: fprintf(ficlog, "\n#********** Variable ");
2610: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2611: fprintf(ficlog, "**********\n#");
1.126 brouard 2612: }
2613: for(i=1; i<=nlstate;i++)
2614: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2615: fprintf(ficresp, "\n");
2616:
2617: for(i=iagemin; i <= iagemax+3; i++){
2618: if(i==iagemax+3){
2619: fprintf(ficlog,"Total");
2620: }else{
2621: if(first==1){
2622: first=0;
2623: printf("See log file for details...\n");
2624: }
2625: fprintf(ficlog,"Age %d", i);
2626: }
2627: for(jk=1; jk <=nlstate ; jk++){
2628: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2629: pp[jk] += freq[jk][m][i];
2630: }
2631: for(jk=1; jk <=nlstate ; jk++){
2632: for(m=-1, pos=0; m <=0 ; m++)
2633: pos += freq[jk][m][i];
2634: if(pp[jk]>=1.e-10){
2635: if(first==1){
1.132 brouard 2636: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2637: }
2638: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2639: }else{
2640: if(first==1)
2641: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2642: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2643: }
2644: }
2645:
2646: for(jk=1; jk <=nlstate ; jk++){
2647: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2648: pp[jk] += freq[jk][m][i];
2649: }
2650: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2651: pos += pp[jk];
2652: posprop += prop[jk][i];
2653: }
2654: for(jk=1; jk <=nlstate ; jk++){
2655: if(pos>=1.e-5){
2656: if(first==1)
2657: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2658: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2659: }else{
2660: if(first==1)
2661: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2662: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2663: }
2664: if( i <= iagemax){
2665: if(pos>=1.e-5){
2666: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2667: /*probs[i][jk][j1]= pp[jk]/pos;*/
2668: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2669: }
2670: else
2671: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2672: }
2673: }
2674:
2675: for(jk=-1; jk <=nlstate+ndeath; jk++)
2676: for(m=-1; m <=nlstate+ndeath; m++)
2677: if(freq[jk][m][i] !=0 ) {
2678: if(first==1)
2679: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2680: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2681: }
2682: if(i <= iagemax)
2683: fprintf(ficresp,"\n");
2684: if(first==1)
2685: printf("Others in log...\n");
2686: fprintf(ficlog,"\n");
2687: }
1.145 brouard 2688: /*}*/
1.126 brouard 2689: }
2690: dateintmean=dateintsum/k2cpt;
2691:
2692: fclose(ficresp);
2693: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2694: free_vector(pp,1,nlstate);
2695: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2696: /* End of Freq */
2697: }
2698:
2699: /************ Prevalence ********************/
2700: 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)
2701: {
2702: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2703: in each health status at the date of interview (if between dateprev1 and dateprev2).
2704: We still use firstpass and lastpass as another selection.
2705: */
2706:
1.164 brouard 2707: int i, m, jk, j1, bool, z1,j;
2708:
2709: double **prop;
2710: double posprop;
1.126 brouard 2711: double y2; /* in fractional years */
2712: int iagemin, iagemax;
1.145 brouard 2713: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2714:
2715: iagemin= (int) agemin;
2716: iagemax= (int) agemax;
2717: /*pp=vector(1,nlstate);*/
2718: prop=matrix(1,nlstate,iagemin,iagemax+3);
2719: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2720: j1=0;
2721:
1.145 brouard 2722: /*j=cptcoveff;*/
1.126 brouard 2723: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2724:
1.145 brouard 2725: first=1;
2726: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2727: /*for(i1=1; i1<=ncodemax[k1];i1++){
2728: j1++;*/
1.126 brouard 2729:
2730: for (i=1; i<=nlstate; i++)
2731: for(m=iagemin; m <= iagemax+3; m++)
2732: prop[i][m]=0.0;
2733:
2734: for (i=1; i<=imx; i++) { /* Each individual */
2735: bool=1;
2736: if (cptcovn>0) {
2737: for (z1=1; z1<=cptcoveff; z1++)
2738: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2739: bool=0;
2740: }
2741: if (bool==1) {
2742: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2743: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2744: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2745: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2746: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2747: 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);
2748: if (s[m][i]>0 && s[m][i]<=nlstate) {
2749: /*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]]);*/
2750: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2751: prop[s[m][i]][iagemax+3] += weight[i];
2752: }
2753: }
2754: } /* end selection of waves */
2755: }
2756: }
2757: for(i=iagemin; i <= iagemax+3; i++){
2758: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2759: posprop += prop[jk][i];
2760: }
1.145 brouard 2761:
1.126 brouard 2762: for(jk=1; jk <=nlstate ; jk++){
2763: if( i <= iagemax){
2764: if(posprop>=1.e-5){
2765: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2766: } else{
2767: if(first==1){
2768: first=0;
2769: 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]);
2770: }
2771: }
1.126 brouard 2772: }
2773: }/* end jk */
2774: }/* end i */
1.145 brouard 2775: /*} *//* end i1 */
2776: } /* end j1 */
1.126 brouard 2777:
2778: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2779: /*free_vector(pp,1,nlstate);*/
2780: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2781: } /* End of prevalence */
2782:
2783: /************* Waves Concatenation ***************/
2784:
2785: 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)
2786: {
2787: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2788: Death is a valid wave (if date is known).
2789: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2790: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2791: and mw[mi+1][i]. dh depends on stepm.
2792: */
2793:
2794: int i, mi, m;
2795: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2796: double sum=0., jmean=0.;*/
2797: int first;
2798: int j, k=0,jk, ju, jl;
2799: double sum=0.;
2800: first=0;
1.164 brouard 2801: jmin=100000;
1.126 brouard 2802: jmax=-1;
2803: jmean=0.;
2804: for(i=1; i<=imx; i++){
2805: mi=0;
2806: m=firstpass;
2807: while(s[m][i] <= nlstate){
2808: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2809: mw[++mi][i]=m;
2810: if(m >=lastpass)
2811: break;
2812: else
2813: m++;
2814: }/* end while */
2815: if (s[m][i] > nlstate){
2816: mi++; /* Death is another wave */
2817: /* if(mi==0) never been interviewed correctly before death */
2818: /* Only death is a correct wave */
2819: mw[mi][i]=m;
2820: }
2821:
2822: wav[i]=mi;
2823: if(mi==0){
2824: nbwarn++;
2825: if(first==0){
2826: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2827: first=1;
2828: }
2829: if(first==1){
2830: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2831: }
2832: } /* end mi==0 */
2833: } /* End individuals */
2834:
2835: for(i=1; i<=imx; i++){
2836: for(mi=1; mi<wav[i];mi++){
2837: if (stepm <=0)
2838: dh[mi][i]=1;
2839: else{
2840: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2841: if (agedc[i] < 2*AGESUP) {
2842: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2843: if(j==0) j=1; /* Survives at least one month after exam */
2844: else if(j<0){
2845: nberr++;
2846: 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]);
2847: j=1; /* Temporary Dangerous patch */
2848: 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);
2849: 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]);
2850: 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);
2851: }
2852: k=k+1;
2853: if (j >= jmax){
2854: jmax=j;
2855: ijmax=i;
2856: }
2857: if (j <= jmin){
2858: jmin=j;
2859: ijmin=i;
2860: }
2861: sum=sum+j;
2862: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2863: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2864: }
2865: }
2866: else{
2867: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2868: /* 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]); */
2869:
2870: k=k+1;
2871: if (j >= jmax) {
2872: jmax=j;
2873: ijmax=i;
2874: }
2875: else if (j <= jmin){
2876: jmin=j;
2877: ijmin=i;
2878: }
2879: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2880: /*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]);*/
2881: if(j<0){
2882: nberr++;
2883: 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]);
2884: 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]);
2885: }
2886: sum=sum+j;
2887: }
2888: jk= j/stepm;
2889: jl= j -jk*stepm;
2890: ju= j -(jk+1)*stepm;
2891: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2892: if(jl==0){
2893: dh[mi][i]=jk;
2894: bh[mi][i]=0;
2895: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2896: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2897: dh[mi][i]=jk+1;
2898: bh[mi][i]=ju;
2899: }
2900: }else{
2901: if(jl <= -ju){
2902: dh[mi][i]=jk;
2903: bh[mi][i]=jl; /* bias is positive if real duration
2904: * is higher than the multiple of stepm and negative otherwise.
2905: */
2906: }
2907: else{
2908: dh[mi][i]=jk+1;
2909: bh[mi][i]=ju;
2910: }
2911: if(dh[mi][i]==0){
2912: dh[mi][i]=1; /* At least one step */
2913: bh[mi][i]=ju; /* At least one step */
2914: /* 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);*/
2915: }
2916: } /* end if mle */
2917: }
2918: } /* end wave */
2919: }
2920: jmean=sum/k;
2921: 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 2922: 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 2923: }
2924:
2925: /*********** Tricode ****************************/
1.145 brouard 2926: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 2927: {
1.144 brouard 2928: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2929: /* 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 2930: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 2931: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 2932: * nbcode[Tvar[j]][1]=
1.144 brouard 2933: */
1.130 brouard 2934:
1.145 brouard 2935: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2936: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 2937: int cptcode=0; /* Modality max of covariates j */
2938: int modmincovj=0; /* Modality min of covariates j */
2939:
2940:
1.126 brouard 2941: cptcoveff=0;
2942:
1.145 brouard 2943: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 2944: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2945:
1.145 brouard 2946: /* Loop on covariates without age and products */
2947: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2948: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 2949: modality of this covariate Vj*/
1.145 brouard 2950: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2951: * If product of Vn*Vm, still boolean *:
2952: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2953: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2954: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 2955: modality of the nth covariate of individual i. */
1.145 brouard 2956: if (ij > modmaxcovj)
2957: modmaxcovj=ij;
2958: else if (ij < modmincovj)
2959: modmincovj=ij;
2960: if ((ij < -1) && (ij > NCOVMAX)){
2961: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2962: exit(1);
2963: }else
1.136 brouard 2964: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 2965: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 2966: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2967: /* getting the maximum value of the modality of the covariate
2968: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2969: female is 1, then modmaxcovj=1.*/
1.126 brouard 2970: }
1.145 brouard 2971: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2972: cptcode=modmaxcovj;
1.137 brouard 2973: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 2974: /*for (i=0; i<=cptcode; i++) {*/
2975: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2976: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2977: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2978: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2979: }
2980: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2981: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 2982: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2983:
1.136 brouard 2984: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 2985: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2986: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2987: modmincovj=3; modmaxcovj = 7;
2988: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2989: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2990: variables V1_1 and V1_2.
2991: nbcode[Tvar[j]][ij]=k;
2992: nbcode[Tvar[j]][1]=0;
2993: nbcode[Tvar[j]][2]=1;
2994: nbcode[Tvar[j]][3]=2;
2995: */
2996: ij=1; /* ij is similar to i but can jumps over null modalities */
2997: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2998: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2999: /*recode from 0 */
1.131 brouard 3000: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3001: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3002: k is a modality. If we have model=V1+V1*sex
3003: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 3004: ij++;
3005: }
3006: if (ij > ncodemax[j]) break;
1.137 brouard 3007: } /* end of loop on */
3008: } /* end of loop on modality */
3009: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3010:
1.145 brouard 3011: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3012:
1.145 brouard 3013: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3014: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3015: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3016: Ndum[ij]++;
3017: }
1.126 brouard 3018:
3019: ij=1;
1.145 brouard 3020: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3021: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3022: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 3023: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3024: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 3025: ij++;
1.145 brouard 3026: }else
3027: Tvaraff[ij]=0;
1.126 brouard 3028: }
1.131 brouard 3029: ij--;
1.144 brouard 3030: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3031:
1.126 brouard 3032: }
3033:
1.145 brouard 3034:
1.126 brouard 3035: /*********** Health Expectancies ****************/
3036:
1.127 brouard 3037: 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 3038:
3039: {
3040: /* Health expectancies, no variances */
1.164 brouard 3041: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3042: int nhstepma, nstepma; /* Decreasing with age */
3043: double age, agelim, hf;
3044: double ***p3mat;
3045: double eip;
3046:
3047: pstamp(ficreseij);
3048: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3049: fprintf(ficreseij,"# Age");
3050: for(i=1; i<=nlstate;i++){
3051: for(j=1; j<=nlstate;j++){
3052: fprintf(ficreseij," e%1d%1d ",i,j);
3053: }
3054: fprintf(ficreseij," e%1d. ",i);
3055: }
3056: fprintf(ficreseij,"\n");
3057:
3058:
3059: if(estepm < stepm){
3060: printf ("Problem %d lower than %d\n",estepm, stepm);
3061: }
3062: else hstepm=estepm;
3063: /* We compute the life expectancy from trapezoids spaced every estepm months
3064: * This is mainly to measure the difference between two models: for example
3065: * if stepm=24 months pijx are given only every 2 years and by summing them
3066: * we are calculating an estimate of the Life Expectancy assuming a linear
3067: * progression in between and thus overestimating or underestimating according
3068: * to the curvature of the survival function. If, for the same date, we
3069: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3070: * to compare the new estimate of Life expectancy with the same linear
3071: * hypothesis. A more precise result, taking into account a more precise
3072: * curvature will be obtained if estepm is as small as stepm. */
3073:
3074: /* For example we decided to compute the life expectancy with the smallest unit */
3075: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3076: nhstepm is the number of hstepm from age to agelim
3077: nstepm is the number of stepm from age to agelin.
3078: Look at hpijx to understand the reason of that which relies in memory size
3079: and note for a fixed period like estepm months */
3080: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3081: survival function given by stepm (the optimization length). Unfortunately it
3082: means that if the survival funtion is printed only each two years of age and if
3083: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3084: results. So we changed our mind and took the option of the best precision.
3085: */
3086: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3087:
3088: agelim=AGESUP;
3089: /* If stepm=6 months */
3090: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3091: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3092:
3093: /* nhstepm age range expressed in number of stepm */
3094: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3095: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3096: /* if (stepm >= YEARM) hstepm=1;*/
3097: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3098: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3099:
3100: for (age=bage; age<=fage; age ++){
3101: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3102: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3103: /* if (stepm >= YEARM) hstepm=1;*/
3104: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3105:
3106: /* If stepm=6 months */
3107: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3108: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3109:
3110: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3111:
3112: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3113:
3114: printf("%d|",(int)age);fflush(stdout);
3115: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3116:
3117: /* Computing expectancies */
3118: for(i=1; i<=nlstate;i++)
3119: for(j=1; j<=nlstate;j++)
3120: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3121: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3122:
3123: /* 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]);*/
3124:
3125: }
3126:
3127: fprintf(ficreseij,"%3.0f",age );
3128: for(i=1; i<=nlstate;i++){
3129: eip=0;
3130: for(j=1; j<=nlstate;j++){
3131: eip +=eij[i][j][(int)age];
3132: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3133: }
3134: fprintf(ficreseij,"%9.4f", eip );
3135: }
3136: fprintf(ficreseij,"\n");
3137:
3138: }
3139: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3140: printf("\n");
3141: fprintf(ficlog,"\n");
3142:
3143: }
3144:
1.127 brouard 3145: 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 3146:
3147: {
3148: /* Covariances of health expectancies eij and of total life expectancies according
3149: to initial status i, ei. .
3150: */
3151: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3152: int nhstepma, nstepma; /* Decreasing with age */
3153: double age, agelim, hf;
3154: double ***p3matp, ***p3matm, ***varhe;
3155: double **dnewm,**doldm;
3156: double *xp, *xm;
3157: double **gp, **gm;
3158: double ***gradg, ***trgradg;
3159: int theta;
3160:
3161: double eip, vip;
3162:
3163: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3164: xp=vector(1,npar);
3165: xm=vector(1,npar);
3166: dnewm=matrix(1,nlstate*nlstate,1,npar);
3167: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3168:
3169: pstamp(ficresstdeij);
3170: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3171: fprintf(ficresstdeij,"# Age");
3172: for(i=1; i<=nlstate;i++){
3173: for(j=1; j<=nlstate;j++)
3174: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3175: fprintf(ficresstdeij," e%1d. ",i);
3176: }
3177: fprintf(ficresstdeij,"\n");
3178:
3179: pstamp(ficrescveij);
3180: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3181: fprintf(ficrescveij,"# Age");
3182: for(i=1; i<=nlstate;i++)
3183: for(j=1; j<=nlstate;j++){
3184: cptj= (j-1)*nlstate+i;
3185: for(i2=1; i2<=nlstate;i2++)
3186: for(j2=1; j2<=nlstate;j2++){
3187: cptj2= (j2-1)*nlstate+i2;
3188: if(cptj2 <= cptj)
3189: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3190: }
3191: }
3192: fprintf(ficrescveij,"\n");
3193:
3194: if(estepm < stepm){
3195: printf ("Problem %d lower than %d\n",estepm, stepm);
3196: }
3197: else hstepm=estepm;
3198: /* We compute the life expectancy from trapezoids spaced every estepm months
3199: * This is mainly to measure the difference between two models: for example
3200: * if stepm=24 months pijx are given only every 2 years and by summing them
3201: * we are calculating an estimate of the Life Expectancy assuming a linear
3202: * progression in between and thus overestimating or underestimating according
3203: * to the curvature of the survival function. If, for the same date, we
3204: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3205: * to compare the new estimate of Life expectancy with the same linear
3206: * hypothesis. A more precise result, taking into account a more precise
3207: * curvature will be obtained if estepm is as small as stepm. */
3208:
3209: /* For example we decided to compute the life expectancy with the smallest unit */
3210: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3211: nhstepm is the number of hstepm from age to agelim
3212: nstepm is the number of stepm from age to agelin.
3213: Look at hpijx to understand the reason of that which relies in memory size
3214: and note for a fixed period like estepm months */
3215: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3216: survival function given by stepm (the optimization length). Unfortunately it
3217: means that if the survival funtion is printed only each two years of age and if
3218: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3219: results. So we changed our mind and took the option of the best precision.
3220: */
3221: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3222:
3223: /* If stepm=6 months */
3224: /* nhstepm age range expressed in number of stepm */
3225: agelim=AGESUP;
3226: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3227: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3228: /* if (stepm >= YEARM) hstepm=1;*/
3229: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3230:
3231: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3232: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3233: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3234: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3235: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3236: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3237:
3238: for (age=bage; age<=fage; age ++){
3239: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3240: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3241: /* if (stepm >= YEARM) hstepm=1;*/
3242: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3243:
3244: /* If stepm=6 months */
3245: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3246: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3247:
3248: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3249:
3250: /* Computing Variances of health expectancies */
3251: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3252: decrease memory allocation */
3253: for(theta=1; theta <=npar; theta++){
3254: for(i=1; i<=npar; i++){
3255: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3256: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3257: }
3258: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3259: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3260:
3261: for(j=1; j<= nlstate; j++){
3262: for(i=1; i<=nlstate; i++){
3263: for(h=0; h<=nhstepm-1; h++){
3264: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3265: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3266: }
3267: }
3268: }
3269:
3270: for(ij=1; ij<= nlstate*nlstate; ij++)
3271: for(h=0; h<=nhstepm-1; h++){
3272: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3273: }
3274: }/* End theta */
3275:
3276:
3277: for(h=0; h<=nhstepm-1; h++)
3278: for(j=1; j<=nlstate*nlstate;j++)
3279: for(theta=1; theta <=npar; theta++)
3280: trgradg[h][j][theta]=gradg[h][theta][j];
3281:
3282:
3283: for(ij=1;ij<=nlstate*nlstate;ij++)
3284: for(ji=1;ji<=nlstate*nlstate;ji++)
3285: varhe[ij][ji][(int)age] =0.;
3286:
3287: printf("%d|",(int)age);fflush(stdout);
3288: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3289: for(h=0;h<=nhstepm-1;h++){
3290: for(k=0;k<=nhstepm-1;k++){
3291: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3292: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3293: for(ij=1;ij<=nlstate*nlstate;ij++)
3294: for(ji=1;ji<=nlstate*nlstate;ji++)
3295: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3296: }
3297: }
3298:
3299: /* Computing expectancies */
3300: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3301: for(i=1; i<=nlstate;i++)
3302: for(j=1; j<=nlstate;j++)
3303: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3304: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3305:
3306: /* 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]);*/
3307:
3308: }
3309:
3310: fprintf(ficresstdeij,"%3.0f",age );
3311: for(i=1; i<=nlstate;i++){
3312: eip=0.;
3313: vip=0.;
3314: for(j=1; j<=nlstate;j++){
3315: eip += eij[i][j][(int)age];
3316: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3317: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3318: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3319: }
3320: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3321: }
3322: fprintf(ficresstdeij,"\n");
3323:
3324: fprintf(ficrescveij,"%3.0f",age );
3325: for(i=1; i<=nlstate;i++)
3326: for(j=1; j<=nlstate;j++){
3327: cptj= (j-1)*nlstate+i;
3328: for(i2=1; i2<=nlstate;i2++)
3329: for(j2=1; j2<=nlstate;j2++){
3330: cptj2= (j2-1)*nlstate+i2;
3331: if(cptj2 <= cptj)
3332: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3333: }
3334: }
3335: fprintf(ficrescveij,"\n");
3336:
3337: }
3338: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3339: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3340: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3341: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3342: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3343: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3344: printf("\n");
3345: fprintf(ficlog,"\n");
3346:
3347: free_vector(xm,1,npar);
3348: free_vector(xp,1,npar);
3349: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3350: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3351: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3352: }
3353:
3354: /************ Variance ******************/
3355: 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[])
3356: {
3357: /* Variance of health expectancies */
3358: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3359: /* double **newm;*/
1.169 brouard 3360: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3361:
3362: int movingaverage();
1.126 brouard 3363: double **dnewm,**doldm;
3364: double **dnewmp,**doldmp;
3365: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3366: int k;
1.126 brouard 3367: double *xp;
3368: double **gp, **gm; /* for var eij */
3369: double ***gradg, ***trgradg; /*for var eij */
3370: double **gradgp, **trgradgp; /* for var p point j */
3371: double *gpp, *gmp; /* for var p point j */
3372: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3373: double ***p3mat;
3374: double age,agelim, hf;
3375: double ***mobaverage;
3376: int theta;
3377: char digit[4];
3378: char digitp[25];
3379:
3380: char fileresprobmorprev[FILENAMELENGTH];
3381:
3382: if(popbased==1){
3383: if(mobilav!=0)
3384: strcpy(digitp,"-populbased-mobilav-");
3385: else strcpy(digitp,"-populbased-nomobil-");
3386: }
3387: else
3388: strcpy(digitp,"-stablbased-");
3389:
3390: if (mobilav!=0) {
3391: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3392: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3393: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3394: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3395: }
3396: }
3397:
3398: strcpy(fileresprobmorprev,"prmorprev");
3399: sprintf(digit,"%-d",ij);
3400: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3401: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3402: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3403: strcat(fileresprobmorprev,fileres);
3404: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3405: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3406: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3407: }
3408: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3409:
3410: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3411: pstamp(ficresprobmorprev);
3412: 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);
3413: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3414: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3415: fprintf(ficresprobmorprev," p.%-d SE",j);
3416: for(i=1; i<=nlstate;i++)
3417: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3418: }
3419: fprintf(ficresprobmorprev,"\n");
3420: fprintf(ficgp,"\n# Routine varevsij");
3421: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3422: 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");
3423: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3424: /* } */
3425: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3426: pstamp(ficresvij);
3427: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3428: if(popbased==1)
1.128 brouard 3429: 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 3430: else
3431: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3432: fprintf(ficresvij,"# Age");
3433: for(i=1; i<=nlstate;i++)
3434: for(j=1; j<=nlstate;j++)
3435: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3436: fprintf(ficresvij,"\n");
3437:
3438: xp=vector(1,npar);
3439: dnewm=matrix(1,nlstate,1,npar);
3440: doldm=matrix(1,nlstate,1,nlstate);
3441: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3442: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3443:
3444: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3445: gpp=vector(nlstate+1,nlstate+ndeath);
3446: gmp=vector(nlstate+1,nlstate+ndeath);
3447: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3448:
3449: if(estepm < stepm){
3450: printf ("Problem %d lower than %d\n",estepm, stepm);
3451: }
3452: else hstepm=estepm;
3453: /* For example we decided to compute the life expectancy with the smallest unit */
3454: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3455: nhstepm is the number of hstepm from age to agelim
3456: nstepm is the number of stepm from age to agelin.
1.128 brouard 3457: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3458: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3459: survival function given by stepm (the optimization length). Unfortunately it
3460: means that if the survival funtion is printed every two years of age and if
3461: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3462: results. So we changed our mind and took the option of the best precision.
3463: */
3464: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3465: agelim = AGESUP;
3466: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3467: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3468: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3469: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3470: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3471: gp=matrix(0,nhstepm,1,nlstate);
3472: gm=matrix(0,nhstepm,1,nlstate);
3473:
3474:
3475: for(theta=1; theta <=npar; theta++){
3476: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3477: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3478: }
3479: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3480: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3481:
3482: if (popbased==1) {
3483: if(mobilav ==0){
3484: for(i=1; i<=nlstate;i++)
3485: prlim[i][i]=probs[(int)age][i][ij];
3486: }else{ /* mobilav */
3487: for(i=1; i<=nlstate;i++)
3488: prlim[i][i]=mobaverage[(int)age][i][ij];
3489: }
3490: }
3491:
3492: for(j=1; j<= nlstate; j++){
3493: for(h=0; h<=nhstepm; h++){
3494: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3495: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3496: }
3497: }
3498: /* This for computing probability of death (h=1 means
3499: computed over hstepm matrices product = hstepm*stepm months)
3500: as a weighted average of prlim.
3501: */
3502: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3503: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3504: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3505: }
3506: /* end probability of death */
3507:
3508: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3509: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3510: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3511: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3512:
3513: if (popbased==1) {
3514: if(mobilav ==0){
3515: for(i=1; i<=nlstate;i++)
3516: prlim[i][i]=probs[(int)age][i][ij];
3517: }else{ /* mobilav */
3518: for(i=1; i<=nlstate;i++)
3519: prlim[i][i]=mobaverage[(int)age][i][ij];
3520: }
3521: }
3522:
1.128 brouard 3523: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3524: for(h=0; h<=nhstepm; h++){
3525: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3526: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3527: }
3528: }
3529: /* This for computing probability of death (h=1 means
3530: computed over hstepm matrices product = hstepm*stepm months)
3531: as a weighted average of prlim.
3532: */
3533: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3534: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3535: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3536: }
3537: /* end probability of death */
3538:
3539: for(j=1; j<= nlstate; j++) /* vareij */
3540: for(h=0; h<=nhstepm; h++){
3541: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3542: }
3543:
3544: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3545: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3546: }
3547:
3548: } /* End theta */
3549:
3550: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3551:
3552: for(h=0; h<=nhstepm; h++) /* veij */
3553: for(j=1; j<=nlstate;j++)
3554: for(theta=1; theta <=npar; theta++)
3555: trgradg[h][j][theta]=gradg[h][theta][j];
3556:
3557: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3558: for(theta=1; theta <=npar; theta++)
3559: trgradgp[j][theta]=gradgp[theta][j];
3560:
3561:
3562: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3563: for(i=1;i<=nlstate;i++)
3564: for(j=1;j<=nlstate;j++)
3565: vareij[i][j][(int)age] =0.;
3566:
3567: for(h=0;h<=nhstepm;h++){
3568: for(k=0;k<=nhstepm;k++){
3569: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3570: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3571: for(i=1;i<=nlstate;i++)
3572: for(j=1;j<=nlstate;j++)
3573: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3574: }
3575: }
3576:
3577: /* pptj */
3578: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3579: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3580: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3581: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3582: varppt[j][i]=doldmp[j][i];
3583: /* end ppptj */
3584: /* x centered again */
3585: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3586: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3587:
3588: if (popbased==1) {
3589: if(mobilav ==0){
3590: for(i=1; i<=nlstate;i++)
3591: prlim[i][i]=probs[(int)age][i][ij];
3592: }else{ /* mobilav */
3593: for(i=1; i<=nlstate;i++)
3594: prlim[i][i]=mobaverage[(int)age][i][ij];
3595: }
3596: }
3597:
3598: /* This for computing probability of death (h=1 means
3599: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3600: as a weighted average of prlim.
3601: */
3602: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3603: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3604: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3605: }
3606: /* end probability of death */
3607:
3608: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3609: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3610: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3611: for(i=1; i<=nlstate;i++){
3612: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3613: }
3614: }
3615: fprintf(ficresprobmorprev,"\n");
3616:
3617: fprintf(ficresvij,"%.0f ",age );
3618: for(i=1; i<=nlstate;i++)
3619: for(j=1; j<=nlstate;j++){
3620: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3621: }
3622: fprintf(ficresvij,"\n");
3623: free_matrix(gp,0,nhstepm,1,nlstate);
3624: free_matrix(gm,0,nhstepm,1,nlstate);
3625: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3626: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3627: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3628: } /* End age */
3629: free_vector(gpp,nlstate+1,nlstate+ndeath);
3630: free_vector(gmp,nlstate+1,nlstate+ndeath);
3631: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3632: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3633: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3634: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3635: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3636: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3637: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3638: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3639: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 3640: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 3641: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3642: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3643: 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);
3644: /* 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);
3645: */
3646: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3647: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3648:
3649: free_vector(xp,1,npar);
3650: free_matrix(doldm,1,nlstate,1,nlstate);
3651: free_matrix(dnewm,1,nlstate,1,npar);
3652: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3653: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3654: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3655: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3656: fclose(ficresprobmorprev);
3657: fflush(ficgp);
3658: fflush(fichtm);
3659: } /* end varevsij */
3660:
3661: /************ Variance of prevlim ******************/
3662: 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[])
3663: {
3664: /* Variance of prevalence limit */
3665: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 3666:
1.126 brouard 3667: double **dnewm,**doldm;
3668: int i, j, nhstepm, hstepm;
3669: double *xp;
3670: double *gp, *gm;
3671: double **gradg, **trgradg;
3672: double age,agelim;
3673: int theta;
3674:
3675: pstamp(ficresvpl);
3676: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3677: fprintf(ficresvpl,"# Age");
3678: for(i=1; i<=nlstate;i++)
3679: fprintf(ficresvpl," %1d-%1d",i,i);
3680: fprintf(ficresvpl,"\n");
3681:
3682: xp=vector(1,npar);
3683: dnewm=matrix(1,nlstate,1,npar);
3684: doldm=matrix(1,nlstate,1,nlstate);
3685:
3686: hstepm=1*YEARM; /* Every year of age */
3687: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3688: agelim = AGESUP;
3689: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3690: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3691: if (stepm >= YEARM) hstepm=1;
3692: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3693: gradg=matrix(1,npar,1,nlstate);
3694: gp=vector(1,nlstate);
3695: gm=vector(1,nlstate);
3696:
3697: for(theta=1; theta <=npar; theta++){
3698: for(i=1; i<=npar; i++){ /* Computes gradient */
3699: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3700: }
3701: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3702: for(i=1;i<=nlstate;i++)
3703: gp[i] = prlim[i][i];
3704:
3705: for(i=1; i<=npar; i++) /* Computes gradient */
3706: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3707: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3708: for(i=1;i<=nlstate;i++)
3709: gm[i] = prlim[i][i];
3710:
3711: for(i=1;i<=nlstate;i++)
3712: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3713: } /* End theta */
3714:
3715: trgradg =matrix(1,nlstate,1,npar);
3716:
3717: for(j=1; j<=nlstate;j++)
3718: for(theta=1; theta <=npar; theta++)
3719: trgradg[j][theta]=gradg[theta][j];
3720:
3721: for(i=1;i<=nlstate;i++)
3722: varpl[i][(int)age] =0.;
3723: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3724: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3725: for(i=1;i<=nlstate;i++)
3726: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3727:
3728: fprintf(ficresvpl,"%.0f ",age );
3729: for(i=1; i<=nlstate;i++)
3730: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3731: fprintf(ficresvpl,"\n");
3732: free_vector(gp,1,nlstate);
3733: free_vector(gm,1,nlstate);
3734: free_matrix(gradg,1,npar,1,nlstate);
3735: free_matrix(trgradg,1,nlstate,1,npar);
3736: } /* End age */
3737:
3738: free_vector(xp,1,npar);
3739: free_matrix(doldm,1,nlstate,1,npar);
3740: free_matrix(dnewm,1,nlstate,1,nlstate);
3741:
3742: }
3743:
3744: /************ Variance of one-step probabilities ******************/
3745: 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[])
3746: {
1.164 brouard 3747: int i, j=0, k1, l1, tj;
1.126 brouard 3748: int k2, l2, j1, z1;
1.164 brouard 3749: int k=0, l;
1.145 brouard 3750: int first=1, first1, first2;
1.126 brouard 3751: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3752: double **dnewm,**doldm;
3753: double *xp;
3754: double *gp, *gm;
3755: double **gradg, **trgradg;
3756: double **mu;
1.164 brouard 3757: double age, cov[NCOVMAX+1];
1.126 brouard 3758: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3759: int theta;
3760: char fileresprob[FILENAMELENGTH];
3761: char fileresprobcov[FILENAMELENGTH];
3762: char fileresprobcor[FILENAMELENGTH];
3763: double ***varpij;
3764:
3765: strcpy(fileresprob,"prob");
3766: strcat(fileresprob,fileres);
3767: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3768: printf("Problem with resultfile: %s\n", fileresprob);
3769: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3770: }
3771: strcpy(fileresprobcov,"probcov");
3772: strcat(fileresprobcov,fileres);
3773: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3774: printf("Problem with resultfile: %s\n", fileresprobcov);
3775: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3776: }
3777: strcpy(fileresprobcor,"probcor");
3778: strcat(fileresprobcor,fileres);
3779: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3780: printf("Problem with resultfile: %s\n", fileresprobcor);
3781: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3782: }
3783: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3784: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3785: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3786: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3787: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3788: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3789: pstamp(ficresprob);
3790: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3791: fprintf(ficresprob,"# Age");
3792: pstamp(ficresprobcov);
3793: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3794: fprintf(ficresprobcov,"# Age");
3795: pstamp(ficresprobcor);
3796: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3797: fprintf(ficresprobcor,"# Age");
3798:
3799:
3800: for(i=1; i<=nlstate;i++)
3801: for(j=1; j<=(nlstate+ndeath);j++){
3802: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3803: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3804: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3805: }
3806: /* fprintf(ficresprob,"\n");
3807: fprintf(ficresprobcov,"\n");
3808: fprintf(ficresprobcor,"\n");
3809: */
1.131 brouard 3810: xp=vector(1,npar);
1.126 brouard 3811: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3812: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3813: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3814: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3815: first=1;
3816: fprintf(ficgp,"\n# Routine varprob");
3817: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3818: fprintf(fichtm,"\n");
3819:
3820: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3821: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3822: file %s<br>\n",optionfilehtmcov);
3823: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3824: and drawn. It helps understanding how is the covariance between two incidences.\
3825: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3826: 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. \
3827: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3828: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3829: standard deviations wide on each axis. <br>\
3830: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3831: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3832: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3833:
3834: cov[1]=1;
1.145 brouard 3835: /* tj=cptcoveff; */
3836: tj = (int) pow(2,cptcoveff);
1.126 brouard 3837: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3838: j1=0;
1.145 brouard 3839: for(j1=1; j1<=tj;j1++){
3840: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3841: /*j1++;*/
1.126 brouard 3842: if (cptcovn>0) {
3843: fprintf(ficresprob, "\n#********** Variable ");
3844: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3845: fprintf(ficresprob, "**********\n#\n");
3846: fprintf(ficresprobcov, "\n#********** Variable ");
3847: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3848: fprintf(ficresprobcov, "**********\n#\n");
3849:
3850: fprintf(ficgp, "\n#********** Variable ");
3851: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3852: fprintf(ficgp, "**********\n#\n");
3853:
3854:
3855: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3856: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3857: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3858:
3859: fprintf(ficresprobcor, "\n#********** Variable ");
3860: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3861: fprintf(ficresprobcor, "**********\n#");
3862: }
3863:
1.145 brouard 3864: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3865: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3866: gp=vector(1,(nlstate)*(nlstate+ndeath));
3867: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 3868: for (age=bage; age<=fage; age ++){
3869: cov[2]=age;
3870: for (k=1; k<=cptcovn;k++) {
1.145 brouard 3871: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3872: * 1 1 1 1 1
3873: * 2 2 1 1 1
3874: * 3 1 2 1 1
3875: */
3876: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 3877: }
3878: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3879: for (k=1; k<=cptcovprod;k++)
3880: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3881:
3882:
3883: for(theta=1; theta <=npar; theta++){
3884: for(i=1; i<=npar; i++)
3885: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3886:
3887: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3888:
3889: k=0;
3890: for(i=1; i<= (nlstate); i++){
3891: for(j=1; j<=(nlstate+ndeath);j++){
3892: k=k+1;
3893: gp[k]=pmmij[i][j];
3894: }
3895: }
3896:
3897: for(i=1; i<=npar; i++)
3898: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3899:
3900: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3901: k=0;
3902: for(i=1; i<=(nlstate); i++){
3903: for(j=1; j<=(nlstate+ndeath);j++){
3904: k=k+1;
3905: gm[k]=pmmij[i][j];
3906: }
3907: }
3908:
3909: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3910: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3911: }
3912:
3913: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3914: for(theta=1; theta <=npar; theta++)
3915: trgradg[j][theta]=gradg[theta][j];
3916:
3917: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3918: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3919:
3920: pmij(pmmij,cov,ncovmodel,x,nlstate);
3921:
3922: k=0;
3923: for(i=1; i<=(nlstate); i++){
3924: for(j=1; j<=(nlstate+ndeath);j++){
3925: k=k+1;
3926: mu[k][(int) age]=pmmij[i][j];
3927: }
3928: }
3929: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3930: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3931: varpij[i][j][(int)age] = doldm[i][j];
3932:
3933: /*printf("\n%d ",(int)age);
3934: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3935: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3936: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3937: }*/
3938:
3939: fprintf(ficresprob,"\n%d ",(int)age);
3940: fprintf(ficresprobcov,"\n%d ",(int)age);
3941: fprintf(ficresprobcor,"\n%d ",(int)age);
3942:
3943: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3944: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3945: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3946: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3947: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3948: }
3949: i=0;
3950: for (k=1; k<=(nlstate);k++){
3951: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 3952: i++;
1.126 brouard 3953: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3954: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3955: for (j=1; j<=i;j++){
1.145 brouard 3956: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 3957: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3958: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3959: }
3960: }
3961: }/* end of loop for state */
3962: } /* end of loop for age */
1.145 brouard 3963: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3964: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3965: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3966: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3967:
1.126 brouard 3968: /* Confidence intervalle of pij */
3969: /*
1.131 brouard 3970: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3971: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3972: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3973: 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);
3974: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3975: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3976: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3977: */
3978:
3979: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 3980: first1=1;first2=2;
1.126 brouard 3981: for (k2=1; k2<=(nlstate);k2++){
3982: for (l2=1; l2<=(nlstate+ndeath);l2++){
3983: if(l2==k2) continue;
3984: j=(k2-1)*(nlstate+ndeath)+l2;
3985: for (k1=1; k1<=(nlstate);k1++){
3986: for (l1=1; l1<=(nlstate+ndeath);l1++){
3987: if(l1==k1) continue;
3988: i=(k1-1)*(nlstate+ndeath)+l1;
3989: if(i<=j) continue;
3990: for (age=bage; age<=fage; age ++){
3991: if ((int)age %5==0){
3992: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3993: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3994: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3995: mu1=mu[i][(int) age]/stepm*YEARM ;
3996: mu2=mu[j][(int) age]/stepm*YEARM;
3997: c12=cv12/sqrt(v1*v2);
3998: /* Computing eigen value of matrix of covariance */
3999: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4000: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4001: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4002: if(first2==1){
4003: first1=0;
4004: 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);
4005: }
4006: 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);
4007: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4008: /* lc2=fabs(lc2); */
1.135 brouard 4009: }
4010:
1.126 brouard 4011: /* Eigen vectors */
4012: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4013: /*v21=sqrt(1.-v11*v11); *//* error */
4014: v21=(lc1-v1)/cv12*v11;
4015: v12=-v21;
4016: v22=v11;
4017: tnalp=v21/v11;
4018: if(first1==1){
4019: first1=0;
4020: 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);
4021: }
4022: 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);
4023: /*printf(fignu*/
4024: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4025: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4026: if(first==1){
4027: first=0;
4028: fprintf(ficgp,"\nset parametric;unset label");
4029: 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 4030: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4031: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4032: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4033: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4034: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4035: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4036: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4037: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4038: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4039: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4040: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4041: 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",\
4042: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4043: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4044: }else{
4045: first=0;
4046: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4047: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4048: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4049: 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",\
4050: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4051: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4052: }/* if first */
4053: } /* age mod 5 */
4054: } /* end loop age */
4055: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4056: first=1;
4057: } /*l12 */
4058: } /* k12 */
4059: } /*l1 */
4060: }/* k1 */
1.169 brouard 4061: /* } */ /* loop covariates */
1.126 brouard 4062: }
4063: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4064: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4065: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4066: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4067: free_vector(xp,1,npar);
4068: fclose(ficresprob);
4069: fclose(ficresprobcov);
4070: fclose(ficresprobcor);
4071: fflush(ficgp);
4072: fflush(fichtmcov);
4073: }
4074:
4075:
4076: /******************* Printing html file ***********/
4077: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4078: int lastpass, int stepm, int weightopt, char model[],\
4079: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4080: int popforecast, int estepm ,\
4081: double jprev1, double mprev1,double anprev1, \
4082: double jprev2, double mprev2,double anprev2){
4083: int jj1, k1, i1, cpt;
4084:
4085: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4086: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4087: </ul>");
4088: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4089: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4090: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4091: fprintf(fichtm,"\
4092: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4093: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4094: fprintf(fichtm,"\
4095: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4096: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4097: fprintf(fichtm,"\
1.128 brouard 4098: - (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 4099: <a href=\"%s\">%s</a> <br>\n",
4100: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4101: fprintf(fichtm,"\
4102: - Population projections by age and states: \
4103: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4104:
4105: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4106:
1.145 brouard 4107: m=pow(2,cptcoveff);
1.126 brouard 4108: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4109:
4110: jj1=0;
4111: for(k1=1; k1<=m;k1++){
4112: for(i1=1; i1<=ncodemax[k1];i1++){
4113: jj1++;
4114: if (cptcovn > 0) {
4115: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4116: for (cpt=1; cpt<=cptcoveff;cpt++)
4117: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4118: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4119: }
4120: /* Pij */
1.145 brouard 4121: 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> \
4122: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4123: /* Quasi-incidences */
4124: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4125: 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> \
4126: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4127: /* Period (stable) prevalence in each health state */
1.154 brouard 4128: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4129: 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> \
4130: <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 4131: }
4132: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4133: 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> \
4134: <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 4135: }
4136: } /* end i1 */
4137: }/* End k1 */
4138: fprintf(fichtm,"</ul>");
4139:
4140:
4141: fprintf(fichtm,"\
4142: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4143: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4144:
4145: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4146: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4147: fprintf(fichtm,"\
4148: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4149: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4150:
4151: fprintf(fichtm,"\
4152: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4153: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4154: fprintf(fichtm,"\
4155: - 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): \
4156: <a href=\"%s\">%s</a> <br>\n</li>",
4157: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4158: fprintf(fichtm,"\
4159: - (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): \
4160: <a href=\"%s\">%s</a> <br>\n</li>",
4161: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4162: fprintf(fichtm,"\
1.128 brouard 4163: - 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 4164: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4165: fprintf(fichtm,"\
1.128 brouard 4166: - 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",
4167: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4168: fprintf(fichtm,"\
4169: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4170: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4171:
4172: /* if(popforecast==1) fprintf(fichtm,"\n */
4173: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4174: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4175: /* <br>",fileres,fileres,fileres,fileres); */
4176: /* else */
4177: /* 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); */
4178: fflush(fichtm);
4179: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4180:
1.145 brouard 4181: m=pow(2,cptcoveff);
1.126 brouard 4182: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4183:
4184: jj1=0;
4185: for(k1=1; k1<=m;k1++){
4186: for(i1=1; i1<=ncodemax[k1];i1++){
4187: jj1++;
4188: if (cptcovn > 0) {
4189: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4190: for (cpt=1; cpt<=cptcoveff;cpt++)
4191: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4192: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4193: }
4194: for(cpt=1; cpt<=nlstate;cpt++) {
4195: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4196: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4197: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4198: }
4199: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4200: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4201: true period expectancies (those weighted with period prevalences are also\
4202: drawn in addition to the population based expectancies computed using\
4203: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4204: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4205: } /* end i1 */
4206: }/* End k1 */
4207: fprintf(fichtm,"</ul>");
4208: fflush(fichtm);
4209: }
4210:
4211: /******************* Gnuplot file **************/
4212: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4213:
4214: char dirfileres[132],optfileres[132];
1.164 brouard 4215: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4216: int ng=0;
1.126 brouard 4217: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4218: /* printf("Problem with file %s",optionfilegnuplot); */
4219: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4220: /* } */
4221:
4222: /*#ifdef windows */
4223: fprintf(ficgp,"cd \"%s\" \n",pathc);
4224: /*#endif */
4225: m=pow(2,cptcoveff);
4226:
4227: strcpy(dirfileres,optionfilefiname);
4228: strcpy(optfileres,"vpl");
4229: /* 1eme*/
1.153 brouard 4230: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4231: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4232: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4233: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4234: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4235: fprintf(ficgp,"set xlabel \"Age\" \n\
4236: set ylabel \"Probability\" \n\
1.145 brouard 4237: set ter png small size 320, 240\n\
1.170 brouard 4238: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4239:
4240: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4241: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4242: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4243: }
1.170 brouard 4244: 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 4245: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4246: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4247: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4248: }
1.170 brouard 4249: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4250: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4251: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4252: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4253: }
1.145 brouard 4254: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4255: }
4256: }
4257: /*2 eme*/
1.153 brouard 4258: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4259: for (k1=1; k1<= m ; k1 ++) {
4260: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4261: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4262:
4263: for (i=1; i<= nlstate+1 ; i ++) {
4264: k=2*i;
1.170 brouard 4265: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4266: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4267: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4268: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4269: }
4270: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4271: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4272: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4273: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4274: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4275: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4276: }
1.145 brouard 4277: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4278: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4279: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4280: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4281: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4282: }
1.145 brouard 4283: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4284: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4285: }
4286: }
4287:
4288: /*3eme*/
4289:
4290: for (k1=1; k1<= m ; k1 ++) {
4291: for (cpt=1; cpt<= nlstate ; cpt ++) {
4292: /* k=2+nlstate*(2*cpt-2); */
4293: k=2+(nlstate+1)*(cpt-1);
4294: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4295: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4296: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4297: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4298: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4299: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4300: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4301: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4302: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4303:
4304: */
4305: for (i=1; i< nlstate ; i ++) {
4306: 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);
4307: /* 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);*/
4308:
4309: }
4310: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4311: }
4312: }
4313:
4314: /* CV preval stable (period) */
1.153 brouard 4315: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4316: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4317: k=3;
1.153 brouard 4318: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4319: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4320: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4321: set ter png small size 320, 240\n\
1.126 brouard 4322: unset log y\n\
1.153 brouard 4323: plot [%.f:%.f] ", ageminpar, agemaxpar);
4324: for (i=1; i<= nlstate ; i ++){
4325: if(i==1)
4326: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4327: else
4328: fprintf(ficgp,", '' ");
1.154 brouard 4329: l=(nlstate+ndeath)*(i-1)+1;
4330: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4331: for (j=1; j<= (nlstate-1) ; j ++)
4332: fprintf(ficgp,"+$%d",k+l+j);
4333: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4334: } /* nlstate */
4335: fprintf(ficgp,"\n");
4336: } /* end cpt state*/
4337: } /* end covariate */
1.126 brouard 4338:
4339: /* proba elementaires */
4340: for(i=1,jk=1; i <=nlstate; i++){
4341: for(k=1; k <=(nlstate+ndeath); k++){
4342: if (k != i) {
4343: for(j=1; j <=ncovmodel; j++){
4344: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4345: jk++;
4346: fprintf(ficgp,"\n");
4347: }
4348: }
4349: }
4350: }
1.145 brouard 4351: /*goto avoid;*/
1.126 brouard 4352: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4353: for(jk=1; jk <=m; jk++) {
1.145 brouard 4354: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4355: if (ng==2)
4356: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4357: else
4358: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4359: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4360: i=1;
4361: for(k2=1; k2<=nlstate; k2++) {
4362: k3=i;
4363: for(k=1; k<=(nlstate+ndeath); k++) {
4364: if (k != k2){
4365: if(ng==2)
4366: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4367: else
4368: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4369: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4370: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4371: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4372: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4373: /* ij++; */
4374: /* } */
4375: /* else */
1.126 brouard 4376: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4377: }
4378: fprintf(ficgp,")/(1");
4379:
4380: for(k1=1; k1 <=nlstate; k1++){
4381: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4382: ij=1;
4383: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4384: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4385: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4386: /* ij++; */
4387: /* } */
4388: /* else */
1.126 brouard 4389: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4390: }
4391: fprintf(ficgp,")");
4392: }
4393: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4394: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4395: i=i+ncovmodel;
4396: }
4397: } /* end k */
4398: } /* end k2 */
4399: } /* end jk */
4400: } /* end ng */
1.164 brouard 4401: /* avoid: */
1.126 brouard 4402: fflush(ficgp);
4403: } /* end gnuplot */
4404:
4405:
4406: /*************** Moving average **************/
4407: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4408:
4409: int i, cpt, cptcod;
4410: int modcovmax =1;
4411: int mobilavrange, mob;
4412: double age;
4413:
4414: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4415: a covariate has 2 modalities */
4416: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4417:
4418: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4419: if(mobilav==1) mobilavrange=5; /* default */
4420: else mobilavrange=mobilav;
4421: for (age=bage; age<=fage; age++)
4422: for (i=1; i<=nlstate;i++)
4423: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4424: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4425: /* We keep the original values on the extreme ages bage, fage and for
4426: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4427: we use a 5 terms etc. until the borders are no more concerned.
4428: */
4429: for (mob=3;mob <=mobilavrange;mob=mob+2){
4430: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4431: for (i=1; i<=nlstate;i++){
4432: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4433: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4434: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4435: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4436: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4437: }
4438: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4439: }
4440: }
4441: }/* end age */
4442: }/* end mob */
4443: }else return -1;
4444: return 0;
4445: }/* End movingaverage */
4446:
4447:
4448: /************** Forecasting ******************/
1.169 brouard 4449: 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 4450: /* proj1, year, month, day of starting projection
4451: agemin, agemax range of age
4452: dateprev1 dateprev2 range of dates during which prevalence is computed
4453: anproj2 year of en of projection (same day and month as proj1).
4454: */
1.164 brouard 4455: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4456: double agec; /* generic age */
4457: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4458: double *popeffectif,*popcount;
4459: double ***p3mat;
4460: double ***mobaverage;
4461: char fileresf[FILENAMELENGTH];
4462:
4463: agelim=AGESUP;
4464: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4465:
4466: strcpy(fileresf,"f");
4467: strcat(fileresf,fileres);
4468: if((ficresf=fopen(fileresf,"w"))==NULL) {
4469: printf("Problem with forecast resultfile: %s\n", fileresf);
4470: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4471: }
4472: printf("Computing forecasting: result on file '%s' \n", fileresf);
4473: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4474:
4475: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4476:
4477: if (mobilav!=0) {
4478: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4479: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4480: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4481: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4482: }
4483: }
4484:
4485: stepsize=(int) (stepm+YEARM-1)/YEARM;
4486: if (stepm<=12) stepsize=1;
4487: if(estepm < stepm){
4488: printf ("Problem %d lower than %d\n",estepm, stepm);
4489: }
4490: else hstepm=estepm;
4491:
4492: hstepm=hstepm/stepm;
4493: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4494: fractional in yp1 */
4495: anprojmean=yp;
4496: yp2=modf((yp1*12),&yp);
4497: mprojmean=yp;
4498: yp1=modf((yp2*30.5),&yp);
4499: jprojmean=yp;
4500: if(jprojmean==0) jprojmean=1;
4501: if(mprojmean==0) jprojmean=1;
4502:
4503: i1=cptcoveff;
4504: if (cptcovn < 1){i1=1;}
4505:
4506: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4507:
4508: fprintf(ficresf,"#****** Routine prevforecast **\n");
4509:
4510: /* if (h==(int)(YEARM*yearp)){ */
4511: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4512: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4513: k=k+1;
4514: fprintf(ficresf,"\n#******");
4515: for(j=1;j<=cptcoveff;j++) {
4516: 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]]);
4517: }
4518: fprintf(ficresf,"******\n");
4519: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4520: for(j=1; j<=nlstate+ndeath;j++){
4521: for(i=1; i<=nlstate;i++)
4522: fprintf(ficresf," p%d%d",i,j);
4523: fprintf(ficresf," p.%d",j);
4524: }
4525: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4526: fprintf(ficresf,"\n");
4527: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4528:
4529: for (agec=fage; agec>=(ageminpar-1); agec--){
4530: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4531: nhstepm = nhstepm/hstepm;
4532: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4533: oldm=oldms;savm=savms;
4534: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4535:
4536: for (h=0; h<=nhstepm; h++){
4537: if (h*hstepm/YEARM*stepm ==yearp) {
4538: fprintf(ficresf,"\n");
4539: for(j=1;j<=cptcoveff;j++)
4540: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4541: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4542: }
4543: for(j=1; j<=nlstate+ndeath;j++) {
4544: ppij=0.;
4545: for(i=1; i<=nlstate;i++) {
4546: if (mobilav==1)
4547: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4548: else {
4549: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4550: }
4551: if (h*hstepm/YEARM*stepm== yearp) {
4552: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4553: }
4554: } /* end i */
4555: if (h*hstepm/YEARM*stepm==yearp) {
4556: fprintf(ficresf," %.3f", ppij);
4557: }
4558: }/* end j */
4559: } /* end h */
4560: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4561: } /* end agec */
4562: } /* end yearp */
4563: } /* end cptcod */
4564: } /* end cptcov */
4565:
4566: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4567:
4568: fclose(ficresf);
4569: }
4570:
4571: /************** Forecasting *****not tested NB*************/
1.169 brouard 4572: 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 4573:
4574: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4575: int *popage;
4576: double calagedatem, agelim, kk1, kk2;
4577: double *popeffectif,*popcount;
4578: double ***p3mat,***tabpop,***tabpopprev;
4579: double ***mobaverage;
4580: char filerespop[FILENAMELENGTH];
4581:
4582: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4583: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4584: agelim=AGESUP;
4585: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4586:
4587: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4588:
4589:
4590: strcpy(filerespop,"pop");
4591: strcat(filerespop,fileres);
4592: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4593: printf("Problem with forecast resultfile: %s\n", filerespop);
4594: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4595: }
4596: printf("Computing forecasting: result on file '%s' \n", filerespop);
4597: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4598:
4599: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4600:
4601: if (mobilav!=0) {
4602: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4603: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4604: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4605: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4606: }
4607: }
4608:
4609: stepsize=(int) (stepm+YEARM-1)/YEARM;
4610: if (stepm<=12) stepsize=1;
4611:
4612: agelim=AGESUP;
4613:
4614: hstepm=1;
4615: hstepm=hstepm/stepm;
4616:
4617: if (popforecast==1) {
4618: if((ficpop=fopen(popfile,"r"))==NULL) {
4619: printf("Problem with population file : %s\n",popfile);exit(0);
4620: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4621: }
4622: popage=ivector(0,AGESUP);
4623: popeffectif=vector(0,AGESUP);
4624: popcount=vector(0,AGESUP);
4625:
4626: i=1;
4627: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4628:
4629: imx=i;
4630: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4631: }
4632:
4633: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4634: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4635: k=k+1;
4636: fprintf(ficrespop,"\n#******");
4637: for(j=1;j<=cptcoveff;j++) {
4638: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4639: }
4640: fprintf(ficrespop,"******\n");
4641: fprintf(ficrespop,"# Age");
4642: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4643: if (popforecast==1) fprintf(ficrespop," [Population]");
4644:
4645: for (cpt=0; cpt<=0;cpt++) {
4646: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4647:
4648: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4649: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4650: nhstepm = nhstepm/hstepm;
4651:
4652: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4653: oldm=oldms;savm=savms;
4654: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4655:
4656: for (h=0; h<=nhstepm; h++){
4657: if (h==(int) (calagedatem+YEARM*cpt)) {
4658: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4659: }
4660: for(j=1; j<=nlstate+ndeath;j++) {
4661: kk1=0.;kk2=0;
4662: for(i=1; i<=nlstate;i++) {
4663: if (mobilav==1)
4664: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4665: else {
4666: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4667: }
4668: }
4669: if (h==(int)(calagedatem+12*cpt)){
4670: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4671: /*fprintf(ficrespop," %.3f", kk1);
4672: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4673: }
4674: }
4675: for(i=1; i<=nlstate;i++){
4676: kk1=0.;
4677: for(j=1; j<=nlstate;j++){
4678: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4679: }
4680: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4681: }
4682:
4683: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4684: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4685: }
4686: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4687: }
4688: }
4689:
4690: /******/
4691:
4692: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4693: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4694: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4695: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4696: nhstepm = nhstepm/hstepm;
4697:
4698: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4699: oldm=oldms;savm=savms;
4700: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4701: for (h=0; h<=nhstepm; h++){
4702: if (h==(int) (calagedatem+YEARM*cpt)) {
4703: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4704: }
4705: for(j=1; j<=nlstate+ndeath;j++) {
4706: kk1=0.;kk2=0;
4707: for(i=1; i<=nlstate;i++) {
4708: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4709: }
4710: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4711: }
4712: }
4713: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4714: }
4715: }
4716: }
4717: }
4718:
4719: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4720:
4721: if (popforecast==1) {
4722: free_ivector(popage,0,AGESUP);
4723: free_vector(popeffectif,0,AGESUP);
4724: free_vector(popcount,0,AGESUP);
4725: }
4726: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4727: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4728: fclose(ficrespop);
4729: } /* End of popforecast */
4730:
4731: int fileappend(FILE *fichier, char *optionfich)
4732: {
4733: if((fichier=fopen(optionfich,"a"))==NULL) {
4734: printf("Problem with file: %s\n", optionfich);
4735: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4736: return (0);
4737: }
4738: fflush(fichier);
4739: return (1);
4740: }
4741:
4742:
4743: /**************** function prwizard **********************/
4744: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4745: {
4746:
4747: /* Wizard to print covariance matrix template */
4748:
1.164 brouard 4749: char ca[32], cb[32];
4750: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 4751: int numlinepar;
4752:
4753: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4754: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4755: for(i=1; i <=nlstate; i++){
4756: jj=0;
4757: for(j=1; j <=nlstate+ndeath; j++){
4758: if(j==i) continue;
4759: jj++;
4760: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4761: printf("%1d%1d",i,j);
4762: fprintf(ficparo,"%1d%1d",i,j);
4763: for(k=1; k<=ncovmodel;k++){
4764: /* printf(" %lf",param[i][j][k]); */
4765: /* fprintf(ficparo," %lf",param[i][j][k]); */
4766: printf(" 0.");
4767: fprintf(ficparo," 0.");
4768: }
4769: printf("\n");
4770: fprintf(ficparo,"\n");
4771: }
4772: }
4773: printf("# Scales (for hessian or gradient estimation)\n");
4774: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4775: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4776: for(i=1; i <=nlstate; i++){
4777: jj=0;
4778: for(j=1; j <=nlstate+ndeath; j++){
4779: if(j==i) continue;
4780: jj++;
4781: fprintf(ficparo,"%1d%1d",i,j);
4782: printf("%1d%1d",i,j);
4783: fflush(stdout);
4784: for(k=1; k<=ncovmodel;k++){
4785: /* printf(" %le",delti3[i][j][k]); */
4786: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4787: printf(" 0.");
4788: fprintf(ficparo," 0.");
4789: }
4790: numlinepar++;
4791: printf("\n");
4792: fprintf(ficparo,"\n");
4793: }
4794: }
4795: printf("# Covariance matrix\n");
4796: /* # 121 Var(a12)\n\ */
4797: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4798: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4799: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4800: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4801: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4802: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4803: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4804: fflush(stdout);
4805: fprintf(ficparo,"# Covariance matrix\n");
4806: /* # 121 Var(a12)\n\ */
4807: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4808: /* # ...\n\ */
4809: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4810:
4811: for(itimes=1;itimes<=2;itimes++){
4812: jj=0;
4813: for(i=1; i <=nlstate; i++){
4814: for(j=1; j <=nlstate+ndeath; j++){
4815: if(j==i) continue;
4816: for(k=1; k<=ncovmodel;k++){
4817: jj++;
4818: ca[0]= k+'a'-1;ca[1]='\0';
4819: if(itimes==1){
4820: printf("#%1d%1d%d",i,j,k);
4821: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4822: }else{
4823: printf("%1d%1d%d",i,j,k);
4824: fprintf(ficparo,"%1d%1d%d",i,j,k);
4825: /* printf(" %.5le",matcov[i][j]); */
4826: }
4827: ll=0;
4828: for(li=1;li <=nlstate; li++){
4829: for(lj=1;lj <=nlstate+ndeath; lj++){
4830: if(lj==li) continue;
4831: for(lk=1;lk<=ncovmodel;lk++){
4832: ll++;
4833: if(ll<=jj){
4834: cb[0]= lk +'a'-1;cb[1]='\0';
4835: if(ll<jj){
4836: if(itimes==1){
4837: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4838: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4839: }else{
4840: printf(" 0.");
4841: fprintf(ficparo," 0.");
4842: }
4843: }else{
4844: if(itimes==1){
4845: printf(" Var(%s%1d%1d)",ca,i,j);
4846: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4847: }else{
4848: printf(" 0.");
4849: fprintf(ficparo," 0.");
4850: }
4851: }
4852: }
4853: } /* end lk */
4854: } /* end lj */
4855: } /* end li */
4856: printf("\n");
4857: fprintf(ficparo,"\n");
4858: numlinepar++;
4859: } /* end k*/
4860: } /*end j */
4861: } /* end i */
4862: } /* end itimes */
4863:
4864: } /* end of prwizard */
4865: /******************* Gompertz Likelihood ******************************/
4866: double gompertz(double x[])
4867: {
4868: double A,B,L=0.0,sump=0.,num=0.;
4869: int i,n=0; /* n is the size of the sample */
4870:
4871: for (i=0;i<=imx-1 ; i++) {
4872: sump=sump+weight[i];
4873: /* sump=sump+1;*/
4874: num=num+1;
4875: }
4876:
4877:
4878: /* for (i=0; i<=imx; i++)
4879: 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]);*/
4880:
4881: for (i=1;i<=imx ; i++)
4882: {
4883: if (cens[i] == 1 && wav[i]>1)
4884: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4885:
4886: if (cens[i] == 0 && wav[i]>1)
4887: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4888: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4889:
4890: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4891: if (wav[i] > 1 ) { /* ??? */
4892: L=L+A*weight[i];
4893: /* 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]);*/
4894: }
4895: }
4896:
4897: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4898:
4899: return -2*L*num/sump;
4900: }
4901:
1.136 brouard 4902: #ifdef GSL
4903: /******************* Gompertz_f Likelihood ******************************/
4904: double gompertz_f(const gsl_vector *v, void *params)
4905: {
4906: double A,B,LL=0.0,sump=0.,num=0.;
4907: double *x= (double *) v->data;
4908: int i,n=0; /* n is the size of the sample */
4909:
4910: for (i=0;i<=imx-1 ; i++) {
4911: sump=sump+weight[i];
4912: /* sump=sump+1;*/
4913: num=num+1;
4914: }
4915:
4916:
4917: /* for (i=0; i<=imx; i++)
4918: 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]);*/
4919: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4920: for (i=1;i<=imx ; i++)
4921: {
4922: if (cens[i] == 1 && wav[i]>1)
4923: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4924:
4925: if (cens[i] == 0 && wav[i]>1)
4926: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4927: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4928:
4929: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4930: if (wav[i] > 1 ) { /* ??? */
4931: LL=LL+A*weight[i];
4932: /* 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]);*/
4933: }
4934: }
4935:
4936: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4937: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4938:
4939: return -2*LL*num/sump;
4940: }
4941: #endif
4942:
1.126 brouard 4943: /******************* Printing html file ***********/
4944: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4945: int lastpass, int stepm, int weightopt, char model[],\
4946: int imx, double p[],double **matcov,double agemortsup){
4947: int i,k;
4948:
4949: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4950: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4951: for (i=1;i<=2;i++)
4952: 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]));
4953: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4954: fprintf(fichtm,"</ul>");
4955:
4956: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4957:
4958: 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>");
4959:
4960: for (k=agegomp;k<(agemortsup-2);k++)
4961: 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]);
4962:
4963:
4964: fflush(fichtm);
4965: }
4966:
4967: /******************* Gnuplot file **************/
4968: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4969:
4970: char dirfileres[132],optfileres[132];
1.164 brouard 4971:
1.126 brouard 4972: int ng;
4973:
4974:
4975: /*#ifdef windows */
4976: fprintf(ficgp,"cd \"%s\" \n",pathc);
4977: /*#endif */
4978:
4979:
4980: strcpy(dirfileres,optionfilefiname);
4981: strcpy(optfileres,"vpl");
4982: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4983: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 4984: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4985: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 4986: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4987:
4988: }
4989:
1.136 brouard 4990: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4991: {
1.126 brouard 4992:
1.136 brouard 4993: /*-------- data file ----------*/
4994: FILE *fic;
4995: char dummy[]=" ";
1.164 brouard 4996: int i=0, j=0, n=0;
1.136 brouard 4997: int linei, month, year,iout;
4998: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 4999: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5000: char *stratrunc;
5001: int lstra;
1.126 brouard 5002:
5003:
1.136 brouard 5004: if((fic=fopen(datafile,"r"))==NULL) {
5005: printf("Problem while opening datafile: %s\n", datafile);return 1;
5006: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5007: }
1.126 brouard 5008:
1.136 brouard 5009: i=1;
5010: linei=0;
5011: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5012: linei=linei+1;
5013: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5014: if(line[j] == '\t')
5015: line[j] = ' ';
5016: }
5017: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5018: ;
5019: };
5020: line[j+1]=0; /* Trims blanks at end of line */
5021: if(line[0]=='#'){
5022: fprintf(ficlog,"Comment line\n%s\n",line);
5023: printf("Comment line\n%s\n",line);
5024: continue;
5025: }
5026: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5027: strcpy(line, linetmp);
1.136 brouard 5028:
1.126 brouard 5029:
1.136 brouard 5030: for (j=maxwav;j>=1;j--){
1.137 brouard 5031: cutv(stra, strb, line, ' ');
1.136 brouard 5032: if(strb[0]=='.') { /* Missing status */
5033: lval=-1;
5034: }else{
5035: errno=0;
5036: lval=strtol(strb,&endptr,10);
5037: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5038: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5039: 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);
5040: 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 5041: return 1;
5042: }
5043: }
5044: s[j][i]=lval;
5045:
5046: strcpy(line,stra);
5047: cutv(stra, strb,line,' ');
1.169 brouard 5048: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5049: }
1.169 brouard 5050: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5051: month=99;
5052: year=9999;
5053: }else{
1.141 brouard 5054: 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);
5055: 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 5056: return 1;
5057: }
5058: anint[j][i]= (double) year;
5059: mint[j][i]= (double)month;
5060: strcpy(line,stra);
5061: } /* ENd Waves */
5062:
5063: cutv(stra, strb,line,' ');
1.169 brouard 5064: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5065: }
1.169 brouard 5066: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5067: month=99;
5068: year=9999;
5069: }else{
1.141 brouard 5070: 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);
5071: 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 5072: return 1;
5073: }
5074: andc[i]=(double) year;
5075: moisdc[i]=(double) month;
5076: strcpy(line,stra);
5077:
5078: cutv(stra, strb,line,' ');
1.169 brouard 5079: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5080: }
1.169 brouard 5081: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5082: month=99;
5083: year=9999;
5084: }else{
1.141 brouard 5085: 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);
5086: 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 5087: return 1;
5088: }
5089: if (year==9999) {
1.141 brouard 5090: 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);
5091: 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 5092: return 1;
1.126 brouard 5093:
1.136 brouard 5094: }
5095: annais[i]=(double)(year);
5096: moisnais[i]=(double)(month);
5097: strcpy(line,stra);
5098:
5099: cutv(stra, strb,line,' ');
5100: errno=0;
5101: dval=strtod(strb,&endptr);
5102: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5103: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5104: 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 5105: fflush(ficlog);
5106: return 1;
5107: }
5108: weight[i]=dval;
5109: strcpy(line,stra);
5110:
5111: for (j=ncovcol;j>=1;j--){
5112: cutv(stra, strb,line,' ');
5113: if(strb[0]=='.') { /* Missing status */
5114: lval=-1;
5115: }else{
5116: errno=0;
5117: lval=strtol(strb,&endptr,10);
5118: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5119: 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);
5120: 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 5121: return 1;
5122: }
5123: }
5124: if(lval <-1 || lval >1){
1.141 brouard 5125: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5126: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5127: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5128: For example, for multinomial values like 1, 2 and 3,\n \
5129: build V1=0 V2=0 for the reference value (1),\n \
5130: V1=1 V2=0 for (2) \n \
5131: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5132: output of IMaCh is often meaningless.\n \
5133: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5134: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5135: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5136: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5137: For example, for multinomial values like 1, 2 and 3,\n \
5138: build V1=0 V2=0 for the reference value (1),\n \
5139: V1=1 V2=0 for (2) \n \
5140: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5141: output of IMaCh is often meaningless.\n \
5142: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5143: return 1;
5144: }
5145: covar[j][i]=(double)(lval);
5146: strcpy(line,stra);
5147: }
5148: lstra=strlen(stra);
5149:
5150: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5151: stratrunc = &(stra[lstra-9]);
5152: num[i]=atol(stratrunc);
5153: }
5154: else
5155: num[i]=atol(stra);
5156: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5157: 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;}*/
5158:
5159: i=i+1;
5160: } /* End loop reading data */
1.126 brouard 5161:
1.136 brouard 5162: *imax=i-1; /* Number of individuals */
5163: fclose(fic);
5164:
5165: return (0);
1.164 brouard 5166: /* endread: */
1.136 brouard 5167: printf("Exiting readdata: ");
5168: fclose(fic);
5169: return (1);
1.126 brouard 5170:
5171:
5172:
1.136 brouard 5173: }
1.145 brouard 5174: void removespace(char *str) {
5175: char *p1 = str, *p2 = str;
5176: do
5177: while (*p2 == ' ')
5178: p2++;
1.169 brouard 5179: while (*p1++ == *p2++);
1.145 brouard 5180: }
5181:
5182: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5183: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5184: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5185: * - cptcovn or number of covariates k of the models excluding age*products =6
5186: * - cptcovage number of covariates with age*products =2
5187: * - cptcovs number of simple covariates
5188: * - 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
5189: * which is a new column after the 9 (ncovcol) variables.
5190: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5191: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5192: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5193: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5194: */
1.136 brouard 5195: {
1.145 brouard 5196: int i, j, k, ks;
1.164 brouard 5197: int j1, k1, k2;
1.136 brouard 5198: char modelsav[80];
1.145 brouard 5199: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5200:
1.145 brouard 5201: /*removespace(model);*/
1.136 brouard 5202: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5203: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5204: j=nbocc(model,'+'); /**< j=Number of '+' */
5205: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5206: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5207: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5208: /* including age products which are counted in cptcovage.
1.169 brouard 5209: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145 brouard 5210: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5211: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5212: strcpy(modelsav,model);
1.137 brouard 5213: if (strstr(model,"AGE") !=0){
5214: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5215: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5216: return 1;
5217: }
1.141 brouard 5218: if (strstr(model,"v") !=0){
5219: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5220: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5221: return 1;
5222: }
1.136 brouard 5223:
1.145 brouard 5224: /* Design
5225: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5226: * < ncovcol=8 >
5227: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5228: * k= 1 2 3 4 5 6 7 8
5229: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5230: * covar[k,i], value of kth covariate if not including age for individual i:
5231: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5232: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5233: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5234: * Tage[++cptcovage]=k
5235: * if products, new covar are created after ncovcol with k1
5236: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5237: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5238: * 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
5239: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5240: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5241: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5242: * < ncovcol=8 >
5243: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5244: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5245: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5246: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5247: * p Tprod[1]@2={ 6, 5}
5248: *p Tvard[1][1]@4= {7, 8, 5, 6}
5249: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5250: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5251: *How to reorganize?
5252: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5253: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5254: * {2, 1, 4, 8, 5, 6, 3, 7}
5255: * Struct []
5256: */
5257:
1.136 brouard 5258: /* This loop fills the array Tvar from the string 'model'.*/
5259: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5260: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5261: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5262: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5263: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5264: /* k=1 Tvar[1]=2 (from V2) */
5265: /* k=5 Tvar[5] */
5266: /* for (k=1; k<=cptcovn;k++) { */
5267: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5268: /* } */
5269: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5270: /*
5271: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5272: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5273: Tvar[k]=0;
5274: cptcovage=0;
5275: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5276: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5277: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5278: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5279: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5280: /*scanf("%d",i);*/
1.145 brouard 5281: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5282: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5283: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5284: /* covar is not filled and then is empty */
1.136 brouard 5285: cptcovprod--;
1.145 brouard 5286: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5287: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5288: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5289: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5290: /*printf("stre=%s ", stre);*/
1.137 brouard 5291: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5292: cptcovprod--;
1.145 brouard 5293: cutl(stre,strb,strc,'V');
1.136 brouard 5294: Tvar[k]=atoi(stre);
5295: cptcovage++;
5296: Tage[cptcovage]=k;
1.137 brouard 5297: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5298: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5299: cptcovn++;
5300: cptcovprodnoage++;k1++;
5301: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5302: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5303: because this model-covariate is a construction we invent a new column
5304: ncovcol + k1
5305: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5306: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5307: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5308: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5309: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5310: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5311: k2=k2+2;
5312: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5313: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5314: for (i=1; i<=lastobs;i++){
5315: /* Computes the new covariate which is a product of
1.145 brouard 5316: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5317: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5318: }
5319: } /* End age is not in the model */
5320: } /* End if model includes a product */
1.136 brouard 5321: else { /* no more sum */
5322: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5323: /* scanf("%d",i);*/
1.145 brouard 5324: cutl(strd,strc,strb,'V');
5325: ks++; /**< Number of simple covariates */
5326: cptcovn++;
5327: Tvar[k]=atoi(strd);
1.136 brouard 5328: }
1.137 brouard 5329: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5330: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5331: scanf("%d",i);*/
5332: } /* end of loop + */
5333: } /* end model */
5334:
5335: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5336: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5337:
5338: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5339: printf("cptcovprod=%d ", cptcovprod);
5340: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5341:
5342: scanf("%d ",i);*/
5343:
5344:
1.137 brouard 5345: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5346: /*endread:*/
1.136 brouard 5347: printf("Exiting decodemodel: ");
5348: return (1);
5349: }
5350:
1.169 brouard 5351: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5352: {
5353: int i, m;
5354:
5355: for (i=1; i<=imx; i++) {
5356: for(m=2; (m<= maxwav); m++) {
5357: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5358: anint[m][i]=9999;
5359: s[m][i]=-1;
5360: }
5361: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5362: *nberr = *nberr + 1;
5363: 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);
5364: 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 5365: s[m][i]=-1;
5366: }
5367: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5368: (*nberr)++;
1.136 brouard 5369: 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]);
5370: 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]);
5371: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5372: }
5373: }
5374: }
5375:
5376: for (i=1; i<=imx; i++) {
5377: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5378: for(m=firstpass; (m<= lastpass); m++){
5379: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5380: if (s[m][i] >= nlstate+1) {
1.169 brouard 5381: if(agedc[i]>0){
5382: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5383: agev[m][i]=agedc[i];
5384: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5385: }else {
1.136 brouard 5386: if ((int)andc[i]!=9999){
5387: nbwarn++;
5388: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5389: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5390: agev[m][i]=-1;
5391: }
5392: }
1.169 brouard 5393: } /* agedc > 0 */
1.136 brouard 5394: }
5395: else if(s[m][i] !=9){ /* Standard case, age in fractional
5396: years but with the precision of a month */
5397: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5398: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5399: agev[m][i]=1;
5400: else if(agev[m][i] < *agemin){
5401: *agemin=agev[m][i];
5402: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5403: }
5404: else if(agev[m][i] >*agemax){
5405: *agemax=agev[m][i];
1.156 brouard 5406: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5407: }
5408: /*agev[m][i]=anint[m][i]-annais[i];*/
5409: /* agev[m][i] = age[i]+2*m;*/
5410: }
5411: else { /* =9 */
5412: agev[m][i]=1;
5413: s[m][i]=-1;
5414: }
5415: }
5416: else /*= 0 Unknown */
5417: agev[m][i]=1;
5418: }
5419:
5420: }
5421: for (i=1; i<=imx; i++) {
5422: for(m=firstpass; (m<=lastpass); m++){
5423: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5424: (*nberr)++;
1.136 brouard 5425: 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);
5426: 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);
5427: return 1;
5428: }
5429: }
5430: }
5431:
5432: /*for (i=1; i<=imx; i++){
5433: for (m=firstpass; (m<lastpass); m++){
5434: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5435: }
5436:
5437: }*/
5438:
5439:
1.139 brouard 5440: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5441: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5442:
5443: return (0);
1.164 brouard 5444: /* endread:*/
1.136 brouard 5445: printf("Exiting calandcheckages: ");
5446: return (1);
5447: }
5448:
1.169 brouard 5449: void syscompilerinfo()
1.167 brouard 5450: {
5451: /* #include "syscompilerinfo.h"*/
1.169 brouard 5452: /* #include <gnu/libc-version.h> */ /* Only on gnu */
1.171 ! brouard 5453: #include <stdint.h>
1.169 brouard 5454: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5455: #if defined(__clang__)
5456: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5457: #endif
5458: #if defined(__ICC) || defined(__INTEL_COMPILER)
5459: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5460: #endif
5461: #if defined(__GNUC__) || defined(__GNUG__)
5462: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5463: #endif
5464: #if defined(__HP_cc) || defined(__HP_aCC)
5465: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5466: #endif
5467: #if defined(__IBMC__) || defined(__IBMCPP__)
5468: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5469: #endif
5470: #if defined(_MSC_VER)
5471: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5472: #endif
5473: #if defined(__PGI)
5474: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5475: #endif
5476: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5477: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 5478: #endif
1.169 brouard 5479: printf(". ");fprintf(ficlog,". ");
5480:
1.167 brouard 5481: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5482: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5483: // Windows (x64 and x86)
5484: #elif __unix__ // all unices, not all compilers
5485: // Unix
5486: #elif __linux__
5487: // linux
5488: #elif __APPLE__
5489: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5490: #endif
5491:
5492: /* __MINGW32__ */
5493: /* __CYGWIN__ */
5494: /* __MINGW64__ */
5495: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5496: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5497: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5498: /* _WIN64 // Defined for applications for Win64. */
5499: /* _M_X64 // Defined for compilations that target x64 processors. */
5500: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 ! brouard 5501:
1.167 brouard 5502: #if UINTPTR_MAX == 0xffffffff
1.171 ! brouard 5503: printf(" 32-bit.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
1.167 brouard 5504: #elif UINTPTR_MAX == 0xffffffffffffffff
1.171 ! brouard 5505: printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
1.167 brouard 5506: #else
1.171 ! brouard 5507: printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* wtf */
1.167 brouard 5508: #endif
5509:
1.171 ! brouard 5510: /* struct utsname sysInfo;
1.167 brouard 5511:
5512: if (uname(&sysInfo) != -1) {
1.169 brouard 5513: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5514: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.167 brouard 5515: }
5516: else
5517: perror("uname() error");
1.171 ! brouard 5518: */
1.169 brouard 5519: #if defined(__GNUC__)
5520: # if defined(__GNUC_PATCHLEVEL__)
5521: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5522: + __GNUC_MINOR__ * 100 \
5523: + __GNUC_PATCHLEVEL__)
5524: # else
5525: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5526: + __GNUC_MINOR__ * 100)
5527: # endif
5528: printf("GNU C version %d.\n", __GNUC_VERSION__);
5529: fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
5530: #endif
5531: #if defined(_MSC_VER)
1.171 ! brouard 5532: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
! 5533: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
1.169 brouard 5534: #endif
5535:
5536: /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
1.167 brouard 5537:
5538: }
1.136 brouard 5539:
5540: /***********************************************/
5541: /**************** Main Program *****************/
5542: /***********************************************/
5543:
5544: int main(int argc, char *argv[])
5545: {
5546: #ifdef GSL
5547: const gsl_multimin_fminimizer_type *T;
5548: size_t iteri = 0, it;
5549: int rval = GSL_CONTINUE;
5550: int status = GSL_SUCCESS;
5551: double ssval;
5552: #endif
5553: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 5554: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5555:
5556: int jj, ll, li, lj, lk;
1.136 brouard 5557: int numlinepar=0; /* Current linenumber of parameter file */
5558: int itimes;
5559: int NDIM=2;
5560: int vpopbased=0;
5561:
1.164 brouard 5562: char ca[32], cb[32];
1.136 brouard 5563: /* FILE *fichtm; *//* Html File */
5564: /* FILE *ficgp;*/ /*Gnuplot File */
5565: struct stat info;
1.164 brouard 5566: double agedeb;
1.136 brouard 5567: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5568:
1.165 brouard 5569: double fret;
1.136 brouard 5570: double dum; /* Dummy variable */
5571: double ***p3mat;
5572: double ***mobaverage;
1.164 brouard 5573:
5574: char line[MAXLINE];
1.136 brouard 5575: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5576: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 5577: char *tok, *val; /* pathtot */
1.136 brouard 5578: int firstobs=1, lastobs=10;
1.164 brouard 5579: int c, h , cpt;
5580: int jl;
5581: int i1, j1, jk, stepsize;
5582: int *tab;
1.136 brouard 5583: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5584: int mobilav=0,popforecast=0;
5585: int hstepm, nhstepm;
5586: int agemortsup;
5587: float sumlpop=0.;
5588: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5589: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5590:
1.164 brouard 5591: double bage=0, fage=110, age, agelim, agebase;
1.136 brouard 5592: double ftolpl=FTOL;
5593: double **prlim;
5594: double ***param; /* Matrix of parameters */
5595: double *p;
5596: double **matcov; /* Matrix of covariance */
5597: double ***delti3; /* Scale */
5598: double *delti; /* Scale */
5599: double ***eij, ***vareij;
5600: double **varpl; /* Variances of prevalence limits by age */
5601: double *epj, vepp;
1.164 brouard 5602:
1.136 brouard 5603: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5604: double **ximort;
1.145 brouard 5605: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5606: int *dcwave;
5607:
1.164 brouard 5608: char z[1]="c";
1.136 brouard 5609:
5610: /*char *strt;*/
5611: char strtend[80];
1.126 brouard 5612:
1.164 brouard 5613:
1.126 brouard 5614: /* setlocale (LC_ALL, ""); */
5615: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5616: /* textdomain (PACKAGE); */
5617: /* setlocale (LC_CTYPE, ""); */
5618: /* setlocale (LC_MESSAGES, ""); */
5619:
5620: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 5621: rstart_time = time(NULL);
5622: /* (void) gettimeofday(&start_time,&tzp);*/
5623: start_time = *localtime(&rstart_time);
1.126 brouard 5624: curr_time=start_time;
1.157 brouard 5625: /*tml = *localtime(&start_time.tm_sec);*/
5626: /* strcpy(strstart,asctime(&tml)); */
5627: strcpy(strstart,asctime(&start_time));
1.126 brouard 5628:
5629: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 5630: /* tp.tm_sec = tp.tm_sec +86400; */
5631: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 5632: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5633: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5634: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 5635: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 5636: /* strt=asctime(&tmg); */
5637: /* printf("Time(after) =%s",strstart); */
5638: /* (void) time (&time_value);
5639: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5640: * tm = *localtime(&time_value);
5641: * strstart=asctime(&tm);
5642: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5643: */
5644:
5645: nberr=0; /* Number of errors and warnings */
5646: nbwarn=0;
5647: getcwd(pathcd, size);
5648:
5649: printf("\n%s\n%s",version,fullversion);
5650: if(argc <=1){
5651: printf("\nEnter the parameter file name: ");
5652: fgets(pathr,FILENAMELENGTH,stdin);
5653: i=strlen(pathr);
5654: if(pathr[i-1]=='\n')
5655: pathr[i-1]='\0';
1.156 brouard 5656: i=strlen(pathr);
5657: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5658: pathr[i-1]='\0';
1.126 brouard 5659: for (tok = pathr; tok != NULL; ){
5660: printf("Pathr |%s|\n",pathr);
5661: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5662: printf("val= |%s| pathr=%s\n",val,pathr);
5663: strcpy (pathtot, val);
5664: if(pathr[0] == '\0') break; /* Dirty */
5665: }
5666: }
5667: else{
5668: strcpy(pathtot,argv[1]);
5669: }
5670: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5671: /*cygwin_split_path(pathtot,path,optionfile);
5672: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5673: /* cutv(path,optionfile,pathtot,'\\');*/
5674:
5675: /* Split argv[0], imach program to get pathimach */
5676: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5677: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5678: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5679: /* strcpy(pathimach,argv[0]); */
5680: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5681: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5682: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5683: chdir(path); /* Can be a relative path */
5684: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5685: printf("Current directory %s!\n",pathcd);
5686: strcpy(command,"mkdir ");
5687: strcat(command,optionfilefiname);
5688: if((outcmd=system(command)) != 0){
1.169 brouard 5689: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 5690: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5691: /* fclose(ficlog); */
5692: /* exit(1); */
5693: }
5694: /* if((imk=mkdir(optionfilefiname))<0){ */
5695: /* perror("mkdir"); */
5696: /* } */
5697:
5698: /*-------- arguments in the command line --------*/
5699:
5700: /* Log file */
5701: strcat(filelog, optionfilefiname);
5702: strcat(filelog,".log"); /* */
5703: if((ficlog=fopen(filelog,"w"))==NULL) {
5704: printf("Problem with logfile %s\n",filelog);
5705: goto end;
5706: }
5707: fprintf(ficlog,"Log filename:%s\n",filelog);
5708: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5709: fprintf(ficlog,"\nEnter the parameter file name: \n");
5710: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5711: path=%s \n\
5712: optionfile=%s\n\
5713: optionfilext=%s\n\
1.156 brouard 5714: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 5715:
1.167 brouard 5716: syscompilerinfo();
5717:
1.126 brouard 5718: printf("Local time (at start):%s",strstart);
5719: fprintf(ficlog,"Local time (at start): %s",strstart);
5720: fflush(ficlog);
5721: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 5722: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 5723:
5724: /* */
5725: strcpy(fileres,"r");
5726: strcat(fileres, optionfilefiname);
5727: strcat(fileres,".txt"); /* Other files have txt extension */
5728:
5729: /*---------arguments file --------*/
5730:
5731: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 5732: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5733: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 5734: fflush(ficlog);
1.149 brouard 5735: /* goto end; */
5736: exit(70);
1.126 brouard 5737: }
5738:
5739:
5740:
5741: strcpy(filereso,"o");
5742: strcat(filereso,fileres);
5743: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5744: printf("Problem with Output resultfile: %s\n", filereso);
5745: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5746: fflush(ficlog);
5747: goto end;
5748: }
5749:
5750: /* Reads comments: lines beginning with '#' */
5751: numlinepar=0;
5752: while((c=getc(ficpar))=='#' && c!= EOF){
5753: ungetc(c,ficpar);
5754: fgets(line, MAXLINE, ficpar);
5755: numlinepar++;
1.141 brouard 5756: fputs(line,stdout);
1.126 brouard 5757: fputs(line,ficparo);
5758: fputs(line,ficlog);
5759: }
5760: ungetc(c,ficpar);
5761:
5762: 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);
5763: numlinepar++;
5764: 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);
5765: 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);
5766: 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);
5767: fflush(ficlog);
5768: while((c=getc(ficpar))=='#' && c!= EOF){
5769: ungetc(c,ficpar);
5770: fgets(line, MAXLINE, ficpar);
5771: numlinepar++;
1.141 brouard 5772: fputs(line, stdout);
5773: //puts(line);
1.126 brouard 5774: fputs(line,ficparo);
5775: fputs(line,ficlog);
5776: }
5777: ungetc(c,ficpar);
5778:
5779:
1.145 brouard 5780: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 5781: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5782: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5783: v1+v2*age+v2*v3 makes cptcovn = 3
5784: */
5785: if (strlen(model)>1)
1.145 brouard 5786: 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*/
5787: else
5788: ncovmodel=2;
1.126 brouard 5789: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5790: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5791: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5792: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5793: 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);
5794: 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);
5795: fflush(stdout);
5796: fclose (ficlog);
5797: goto end;
5798: }
1.126 brouard 5799: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5800: delti=delti3[1][1];
5801: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5802: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5803: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5804: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5805: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5806: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5807: fclose (ficparo);
5808: fclose (ficlog);
5809: goto end;
5810: exit(0);
5811: }
5812: else if(mle==-3) {
5813: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5814: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5815: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5816: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5817: matcov=matrix(1,npar,1,npar);
5818: }
5819: else{
1.145 brouard 5820: /* Read guessed parameters */
1.126 brouard 5821: /* Reads comments: lines beginning with '#' */
5822: while((c=getc(ficpar))=='#' && c!= EOF){
5823: ungetc(c,ficpar);
5824: fgets(line, MAXLINE, ficpar);
5825: numlinepar++;
1.141 brouard 5826: fputs(line,stdout);
1.126 brouard 5827: fputs(line,ficparo);
5828: fputs(line,ficlog);
5829: }
5830: ungetc(c,ficpar);
5831:
5832: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5833: for(i=1; i <=nlstate; i++){
5834: j=0;
5835: for(jj=1; jj <=nlstate+ndeath; jj++){
5836: if(jj==i) continue;
5837: j++;
5838: fscanf(ficpar,"%1d%1d",&i1,&j1);
5839: if ((i1 != i) && (j1 != j)){
5840: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5841: It might be a problem of design; if ncovcol and the model are correct\n \
5842: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5843: exit(1);
5844: }
5845: fprintf(ficparo,"%1d%1d",i1,j1);
5846: if(mle==1)
5847: printf("%1d%1d",i,j);
5848: fprintf(ficlog,"%1d%1d",i,j);
5849: for(k=1; k<=ncovmodel;k++){
5850: fscanf(ficpar," %lf",¶m[i][j][k]);
5851: if(mle==1){
5852: printf(" %lf",param[i][j][k]);
5853: fprintf(ficlog," %lf",param[i][j][k]);
5854: }
5855: else
5856: fprintf(ficlog," %lf",param[i][j][k]);
5857: fprintf(ficparo," %lf",param[i][j][k]);
5858: }
5859: fscanf(ficpar,"\n");
5860: numlinepar++;
5861: if(mle==1)
5862: printf("\n");
5863: fprintf(ficlog,"\n");
5864: fprintf(ficparo,"\n");
5865: }
5866: }
5867: fflush(ficlog);
5868:
1.145 brouard 5869: /* Reads scales values */
1.126 brouard 5870: p=param[1][1];
5871:
5872: /* Reads comments: lines beginning with '#' */
5873: while((c=getc(ficpar))=='#' && c!= EOF){
5874: ungetc(c,ficpar);
5875: fgets(line, MAXLINE, ficpar);
5876: numlinepar++;
1.141 brouard 5877: fputs(line,stdout);
1.126 brouard 5878: fputs(line,ficparo);
5879: fputs(line,ficlog);
5880: }
5881: ungetc(c,ficpar);
5882:
5883: for(i=1; i <=nlstate; i++){
5884: for(j=1; j <=nlstate+ndeath-1; j++){
5885: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 5886: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 5887: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5888: exit(1);
5889: }
5890: printf("%1d%1d",i,j);
5891: fprintf(ficparo,"%1d%1d",i1,j1);
5892: fprintf(ficlog,"%1d%1d",i1,j1);
5893: for(k=1; k<=ncovmodel;k++){
5894: fscanf(ficpar,"%le",&delti3[i][j][k]);
5895: printf(" %le",delti3[i][j][k]);
5896: fprintf(ficparo," %le",delti3[i][j][k]);
5897: fprintf(ficlog," %le",delti3[i][j][k]);
5898: }
5899: fscanf(ficpar,"\n");
5900: numlinepar++;
5901: printf("\n");
5902: fprintf(ficparo,"\n");
5903: fprintf(ficlog,"\n");
5904: }
5905: }
5906: fflush(ficlog);
5907:
1.145 brouard 5908: /* Reads covariance matrix */
1.126 brouard 5909: delti=delti3[1][1];
5910:
5911:
5912: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5913:
5914: /* Reads comments: lines beginning with '#' */
5915: while((c=getc(ficpar))=='#' && c!= EOF){
5916: ungetc(c,ficpar);
5917: fgets(line, MAXLINE, ficpar);
5918: numlinepar++;
1.141 brouard 5919: fputs(line,stdout);
1.126 brouard 5920: fputs(line,ficparo);
5921: fputs(line,ficlog);
5922: }
5923: ungetc(c,ficpar);
5924:
5925: matcov=matrix(1,npar,1,npar);
1.131 brouard 5926: for(i=1; i <=npar; i++)
5927: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5928:
1.126 brouard 5929: for(i=1; i <=npar; i++){
1.145 brouard 5930: fscanf(ficpar,"%s",str);
1.126 brouard 5931: if(mle==1)
5932: printf("%s",str);
5933: fprintf(ficlog,"%s",str);
5934: fprintf(ficparo,"%s",str);
5935: for(j=1; j <=i; j++){
5936: fscanf(ficpar," %le",&matcov[i][j]);
5937: if(mle==1){
5938: printf(" %.5le",matcov[i][j]);
5939: }
5940: fprintf(ficlog," %.5le",matcov[i][j]);
5941: fprintf(ficparo," %.5le",matcov[i][j]);
5942: }
5943: fscanf(ficpar,"\n");
5944: numlinepar++;
5945: if(mle==1)
5946: printf("\n");
5947: fprintf(ficlog,"\n");
5948: fprintf(ficparo,"\n");
5949: }
5950: for(i=1; i <=npar; i++)
5951: for(j=i+1;j<=npar;j++)
5952: matcov[i][j]=matcov[j][i];
5953:
5954: if(mle==1)
5955: printf("\n");
5956: fprintf(ficlog,"\n");
5957:
5958: fflush(ficlog);
5959:
5960: /*-------- Rewriting parameter file ----------*/
5961: strcpy(rfileres,"r"); /* "Rparameterfile */
5962: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5963: strcat(rfileres,"."); /* */
5964: strcat(rfileres,optionfilext); /* Other files have txt extension */
5965: if((ficres =fopen(rfileres,"w"))==NULL) {
5966: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5967: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5968: }
5969: fprintf(ficres,"#%s\n",version);
5970: } /* End of mle != -3 */
5971:
5972:
5973: n= lastobs;
5974: num=lvector(1,n);
5975: moisnais=vector(1,n);
5976: annais=vector(1,n);
5977: moisdc=vector(1,n);
5978: andc=vector(1,n);
5979: agedc=vector(1,n);
5980: cod=ivector(1,n);
5981: weight=vector(1,n);
5982: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5983: mint=matrix(1,maxwav,1,n);
5984: anint=matrix(1,maxwav,1,n);
1.131 brouard 5985: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5986: tab=ivector(1,NCOVMAX);
1.144 brouard 5987: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 5988:
1.136 brouard 5989: /* Reads data from file datafile */
5990: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5991: goto end;
5992:
5993: /* Calculation of the number of parameters from char model */
1.137 brouard 5994: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5995: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5996: k=3 V4 Tvar[k=3]= 4 (from V4)
5997: k=2 V1 Tvar[k=2]= 1 (from V1)
5998: k=1 Tvar[1]=2 (from V2)
5999: */
6000: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6001: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6002: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6003: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6004: */
6005: /* For model-covariate k tells which data-covariate to use but
6006: because this model-covariate is a construction we invent a new column
6007: ncovcol + k1
6008: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6009: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6010: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6011: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6012: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6013: */
1.145 brouard 6014: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6015: 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 6016: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6017: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6018: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6019: 4 covariates (3 plus signs)
6020: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6021: */
1.136 brouard 6022:
6023: if(decodemodel(model, lastobs) == 1)
6024: goto end;
6025:
1.137 brouard 6026: if((double)(lastobs-imx)/(double)imx > 1.10){
6027: nbwarn++;
6028: 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);
6029: 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);
6030: }
1.136 brouard 6031: /* if(mle==1){*/
1.137 brouard 6032: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6033: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6034: }
6035:
6036: /*-calculation of age at interview from date of interview and age at death -*/
6037: agev=matrix(1,maxwav,1,imx);
6038:
6039: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6040: goto end;
6041:
1.126 brouard 6042:
1.136 brouard 6043: agegomp=(int)agemin;
6044: free_vector(moisnais,1,n);
6045: free_vector(annais,1,n);
1.126 brouard 6046: /* free_matrix(mint,1,maxwav,1,n);
6047: free_matrix(anint,1,maxwav,1,n);*/
6048: free_vector(moisdc,1,n);
6049: free_vector(andc,1,n);
1.145 brouard 6050: /* */
6051:
1.126 brouard 6052: wav=ivector(1,imx);
6053: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6054: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6055: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6056:
6057: /* Concatenates waves */
6058: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6059: /* */
6060:
1.126 brouard 6061: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6062:
6063: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6064: ncodemax[1]=1;
1.145 brouard 6065: Ndum =ivector(-1,NCOVMAX);
6066: if (ncovmodel > 2)
6067: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6068:
6069: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6070: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6071: h=0;
6072:
6073:
6074: /*if (cptcovn > 0) */
1.126 brouard 6075:
1.145 brouard 6076:
1.126 brouard 6077: m=pow(2,cptcoveff);
6078:
1.131 brouard 6079: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 6080: 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 */
6081: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6082: 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 6083: h++;
1.141 brouard 6084: if (h>m)
1.136 brouard 6085: h=1;
1.144 brouard 6086: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 6087: * h 1 2 3 4
6088: *______________________________
6089: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6090: * 2 2 1 1 1
6091: * 3 i=2 1 2 1 1
6092: * 4 2 2 1 1
6093: * 5 i=3 1 i=2 1 2 1
6094: * 6 2 1 2 1
6095: * 7 i=4 1 2 2 1
6096: * 8 2 2 2 1
6097: * 9 i=5 1 i=3 1 i=2 1 1
6098: * 10 2 1 1 1
6099: * 11 i=6 1 2 1 1
6100: * 12 2 2 1 1
6101: * 13 i=7 1 i=4 1 2 1
6102: * 14 2 1 2 1
6103: * 15 i=8 1 2 2 1
6104: * 16 2 2 2 1
6105: */
1.141 brouard 6106: codtab[h][k]=j;
1.145 brouard 6107: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 6108: 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 6109: }
6110: }
6111: }
6112: }
6113: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6114: codtab[1][2]=1;codtab[2][2]=2; */
6115: /* for(i=1; i <=m ;i++){
6116: for(k=1; k <=cptcovn; k++){
1.131 brouard 6117: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 6118: }
6119: printf("\n");
6120: }
6121: scanf("%d",i);*/
1.145 brouard 6122:
6123: free_ivector(Ndum,-1,NCOVMAX);
6124:
6125:
1.126 brouard 6126:
6127: /*------------ gnuplot -------------*/
6128: strcpy(optionfilegnuplot,optionfilefiname);
6129: if(mle==-3)
6130: strcat(optionfilegnuplot,"-mort");
6131: strcat(optionfilegnuplot,".gp");
6132:
6133: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6134: printf("Problem with file %s",optionfilegnuplot);
6135: }
6136: else{
6137: fprintf(ficgp,"\n# %s\n", version);
6138: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6139: //fprintf(ficgp,"set missing 'NaNq'\n");
6140: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6141: }
6142: /* fclose(ficgp);*/
6143: /*--------- index.htm --------*/
6144:
6145: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6146: if(mle==-3)
6147: strcat(optionfilehtm,"-mort");
6148: strcat(optionfilehtm,".htm");
6149: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6150: printf("Problem with %s \n",optionfilehtm);
6151: exit(0);
1.126 brouard 6152: }
6153:
6154: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6155: strcat(optionfilehtmcov,"-cov.htm");
6156: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6157: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6158: }
6159: else{
6160: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6161: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6162: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6163: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6164: }
6165:
6166: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6167: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6168: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6169: \n\
6170: <hr size=\"2\" color=\"#EC5E5E\">\
6171: <ul><li><h4>Parameter files</h4>\n\
6172: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6173: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6174: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6175: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6176: - Date and time at start: %s</ul>\n",\
6177: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6178: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6179: fileres,fileres,\
6180: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6181: fflush(fichtm);
6182:
6183: strcpy(pathr,path);
6184: strcat(pathr,optionfilefiname);
6185: chdir(optionfilefiname); /* Move to directory named optionfile */
6186:
6187: /* Calculates basic frequencies. Computes observed prevalence at single age
6188: and prints on file fileres'p'. */
6189: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6190:
6191: fprintf(fichtm,"\n");
6192: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6193: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6194: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6195: imx,agemin,agemax,jmin,jmax,jmean);
6196: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6197: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6198: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6199: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6200: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6201:
6202:
6203: /* For Powell, parameters are in a vector p[] starting at p[1]
6204: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6205: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6206:
6207: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6208:
6209: if (mle==-3){
1.136 brouard 6210: ximort=matrix(1,NDIM,1,NDIM);
6211: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6212: cens=ivector(1,n);
6213: ageexmed=vector(1,n);
6214: agecens=vector(1,n);
6215: dcwave=ivector(1,n);
6216:
6217: for (i=1; i<=imx; i++){
6218: dcwave[i]=-1;
6219: for (m=firstpass; m<=lastpass; m++)
6220: if (s[m][i]>nlstate) {
6221: dcwave[i]=m;
6222: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6223: break;
6224: }
6225: }
6226:
6227: for (i=1; i<=imx; i++) {
6228: if (wav[i]>0){
6229: ageexmed[i]=agev[mw[1][i]][i];
6230: j=wav[i];
6231: agecens[i]=1.;
6232:
6233: if (ageexmed[i]> 1 && wav[i] > 0){
6234: agecens[i]=agev[mw[j][i]][i];
6235: cens[i]= 1;
6236: }else if (ageexmed[i]< 1)
6237: cens[i]= -1;
6238: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6239: cens[i]=0 ;
6240: }
6241: else cens[i]=-1;
6242: }
6243:
6244: for (i=1;i<=NDIM;i++) {
6245: for (j=1;j<=NDIM;j++)
6246: ximort[i][j]=(i == j ? 1.0 : 0.0);
6247: }
6248:
1.145 brouard 6249: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6250: /*printf("%lf %lf", p[1], p[2]);*/
6251:
6252:
1.136 brouard 6253: #ifdef GSL
6254: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6255: #else
1.126 brouard 6256: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6257: #endif
1.126 brouard 6258: strcpy(filerespow,"pow-mort");
6259: strcat(filerespow,fileres);
6260: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6261: printf("Problem with resultfile: %s\n", filerespow);
6262: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6263: }
1.136 brouard 6264: #ifdef GSL
6265: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6266: #else
1.126 brouard 6267: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6268: #endif
1.126 brouard 6269: /* for (i=1;i<=nlstate;i++)
6270: for(j=1;j<=nlstate+ndeath;j++)
6271: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6272: */
6273: fprintf(ficrespow,"\n");
1.136 brouard 6274: #ifdef GSL
6275: /* gsl starts here */
6276: T = gsl_multimin_fminimizer_nmsimplex;
6277: gsl_multimin_fminimizer *sfm = NULL;
6278: gsl_vector *ss, *x;
6279: gsl_multimin_function minex_func;
6280:
6281: /* Initial vertex size vector */
6282: ss = gsl_vector_alloc (NDIM);
6283:
6284: if (ss == NULL){
6285: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6286: }
6287: /* Set all step sizes to 1 */
6288: gsl_vector_set_all (ss, 0.001);
6289:
6290: /* Starting point */
1.126 brouard 6291:
1.136 brouard 6292: x = gsl_vector_alloc (NDIM);
6293:
6294: if (x == NULL){
6295: gsl_vector_free(ss);
6296: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6297: }
6298:
6299: /* Initialize method and iterate */
6300: /* p[1]=0.0268; p[NDIM]=0.083; */
6301: /* gsl_vector_set(x, 0, 0.0268); */
6302: /* gsl_vector_set(x, 1, 0.083); */
6303: gsl_vector_set(x, 0, p[1]);
6304: gsl_vector_set(x, 1, p[2]);
6305:
6306: minex_func.f = &gompertz_f;
6307: minex_func.n = NDIM;
6308: minex_func.params = (void *)&p; /* ??? */
6309:
6310: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6311: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6312:
6313: printf("Iterations beginning .....\n\n");
6314: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6315:
6316: iteri=0;
6317: while (rval == GSL_CONTINUE){
6318: iteri++;
6319: status = gsl_multimin_fminimizer_iterate(sfm);
6320:
6321: if (status) printf("error: %s\n", gsl_strerror (status));
6322: fflush(0);
6323:
6324: if (status)
6325: break;
6326:
6327: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6328: ssval = gsl_multimin_fminimizer_size (sfm);
6329:
6330: if (rval == GSL_SUCCESS)
6331: printf ("converged to a local maximum at\n");
6332:
6333: printf("%5d ", iteri);
6334: for (it = 0; it < NDIM; it++){
6335: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6336: }
6337: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6338: }
6339:
6340: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6341:
6342: gsl_vector_free(x); /* initial values */
6343: gsl_vector_free(ss); /* inital step size */
6344: for (it=0; it<NDIM; it++){
6345: p[it+1]=gsl_vector_get(sfm->x,it);
6346: fprintf(ficrespow," %.12lf", p[it]);
6347: }
6348: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6349: #endif
6350: #ifdef POWELL
6351: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6352: #endif
1.126 brouard 6353: fclose(ficrespow);
6354:
6355: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6356:
6357: for(i=1; i <=NDIM; i++)
6358: for(j=i+1;j<=NDIM;j++)
6359: matcov[i][j]=matcov[j][i];
6360:
6361: printf("\nCovariance matrix\n ");
6362: for(i=1; i <=NDIM; i++) {
6363: for(j=1;j<=NDIM;j++){
6364: printf("%f ",matcov[i][j]);
6365: }
6366: printf("\n ");
6367: }
6368:
6369: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6370: for (i=1;i<=NDIM;i++)
6371: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6372:
6373: lsurv=vector(1,AGESUP);
6374: lpop=vector(1,AGESUP);
6375: tpop=vector(1,AGESUP);
6376: lsurv[agegomp]=100000;
6377:
6378: for (k=agegomp;k<=AGESUP;k++) {
6379: agemortsup=k;
6380: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6381: }
6382:
6383: for (k=agegomp;k<agemortsup;k++)
6384: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6385:
6386: for (k=agegomp;k<agemortsup;k++){
6387: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6388: sumlpop=sumlpop+lpop[k];
6389: }
6390:
6391: tpop[agegomp]=sumlpop;
6392: for (k=agegomp;k<(agemortsup-3);k++){
6393: /* tpop[k+1]=2;*/
6394: tpop[k+1]=tpop[k]-lpop[k];
6395: }
6396:
6397:
6398: printf("\nAge lx qx dx Lx Tx e(x)\n");
6399: for (k=agegomp;k<(agemortsup-2);k++)
6400: 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]);
6401:
6402:
6403: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6404: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6405:
6406: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6407: stepm, weightopt,\
6408: model,imx,p,matcov,agemortsup);
6409:
6410: free_vector(lsurv,1,AGESUP);
6411: free_vector(lpop,1,AGESUP);
6412: free_vector(tpop,1,AGESUP);
1.136 brouard 6413: #ifdef GSL
6414: free_ivector(cens,1,n);
6415: free_vector(agecens,1,n);
6416: free_ivector(dcwave,1,n);
6417: free_matrix(ximort,1,NDIM,1,NDIM);
6418: #endif
1.126 brouard 6419: } /* Endof if mle==-3 */
6420:
6421: else{ /* For mle >=1 */
1.132 brouard 6422: globpr=0;/* debug */
6423: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6424: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6425: for (k=1; k<=npar;k++)
6426: printf(" %d %8.5f",k,p[k]);
6427: printf("\n");
6428: globpr=1; /* to print the contributions */
6429: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6430: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6431: for (k=1; k<=npar;k++)
6432: printf(" %d %8.5f",k,p[k]);
6433: printf("\n");
6434: if(mle>=1){ /* Could be 1 or 2 */
6435: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6436: }
6437:
6438: /*--------- results files --------------*/
6439: 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);
6440:
6441:
6442: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6443: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6444: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6445: for(i=1,jk=1; i <=nlstate; i++){
6446: for(k=1; k <=(nlstate+ndeath); k++){
6447: if (k != i) {
6448: printf("%d%d ",i,k);
6449: fprintf(ficlog,"%d%d ",i,k);
6450: fprintf(ficres,"%1d%1d ",i,k);
6451: for(j=1; j <=ncovmodel; j++){
6452: printf("%lf ",p[jk]);
6453: fprintf(ficlog,"%lf ",p[jk]);
6454: fprintf(ficres,"%lf ",p[jk]);
6455: jk++;
6456: }
6457: printf("\n");
6458: fprintf(ficlog,"\n");
6459: fprintf(ficres,"\n");
6460: }
6461: }
6462: }
6463: if(mle!=0){
6464: /* Computing hessian and covariance matrix */
6465: ftolhess=ftol; /* Usually correct */
6466: hesscov(matcov, p, npar, delti, ftolhess, func);
6467: }
6468: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6469: printf("# Scales (for hessian or gradient estimation)\n");
6470: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6471: for(i=1,jk=1; i <=nlstate; i++){
6472: for(j=1; j <=nlstate+ndeath; j++){
6473: if (j!=i) {
6474: fprintf(ficres,"%1d%1d",i,j);
6475: printf("%1d%1d",i,j);
6476: fprintf(ficlog,"%1d%1d",i,j);
6477: for(k=1; k<=ncovmodel;k++){
6478: printf(" %.5e",delti[jk]);
6479: fprintf(ficlog," %.5e",delti[jk]);
6480: fprintf(ficres," %.5e",delti[jk]);
6481: jk++;
6482: }
6483: printf("\n");
6484: fprintf(ficlog,"\n");
6485: fprintf(ficres,"\n");
6486: }
6487: }
6488: }
6489:
6490: 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");
6491: if(mle>=1)
6492: 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");
6493: 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");
6494: /* # 121 Var(a12)\n\ */
6495: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6496: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6497: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6498: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6499: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6500: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6501: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6502:
6503:
6504: /* Just to have a covariance matrix which will be more understandable
6505: even is we still don't want to manage dictionary of variables
6506: */
6507: for(itimes=1;itimes<=2;itimes++){
6508: jj=0;
6509: for(i=1; i <=nlstate; i++){
6510: for(j=1; j <=nlstate+ndeath; j++){
6511: if(j==i) continue;
6512: for(k=1; k<=ncovmodel;k++){
6513: jj++;
6514: ca[0]= k+'a'-1;ca[1]='\0';
6515: if(itimes==1){
6516: if(mle>=1)
6517: printf("#%1d%1d%d",i,j,k);
6518: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6519: fprintf(ficres,"#%1d%1d%d",i,j,k);
6520: }else{
6521: if(mle>=1)
6522: printf("%1d%1d%d",i,j,k);
6523: fprintf(ficlog,"%1d%1d%d",i,j,k);
6524: fprintf(ficres,"%1d%1d%d",i,j,k);
6525: }
6526: ll=0;
6527: for(li=1;li <=nlstate; li++){
6528: for(lj=1;lj <=nlstate+ndeath; lj++){
6529: if(lj==li) continue;
6530: for(lk=1;lk<=ncovmodel;lk++){
6531: ll++;
6532: if(ll<=jj){
6533: cb[0]= lk +'a'-1;cb[1]='\0';
6534: if(ll<jj){
6535: if(itimes==1){
6536: if(mle>=1)
6537: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6538: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6539: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6540: }else{
6541: if(mle>=1)
6542: printf(" %.5e",matcov[jj][ll]);
6543: fprintf(ficlog," %.5e",matcov[jj][ll]);
6544: fprintf(ficres," %.5e",matcov[jj][ll]);
6545: }
6546: }else{
6547: if(itimes==1){
6548: if(mle>=1)
6549: printf(" Var(%s%1d%1d)",ca,i,j);
6550: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6551: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6552: }else{
6553: if(mle>=1)
6554: printf(" %.5e",matcov[jj][ll]);
6555: fprintf(ficlog," %.5e",matcov[jj][ll]);
6556: fprintf(ficres," %.5e",matcov[jj][ll]);
6557: }
6558: }
6559: }
6560: } /* end lk */
6561: } /* end lj */
6562: } /* end li */
6563: if(mle>=1)
6564: printf("\n");
6565: fprintf(ficlog,"\n");
6566: fprintf(ficres,"\n");
6567: numlinepar++;
6568: } /* end k*/
6569: } /*end j */
6570: } /* end i */
6571: } /* end itimes */
6572:
6573: fflush(ficlog);
6574: fflush(ficres);
6575:
6576: while((c=getc(ficpar))=='#' && c!= EOF){
6577: ungetc(c,ficpar);
6578: fgets(line, MAXLINE, ficpar);
1.141 brouard 6579: fputs(line,stdout);
1.126 brouard 6580: fputs(line,ficparo);
6581: }
6582: ungetc(c,ficpar);
6583:
6584: estepm=0;
6585: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6586: if (estepm==0 || estepm < stepm) estepm=stepm;
6587: if (fage <= 2) {
6588: bage = ageminpar;
6589: fage = agemaxpar;
6590: }
6591:
6592: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6593: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6594: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6595:
6596: while((c=getc(ficpar))=='#' && c!= EOF){
6597: ungetc(c,ficpar);
6598: fgets(line, MAXLINE, ficpar);
1.141 brouard 6599: fputs(line,stdout);
1.126 brouard 6600: fputs(line,ficparo);
6601: }
6602: ungetc(c,ficpar);
6603:
6604: 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);
6605: 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);
6606: 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);
6607: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6608: 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);
6609:
6610: while((c=getc(ficpar))=='#' && c!= EOF){
6611: ungetc(c,ficpar);
6612: fgets(line, MAXLINE, ficpar);
1.141 brouard 6613: fputs(line,stdout);
1.126 brouard 6614: fputs(line,ficparo);
6615: }
6616: ungetc(c,ficpar);
6617:
6618:
6619: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6620: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6621:
6622: fscanf(ficpar,"pop_based=%d\n",&popbased);
6623: fprintf(ficparo,"pop_based=%d\n",popbased);
6624: fprintf(ficres,"pop_based=%d\n",popbased);
6625:
6626: while((c=getc(ficpar))=='#' && c!= EOF){
6627: ungetc(c,ficpar);
6628: fgets(line, MAXLINE, ficpar);
1.141 brouard 6629: fputs(line,stdout);
1.126 brouard 6630: fputs(line,ficparo);
6631: }
6632: ungetc(c,ficpar);
6633:
6634: 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);
6635: 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);
6636: 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);
6637: 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);
6638: 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);
6639: /* day and month of proj2 are not used but only year anproj2.*/
6640:
6641:
6642:
1.145 brouard 6643: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6644: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 6645:
6646: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6647: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6648:
6649: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6650: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6651: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6652:
6653: /*------------ free_vector -------------*/
6654: /* chdir(path); */
6655:
6656: free_ivector(wav,1,imx);
6657: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6658: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6659: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6660: free_lvector(num,1,n);
6661: free_vector(agedc,1,n);
6662: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6663: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6664: fclose(ficparo);
6665: fclose(ficres);
6666:
6667:
6668: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.145 brouard 6669: #include "prevlim.h" /* Use ficrespl, ficlog */
1.126 brouard 6670: fclose(ficrespl);
6671:
1.145 brouard 6672: #ifdef FREEEXIT2
6673: #include "freeexit2.h"
6674: #endif
6675:
1.126 brouard 6676: /*------------- h Pij x at various ages ------------*/
1.145 brouard 6677: #include "hpijx.h"
6678: fclose(ficrespij);
1.126 brouard 6679:
1.145 brouard 6680: /*-------------- Variance of one-step probabilities---*/
6681: k=1;
1.126 brouard 6682: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6683:
6684:
6685: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6686: for(i=1;i<=AGESUP;i++)
6687: for(j=1;j<=NCOVMAX;j++)
6688: for(k=1;k<=NCOVMAX;k++)
6689: probs[i][j][k]=0.;
6690:
6691: /*---------- Forecasting ------------------*/
6692: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6693: if(prevfcast==1){
6694: /* if(stepm ==1){*/
6695: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6696: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6697: /* } */
6698: /* else{ */
6699: /* erreur=108; */
6700: /* 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); */
6701: /* 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); */
6702: /* } */
6703: }
6704:
6705:
1.127 brouard 6706: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6707:
6708: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6709: /* 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",\
6710: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6711: */
1.126 brouard 6712:
1.127 brouard 6713: if (mobilav!=0) {
6714: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6715: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6716: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6717: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6718: }
1.126 brouard 6719: }
6720:
6721:
1.127 brouard 6722: /*---------- Health expectancies, no variances ------------*/
6723:
1.126 brouard 6724: strcpy(filerese,"e");
6725: strcat(filerese,fileres);
6726: if((ficreseij=fopen(filerese,"w"))==NULL) {
6727: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6728: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6729: }
6730: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6731: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 6732: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6733: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6734:
6735: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 6736: fprintf(ficreseij,"\n#****** ");
6737: for(j=1;j<=cptcoveff;j++) {
6738: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6739: }
6740: fprintf(ficreseij,"******\n");
6741:
6742: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6743: oldm=oldms;savm=savms;
6744: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6745:
6746: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6747: /*}*/
1.127 brouard 6748: }
6749: fclose(ficreseij);
6750:
6751:
6752: /*---------- Health expectancies and variances ------------*/
6753:
6754:
6755: strcpy(filerest,"t");
6756: strcat(filerest,fileres);
6757: if((ficrest=fopen(filerest,"w"))==NULL) {
6758: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6759: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6760: }
6761: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6762: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6763:
1.126 brouard 6764:
6765: strcpy(fileresstde,"stde");
6766: strcat(fileresstde,fileres);
6767: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6768: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6769: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6770: }
6771: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6772: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6773:
6774: strcpy(filerescve,"cve");
6775: strcat(filerescve,fileres);
6776: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6777: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6778: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6779: }
6780: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6781: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6782:
6783: strcpy(fileresv,"v");
6784: strcat(fileresv,fileres);
6785: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6786: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6787: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6788: }
6789: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6790: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6791:
1.145 brouard 6792: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6793: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6794:
6795: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6796: fprintf(ficrest,"\n#****** ");
1.126 brouard 6797: for(j=1;j<=cptcoveff;j++)
6798: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6799: fprintf(ficrest,"******\n");
6800:
6801: fprintf(ficresstdeij,"\n#****** ");
6802: fprintf(ficrescveij,"\n#****** ");
6803: for(j=1;j<=cptcoveff;j++) {
6804: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6805: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6806: }
6807: fprintf(ficresstdeij,"******\n");
6808: fprintf(ficrescveij,"******\n");
6809:
6810: fprintf(ficresvij,"\n#****** ");
6811: for(j=1;j<=cptcoveff;j++)
6812: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6813: fprintf(ficresvij,"******\n");
6814:
6815: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6816: oldm=oldms;savm=savms;
1.127 brouard 6817: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 6818: /*
6819: */
6820: /* goto endfree; */
1.126 brouard 6821:
6822: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6823: pstamp(ficrest);
1.145 brouard 6824:
6825:
1.128 brouard 6826: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 6827: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 6828: cptcod= 0; /* To be deleted */
6829: 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 6830: 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 6831: if(vpopbased==1)
6832: 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);
6833: else
6834: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6835: fprintf(ficrest,"# Age e.. (std) ");
6836: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6837: fprintf(ficrest,"\n");
1.126 brouard 6838:
1.128 brouard 6839: epj=vector(1,nlstate+1);
6840: for(age=bage; age <=fage ;age++){
6841: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6842: if (vpopbased==1) {
6843: if(mobilav ==0){
6844: for(i=1; i<=nlstate;i++)
6845: prlim[i][i]=probs[(int)age][i][k];
6846: }else{ /* mobilav */
6847: for(i=1; i<=nlstate;i++)
6848: prlim[i][i]=mobaverage[(int)age][i][k];
6849: }
1.126 brouard 6850: }
6851:
1.128 brouard 6852: fprintf(ficrest," %4.0f",age);
6853: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6854: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6855: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6856: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6857: }
6858: epj[nlstate+1] +=epj[j];
1.126 brouard 6859: }
6860:
1.128 brouard 6861: for(i=1, vepp=0.;i <=nlstate;i++)
6862: for(j=1;j <=nlstate;j++)
6863: vepp += vareij[i][j][(int)age];
6864: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6865: for(j=1;j <=nlstate;j++){
6866: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6867: }
6868: fprintf(ficrest,"\n");
1.126 brouard 6869: }
6870: }
6871: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6872: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6873: free_vector(epj,1,nlstate+1);
1.145 brouard 6874: /*}*/
1.126 brouard 6875: }
6876: free_vector(weight,1,n);
1.145 brouard 6877: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 6878: free_imatrix(s,1,maxwav+1,1,n);
6879: free_matrix(anint,1,maxwav,1,n);
6880: free_matrix(mint,1,maxwav,1,n);
6881: free_ivector(cod,1,n);
6882: free_ivector(tab,1,NCOVMAX);
6883: fclose(ficresstdeij);
6884: fclose(ficrescveij);
6885: fclose(ficresvij);
6886: fclose(ficrest);
6887: fclose(ficpar);
6888:
6889: /*------- Variance of period (stable) prevalence------*/
6890:
6891: strcpy(fileresvpl,"vpl");
6892: strcat(fileresvpl,fileres);
6893: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6894: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6895: exit(0);
6896: }
6897: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6898:
1.145 brouard 6899: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6900: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6901:
6902: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6903: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 6904: for(j=1;j<=cptcoveff;j++)
6905: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6906: fprintf(ficresvpl,"******\n");
6907:
6908: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6909: oldm=oldms;savm=savms;
6910: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6911: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6912: /*}*/
1.126 brouard 6913: }
6914:
6915: fclose(ficresvpl);
6916:
6917: /*---------- End : free ----------------*/
6918: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6919: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6920: } /* mle==-3 arrives here for freeing */
1.164 brouard 6921: /* endfree:*/
1.141 brouard 6922: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 6923: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6924: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6925: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6926: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6927: free_matrix(covar,0,NCOVMAX,1,n);
6928: free_matrix(matcov,1,npar,1,npar);
6929: /*free_vector(delti,1,npar);*/
6930: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6931: free_matrix(agev,1,maxwav,1,imx);
6932: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6933:
1.145 brouard 6934: free_ivector(ncodemax,1,NCOVMAX);
6935: free_ivector(Tvar,1,NCOVMAX);
6936: free_ivector(Tprod,1,NCOVMAX);
6937: free_ivector(Tvaraff,1,NCOVMAX);
6938: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 6939:
6940: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6941: free_imatrix(codtab,1,100,1,10);
6942: fflush(fichtm);
6943: fflush(ficgp);
6944:
6945:
6946: if((nberr >0) || (nbwarn>0)){
6947: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6948: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6949: }else{
6950: printf("End of Imach\n");
6951: fprintf(ficlog,"End of Imach\n");
6952: }
6953: printf("See log file on %s\n",filelog);
6954: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 6955: /*(void) gettimeofday(&end_time,&tzp);*/
6956: rend_time = time(NULL);
6957: end_time = *localtime(&rend_time);
6958: /* tml = *localtime(&end_time.tm_sec); */
6959: strcpy(strtend,asctime(&end_time));
1.126 brouard 6960: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6961: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 6962: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 6963:
1.157 brouard 6964: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6965: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6966: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 6967: /* printf("Total time was %d uSec.\n", total_usecs);*/
6968: /* if(fileappend(fichtm,optionfilehtm)){ */
6969: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6970: fclose(fichtm);
6971: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6972: fclose(fichtmcov);
6973: fclose(ficgp);
6974: fclose(ficlog);
6975: /*------ End -----------*/
6976:
6977:
6978: printf("Before Current directory %s!\n",pathcd);
6979: if(chdir(pathcd) != 0)
6980: printf("Can't move to directory %s!\n",path);
6981: if(getcwd(pathcd,MAXLINE) > 0)
6982: printf("Current directory %s!\n",pathcd);
6983: /*strcat(plotcmd,CHARSEPARATOR);*/
6984: sprintf(plotcmd,"gnuplot");
1.157 brouard 6985: #ifdef _WIN32
1.126 brouard 6986: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6987: #endif
6988: if(!stat(plotcmd,&info)){
1.158 brouard 6989: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6990: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 6991: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 6992: }else
6993: strcpy(pplotcmd,plotcmd);
1.157 brouard 6994: #ifdef __unix
1.126 brouard 6995: strcpy(plotcmd,GNUPLOTPROGRAM);
6996: if(!stat(plotcmd,&info)){
1.158 brouard 6997: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6998: }else
6999: strcpy(pplotcmd,plotcmd);
7000: #endif
7001: }else
7002: strcpy(pplotcmd,plotcmd);
7003:
7004: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7005: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7006:
7007: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7008: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7009: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7010: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7011: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7012: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7013: }
1.158 brouard 7014: printf(" Successful, please wait...");
1.126 brouard 7015: while (z[0] != 'q') {
7016: /* chdir(path); */
1.154 brouard 7017: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7018: scanf("%s",z);
7019: /* if (z[0] == 'c') system("./imach"); */
7020: if (z[0] == 'e') {
1.158 brouard 7021: #ifdef __APPLE__
1.152 brouard 7022: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7023: #elif __linux
7024: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7025: #else
1.152 brouard 7026: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7027: #endif
7028: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7029: system(pplotcmd);
1.126 brouard 7030: }
7031: else if (z[0] == 'g') system(plotcmd);
7032: else if (z[0] == 'q') exit(0);
7033: }
7034: end:
7035: while (z[0] != 'q') {
7036: printf("\nType q for exiting: ");
7037: scanf("%s",z);
7038: }
7039: }
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