1: /* $Id: imach.c,v 1.177 2015/01/03 18:40:56 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.177 2015/01/03 18:40:56 brouard
5: Summary: Still testing ilc32 on OSX
6:
7: Revision 1.176 2015/01/03 16:45:04 brouard
8: *** empty log message ***
9:
10: Revision 1.175 2015/01/03 16:33:42 brouard
11: *** empty log message ***
12:
13: Revision 1.174 2015/01/03 16:15:49 brouard
14: Summary: Still in cross-compilation
15:
16: Revision 1.173 2015/01/03 12:06:26 brouard
17: Summary: trying to detect cross-compilation
18:
19: Revision 1.172 2014/12/27 12:07:47 brouard
20: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
21:
22: Revision 1.171 2014/12/23 13:26:59 brouard
23: Summary: Back from Visual C
24:
25: Still problem with utsname.h on Windows
26:
27: Revision 1.170 2014/12/23 11:17:12 brouard
28: Summary: Cleaning some \%% back to %%
29:
30: The escape was mandatory for a specific compiler (which one?), but too many warnings.
31:
32: Revision 1.169 2014/12/22 23:08:31 brouard
33: Summary: 0.98p
34:
35: Outputs some informations on compiler used, OS etc. Testing on different platforms.
36:
37: Revision 1.168 2014/12/22 15:17:42 brouard
38: Summary: update
39:
40: Revision 1.167 2014/12/22 13:50:56 brouard
41: Summary: Testing uname and compiler version and if compiled 32 or 64
42:
43: Testing on Linux 64
44:
45: Revision 1.166 2014/12/22 11:40:47 brouard
46: *** empty log message ***
47:
48: Revision 1.165 2014/12/16 11:20:36 brouard
49: Summary: After compiling on Visual C
50:
51: * imach.c (Module): Merging 1.61 to 1.162
52:
53: Revision 1.164 2014/12/16 10:52:11 brouard
54: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
55:
56: * imach.c (Module): Merging 1.61 to 1.162
57:
58: Revision 1.163 2014/12/16 10:30:11 brouard
59: * imach.c (Module): Merging 1.61 to 1.162
60:
61: Revision 1.162 2014/09/25 11:43:39 brouard
62: Summary: temporary backup 0.99!
63:
64: Revision 1.1 2014/09/16 11:06:58 brouard
65: Summary: With some code (wrong) for nlopt
66:
67: Author:
68:
69: Revision 1.161 2014/09/15 20:41:41 brouard
70: Summary: Problem with macro SQR on Intel compiler
71:
72: Revision 1.160 2014/09/02 09:24:05 brouard
73: *** empty log message ***
74:
75: Revision 1.159 2014/09/01 10:34:10 brouard
76: Summary: WIN32
77: Author: Brouard
78:
79: Revision 1.158 2014/08/27 17:11:51 brouard
80: *** empty log message ***
81:
82: Revision 1.157 2014/08/27 16:26:55 brouard
83: Summary: Preparing windows Visual studio version
84: Author: Brouard
85:
86: In order to compile on Visual studio, time.h is now correct and time_t
87: and tm struct should be used. difftime should be used but sometimes I
88: just make the differences in raw time format (time(&now).
89: Trying to suppress #ifdef LINUX
90: Add xdg-open for __linux in order to open default browser.
91:
92: Revision 1.156 2014/08/25 20:10:10 brouard
93: *** empty log message ***
94:
95: Revision 1.155 2014/08/25 18:32:34 brouard
96: Summary: New compile, minor changes
97: Author: Brouard
98:
99: Revision 1.154 2014/06/20 17:32:08 brouard
100: Summary: Outputs now all graphs of convergence to period prevalence
101:
102: Revision 1.153 2014/06/20 16:45:46 brouard
103: Summary: If 3 live state, convergence to period prevalence on same graph
104: Author: Brouard
105:
106: Revision 1.152 2014/06/18 17:54:09 brouard
107: Summary: open browser, use gnuplot on same dir than imach if not found in the path
108:
109: Revision 1.151 2014/06/18 16:43:30 brouard
110: *** empty log message ***
111:
112: Revision 1.150 2014/06/18 16:42:35 brouard
113: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
114: Author: brouard
115:
116: Revision 1.149 2014/06/18 15:51:14 brouard
117: Summary: Some fixes in parameter files errors
118: Author: Nicolas Brouard
119:
120: Revision 1.148 2014/06/17 17:38:48 brouard
121: Summary: Nothing new
122: Author: Brouard
123:
124: Just a new packaging for OS/X version 0.98nS
125:
126: Revision 1.147 2014/06/16 10:33:11 brouard
127: *** empty log message ***
128:
129: Revision 1.146 2014/06/16 10:20:28 brouard
130: Summary: Merge
131: Author: Brouard
132:
133: Merge, before building revised version.
134:
135: Revision 1.145 2014/06/10 21:23:15 brouard
136: Summary: Debugging with valgrind
137: Author: Nicolas Brouard
138:
139: Lot of changes in order to output the results with some covariates
140: After the Edimburgh REVES conference 2014, it seems mandatory to
141: improve the code.
142: No more memory valgrind error but a lot has to be done in order to
143: continue the work of splitting the code into subroutines.
144: Also, decodemodel has been improved. Tricode is still not
145: optimal. nbcode should be improved. Documentation has been added in
146: the source code.
147:
148: Revision 1.143 2014/01/26 09:45:38 brouard
149: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
150:
151: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
152: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
153:
154: Revision 1.142 2014/01/26 03:57:36 brouard
155: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
156:
157: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
158:
159: Revision 1.141 2014/01/26 02:42:01 brouard
160: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
161:
162: Revision 1.140 2011/09/02 10:37:54 brouard
163: Summary: times.h is ok with mingw32 now.
164:
165: Revision 1.139 2010/06/14 07:50:17 brouard
166: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
167: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
168:
169: Revision 1.138 2010/04/30 18:19:40 brouard
170: *** empty log message ***
171:
172: Revision 1.137 2010/04/29 18:11:38 brouard
173: (Module): Checking covariates for more complex models
174: than V1+V2. A lot of change to be done. Unstable.
175:
176: Revision 1.136 2010/04/26 20:30:53 brouard
177: (Module): merging some libgsl code. Fixing computation
178: of likelione (using inter/intrapolation if mle = 0) in order to
179: get same likelihood as if mle=1.
180: Some cleaning of code and comments added.
181:
182: Revision 1.135 2009/10/29 15:33:14 brouard
183: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
184:
185: Revision 1.134 2009/10/29 13:18:53 brouard
186: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
187:
188: Revision 1.133 2009/07/06 10:21:25 brouard
189: just nforces
190:
191: Revision 1.132 2009/07/06 08:22:05 brouard
192: Many tings
193:
194: Revision 1.131 2009/06/20 16:22:47 brouard
195: Some dimensions resccaled
196:
197: Revision 1.130 2009/05/26 06:44:34 brouard
198: (Module): Max Covariate is now set to 20 instead of 8. A
199: lot of cleaning with variables initialized to 0. Trying to make
200: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
201:
202: Revision 1.129 2007/08/31 13:49:27 lievre
203: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
204:
205: Revision 1.128 2006/06/30 13:02:05 brouard
206: (Module): Clarifications on computing e.j
207:
208: Revision 1.127 2006/04/28 18:11:50 brouard
209: (Module): Yes the sum of survivors was wrong since
210: imach-114 because nhstepm was no more computed in the age
211: loop. Now we define nhstepma in the age loop.
212: (Module): In order to speed up (in case of numerous covariates) we
213: compute health expectancies (without variances) in a first step
214: and then all the health expectancies with variances or standard
215: deviation (needs data from the Hessian matrices) which slows the
216: computation.
217: In the future we should be able to stop the program is only health
218: expectancies and graph are needed without standard deviations.
219:
220: Revision 1.126 2006/04/28 17:23:28 brouard
221: (Module): Yes the sum of survivors was wrong since
222: imach-114 because nhstepm was no more computed in the age
223: loop. Now we define nhstepma in the age loop.
224: Version 0.98h
225:
226: Revision 1.125 2006/04/04 15:20:31 lievre
227: Errors in calculation of health expectancies. Age was not initialized.
228: Forecasting file added.
229:
230: Revision 1.124 2006/03/22 17:13:53 lievre
231: Parameters are printed with %lf instead of %f (more numbers after the comma).
232: The log-likelihood is printed in the log file
233:
234: Revision 1.123 2006/03/20 10:52:43 brouard
235: * imach.c (Module): <title> changed, corresponds to .htm file
236: name. <head> headers where missing.
237:
238: * imach.c (Module): Weights can have a decimal point as for
239: English (a comma might work with a correct LC_NUMERIC environment,
240: otherwise the weight is truncated).
241: Modification of warning when the covariates values are not 0 or
242: 1.
243: Version 0.98g
244:
245: Revision 1.122 2006/03/20 09:45:41 brouard
246: (Module): Weights can have a decimal point as for
247: English (a comma might work with a correct LC_NUMERIC environment,
248: otherwise the weight is truncated).
249: Modification of warning when the covariates values are not 0 or
250: 1.
251: Version 0.98g
252:
253: Revision 1.121 2006/03/16 17:45:01 lievre
254: * imach.c (Module): Comments concerning covariates added
255:
256: * imach.c (Module): refinements in the computation of lli if
257: status=-2 in order to have more reliable computation if stepm is
258: not 1 month. Version 0.98f
259:
260: Revision 1.120 2006/03/16 15:10:38 lievre
261: (Module): refinements in the computation of lli if
262: status=-2 in order to have more reliable computation if stepm is
263: not 1 month. Version 0.98f
264:
265: Revision 1.119 2006/03/15 17:42:26 brouard
266: (Module): Bug if status = -2, the loglikelihood was
267: computed as likelihood omitting the logarithm. Version O.98e
268:
269: Revision 1.118 2006/03/14 18:20:07 brouard
270: (Module): varevsij Comments added explaining the second
271: table of variances if popbased=1 .
272: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
273: (Module): Function pstamp added
274: (Module): Version 0.98d
275:
276: Revision 1.117 2006/03/14 17:16:22 brouard
277: (Module): varevsij Comments added explaining the second
278: table of variances if popbased=1 .
279: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
280: (Module): Function pstamp added
281: (Module): Version 0.98d
282:
283: Revision 1.116 2006/03/06 10:29:27 brouard
284: (Module): Variance-covariance wrong links and
285: varian-covariance of ej. is needed (Saito).
286:
287: Revision 1.115 2006/02/27 12:17:45 brouard
288: (Module): One freematrix added in mlikeli! 0.98c
289:
290: Revision 1.114 2006/02/26 12:57:58 brouard
291: (Module): Some improvements in processing parameter
292: filename with strsep.
293:
294: Revision 1.113 2006/02/24 14:20:24 brouard
295: (Module): Memory leaks checks with valgrind and:
296: datafile was not closed, some imatrix were not freed and on matrix
297: allocation too.
298:
299: Revision 1.112 2006/01/30 09:55:26 brouard
300: (Module): Back to gnuplot.exe instead of wgnuplot.exe
301:
302: Revision 1.111 2006/01/25 20:38:18 brouard
303: (Module): Lots of cleaning and bugs added (Gompertz)
304: (Module): Comments can be added in data file. Missing date values
305: can be a simple dot '.'.
306:
307: Revision 1.110 2006/01/25 00:51:50 brouard
308: (Module): Lots of cleaning and bugs added (Gompertz)
309:
310: Revision 1.109 2006/01/24 19:37:15 brouard
311: (Module): Comments (lines starting with a #) are allowed in data.
312:
313: Revision 1.108 2006/01/19 18:05:42 lievre
314: Gnuplot problem appeared...
315: To be fixed
316:
317: Revision 1.107 2006/01/19 16:20:37 brouard
318: Test existence of gnuplot in imach path
319:
320: Revision 1.106 2006/01/19 13:24:36 brouard
321: Some cleaning and links added in html output
322:
323: Revision 1.105 2006/01/05 20:23:19 lievre
324: *** empty log message ***
325:
326: Revision 1.104 2005/09/30 16:11:43 lievre
327: (Module): sump fixed, loop imx fixed, and simplifications.
328: (Module): If the status is missing at the last wave but we know
329: that the person is alive, then we can code his/her status as -2
330: (instead of missing=-1 in earlier versions) and his/her
331: contributions to the likelihood is 1 - Prob of dying from last
332: health status (= 1-p13= p11+p12 in the easiest case of somebody in
333: the healthy state at last known wave). Version is 0.98
334:
335: Revision 1.103 2005/09/30 15:54:49 lievre
336: (Module): sump fixed, loop imx fixed, and simplifications.
337:
338: Revision 1.102 2004/09/15 17:31:30 brouard
339: Add the possibility to read data file including tab characters.
340:
341: Revision 1.101 2004/09/15 10:38:38 brouard
342: Fix on curr_time
343:
344: Revision 1.100 2004/07/12 18:29:06 brouard
345: Add version for Mac OS X. Just define UNIX in Makefile
346:
347: Revision 1.99 2004/06/05 08:57:40 brouard
348: *** empty log message ***
349:
350: Revision 1.98 2004/05/16 15:05:56 brouard
351: New version 0.97 . First attempt to estimate force of mortality
352: directly from the data i.e. without the need of knowing the health
353: state at each age, but using a Gompertz model: log u =a + b*age .
354: This is the basic analysis of mortality and should be done before any
355: other analysis, in order to test if the mortality estimated from the
356: cross-longitudinal survey is different from the mortality estimated
357: from other sources like vital statistic data.
358:
359: The same imach parameter file can be used but the option for mle should be -3.
360:
361: Agnès, who wrote this part of the code, tried to keep most of the
362: former routines in order to include the new code within the former code.
363:
364: The output is very simple: only an estimate of the intercept and of
365: the slope with 95% confident intervals.
366:
367: Current limitations:
368: A) Even if you enter covariates, i.e. with the
369: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
370: B) There is no computation of Life Expectancy nor Life Table.
371:
372: Revision 1.97 2004/02/20 13:25:42 lievre
373: Version 0.96d. Population forecasting command line is (temporarily)
374: suppressed.
375:
376: Revision 1.96 2003/07/15 15:38:55 brouard
377: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
378: rewritten within the same printf. Workaround: many printfs.
379:
380: Revision 1.95 2003/07/08 07:54:34 brouard
381: * imach.c (Repository):
382: (Repository): Using imachwizard code to output a more meaningful covariance
383: matrix (cov(a12,c31) instead of numbers.
384:
385: Revision 1.94 2003/06/27 13:00:02 brouard
386: Just cleaning
387:
388: Revision 1.93 2003/06/25 16:33:55 brouard
389: (Module): On windows (cygwin) function asctime_r doesn't
390: exist so I changed back to asctime which exists.
391: (Module): Version 0.96b
392:
393: Revision 1.92 2003/06/25 16:30:45 brouard
394: (Module): On windows (cygwin) function asctime_r doesn't
395: exist so I changed back to asctime which exists.
396:
397: Revision 1.91 2003/06/25 15:30:29 brouard
398: * imach.c (Repository): Duplicated warning errors corrected.
399: (Repository): Elapsed time after each iteration is now output. It
400: helps to forecast when convergence will be reached. Elapsed time
401: is stamped in powell. We created a new html file for the graphs
402: concerning matrix of covariance. It has extension -cov.htm.
403:
404: Revision 1.90 2003/06/24 12:34:15 brouard
405: (Module): Some bugs corrected for windows. Also, when
406: mle=-1 a template is output in file "or"mypar.txt with the design
407: of the covariance matrix to be input.
408:
409: Revision 1.89 2003/06/24 12:30:52 brouard
410: (Module): Some bugs corrected for windows. Also, when
411: mle=-1 a template is output in file "or"mypar.txt with the design
412: of the covariance matrix to be input.
413:
414: Revision 1.88 2003/06/23 17:54:56 brouard
415: * 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.
416:
417: Revision 1.87 2003/06/18 12:26:01 brouard
418: Version 0.96
419:
420: Revision 1.86 2003/06/17 20:04:08 brouard
421: (Module): Change position of html and gnuplot routines and added
422: routine fileappend.
423:
424: Revision 1.85 2003/06/17 13:12:43 brouard
425: * imach.c (Repository): Check when date of death was earlier that
426: current date of interview. It may happen when the death was just
427: prior to the death. In this case, dh was negative and likelihood
428: was wrong (infinity). We still send an "Error" but patch by
429: assuming that the date of death was just one stepm after the
430: interview.
431: (Repository): Because some people have very long ID (first column)
432: we changed int to long in num[] and we added a new lvector for
433: memory allocation. But we also truncated to 8 characters (left
434: truncation)
435: (Repository): No more line truncation errors.
436:
437: Revision 1.84 2003/06/13 21:44:43 brouard
438: * imach.c (Repository): Replace "freqsummary" at a correct
439: place. It differs from routine "prevalence" which may be called
440: many times. Probs is memory consuming and must be used with
441: parcimony.
442: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
443:
444: Revision 1.83 2003/06/10 13:39:11 lievre
445: *** empty log message ***
446:
447: Revision 1.82 2003/06/05 15:57:20 brouard
448: Add log in imach.c and fullversion number is now printed.
449:
450: */
451: /*
452: Interpolated Markov Chain
453:
454: Short summary of the programme:
455:
456: This program computes Healthy Life Expectancies from
457: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
458: first survey ("cross") where individuals from different ages are
459: interviewed on their health status or degree of disability (in the
460: case of a health survey which is our main interest) -2- at least a
461: second wave of interviews ("longitudinal") which measure each change
462: (if any) in individual health status. Health expectancies are
463: computed from the time spent in each health state according to a
464: model. More health states you consider, more time is necessary to reach the
465: Maximum Likelihood of the parameters involved in the model. The
466: simplest model is the multinomial logistic model where pij is the
467: probability to be observed in state j at the second wave
468: conditional to be observed in state i at the first wave. Therefore
469: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
470: 'age' is age and 'sex' is a covariate. If you want to have a more
471: complex model than "constant and age", you should modify the program
472: where the markup *Covariates have to be included here again* invites
473: you to do it. More covariates you add, slower the
474: convergence.
475:
476: The advantage of this computer programme, compared to a simple
477: multinomial logistic model, is clear when the delay between waves is not
478: identical for each individual. Also, if a individual missed an
479: intermediate interview, the information is lost, but taken into
480: account using an interpolation or extrapolation.
481:
482: hPijx is the probability to be observed in state i at age x+h
483: conditional to the observed state i at age x. The delay 'h' can be
484: split into an exact number (nh*stepm) of unobserved intermediate
485: states. This elementary transition (by month, quarter,
486: semester or year) is modelled as a multinomial logistic. The hPx
487: matrix is simply the matrix product of nh*stepm elementary matrices
488: and the contribution of each individual to the likelihood is simply
489: hPijx.
490:
491: Also this programme outputs the covariance matrix of the parameters but also
492: of the life expectancies. It also computes the period (stable) prevalence.
493:
494: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
495: Institut national d'études démographiques, Paris.
496: This software have been partly granted by Euro-REVES, a concerted action
497: from the European Union.
498: It is copyrighted identically to a GNU software product, ie programme and
499: software can be distributed freely for non commercial use. Latest version
500: can be accessed at http://euroreves.ined.fr/imach .
501:
502: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
503: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
504:
505: **********************************************************************/
506: /*
507: main
508: read parameterfile
509: read datafile
510: concatwav
511: freqsummary
512: if (mle >= 1)
513: mlikeli
514: print results files
515: if mle==1
516: computes hessian
517: read end of parameter file: agemin, agemax, bage, fage, estepm
518: begin-prev-date,...
519: open gnuplot file
520: open html file
521: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
522: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
523: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
524: freexexit2 possible for memory heap.
525:
526: h Pij x | pij_nom ficrestpij
527: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
528: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
529: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
530:
531: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
532: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
533: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
534: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
535: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
536:
537: forecasting if prevfcast==1 prevforecast call prevalence()
538: health expectancies
539: Variance-covariance of DFLE
540: prevalence()
541: movingaverage()
542: varevsij()
543: if popbased==1 varevsij(,popbased)
544: total life expectancies
545: Variance of period (stable) prevalence
546: end
547: */
548:
549: #define POWELL /* Instead of NLOPT */
550:
551: #include <math.h>
552: #include <stdio.h>
553: #include <stdlib.h>
554: #include <string.h>
555:
556: #ifdef _WIN32
557: #include <io.h>
558: #include <windows.h>
559: #include <tchar.h>
560: #else
561: #include <unistd.h>
562: #endif
563:
564: #include <limits.h>
565: #include <sys/types.h>
566:
567: #if defined(__GNUC__)
568: #include <sys/utsname.h> /* Doesn't work on Windows */
569: #endif
570:
571: #include <sys/stat.h>
572: #include <errno.h>
573: /* extern int errno; */
574:
575: /* #ifdef LINUX */
576: /* #include <time.h> */
577: /* #include "timeval.h" */
578: /* #else */
579: /* #include <sys/time.h> */
580: /* #endif */
581:
582: #include <time.h>
583:
584: #ifdef GSL
585: #include <gsl/gsl_errno.h>
586: #include <gsl/gsl_multimin.h>
587: #endif
588:
589:
590: #ifdef NLOPT
591: #include <nlopt.h>
592: typedef struct {
593: double (* function)(double [] );
594: } myfunc_data ;
595: #endif
596:
597: /* #include <libintl.h> */
598: /* #define _(String) gettext (String) */
599:
600: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
601:
602: #define GNUPLOTPROGRAM "gnuplot"
603: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
604: #define FILENAMELENGTH 132
605:
606: #define GLOCK_ERROR_NOPATH -1 /* empty path */
607: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
608:
609: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
610: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
611:
612: #define NINTERVMAX 8
613: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
614: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
615: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
616: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
617: #define MAXN 20000
618: #define YEARM 12. /**< Number of months per year */
619: #define AGESUP 130
620: #define AGEBASE 40
621: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
622: #ifdef _WIN32
623: #define DIRSEPARATOR '\\'
624: #define CHARSEPARATOR "\\"
625: #define ODIRSEPARATOR '/'
626: #else
627: #define DIRSEPARATOR '/'
628: #define CHARSEPARATOR "/"
629: #define ODIRSEPARATOR '\\'
630: #endif
631:
632: /* $Id: imach.c,v 1.177 2015/01/03 18:40:56 brouard Exp $ */
633: /* $State: Exp $ */
634:
635: 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";
636: char fullversion[]="$Revision: 1.177 $ $Date: 2015/01/03 18:40:56 $";
637: char strstart[80];
638: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
639: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
640: int nvar=0, nforce=0; /* Number of variables, number of forces */
641: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
642: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
643: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
644: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
645: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
646: int cptcovprodnoage=0; /**< Number of covariate products without age */
647: int cptcoveff=0; /* Total number of covariates to vary for printing results */
648: int cptcov=0; /* Working variable */
649: int npar=NPARMAX;
650: int nlstate=2; /* Number of live states */
651: int ndeath=1; /* Number of dead states */
652: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
653: int popbased=0;
654:
655: int *wav; /* Number of waves for this individuual 0 is possible */
656: int maxwav=0; /* Maxim number of waves */
657: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
658: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
659: int gipmx=0, gsw=0; /* Global variables on the number of contributions
660: to the likelihood and the sum of weights (done by funcone)*/
661: int mle=1, weightopt=0;
662: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
663: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
664: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
665: * wave mi and wave mi+1 is not an exact multiple of stepm. */
666: int countcallfunc=0; /* Count the number of calls to func */
667: double jmean=1; /* Mean space between 2 waves */
668: double **matprod2(); /* test */
669: double **oldm, **newm, **savm; /* Working pointers to matrices */
670: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
671: /*FILE *fic ; */ /* Used in readdata only */
672: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
673: FILE *ficlog, *ficrespow;
674: int globpr=0; /* Global variable for printing or not */
675: double fretone; /* Only one call to likelihood */
676: long ipmx=0; /* Number of contributions */
677: double sw; /* Sum of weights */
678: char filerespow[FILENAMELENGTH];
679: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
680: FILE *ficresilk;
681: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
682: FILE *ficresprobmorprev;
683: FILE *fichtm, *fichtmcov; /* Html File */
684: FILE *ficreseij;
685: char filerese[FILENAMELENGTH];
686: FILE *ficresstdeij;
687: char fileresstde[FILENAMELENGTH];
688: FILE *ficrescveij;
689: char filerescve[FILENAMELENGTH];
690: FILE *ficresvij;
691: char fileresv[FILENAMELENGTH];
692: FILE *ficresvpl;
693: char fileresvpl[FILENAMELENGTH];
694: char title[MAXLINE];
695: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
696: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
697: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
698: char command[FILENAMELENGTH];
699: int outcmd=0;
700:
701: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
702:
703: char filelog[FILENAMELENGTH]; /* Log file */
704: char filerest[FILENAMELENGTH];
705: char fileregp[FILENAMELENGTH];
706: char popfile[FILENAMELENGTH];
707:
708: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
709:
710: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
711: /* struct timezone tzp; */
712: /* extern int gettimeofday(); */
713: struct tm tml, *gmtime(), *localtime();
714:
715: extern time_t time();
716:
717: struct tm start_time, end_time, curr_time, last_time, forecast_time;
718: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
719: struct tm tm;
720:
721: char strcurr[80], strfor[80];
722:
723: char *endptr;
724: long lval;
725: double dval;
726:
727: #define NR_END 1
728: #define FREE_ARG char*
729: #define FTOL 1.0e-10
730:
731: #define NRANSI
732: #define ITMAX 200
733:
734: #define TOL 2.0e-4
735:
736: #define CGOLD 0.3819660
737: #define ZEPS 1.0e-10
738: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
739:
740: #define GOLD 1.618034
741: #define GLIMIT 100.0
742: #define TINY 1.0e-20
743:
744: static double maxarg1,maxarg2;
745: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
746: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
747:
748: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
749: #define rint(a) floor(a+0.5)
750: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
751: /* #define mytinydouble 1.0e-16 */
752: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
753: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
754: /* static double dsqrarg; */
755: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
756: static double sqrarg;
757: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
758: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
759: int agegomp= AGEGOMP;
760:
761: int imx;
762: int stepm=1;
763: /* Stepm, step in month: minimum step interpolation*/
764:
765: int estepm;
766: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
767:
768: int m,nb;
769: long *num;
770: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
771: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
772: double **pmmij, ***probs;
773: double *ageexmed,*agecens;
774: double dateintmean=0;
775:
776: double *weight;
777: int **s; /* Status */
778: double *agedc;
779: double **covar; /**< covar[j,i], value of jth covariate for individual i,
780: * covar=matrix(0,NCOVMAX,1,n);
781: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
782: double idx;
783: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
784: int *Ndum; /** Freq of modality (tricode */
785: int **codtab; /**< codtab=imatrix(1,100,1,10); */
786: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
787: double *lsurv, *lpop, *tpop;
788:
789: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
790: double ftolhess; /**< Tolerance for computing hessian */
791:
792: /**************** split *************************/
793: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
794: {
795: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
796: the name of the file (name), its extension only (ext) and its first part of the name (finame)
797: */
798: char *ss; /* pointer */
799: int l1, l2; /* length counters */
800:
801: l1 = strlen(path ); /* length of path */
802: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
803: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
804: if ( ss == NULL ) { /* no directory, so determine current directory */
805: strcpy( name, path ); /* we got the fullname name because no directory */
806: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
807: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
808: /* get current working directory */
809: /* extern char* getcwd ( char *buf , int len);*/
810: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
811: return( GLOCK_ERROR_GETCWD );
812: }
813: /* got dirc from getcwd*/
814: printf(" DIRC = %s \n",dirc);
815: } else { /* strip direcotry from path */
816: ss++; /* after this, the filename */
817: l2 = strlen( ss ); /* length of filename */
818: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
819: strcpy( name, ss ); /* save file name */
820: strncpy( dirc, path, l1 - l2 ); /* now the directory */
821: dirc[l1-l2] = 0; /* add zero */
822: printf(" DIRC2 = %s \n",dirc);
823: }
824: /* We add a separator at the end of dirc if not exists */
825: l1 = strlen( dirc ); /* length of directory */
826: if( dirc[l1-1] != DIRSEPARATOR ){
827: dirc[l1] = DIRSEPARATOR;
828: dirc[l1+1] = 0;
829: printf(" DIRC3 = %s \n",dirc);
830: }
831: ss = strrchr( name, '.' ); /* find last / */
832: if (ss >0){
833: ss++;
834: strcpy(ext,ss); /* save extension */
835: l1= strlen( name);
836: l2= strlen(ss)+1;
837: strncpy( finame, name, l1-l2);
838: finame[l1-l2]= 0;
839: }
840:
841: return( 0 ); /* we're done */
842: }
843:
844:
845: /******************************************/
846:
847: void replace_back_to_slash(char *s, char*t)
848: {
849: int i;
850: int lg=0;
851: i=0;
852: lg=strlen(t);
853: for(i=0; i<= lg; i++) {
854: (s[i] = t[i]);
855: if (t[i]== '\\') s[i]='/';
856: }
857: }
858:
859: char *trimbb(char *out, char *in)
860: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
861: char *s;
862: s=out;
863: while (*in != '\0'){
864: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
865: in++;
866: }
867: *out++ = *in++;
868: }
869: *out='\0';
870: return s;
871: }
872:
873: char *cutl(char *blocc, char *alocc, char *in, char occ)
874: {
875: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
876: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
877: gives blocc="abcdef2ghi" and alocc="j".
878: If occ is not found blocc is null and alocc is equal to in. Returns blocc
879: */
880: char *s, *t;
881: t=in;s=in;
882: while ((*in != occ) && (*in != '\0')){
883: *alocc++ = *in++;
884: }
885: if( *in == occ){
886: *(alocc)='\0';
887: s=++in;
888: }
889:
890: if (s == t) {/* occ not found */
891: *(alocc-(in-s))='\0';
892: in=s;
893: }
894: while ( *in != '\0'){
895: *blocc++ = *in++;
896: }
897:
898: *blocc='\0';
899: return t;
900: }
901: char *cutv(char *blocc, char *alocc, char *in, char occ)
902: {
903: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
904: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
905: gives blocc="abcdef2ghi" and alocc="j".
906: If occ is not found blocc is null and alocc is equal to in. Returns alocc
907: */
908: char *s, *t;
909: t=in;s=in;
910: while (*in != '\0'){
911: while( *in == occ){
912: *blocc++ = *in++;
913: s=in;
914: }
915: *blocc++ = *in++;
916: }
917: if (s == t) /* occ not found */
918: *(blocc-(in-s))='\0';
919: else
920: *(blocc-(in-s)-1)='\0';
921: in=s;
922: while ( *in != '\0'){
923: *alocc++ = *in++;
924: }
925:
926: *alocc='\0';
927: return s;
928: }
929:
930: int nbocc(char *s, char occ)
931: {
932: int i,j=0;
933: int lg=20;
934: i=0;
935: lg=strlen(s);
936: for(i=0; i<= lg; i++) {
937: if (s[i] == occ ) j++;
938: }
939: return j;
940: }
941:
942: /* void cutv(char *u,char *v, char*t, char occ) */
943: /* { */
944: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
945: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
946: /* gives u="abcdef2ghi" and v="j" *\/ */
947: /* int i,lg,j,p=0; */
948: /* i=0; */
949: /* lg=strlen(t); */
950: /* for(j=0; j<=lg-1; j++) { */
951: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
952: /* } */
953:
954: /* for(j=0; j<p; j++) { */
955: /* (u[j] = t[j]); */
956: /* } */
957: /* u[p]='\0'; */
958:
959: /* for(j=0; j<= lg; j++) { */
960: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
961: /* } */
962: /* } */
963:
964: #ifdef _WIN32
965: char * strsep(char **pp, const char *delim)
966: {
967: char *p, *q;
968:
969: if ((p = *pp) == NULL)
970: return 0;
971: if ((q = strpbrk (p, delim)) != NULL)
972: {
973: *pp = q + 1;
974: *q = '\0';
975: }
976: else
977: *pp = 0;
978: return p;
979: }
980: #endif
981:
982: /********************** nrerror ********************/
983:
984: void nrerror(char error_text[])
985: {
986: fprintf(stderr,"ERREUR ...\n");
987: fprintf(stderr,"%s\n",error_text);
988: exit(EXIT_FAILURE);
989: }
990: /*********************** vector *******************/
991: double *vector(int nl, int nh)
992: {
993: double *v;
994: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
995: if (!v) nrerror("allocation failure in vector");
996: return v-nl+NR_END;
997: }
998:
999: /************************ free vector ******************/
1000: void free_vector(double*v, int nl, int nh)
1001: {
1002: free((FREE_ARG)(v+nl-NR_END));
1003: }
1004:
1005: /************************ivector *******************************/
1006: int *ivector(long nl,long nh)
1007: {
1008: int *v;
1009: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1010: if (!v) nrerror("allocation failure in ivector");
1011: return v-nl+NR_END;
1012: }
1013:
1014: /******************free ivector **************************/
1015: void free_ivector(int *v, long nl, long nh)
1016: {
1017: free((FREE_ARG)(v+nl-NR_END));
1018: }
1019:
1020: /************************lvector *******************************/
1021: long *lvector(long nl,long nh)
1022: {
1023: long *v;
1024: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1025: if (!v) nrerror("allocation failure in ivector");
1026: return v-nl+NR_END;
1027: }
1028:
1029: /******************free lvector **************************/
1030: void free_lvector(long *v, long nl, long nh)
1031: {
1032: free((FREE_ARG)(v+nl-NR_END));
1033: }
1034:
1035: /******************* imatrix *******************************/
1036: int **imatrix(long nrl, long nrh, long ncl, long nch)
1037: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1038: {
1039: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1040: int **m;
1041:
1042: /* allocate pointers to rows */
1043: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1044: if (!m) nrerror("allocation failure 1 in matrix()");
1045: m += NR_END;
1046: m -= nrl;
1047:
1048:
1049: /* allocate rows and set pointers to them */
1050: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1051: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1052: m[nrl] += NR_END;
1053: m[nrl] -= ncl;
1054:
1055: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1056:
1057: /* return pointer to array of pointers to rows */
1058: return m;
1059: }
1060:
1061: /****************** free_imatrix *************************/
1062: void free_imatrix(m,nrl,nrh,ncl,nch)
1063: int **m;
1064: long nch,ncl,nrh,nrl;
1065: /* free an int matrix allocated by imatrix() */
1066: {
1067: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1068: free((FREE_ARG) (m+nrl-NR_END));
1069: }
1070:
1071: /******************* matrix *******************************/
1072: double **matrix(long nrl, long nrh, long ncl, long nch)
1073: {
1074: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1075: double **m;
1076:
1077: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1078: if (!m) nrerror("allocation failure 1 in matrix()");
1079: m += NR_END;
1080: m -= nrl;
1081:
1082: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1083: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1084: m[nrl] += NR_END;
1085: m[nrl] -= ncl;
1086:
1087: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1088: return m;
1089: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1090: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1091: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1092: */
1093: }
1094:
1095: /*************************free matrix ************************/
1096: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1097: {
1098: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1099: free((FREE_ARG)(m+nrl-NR_END));
1100: }
1101:
1102: /******************* ma3x *******************************/
1103: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1104: {
1105: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1106: double ***m;
1107:
1108: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1109: if (!m) nrerror("allocation failure 1 in matrix()");
1110: m += NR_END;
1111: m -= nrl;
1112:
1113: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1114: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1115: m[nrl] += NR_END;
1116: m[nrl] -= ncl;
1117:
1118: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1119:
1120: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1121: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1122: m[nrl][ncl] += NR_END;
1123: m[nrl][ncl] -= nll;
1124: for (j=ncl+1; j<=nch; j++)
1125: m[nrl][j]=m[nrl][j-1]+nlay;
1126:
1127: for (i=nrl+1; i<=nrh; i++) {
1128: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1129: for (j=ncl+1; j<=nch; j++)
1130: m[i][j]=m[i][j-1]+nlay;
1131: }
1132: return m;
1133: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1134: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1135: */
1136: }
1137:
1138: /*************************free ma3x ************************/
1139: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1140: {
1141: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1142: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1143: free((FREE_ARG)(m+nrl-NR_END));
1144: }
1145:
1146: /*************** function subdirf ***********/
1147: char *subdirf(char fileres[])
1148: {
1149: /* Caution optionfilefiname is hidden */
1150: strcpy(tmpout,optionfilefiname);
1151: strcat(tmpout,"/"); /* Add to the right */
1152: strcat(tmpout,fileres);
1153: return tmpout;
1154: }
1155:
1156: /*************** function subdirf2 ***********/
1157: char *subdirf2(char fileres[], char *preop)
1158: {
1159:
1160: /* Caution optionfilefiname is hidden */
1161: strcpy(tmpout,optionfilefiname);
1162: strcat(tmpout,"/");
1163: strcat(tmpout,preop);
1164: strcat(tmpout,fileres);
1165: return tmpout;
1166: }
1167:
1168: /*************** function subdirf3 ***********/
1169: char *subdirf3(char fileres[], char *preop, char *preop2)
1170: {
1171:
1172: /* Caution optionfilefiname is hidden */
1173: strcpy(tmpout,optionfilefiname);
1174: strcat(tmpout,"/");
1175: strcat(tmpout,preop);
1176: strcat(tmpout,preop2);
1177: strcat(tmpout,fileres);
1178: return tmpout;
1179: }
1180:
1181: char *asc_diff_time(long time_sec, char ascdiff[])
1182: {
1183: long sec_left, days, hours, minutes;
1184: days = (time_sec) / (60*60*24);
1185: sec_left = (time_sec) % (60*60*24);
1186: hours = (sec_left) / (60*60) ;
1187: sec_left = (sec_left) %(60*60);
1188: minutes = (sec_left) /60;
1189: sec_left = (sec_left) % (60);
1190: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1191: return ascdiff;
1192: }
1193:
1194: /***************** f1dim *************************/
1195: extern int ncom;
1196: extern double *pcom,*xicom;
1197: extern double (*nrfunc)(double []);
1198:
1199: double f1dim(double x)
1200: {
1201: int j;
1202: double f;
1203: double *xt;
1204:
1205: xt=vector(1,ncom);
1206: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1207: f=(*nrfunc)(xt);
1208: free_vector(xt,1,ncom);
1209: return f;
1210: }
1211:
1212: /*****************brent *************************/
1213: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1214: {
1215: int iter;
1216: double a,b,d,etemp;
1217: double fu=0,fv,fw,fx;
1218: double ftemp=0.;
1219: double p,q,r,tol1,tol2,u,v,w,x,xm;
1220: double e=0.0;
1221:
1222: a=(ax < cx ? ax : cx);
1223: b=(ax > cx ? ax : cx);
1224: x=w=v=bx;
1225: fw=fv=fx=(*f)(x);
1226: for (iter=1;iter<=ITMAX;iter++) {
1227: xm=0.5*(a+b);
1228: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1229: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1230: printf(".");fflush(stdout);
1231: fprintf(ficlog,".");fflush(ficlog);
1232: #ifdef DEBUGBRENT
1233: 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);
1234: 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);
1235: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1236: #endif
1237: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1238: *xmin=x;
1239: return fx;
1240: }
1241: ftemp=fu;
1242: if (fabs(e) > tol1) {
1243: r=(x-w)*(fx-fv);
1244: q=(x-v)*(fx-fw);
1245: p=(x-v)*q-(x-w)*r;
1246: q=2.0*(q-r);
1247: if (q > 0.0) p = -p;
1248: q=fabs(q);
1249: etemp=e;
1250: e=d;
1251: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1252: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1253: else {
1254: d=p/q;
1255: u=x+d;
1256: if (u-a < tol2 || b-u < tol2)
1257: d=SIGN(tol1,xm-x);
1258: }
1259: } else {
1260: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1261: }
1262: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1263: fu=(*f)(u);
1264: if (fu <= fx) {
1265: if (u >= x) a=x; else b=x;
1266: SHFT(v,w,x,u)
1267: SHFT(fv,fw,fx,fu)
1268: } else {
1269: if (u < x) a=u; else b=u;
1270: if (fu <= fw || w == x) {
1271: v=w;
1272: w=u;
1273: fv=fw;
1274: fw=fu;
1275: } else if (fu <= fv || v == x || v == w) {
1276: v=u;
1277: fv=fu;
1278: }
1279: }
1280: }
1281: nrerror("Too many iterations in brent");
1282: *xmin=x;
1283: return fx;
1284: }
1285:
1286: /****************** mnbrak ***********************/
1287:
1288: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1289: double (*func)(double))
1290: {
1291: double ulim,u,r,q, dum;
1292: double fu;
1293:
1294: *fa=(*func)(*ax);
1295: *fb=(*func)(*bx);
1296: if (*fb > *fa) {
1297: SHFT(dum,*ax,*bx,dum)
1298: SHFT(dum,*fb,*fa,dum)
1299: }
1300: *cx=(*bx)+GOLD*(*bx-*ax);
1301: *fc=(*func)(*cx);
1302: while (*fb > *fc) { /* Declining fa, fb, fc */
1303: r=(*bx-*ax)*(*fb-*fc);
1304: q=(*bx-*cx)*(*fb-*fa);
1305: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1306: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1307: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1308: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1309: fu=(*func)(u);
1310: #ifdef DEBUG
1311: /* f(x)=A(x-u)**2+f(u) */
1312: double A, fparabu;
1313: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1314: fparabu= *fa - A*(*ax-u)*(*ax-u);
1315: 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);
1316: 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);
1317: #endif
1318: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1319: fu=(*func)(u);
1320: if (fu < *fc) {
1321: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1322: SHFT(*fb,*fc,fu,(*func)(u))
1323: }
1324: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1325: u=ulim;
1326: fu=(*func)(u);
1327: } else {
1328: u=(*cx)+GOLD*(*cx-*bx);
1329: fu=(*func)(u);
1330: }
1331: SHFT(*ax,*bx,*cx,u)
1332: SHFT(*fa,*fb,*fc,fu)
1333: }
1334: }
1335:
1336: /*************** linmin ************************/
1337: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1338: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1339: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1340: the value of func at the returned location p . This is actually all accomplished by calling the
1341: routines mnbrak and brent .*/
1342: int ncom;
1343: double *pcom,*xicom;
1344: double (*nrfunc)(double []);
1345:
1346: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1347: {
1348: double brent(double ax, double bx, double cx,
1349: double (*f)(double), double tol, double *xmin);
1350: double f1dim(double x);
1351: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1352: double *fc, double (*func)(double));
1353: int j;
1354: double xx,xmin,bx,ax;
1355: double fx,fb,fa;
1356:
1357: ncom=n;
1358: pcom=vector(1,n);
1359: xicom=vector(1,n);
1360: nrfunc=func;
1361: for (j=1;j<=n;j++) {
1362: pcom[j]=p[j];
1363: xicom[j]=xi[j];
1364: }
1365: ax=0.0;
1366: xx=1.0;
1367: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1368: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1369: #ifdef DEBUG
1370: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1371: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1372: #endif
1373: for (j=1;j<=n;j++) {
1374: xi[j] *= xmin;
1375: p[j] += xi[j];
1376: }
1377: free_vector(xicom,1,n);
1378: free_vector(pcom,1,n);
1379: }
1380:
1381:
1382: /*************** powell ************************/
1383: /*
1384: Minimization of a function func of n variables. Input consists of an initial starting point
1385: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1386: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1387: such that failure to decrease by more than this amount on one iteration signals doneness. On
1388: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1389: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1390: */
1391: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1392: double (*func)(double []))
1393: {
1394: void linmin(double p[], double xi[], int n, double *fret,
1395: double (*func)(double []));
1396: int i,ibig,j;
1397: double del,t,*pt,*ptt,*xit;
1398: double fp,fptt;
1399: double *xits;
1400: int niterf, itmp;
1401:
1402: pt=vector(1,n);
1403: ptt=vector(1,n);
1404: xit=vector(1,n);
1405: xits=vector(1,n);
1406: *fret=(*func)(p);
1407: for (j=1;j<=n;j++) pt[j]=p[j];
1408: rcurr_time = time(NULL);
1409: for (*iter=1;;++(*iter)) {
1410: fp=(*fret);
1411: ibig=0;
1412: del=0.0;
1413: rlast_time=rcurr_time;
1414: /* (void) gettimeofday(&curr_time,&tzp); */
1415: rcurr_time = time(NULL);
1416: curr_time = *localtime(&rcurr_time);
1417: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1418: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1419: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1420: for (i=1;i<=n;i++) {
1421: printf(" %d %.12f",i, p[i]);
1422: fprintf(ficlog," %d %.12lf",i, p[i]);
1423: fprintf(ficrespow," %.12lf", p[i]);
1424: }
1425: printf("\n");
1426: fprintf(ficlog,"\n");
1427: fprintf(ficrespow,"\n");fflush(ficrespow);
1428: if(*iter <=3){
1429: tml = *localtime(&rcurr_time);
1430: strcpy(strcurr,asctime(&tml));
1431: rforecast_time=rcurr_time;
1432: itmp = strlen(strcurr);
1433: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1434: strcurr[itmp-1]='\0';
1435: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1436: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1437: for(niterf=10;niterf<=30;niterf+=10){
1438: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1439: forecast_time = *localtime(&rforecast_time);
1440: strcpy(strfor,asctime(&forecast_time));
1441: itmp = strlen(strfor);
1442: if(strfor[itmp-1]=='\n')
1443: strfor[itmp-1]='\0';
1444: 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);
1445: 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);
1446: }
1447: }
1448: for (i=1;i<=n;i++) {
1449: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1450: fptt=(*fret);
1451: #ifdef DEBUG
1452: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1453: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1454: #endif
1455: printf("%d",i);fflush(stdout);
1456: fprintf(ficlog,"%d",i);fflush(ficlog);
1457: linmin(p,xit,n,fret,func);
1458: if (fabs(fptt-(*fret)) > del) {
1459: del=fabs(fptt-(*fret));
1460: ibig=i;
1461: }
1462: #ifdef DEBUG
1463: printf("%d %.12e",i,(*fret));
1464: fprintf(ficlog,"%d %.12e",i,(*fret));
1465: for (j=1;j<=n;j++) {
1466: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1467: printf(" x(%d)=%.12e",j,xit[j]);
1468: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1469: }
1470: for(j=1;j<=n;j++) {
1471: printf(" p(%d)=%.12e",j,p[j]);
1472: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1473: }
1474: printf("\n");
1475: fprintf(ficlog,"\n");
1476: #endif
1477: } /* end i */
1478: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1479: #ifdef DEBUG
1480: int k[2],l;
1481: k[0]=1;
1482: k[1]=-1;
1483: printf("Max: %.12e",(*func)(p));
1484: fprintf(ficlog,"Max: %.12e",(*func)(p));
1485: for (j=1;j<=n;j++) {
1486: printf(" %.12e",p[j]);
1487: fprintf(ficlog," %.12e",p[j]);
1488: }
1489: printf("\n");
1490: fprintf(ficlog,"\n");
1491: for(l=0;l<=1;l++) {
1492: for (j=1;j<=n;j++) {
1493: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1494: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1495: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1496: }
1497: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1498: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1499: }
1500: #endif
1501:
1502:
1503: free_vector(xit,1,n);
1504: free_vector(xits,1,n);
1505: free_vector(ptt,1,n);
1506: free_vector(pt,1,n);
1507: return;
1508: }
1509: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1510: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1511: ptt[j]=2.0*p[j]-pt[j];
1512: xit[j]=p[j]-pt[j];
1513: pt[j]=p[j];
1514: }
1515: fptt=(*func)(ptt);
1516: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1517: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1518: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1519: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1520: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1521: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1522: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1523: /* Thus we compare delta(2h) with observed f1-f3 */
1524: /* or best gain on one ancient line 'del' with total */
1525: /* gain f1-f2 = f1 - f2 - 'del' with del */
1526: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1527:
1528: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1529: t= t- del*SQR(fp-fptt);
1530: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1531: 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);
1532: #ifdef DEBUG
1533: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1534: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1535: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1536: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1537: 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);
1538: 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);
1539: #endif
1540: if (t < 0.0) { /* Then we use it for last direction */
1541: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1542: for (j=1;j<=n;j++) {
1543: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1544: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1545: }
1546: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1547: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1548:
1549: #ifdef DEBUG
1550: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1551: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1552: for(j=1;j<=n;j++){
1553: printf(" %.12e",xit[j]);
1554: fprintf(ficlog," %.12e",xit[j]);
1555: }
1556: printf("\n");
1557: fprintf(ficlog,"\n");
1558: #endif
1559: } /* end of t negative */
1560: } /* end if (fptt < fp) */
1561: }
1562: }
1563:
1564: /**** Prevalence limit (stable or period prevalence) ****************/
1565:
1566: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1567: {
1568: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1569: matrix by transitions matrix until convergence is reached */
1570:
1571: int i, ii,j,k;
1572: double min, max, maxmin, maxmax,sumnew=0.;
1573: /* double **matprod2(); */ /* test */
1574: double **out, cov[NCOVMAX+1], **pmij();
1575: double **newm;
1576: double agefin, delaymax=50 ; /* Max number of years to converge */
1577:
1578: for (ii=1;ii<=nlstate+ndeath;ii++)
1579: for (j=1;j<=nlstate+ndeath;j++){
1580: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1581: }
1582:
1583: cov[1]=1.;
1584:
1585: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1586: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1587: newm=savm;
1588: /* Covariates have to be included here again */
1589: cov[2]=agefin;
1590:
1591: for (k=1; k<=cptcovn;k++) {
1592: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1593: /*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]]);*/
1594: }
1595: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1596: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1597: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1598:
1599: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1600: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1601: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1602: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1603: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1604: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1605:
1606: savm=oldm;
1607: oldm=newm;
1608: maxmax=0.;
1609: for(j=1;j<=nlstate;j++){
1610: min=1.;
1611: max=0.;
1612: for(i=1; i<=nlstate; i++) {
1613: sumnew=0;
1614: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1615: prlim[i][j]= newm[i][j]/(1-sumnew);
1616: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1617: max=FMAX(max,prlim[i][j]);
1618: min=FMIN(min,prlim[i][j]);
1619: }
1620: maxmin=max-min;
1621: maxmax=FMAX(maxmax,maxmin);
1622: } /* j loop */
1623: if(maxmax < ftolpl){
1624: return prlim;
1625: }
1626: } /* age loop */
1627: return prlim; /* should not reach here */
1628: }
1629:
1630: /*************** transition probabilities ***************/
1631:
1632: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1633: {
1634: /* According to parameters values stored in x and the covariate's values stored in cov,
1635: computes the probability to be observed in state j being in state i by appying the
1636: model to the ncovmodel covariates (including constant and age).
1637: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1638: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1639: ncth covariate in the global vector x is given by the formula:
1640: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1641: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1642: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1643: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1644: Outputs ps[i][j] the probability to be observed in j being in j according to
1645: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1646: */
1647: double s1, lnpijopii;
1648: /*double t34;*/
1649: int i,j, nc, ii, jj;
1650:
1651: for(i=1; i<= nlstate; i++){
1652: for(j=1; j<i;j++){
1653: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1654: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1655: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1656: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1657: }
1658: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1659: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1660: }
1661: for(j=i+1; j<=nlstate+ndeath;j++){
1662: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1663: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1664: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1665: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1666: }
1667: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1668: }
1669: }
1670:
1671: for(i=1; i<= nlstate; i++){
1672: s1=0;
1673: for(j=1; j<i; j++){
1674: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1675: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1676: }
1677: for(j=i+1; j<=nlstate+ndeath; j++){
1678: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1679: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1680: }
1681: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1682: ps[i][i]=1./(s1+1.);
1683: /* Computing other pijs */
1684: for(j=1; j<i; j++)
1685: ps[i][j]= exp(ps[i][j])*ps[i][i];
1686: for(j=i+1; j<=nlstate+ndeath; j++)
1687: ps[i][j]= exp(ps[i][j])*ps[i][i];
1688: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1689: } /* end i */
1690:
1691: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1692: for(jj=1; jj<= nlstate+ndeath; jj++){
1693: ps[ii][jj]=0;
1694: ps[ii][ii]=1;
1695: }
1696: }
1697:
1698:
1699: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1700: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1701: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1702: /* } */
1703: /* printf("\n "); */
1704: /* } */
1705: /* printf("\n ");printf("%lf ",cov[2]);*/
1706: /*
1707: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1708: goto end;*/
1709: return ps;
1710: }
1711:
1712: /**************** Product of 2 matrices ******************/
1713:
1714: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1715: {
1716: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1717: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1718: /* in, b, out are matrice of pointers which should have been initialized
1719: before: only the contents of out is modified. The function returns
1720: a pointer to pointers identical to out */
1721: int i, j, k;
1722: for(i=nrl; i<= nrh; i++)
1723: for(k=ncolol; k<=ncoloh; k++){
1724: out[i][k]=0.;
1725: for(j=ncl; j<=nch; j++)
1726: out[i][k] +=in[i][j]*b[j][k];
1727: }
1728: return out;
1729: }
1730:
1731:
1732: /************* Higher Matrix Product ***************/
1733:
1734: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1735: {
1736: /* Computes the transition matrix starting at age 'age' over
1737: 'nhstepm*hstepm*stepm' months (i.e. until
1738: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1739: nhstepm*hstepm matrices.
1740: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1741: (typically every 2 years instead of every month which is too big
1742: for the memory).
1743: Model is determined by parameters x and covariates have to be
1744: included manually here.
1745:
1746: */
1747:
1748: int i, j, d, h, k;
1749: double **out, cov[NCOVMAX+1];
1750: double **newm;
1751:
1752: /* Hstepm could be zero and should return the unit matrix */
1753: for (i=1;i<=nlstate+ndeath;i++)
1754: for (j=1;j<=nlstate+ndeath;j++){
1755: oldm[i][j]=(i==j ? 1.0 : 0.0);
1756: po[i][j][0]=(i==j ? 1.0 : 0.0);
1757: }
1758: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1759: for(h=1; h <=nhstepm; h++){
1760: for(d=1; d <=hstepm; d++){
1761: newm=savm;
1762: /* Covariates have to be included here again */
1763: cov[1]=1.;
1764: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1765: for (k=1; k<=cptcovn;k++)
1766: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1767: for (k=1; k<=cptcovage;k++)
1768: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1769: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1770: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1771:
1772:
1773: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1774: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1775: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1776: pmij(pmmij,cov,ncovmodel,x,nlstate));
1777: savm=oldm;
1778: oldm=newm;
1779: }
1780: for(i=1; i<=nlstate+ndeath; i++)
1781: for(j=1;j<=nlstate+ndeath;j++) {
1782: po[i][j][h]=newm[i][j];
1783: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1784: }
1785: /*printf("h=%d ",h);*/
1786: } /* end h */
1787: /* printf("\n H=%d \n",h); */
1788: return po;
1789: }
1790:
1791: #ifdef NLOPT
1792: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1793: double fret;
1794: double *xt;
1795: int j;
1796: myfunc_data *d2 = (myfunc_data *) pd;
1797: /* xt = (p1-1); */
1798: xt=vector(1,n);
1799: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1800:
1801: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1802: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1803: printf("Function = %.12lf ",fret);
1804: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1805: printf("\n");
1806: free_vector(xt,1,n);
1807: return fret;
1808: }
1809: #endif
1810:
1811: /*************** log-likelihood *************/
1812: double func( double *x)
1813: {
1814: int i, ii, j, k, mi, d, kk;
1815: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1816: double **out;
1817: double sw; /* Sum of weights */
1818: double lli; /* Individual log likelihood */
1819: int s1, s2;
1820: double bbh, survp;
1821: long ipmx;
1822: /*extern weight */
1823: /* We are differentiating ll according to initial status */
1824: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1825: /*for(i=1;i<imx;i++)
1826: printf(" %d\n",s[4][i]);
1827: */
1828:
1829: ++countcallfunc;
1830:
1831: cov[1]=1.;
1832:
1833: for(k=1; k<=nlstate; k++) ll[k]=0.;
1834:
1835: if(mle==1){
1836: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1837: /* Computes the values of the ncovmodel covariates of the model
1838: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1839: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1840: to be observed in j being in i according to the model.
1841: */
1842: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1843: cov[2+k]=covar[Tvar[k]][i];
1844: }
1845: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1846: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1847: has been calculated etc */
1848: for(mi=1; mi<= wav[i]-1; mi++){
1849: for (ii=1;ii<=nlstate+ndeath;ii++)
1850: for (j=1;j<=nlstate+ndeath;j++){
1851: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1852: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1853: }
1854: for(d=0; d<dh[mi][i]; d++){
1855: newm=savm;
1856: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1857: for (kk=1; kk<=cptcovage;kk++) {
1858: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1859: }
1860: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1861: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1862: savm=oldm;
1863: oldm=newm;
1864: } /* end mult */
1865:
1866: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1867: /* But now since version 0.9 we anticipate for bias at large stepm.
1868: * If stepm is larger than one month (smallest stepm) and if the exact delay
1869: * (in months) between two waves is not a multiple of stepm, we rounded to
1870: * the nearest (and in case of equal distance, to the lowest) interval but now
1871: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1872: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1873: * probability in order to take into account the bias as a fraction of the way
1874: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1875: * -stepm/2 to stepm/2 .
1876: * For stepm=1 the results are the same as for previous versions of Imach.
1877: * For stepm > 1 the results are less biased than in previous versions.
1878: */
1879: s1=s[mw[mi][i]][i];
1880: s2=s[mw[mi+1][i]][i];
1881: bbh=(double)bh[mi][i]/(double)stepm;
1882: /* bias bh is positive if real duration
1883: * is higher than the multiple of stepm and negative otherwise.
1884: */
1885: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1886: if( s2 > nlstate){
1887: /* i.e. if s2 is a death state and if the date of death is known
1888: then the contribution to the likelihood is the probability to
1889: die between last step unit time and current step unit time,
1890: which is also equal to probability to die before dh
1891: minus probability to die before dh-stepm .
1892: In version up to 0.92 likelihood was computed
1893: as if date of death was unknown. Death was treated as any other
1894: health state: the date of the interview describes the actual state
1895: and not the date of a change in health state. The former idea was
1896: to consider that at each interview the state was recorded
1897: (healthy, disable or death) and IMaCh was corrected; but when we
1898: introduced the exact date of death then we should have modified
1899: the contribution of an exact death to the likelihood. This new
1900: contribution is smaller and very dependent of the step unit
1901: stepm. It is no more the probability to die between last interview
1902: and month of death but the probability to survive from last
1903: interview up to one month before death multiplied by the
1904: probability to die within a month. Thanks to Chris
1905: Jackson for correcting this bug. Former versions increased
1906: mortality artificially. The bad side is that we add another loop
1907: which slows down the processing. The difference can be up to 10%
1908: lower mortality.
1909: */
1910: lli=log(out[s1][s2] - savm[s1][s2]);
1911:
1912:
1913: } else if (s2==-2) {
1914: for (j=1,survp=0. ; j<=nlstate; j++)
1915: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1916: /*survp += out[s1][j]; */
1917: lli= log(survp);
1918: }
1919:
1920: else if (s2==-4) {
1921: for (j=3,survp=0. ; j<=nlstate; j++)
1922: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1923: lli= log(survp);
1924: }
1925:
1926: else if (s2==-5) {
1927: for (j=1,survp=0. ; j<=2; j++)
1928: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1929: lli= log(survp);
1930: }
1931:
1932: else{
1933: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1934: /* 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 */
1935: }
1936: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1937: /*if(lli ==000.0)*/
1938: /*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); */
1939: ipmx +=1;
1940: sw += weight[i];
1941: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1942: } /* end of wave */
1943: } /* end of individual */
1944: } else if(mle==2){
1945: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1946: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1947: for(mi=1; mi<= wav[i]-1; mi++){
1948: for (ii=1;ii<=nlstate+ndeath;ii++)
1949: for (j=1;j<=nlstate+ndeath;j++){
1950: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1951: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1952: }
1953: for(d=0; d<=dh[mi][i]; d++){
1954: newm=savm;
1955: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1956: for (kk=1; kk<=cptcovage;kk++) {
1957: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1958: }
1959: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1960: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1961: savm=oldm;
1962: oldm=newm;
1963: } /* end mult */
1964:
1965: s1=s[mw[mi][i]][i];
1966: s2=s[mw[mi+1][i]][i];
1967: bbh=(double)bh[mi][i]/(double)stepm;
1968: 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 */
1969: ipmx +=1;
1970: sw += weight[i];
1971: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1972: } /* end of wave */
1973: } /* end of individual */
1974: } else if(mle==3){ /* exponential inter-extrapolation */
1975: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1976: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1977: for(mi=1; mi<= wav[i]-1; mi++){
1978: for (ii=1;ii<=nlstate+ndeath;ii++)
1979: for (j=1;j<=nlstate+ndeath;j++){
1980: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1981: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1982: }
1983: for(d=0; d<dh[mi][i]; d++){
1984: newm=savm;
1985: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1986: for (kk=1; kk<=cptcovage;kk++) {
1987: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1988: }
1989: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1990: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1991: savm=oldm;
1992: oldm=newm;
1993: } /* end mult */
1994:
1995: s1=s[mw[mi][i]][i];
1996: s2=s[mw[mi+1][i]][i];
1997: bbh=(double)bh[mi][i]/(double)stepm;
1998: 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 */
1999: ipmx +=1;
2000: sw += weight[i];
2001: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2002: } /* end of wave */
2003: } /* end of individual */
2004: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2005: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2006: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2007: for(mi=1; mi<= wav[i]-1; mi++){
2008: for (ii=1;ii<=nlstate+ndeath;ii++)
2009: for (j=1;j<=nlstate+ndeath;j++){
2010: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2011: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2012: }
2013: for(d=0; d<dh[mi][i]; d++){
2014: newm=savm;
2015: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2016: for (kk=1; kk<=cptcovage;kk++) {
2017: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2018: }
2019:
2020: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2021: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2022: savm=oldm;
2023: oldm=newm;
2024: } /* end mult */
2025:
2026: s1=s[mw[mi][i]][i];
2027: s2=s[mw[mi+1][i]][i];
2028: if( s2 > nlstate){
2029: lli=log(out[s1][s2] - savm[s1][s2]);
2030: }else{
2031: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2032: }
2033: ipmx +=1;
2034: sw += weight[i];
2035: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2036: /* 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]); */
2037: } /* end of wave */
2038: } /* end of individual */
2039: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2040: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2041: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2042: for(mi=1; mi<= wav[i]-1; mi++){
2043: for (ii=1;ii<=nlstate+ndeath;ii++)
2044: for (j=1;j<=nlstate+ndeath;j++){
2045: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2046: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2047: }
2048: for(d=0; d<dh[mi][i]; d++){
2049: newm=savm;
2050: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2051: for (kk=1; kk<=cptcovage;kk++) {
2052: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2053: }
2054:
2055: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2056: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2057: savm=oldm;
2058: oldm=newm;
2059: } /* end mult */
2060:
2061: s1=s[mw[mi][i]][i];
2062: s2=s[mw[mi+1][i]][i];
2063: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2064: ipmx +=1;
2065: sw += weight[i];
2066: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2067: /*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]);*/
2068: } /* end of wave */
2069: } /* end of individual */
2070: } /* End of if */
2071: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2072: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2073: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2074: return -l;
2075: }
2076:
2077: /*************** log-likelihood *************/
2078: double funcone( double *x)
2079: {
2080: /* Same as likeli but slower because of a lot of printf and if */
2081: int i, ii, j, k, mi, d, kk;
2082: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2083: double **out;
2084: double lli; /* Individual log likelihood */
2085: double llt;
2086: int s1, s2;
2087: double bbh, survp;
2088: /*extern weight */
2089: /* We are differentiating ll according to initial status */
2090: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2091: /*for(i=1;i<imx;i++)
2092: printf(" %d\n",s[4][i]);
2093: */
2094: cov[1]=1.;
2095:
2096: for(k=1; k<=nlstate; k++) ll[k]=0.;
2097:
2098: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2099: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2100: for(mi=1; mi<= wav[i]-1; mi++){
2101: for (ii=1;ii<=nlstate+ndeath;ii++)
2102: for (j=1;j<=nlstate+ndeath;j++){
2103: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2104: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2105: }
2106: for(d=0; d<dh[mi][i]; d++){
2107: newm=savm;
2108: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2109: for (kk=1; kk<=cptcovage;kk++) {
2110: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2111: }
2112: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2113: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2114: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2115: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2116: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2117: savm=oldm;
2118: oldm=newm;
2119: } /* end mult */
2120:
2121: s1=s[mw[mi][i]][i];
2122: s2=s[mw[mi+1][i]][i];
2123: bbh=(double)bh[mi][i]/(double)stepm;
2124: /* bias is positive if real duration
2125: * is higher than the multiple of stepm and negative otherwise.
2126: */
2127: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2128: lli=log(out[s1][s2] - savm[s1][s2]);
2129: } else if (s2==-2) {
2130: for (j=1,survp=0. ; j<=nlstate; j++)
2131: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2132: lli= log(survp);
2133: }else if (mle==1){
2134: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2135: } else if(mle==2){
2136: 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 */
2137: } else if(mle==3){ /* exponential inter-extrapolation */
2138: 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 */
2139: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2140: lli=log(out[s1][s2]); /* Original formula */
2141: } else{ /* mle=0 back to 1 */
2142: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2143: /*lli=log(out[s1][s2]); */ /* Original formula */
2144: } /* End of if */
2145: ipmx +=1;
2146: sw += weight[i];
2147: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2148: /*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]); */
2149: if(globpr){
2150: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2151: %11.6f %11.6f %11.6f ", \
2152: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2153: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2154: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2155: llt +=ll[k]*gipmx/gsw;
2156: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2157: }
2158: fprintf(ficresilk," %10.6f\n", -llt);
2159: }
2160: } /* end of wave */
2161: } /* end of individual */
2162: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2163: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2164: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2165: if(globpr==0){ /* First time we count the contributions and weights */
2166: gipmx=ipmx;
2167: gsw=sw;
2168: }
2169: return -l;
2170: }
2171:
2172:
2173: /*************** function likelione ***********/
2174: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2175: {
2176: /* This routine should help understanding what is done with
2177: the selection of individuals/waves and
2178: to check the exact contribution to the likelihood.
2179: Plotting could be done.
2180: */
2181: int k;
2182:
2183: if(*globpri !=0){ /* Just counts and sums, no printings */
2184: strcpy(fileresilk,"ilk");
2185: strcat(fileresilk,fileres);
2186: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2187: printf("Problem with resultfile: %s\n", fileresilk);
2188: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2189: }
2190: 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");
2191: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2192: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2193: for(k=1; k<=nlstate; k++)
2194: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2195: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2196: }
2197:
2198: *fretone=(*funcone)(p);
2199: if(*globpri !=0){
2200: fclose(ficresilk);
2201: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2202: fflush(fichtm);
2203: }
2204: return;
2205: }
2206:
2207:
2208: /*********** Maximum Likelihood Estimation ***************/
2209:
2210: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2211: {
2212: int i,j, iter=0;
2213: double **xi;
2214: double fret;
2215: double fretone; /* Only one call to likelihood */
2216: /* char filerespow[FILENAMELENGTH];*/
2217:
2218: #ifdef NLOPT
2219: int creturn;
2220: nlopt_opt opt;
2221: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2222: double *lb;
2223: double minf; /* the minimum objective value, upon return */
2224: double * p1; /* Shifted parameters from 0 instead of 1 */
2225: myfunc_data dinst, *d = &dinst;
2226: #endif
2227:
2228:
2229: xi=matrix(1,npar,1,npar);
2230: for (i=1;i<=npar;i++)
2231: for (j=1;j<=npar;j++)
2232: xi[i][j]=(i==j ? 1.0 : 0.0);
2233: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2234: strcpy(filerespow,"pow");
2235: strcat(filerespow,fileres);
2236: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2237: printf("Problem with resultfile: %s\n", filerespow);
2238: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2239: }
2240: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2241: for (i=1;i<=nlstate;i++)
2242: for(j=1;j<=nlstate+ndeath;j++)
2243: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2244: fprintf(ficrespow,"\n");
2245: #ifdef POWELL
2246: powell(p,xi,npar,ftol,&iter,&fret,func);
2247: #endif
2248:
2249: #ifdef NLOPT
2250: #ifdef NEWUOA
2251: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2252: #else
2253: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2254: #endif
2255: lb=vector(0,npar-1);
2256: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2257: nlopt_set_lower_bounds(opt, lb);
2258: nlopt_set_initial_step1(opt, 0.1);
2259:
2260: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2261: d->function = func;
2262: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2263: nlopt_set_min_objective(opt, myfunc, d);
2264: nlopt_set_xtol_rel(opt, ftol);
2265: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2266: printf("nlopt failed! %d\n",creturn);
2267: }
2268: else {
2269: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2270: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2271: iter=1; /* not equal */
2272: }
2273: nlopt_destroy(opt);
2274: #endif
2275: free_matrix(xi,1,npar,1,npar);
2276: fclose(ficrespow);
2277: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2278: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2279: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2280:
2281: }
2282:
2283: /**** Computes Hessian and covariance matrix ***/
2284: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2285: {
2286: double **a,**y,*x,pd;
2287: double **hess;
2288: int i, j;
2289: int *indx;
2290:
2291: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2292: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2293: void lubksb(double **a, int npar, int *indx, double b[]) ;
2294: void ludcmp(double **a, int npar, int *indx, double *d) ;
2295: double gompertz(double p[]);
2296: hess=matrix(1,npar,1,npar);
2297:
2298: printf("\nCalculation of the hessian matrix. Wait...\n");
2299: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2300: for (i=1;i<=npar;i++){
2301: printf("%d",i);fflush(stdout);
2302: fprintf(ficlog,"%d",i);fflush(ficlog);
2303:
2304: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2305:
2306: /* printf(" %f ",p[i]);
2307: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2308: }
2309:
2310: for (i=1;i<=npar;i++) {
2311: for (j=1;j<=npar;j++) {
2312: if (j>i) {
2313: printf(".%d%d",i,j);fflush(stdout);
2314: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2315: hess[i][j]=hessij(p,delti,i,j,func,npar);
2316:
2317: hess[j][i]=hess[i][j];
2318: /*printf(" %lf ",hess[i][j]);*/
2319: }
2320: }
2321: }
2322: printf("\n");
2323: fprintf(ficlog,"\n");
2324:
2325: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2326: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2327:
2328: a=matrix(1,npar,1,npar);
2329: y=matrix(1,npar,1,npar);
2330: x=vector(1,npar);
2331: indx=ivector(1,npar);
2332: for (i=1;i<=npar;i++)
2333: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2334: ludcmp(a,npar,indx,&pd);
2335:
2336: for (j=1;j<=npar;j++) {
2337: for (i=1;i<=npar;i++) x[i]=0;
2338: x[j]=1;
2339: lubksb(a,npar,indx,x);
2340: for (i=1;i<=npar;i++){
2341: matcov[i][j]=x[i];
2342: }
2343: }
2344:
2345: printf("\n#Hessian matrix#\n");
2346: fprintf(ficlog,"\n#Hessian matrix#\n");
2347: for (i=1;i<=npar;i++) {
2348: for (j=1;j<=npar;j++) {
2349: printf("%.3e ",hess[i][j]);
2350: fprintf(ficlog,"%.3e ",hess[i][j]);
2351: }
2352: printf("\n");
2353: fprintf(ficlog,"\n");
2354: }
2355:
2356: /* Recompute Inverse */
2357: for (i=1;i<=npar;i++)
2358: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2359: ludcmp(a,npar,indx,&pd);
2360:
2361: /* printf("\n#Hessian matrix recomputed#\n");
2362:
2363: for (j=1;j<=npar;j++) {
2364: for (i=1;i<=npar;i++) x[i]=0;
2365: x[j]=1;
2366: lubksb(a,npar,indx,x);
2367: for (i=1;i<=npar;i++){
2368: y[i][j]=x[i];
2369: printf("%.3e ",y[i][j]);
2370: fprintf(ficlog,"%.3e ",y[i][j]);
2371: }
2372: printf("\n");
2373: fprintf(ficlog,"\n");
2374: }
2375: */
2376:
2377: free_matrix(a,1,npar,1,npar);
2378: free_matrix(y,1,npar,1,npar);
2379: free_vector(x,1,npar);
2380: free_ivector(indx,1,npar);
2381: free_matrix(hess,1,npar,1,npar);
2382:
2383:
2384: }
2385:
2386: /*************** hessian matrix ****************/
2387: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2388: {
2389: int i;
2390: int l=1, lmax=20;
2391: double k1,k2;
2392: double p2[MAXPARM+1]; /* identical to x */
2393: double res;
2394: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2395: double fx;
2396: int k=0,kmax=10;
2397: double l1;
2398:
2399: fx=func(x);
2400: for (i=1;i<=npar;i++) p2[i]=x[i];
2401: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2402: l1=pow(10,l);
2403: delts=delt;
2404: for(k=1 ; k <kmax; k=k+1){
2405: delt = delta*(l1*k);
2406: p2[theta]=x[theta] +delt;
2407: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2408: p2[theta]=x[theta]-delt;
2409: k2=func(p2)-fx;
2410: /*res= (k1-2.0*fx+k2)/delt/delt; */
2411: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2412:
2413: #ifdef DEBUGHESS
2414: 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);
2415: 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);
2416: #endif
2417: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2418: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2419: k=kmax;
2420: }
2421: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2422: k=kmax; l=lmax*10;
2423: }
2424: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2425: delts=delt;
2426: }
2427: }
2428: }
2429: delti[theta]=delts;
2430: return res;
2431:
2432: }
2433:
2434: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2435: {
2436: int i;
2437: int l=1, lmax=20;
2438: double k1,k2,k3,k4,res,fx;
2439: double p2[MAXPARM+1];
2440: int k;
2441:
2442: fx=func(x);
2443: for (k=1; k<=2; k++) {
2444: for (i=1;i<=npar;i++) p2[i]=x[i];
2445: p2[thetai]=x[thetai]+delti[thetai]/k;
2446: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2447: k1=func(p2)-fx;
2448:
2449: p2[thetai]=x[thetai]+delti[thetai]/k;
2450: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2451: k2=func(p2)-fx;
2452:
2453: p2[thetai]=x[thetai]-delti[thetai]/k;
2454: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2455: k3=func(p2)-fx;
2456:
2457: p2[thetai]=x[thetai]-delti[thetai]/k;
2458: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2459: k4=func(p2)-fx;
2460: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2461: #ifdef DEBUG
2462: 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);
2463: 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);
2464: #endif
2465: }
2466: return res;
2467: }
2468:
2469: /************** Inverse of matrix **************/
2470: void ludcmp(double **a, int n, int *indx, double *d)
2471: {
2472: int i,imax,j,k;
2473: double big,dum,sum,temp;
2474: double *vv;
2475:
2476: vv=vector(1,n);
2477: *d=1.0;
2478: for (i=1;i<=n;i++) {
2479: big=0.0;
2480: for (j=1;j<=n;j++)
2481: if ((temp=fabs(a[i][j])) > big) big=temp;
2482: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2483: vv[i]=1.0/big;
2484: }
2485: for (j=1;j<=n;j++) {
2486: for (i=1;i<j;i++) {
2487: sum=a[i][j];
2488: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2489: a[i][j]=sum;
2490: }
2491: big=0.0;
2492: for (i=j;i<=n;i++) {
2493: sum=a[i][j];
2494: for (k=1;k<j;k++)
2495: sum -= a[i][k]*a[k][j];
2496: a[i][j]=sum;
2497: if ( (dum=vv[i]*fabs(sum)) >= big) {
2498: big=dum;
2499: imax=i;
2500: }
2501: }
2502: if (j != imax) {
2503: for (k=1;k<=n;k++) {
2504: dum=a[imax][k];
2505: a[imax][k]=a[j][k];
2506: a[j][k]=dum;
2507: }
2508: *d = -(*d);
2509: vv[imax]=vv[j];
2510: }
2511: indx[j]=imax;
2512: if (a[j][j] == 0.0) a[j][j]=TINY;
2513: if (j != n) {
2514: dum=1.0/(a[j][j]);
2515: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2516: }
2517: }
2518: free_vector(vv,1,n); /* Doesn't work */
2519: ;
2520: }
2521:
2522: void lubksb(double **a, int n, int *indx, double b[])
2523: {
2524: int i,ii=0,ip,j;
2525: double sum;
2526:
2527: for (i=1;i<=n;i++) {
2528: ip=indx[i];
2529: sum=b[ip];
2530: b[ip]=b[i];
2531: if (ii)
2532: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2533: else if (sum) ii=i;
2534: b[i]=sum;
2535: }
2536: for (i=n;i>=1;i--) {
2537: sum=b[i];
2538: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2539: b[i]=sum/a[i][i];
2540: }
2541: }
2542:
2543: void pstamp(FILE *fichier)
2544: {
2545: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2546: }
2547:
2548: /************ Frequencies ********************/
2549: 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[])
2550: { /* Some frequencies */
2551:
2552: int i, m, jk, j1, bool, z1,j;
2553: int first;
2554: double ***freq; /* Frequencies */
2555: double *pp, **prop;
2556: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2557: char fileresp[FILENAMELENGTH];
2558:
2559: pp=vector(1,nlstate);
2560: prop=matrix(1,nlstate,iagemin,iagemax+3);
2561: strcpy(fileresp,"p");
2562: strcat(fileresp,fileres);
2563: if((ficresp=fopen(fileresp,"w"))==NULL) {
2564: printf("Problem with prevalence resultfile: %s\n", fileresp);
2565: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2566: exit(0);
2567: }
2568: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2569: j1=0;
2570:
2571: j=cptcoveff;
2572: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2573:
2574: first=1;
2575:
2576: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2577: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2578: /* j1++; */
2579: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2580: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2581: scanf("%d", i);*/
2582: for (i=-5; i<=nlstate+ndeath; i++)
2583: for (jk=-5; jk<=nlstate+ndeath; jk++)
2584: for(m=iagemin; m <= iagemax+3; m++)
2585: freq[i][jk][m]=0;
2586:
2587: for (i=1; i<=nlstate; i++)
2588: for(m=iagemin; m <= iagemax+3; m++)
2589: prop[i][m]=0;
2590:
2591: dateintsum=0;
2592: k2cpt=0;
2593: for (i=1; i<=imx; i++) {
2594: bool=1;
2595: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2596: for (z1=1; z1<=cptcoveff; z1++)
2597: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2598: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2599: bool=0;
2600: /* 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",
2601: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2602: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2603: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2604: }
2605: }
2606:
2607: if (bool==1){
2608: for(m=firstpass; m<=lastpass; m++){
2609: k2=anint[m][i]+(mint[m][i]/12.);
2610: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2611: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2612: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2613: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2614: if (m<lastpass) {
2615: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2616: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2617: }
2618:
2619: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2620: dateintsum=dateintsum+k2;
2621: k2cpt++;
2622: }
2623: /*}*/
2624: }
2625: }
2626: } /* end i */
2627:
2628: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2629: pstamp(ficresp);
2630: if (cptcovn>0) {
2631: fprintf(ficresp, "\n#********** Variable ");
2632: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2633: fprintf(ficresp, "**********\n#");
2634: fprintf(ficlog, "\n#********** Variable ");
2635: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2636: fprintf(ficlog, "**********\n#");
2637: }
2638: for(i=1; i<=nlstate;i++)
2639: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2640: fprintf(ficresp, "\n");
2641:
2642: for(i=iagemin; i <= iagemax+3; i++){
2643: if(i==iagemax+3){
2644: fprintf(ficlog,"Total");
2645: }else{
2646: if(first==1){
2647: first=0;
2648: printf("See log file for details...\n");
2649: }
2650: fprintf(ficlog,"Age %d", i);
2651: }
2652: for(jk=1; jk <=nlstate ; jk++){
2653: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2654: pp[jk] += freq[jk][m][i];
2655: }
2656: for(jk=1; jk <=nlstate ; jk++){
2657: for(m=-1, pos=0; m <=0 ; m++)
2658: pos += freq[jk][m][i];
2659: if(pp[jk]>=1.e-10){
2660: if(first==1){
2661: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2662: }
2663: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2664: }else{
2665: if(first==1)
2666: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2667: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2668: }
2669: }
2670:
2671: for(jk=1; jk <=nlstate ; jk++){
2672: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2673: pp[jk] += freq[jk][m][i];
2674: }
2675: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2676: pos += pp[jk];
2677: posprop += prop[jk][i];
2678: }
2679: for(jk=1; jk <=nlstate ; jk++){
2680: if(pos>=1.e-5){
2681: if(first==1)
2682: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2683: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2684: }else{
2685: if(first==1)
2686: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2687: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2688: }
2689: if( i <= iagemax){
2690: if(pos>=1.e-5){
2691: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2692: /*probs[i][jk][j1]= pp[jk]/pos;*/
2693: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2694: }
2695: else
2696: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2697: }
2698: }
2699:
2700: for(jk=-1; jk <=nlstate+ndeath; jk++)
2701: for(m=-1; m <=nlstate+ndeath; m++)
2702: if(freq[jk][m][i] !=0 ) {
2703: if(first==1)
2704: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2705: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2706: }
2707: if(i <= iagemax)
2708: fprintf(ficresp,"\n");
2709: if(first==1)
2710: printf("Others in log...\n");
2711: fprintf(ficlog,"\n");
2712: }
2713: /*}*/
2714: }
2715: dateintmean=dateintsum/k2cpt;
2716:
2717: fclose(ficresp);
2718: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2719: free_vector(pp,1,nlstate);
2720: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2721: /* End of Freq */
2722: }
2723:
2724: /************ Prevalence ********************/
2725: 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)
2726: {
2727: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2728: in each health status at the date of interview (if between dateprev1 and dateprev2).
2729: We still use firstpass and lastpass as another selection.
2730: */
2731:
2732: int i, m, jk, j1, bool, z1,j;
2733:
2734: double **prop;
2735: double posprop;
2736: double y2; /* in fractional years */
2737: int iagemin, iagemax;
2738: int first; /** to stop verbosity which is redirected to log file */
2739:
2740: iagemin= (int) agemin;
2741: iagemax= (int) agemax;
2742: /*pp=vector(1,nlstate);*/
2743: prop=matrix(1,nlstate,iagemin,iagemax+3);
2744: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2745: j1=0;
2746:
2747: /*j=cptcoveff;*/
2748: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2749:
2750: first=1;
2751: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2752: /*for(i1=1; i1<=ncodemax[k1];i1++){
2753: j1++;*/
2754:
2755: for (i=1; i<=nlstate; i++)
2756: for(m=iagemin; m <= iagemax+3; m++)
2757: prop[i][m]=0.0;
2758:
2759: for (i=1; i<=imx; i++) { /* Each individual */
2760: bool=1;
2761: if (cptcovn>0) {
2762: for (z1=1; z1<=cptcoveff; z1++)
2763: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2764: bool=0;
2765: }
2766: if (bool==1) {
2767: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2768: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2769: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2770: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2771: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2772: 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);
2773: if (s[m][i]>0 && s[m][i]<=nlstate) {
2774: /*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]]);*/
2775: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2776: prop[s[m][i]][iagemax+3] += weight[i];
2777: }
2778: }
2779: } /* end selection of waves */
2780: }
2781: }
2782: for(i=iagemin; i <= iagemax+3; i++){
2783: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2784: posprop += prop[jk][i];
2785: }
2786:
2787: for(jk=1; jk <=nlstate ; jk++){
2788: if( i <= iagemax){
2789: if(posprop>=1.e-5){
2790: probs[i][jk][j1]= prop[jk][i]/posprop;
2791: } else{
2792: if(first==1){
2793: first=0;
2794: 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]);
2795: }
2796: }
2797: }
2798: }/* end jk */
2799: }/* end i */
2800: /*} *//* end i1 */
2801: } /* end j1 */
2802:
2803: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2804: /*free_vector(pp,1,nlstate);*/
2805: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2806: } /* End of prevalence */
2807:
2808: /************* Waves Concatenation ***************/
2809:
2810: 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)
2811: {
2812: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2813: Death is a valid wave (if date is known).
2814: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2815: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2816: and mw[mi+1][i]. dh depends on stepm.
2817: */
2818:
2819: int i, mi, m;
2820: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2821: double sum=0., jmean=0.;*/
2822: int first;
2823: int j, k=0,jk, ju, jl;
2824: double sum=0.;
2825: first=0;
2826: jmin=100000;
2827: jmax=-1;
2828: jmean=0.;
2829: for(i=1; i<=imx; i++){
2830: mi=0;
2831: m=firstpass;
2832: while(s[m][i] <= nlstate){
2833: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2834: mw[++mi][i]=m;
2835: if(m >=lastpass)
2836: break;
2837: else
2838: m++;
2839: }/* end while */
2840: if (s[m][i] > nlstate){
2841: mi++; /* Death is another wave */
2842: /* if(mi==0) never been interviewed correctly before death */
2843: /* Only death is a correct wave */
2844: mw[mi][i]=m;
2845: }
2846:
2847: wav[i]=mi;
2848: if(mi==0){
2849: nbwarn++;
2850: if(first==0){
2851: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2852: first=1;
2853: }
2854: if(first==1){
2855: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2856: }
2857: } /* end mi==0 */
2858: } /* End individuals */
2859:
2860: for(i=1; i<=imx; i++){
2861: for(mi=1; mi<wav[i];mi++){
2862: if (stepm <=0)
2863: dh[mi][i]=1;
2864: else{
2865: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2866: if (agedc[i] < 2*AGESUP) {
2867: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2868: if(j==0) j=1; /* Survives at least one month after exam */
2869: else if(j<0){
2870: nberr++;
2871: 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]);
2872: j=1; /* Temporary Dangerous patch */
2873: 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);
2874: 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]);
2875: 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);
2876: }
2877: k=k+1;
2878: if (j >= jmax){
2879: jmax=j;
2880: ijmax=i;
2881: }
2882: if (j <= jmin){
2883: jmin=j;
2884: ijmin=i;
2885: }
2886: sum=sum+j;
2887: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2888: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2889: }
2890: }
2891: else{
2892: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2893: /* 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]); */
2894:
2895: k=k+1;
2896: if (j >= jmax) {
2897: jmax=j;
2898: ijmax=i;
2899: }
2900: else if (j <= jmin){
2901: jmin=j;
2902: ijmin=i;
2903: }
2904: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2905: /*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]);*/
2906: if(j<0){
2907: nberr++;
2908: 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]);
2909: 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]);
2910: }
2911: sum=sum+j;
2912: }
2913: jk= j/stepm;
2914: jl= j -jk*stepm;
2915: ju= j -(jk+1)*stepm;
2916: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2917: if(jl==0){
2918: dh[mi][i]=jk;
2919: bh[mi][i]=0;
2920: }else{ /* We want a negative bias in order to only have interpolation ie
2921: * to avoid the price of an extra matrix product in likelihood */
2922: dh[mi][i]=jk+1;
2923: bh[mi][i]=ju;
2924: }
2925: }else{
2926: if(jl <= -ju){
2927: dh[mi][i]=jk;
2928: bh[mi][i]=jl; /* bias is positive if real duration
2929: * is higher than the multiple of stepm and negative otherwise.
2930: */
2931: }
2932: else{
2933: dh[mi][i]=jk+1;
2934: bh[mi][i]=ju;
2935: }
2936: if(dh[mi][i]==0){
2937: dh[mi][i]=1; /* At least one step */
2938: bh[mi][i]=ju; /* At least one step */
2939: /* 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);*/
2940: }
2941: } /* end if mle */
2942: }
2943: } /* end wave */
2944: }
2945: jmean=sum/k;
2946: 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);
2947: 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);
2948: }
2949:
2950: /*********** Tricode ****************************/
2951: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2952: {
2953: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2954: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2955: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2956: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2957: * nbcode[Tvar[j]][1]=
2958: */
2959:
2960: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2961: int modmaxcovj=0; /* Modality max of covariates j */
2962: int cptcode=0; /* Modality max of covariates j */
2963: int modmincovj=0; /* Modality min of covariates j */
2964:
2965:
2966: cptcoveff=0;
2967:
2968: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2969: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2970:
2971: /* Loop on covariates without age and products */
2972: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2973: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2974: modality of this covariate Vj*/
2975: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2976: * If product of Vn*Vm, still boolean *:
2977: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2978: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2979: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2980: modality of the nth covariate of individual i. */
2981: if (ij > modmaxcovj)
2982: modmaxcovj=ij;
2983: else if (ij < modmincovj)
2984: modmincovj=ij;
2985: if ((ij < -1) && (ij > NCOVMAX)){
2986: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2987: exit(1);
2988: }else
2989: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2990: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2991: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2992: /* getting the maximum value of the modality of the covariate
2993: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2994: female is 1, then modmaxcovj=1.*/
2995: }
2996: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2997: cptcode=modmaxcovj;
2998: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2999: /*for (i=0; i<=cptcode; i++) {*/
3000: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
3001: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
3002: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
3003: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
3004: }
3005: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3006: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3007: } /* Ndum[-1] number of undefined modalities */
3008:
3009: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3010: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
3011: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
3012: modmincovj=3; modmaxcovj = 7;
3013: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
3014: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
3015: variables V1_1 and V1_2.
3016: nbcode[Tvar[j]][ij]=k;
3017: nbcode[Tvar[j]][1]=0;
3018: nbcode[Tvar[j]][2]=1;
3019: nbcode[Tvar[j]][3]=2;
3020: */
3021: ij=1; /* ij is similar to i but can jumps over null modalities */
3022: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3023: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3024: /*recode from 0 */
3025: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3026: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3027: k is a modality. If we have model=V1+V1*sex
3028: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3029: ij++;
3030: }
3031: if (ij > ncodemax[j]) break;
3032: } /* end of loop on */
3033: } /* end of loop on modality */
3034: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3035:
3036: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3037:
3038: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3039: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3040: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3041: Ndum[ij]++;
3042: }
3043:
3044: ij=1;
3045: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3046: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3047: if((Ndum[i]!=0) && (i<=ncovcol)){
3048: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3049: Tvaraff[ij]=i; /*For printing (unclear) */
3050: ij++;
3051: }else
3052: Tvaraff[ij]=0;
3053: }
3054: ij--;
3055: cptcoveff=ij; /*Number of total covariates*/
3056:
3057: }
3058:
3059:
3060: /*********** Health Expectancies ****************/
3061:
3062: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3063:
3064: {
3065: /* Health expectancies, no variances */
3066: int i, j, nhstepm, hstepm, h, nstepm;
3067: int nhstepma, nstepma; /* Decreasing with age */
3068: double age, agelim, hf;
3069: double ***p3mat;
3070: double eip;
3071:
3072: pstamp(ficreseij);
3073: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3074: fprintf(ficreseij,"# Age");
3075: for(i=1; i<=nlstate;i++){
3076: for(j=1; j<=nlstate;j++){
3077: fprintf(ficreseij," e%1d%1d ",i,j);
3078: }
3079: fprintf(ficreseij," e%1d. ",i);
3080: }
3081: fprintf(ficreseij,"\n");
3082:
3083:
3084: if(estepm < stepm){
3085: printf ("Problem %d lower than %d\n",estepm, stepm);
3086: }
3087: else hstepm=estepm;
3088: /* We compute the life expectancy from trapezoids spaced every estepm months
3089: * This is mainly to measure the difference between two models: for example
3090: * if stepm=24 months pijx are given only every 2 years and by summing them
3091: * we are calculating an estimate of the Life Expectancy assuming a linear
3092: * progression in between and thus overestimating or underestimating according
3093: * to the curvature of the survival function. If, for the same date, we
3094: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3095: * to compare the new estimate of Life expectancy with the same linear
3096: * hypothesis. A more precise result, taking into account a more precise
3097: * curvature will be obtained if estepm is as small as stepm. */
3098:
3099: /* For example we decided to compute the life expectancy with the smallest unit */
3100: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3101: nhstepm is the number of hstepm from age to agelim
3102: nstepm is the number of stepm from age to agelin.
3103: Look at hpijx to understand the reason of that which relies in memory size
3104: and note for a fixed period like estepm months */
3105: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3106: survival function given by stepm (the optimization length). Unfortunately it
3107: means that if the survival funtion is printed only each two years of age and if
3108: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3109: results. So we changed our mind and took the option of the best precision.
3110: */
3111: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3112:
3113: agelim=AGESUP;
3114: /* If stepm=6 months */
3115: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3116: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3117:
3118: /* nhstepm age range expressed in number of stepm */
3119: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3120: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3121: /* if (stepm >= YEARM) hstepm=1;*/
3122: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3123: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3124:
3125: for (age=bage; age<=fage; age ++){
3126: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3127: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3128: /* if (stepm >= YEARM) hstepm=1;*/
3129: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3130:
3131: /* If stepm=6 months */
3132: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3133: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3134:
3135: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3136:
3137: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3138:
3139: printf("%d|",(int)age);fflush(stdout);
3140: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3141:
3142: /* Computing expectancies */
3143: for(i=1; i<=nlstate;i++)
3144: for(j=1; j<=nlstate;j++)
3145: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3146: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3147:
3148: /* 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]);*/
3149:
3150: }
3151:
3152: fprintf(ficreseij,"%3.0f",age );
3153: for(i=1; i<=nlstate;i++){
3154: eip=0;
3155: for(j=1; j<=nlstate;j++){
3156: eip +=eij[i][j][(int)age];
3157: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3158: }
3159: fprintf(ficreseij,"%9.4f", eip );
3160: }
3161: fprintf(ficreseij,"\n");
3162:
3163: }
3164: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3165: printf("\n");
3166: fprintf(ficlog,"\n");
3167:
3168: }
3169:
3170: 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[] )
3171:
3172: {
3173: /* Covariances of health expectancies eij and of total life expectancies according
3174: to initial status i, ei. .
3175: */
3176: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3177: int nhstepma, nstepma; /* Decreasing with age */
3178: double age, agelim, hf;
3179: double ***p3matp, ***p3matm, ***varhe;
3180: double **dnewm,**doldm;
3181: double *xp, *xm;
3182: double **gp, **gm;
3183: double ***gradg, ***trgradg;
3184: int theta;
3185:
3186: double eip, vip;
3187:
3188: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3189: xp=vector(1,npar);
3190: xm=vector(1,npar);
3191: dnewm=matrix(1,nlstate*nlstate,1,npar);
3192: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3193:
3194: pstamp(ficresstdeij);
3195: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3196: fprintf(ficresstdeij,"# Age");
3197: for(i=1; i<=nlstate;i++){
3198: for(j=1; j<=nlstate;j++)
3199: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3200: fprintf(ficresstdeij," e%1d. ",i);
3201: }
3202: fprintf(ficresstdeij,"\n");
3203:
3204: pstamp(ficrescveij);
3205: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3206: fprintf(ficrescveij,"# Age");
3207: for(i=1; i<=nlstate;i++)
3208: for(j=1; j<=nlstate;j++){
3209: cptj= (j-1)*nlstate+i;
3210: for(i2=1; i2<=nlstate;i2++)
3211: for(j2=1; j2<=nlstate;j2++){
3212: cptj2= (j2-1)*nlstate+i2;
3213: if(cptj2 <= cptj)
3214: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3215: }
3216: }
3217: fprintf(ficrescveij,"\n");
3218:
3219: if(estepm < stepm){
3220: printf ("Problem %d lower than %d\n",estepm, stepm);
3221: }
3222: else hstepm=estepm;
3223: /* We compute the life expectancy from trapezoids spaced every estepm months
3224: * This is mainly to measure the difference between two models: for example
3225: * if stepm=24 months pijx are given only every 2 years and by summing them
3226: * we are calculating an estimate of the Life Expectancy assuming a linear
3227: * progression in between and thus overestimating or underestimating according
3228: * to the curvature of the survival function. If, for the same date, we
3229: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3230: * to compare the new estimate of Life expectancy with the same linear
3231: * hypothesis. A more precise result, taking into account a more precise
3232: * curvature will be obtained if estepm is as small as stepm. */
3233:
3234: /* For example we decided to compute the life expectancy with the smallest unit */
3235: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3236: nhstepm is the number of hstepm from age to agelim
3237: nstepm is the number of stepm from age to agelin.
3238: Look at hpijx to understand the reason of that which relies in memory size
3239: and note for a fixed period like estepm months */
3240: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3241: survival function given by stepm (the optimization length). Unfortunately it
3242: means that if the survival funtion is printed only each two years of age and if
3243: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3244: results. So we changed our mind and took the option of the best precision.
3245: */
3246: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3247:
3248: /* If stepm=6 months */
3249: /* nhstepm age range expressed in number of stepm */
3250: agelim=AGESUP;
3251: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3252: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3253: /* if (stepm >= YEARM) hstepm=1;*/
3254: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3255:
3256: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3257: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3258: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3259: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3260: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3261: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3262:
3263: for (age=bage; age<=fage; age ++){
3264: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3265: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3266: /* if (stepm >= YEARM) hstepm=1;*/
3267: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3268:
3269: /* If stepm=6 months */
3270: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3271: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3272:
3273: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3274:
3275: /* Computing Variances of health expectancies */
3276: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3277: decrease memory allocation */
3278: for(theta=1; theta <=npar; theta++){
3279: for(i=1; i<=npar; i++){
3280: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3281: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3282: }
3283: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3284: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3285:
3286: for(j=1; j<= nlstate; j++){
3287: for(i=1; i<=nlstate; i++){
3288: for(h=0; h<=nhstepm-1; h++){
3289: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3290: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3291: }
3292: }
3293: }
3294:
3295: for(ij=1; ij<= nlstate*nlstate; ij++)
3296: for(h=0; h<=nhstepm-1; h++){
3297: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3298: }
3299: }/* End theta */
3300:
3301:
3302: for(h=0; h<=nhstepm-1; h++)
3303: for(j=1; j<=nlstate*nlstate;j++)
3304: for(theta=1; theta <=npar; theta++)
3305: trgradg[h][j][theta]=gradg[h][theta][j];
3306:
3307:
3308: for(ij=1;ij<=nlstate*nlstate;ij++)
3309: for(ji=1;ji<=nlstate*nlstate;ji++)
3310: varhe[ij][ji][(int)age] =0.;
3311:
3312: printf("%d|",(int)age);fflush(stdout);
3313: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3314: for(h=0;h<=nhstepm-1;h++){
3315: for(k=0;k<=nhstepm-1;k++){
3316: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3317: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3318: for(ij=1;ij<=nlstate*nlstate;ij++)
3319: for(ji=1;ji<=nlstate*nlstate;ji++)
3320: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3321: }
3322: }
3323:
3324: /* Computing expectancies */
3325: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3326: for(i=1; i<=nlstate;i++)
3327: for(j=1; j<=nlstate;j++)
3328: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3329: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3330:
3331: /* 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]);*/
3332:
3333: }
3334:
3335: fprintf(ficresstdeij,"%3.0f",age );
3336: for(i=1; i<=nlstate;i++){
3337: eip=0.;
3338: vip=0.;
3339: for(j=1; j<=nlstate;j++){
3340: eip += eij[i][j][(int)age];
3341: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3342: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3343: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3344: }
3345: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3346: }
3347: fprintf(ficresstdeij,"\n");
3348:
3349: fprintf(ficrescveij,"%3.0f",age );
3350: for(i=1; i<=nlstate;i++)
3351: for(j=1; j<=nlstate;j++){
3352: cptj= (j-1)*nlstate+i;
3353: for(i2=1; i2<=nlstate;i2++)
3354: for(j2=1; j2<=nlstate;j2++){
3355: cptj2= (j2-1)*nlstate+i2;
3356: if(cptj2 <= cptj)
3357: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3358: }
3359: }
3360: fprintf(ficrescveij,"\n");
3361:
3362: }
3363: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3364: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3365: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3366: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3367: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3368: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3369: printf("\n");
3370: fprintf(ficlog,"\n");
3371:
3372: free_vector(xm,1,npar);
3373: free_vector(xp,1,npar);
3374: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3375: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3376: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3377: }
3378:
3379: /************ Variance ******************/
3380: 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[])
3381: {
3382: /* Variance of health expectancies */
3383: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3384: /* double **newm;*/
3385: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3386:
3387: int movingaverage();
3388: double **dnewm,**doldm;
3389: double **dnewmp,**doldmp;
3390: int i, j, nhstepm, hstepm, h, nstepm ;
3391: int k;
3392: double *xp;
3393: double **gp, **gm; /* for var eij */
3394: double ***gradg, ***trgradg; /*for var eij */
3395: double **gradgp, **trgradgp; /* for var p point j */
3396: double *gpp, *gmp; /* for var p point j */
3397: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3398: double ***p3mat;
3399: double age,agelim, hf;
3400: double ***mobaverage;
3401: int theta;
3402: char digit[4];
3403: char digitp[25];
3404:
3405: char fileresprobmorprev[FILENAMELENGTH];
3406:
3407: if(popbased==1){
3408: if(mobilav!=0)
3409: strcpy(digitp,"-populbased-mobilav-");
3410: else strcpy(digitp,"-populbased-nomobil-");
3411: }
3412: else
3413: strcpy(digitp,"-stablbased-");
3414:
3415: if (mobilav!=0) {
3416: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3417: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3418: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3419: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3420: }
3421: }
3422:
3423: strcpy(fileresprobmorprev,"prmorprev");
3424: sprintf(digit,"%-d",ij);
3425: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3426: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3427: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3428: strcat(fileresprobmorprev,fileres);
3429: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3430: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3431: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3432: }
3433: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3434:
3435: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3436: pstamp(ficresprobmorprev);
3437: 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);
3438: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3439: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3440: fprintf(ficresprobmorprev," p.%-d SE",j);
3441: for(i=1; i<=nlstate;i++)
3442: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3443: }
3444: fprintf(ficresprobmorprev,"\n");
3445: fprintf(ficgp,"\n# Routine varevsij");
3446: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3447: 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");
3448: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3449: /* } */
3450: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3451: pstamp(ficresvij);
3452: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3453: if(popbased==1)
3454: 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);
3455: else
3456: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3457: fprintf(ficresvij,"# Age");
3458: for(i=1; i<=nlstate;i++)
3459: for(j=1; j<=nlstate;j++)
3460: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3461: fprintf(ficresvij,"\n");
3462:
3463: xp=vector(1,npar);
3464: dnewm=matrix(1,nlstate,1,npar);
3465: doldm=matrix(1,nlstate,1,nlstate);
3466: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3467: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3468:
3469: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3470: gpp=vector(nlstate+1,nlstate+ndeath);
3471: gmp=vector(nlstate+1,nlstate+ndeath);
3472: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3473:
3474: if(estepm < stepm){
3475: printf ("Problem %d lower than %d\n",estepm, stepm);
3476: }
3477: else hstepm=estepm;
3478: /* For example we decided to compute the life expectancy with the smallest unit */
3479: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3480: nhstepm is the number of hstepm from age to agelim
3481: nstepm is the number of stepm from age to agelin.
3482: Look at function hpijx to understand why (it is linked to memory size questions) */
3483: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3484: survival function given by stepm (the optimization length). Unfortunately it
3485: means that if the survival funtion is printed every two years of age and if
3486: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3487: results. So we changed our mind and took the option of the best precision.
3488: */
3489: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3490: agelim = AGESUP;
3491: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3492: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3493: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3494: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3495: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3496: gp=matrix(0,nhstepm,1,nlstate);
3497: gm=matrix(0,nhstepm,1,nlstate);
3498:
3499:
3500: for(theta=1; theta <=npar; theta++){
3501: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3502: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3503: }
3504: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3505: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3506:
3507: if (popbased==1) {
3508: if(mobilav ==0){
3509: for(i=1; i<=nlstate;i++)
3510: prlim[i][i]=probs[(int)age][i][ij];
3511: }else{ /* mobilav */
3512: for(i=1; i<=nlstate;i++)
3513: prlim[i][i]=mobaverage[(int)age][i][ij];
3514: }
3515: }
3516:
3517: for(j=1; j<= nlstate; j++){
3518: for(h=0; h<=nhstepm; h++){
3519: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3520: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3521: }
3522: }
3523: /* This for computing probability of death (h=1 means
3524: computed over hstepm matrices product = hstepm*stepm months)
3525: as a weighted average of prlim.
3526: */
3527: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3528: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3529: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3530: }
3531: /* end probability of death */
3532:
3533: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3534: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3535: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3536: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3537:
3538: if (popbased==1) {
3539: if(mobilav ==0){
3540: for(i=1; i<=nlstate;i++)
3541: prlim[i][i]=probs[(int)age][i][ij];
3542: }else{ /* mobilav */
3543: for(i=1; i<=nlstate;i++)
3544: prlim[i][i]=mobaverage[(int)age][i][ij];
3545: }
3546: }
3547:
3548: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3549: for(h=0; h<=nhstepm; h++){
3550: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3551: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3552: }
3553: }
3554: /* This for computing probability of death (h=1 means
3555: computed over hstepm matrices product = hstepm*stepm months)
3556: as a weighted average of prlim.
3557: */
3558: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3559: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3560: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3561: }
3562: /* end probability of death */
3563:
3564: for(j=1; j<= nlstate; j++) /* vareij */
3565: for(h=0; h<=nhstepm; h++){
3566: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3567: }
3568:
3569: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3570: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3571: }
3572:
3573: } /* End theta */
3574:
3575: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3576:
3577: for(h=0; h<=nhstepm; h++) /* veij */
3578: for(j=1; j<=nlstate;j++)
3579: for(theta=1; theta <=npar; theta++)
3580: trgradg[h][j][theta]=gradg[h][theta][j];
3581:
3582: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3583: for(theta=1; theta <=npar; theta++)
3584: trgradgp[j][theta]=gradgp[theta][j];
3585:
3586:
3587: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3588: for(i=1;i<=nlstate;i++)
3589: for(j=1;j<=nlstate;j++)
3590: vareij[i][j][(int)age] =0.;
3591:
3592: for(h=0;h<=nhstepm;h++){
3593: for(k=0;k<=nhstepm;k++){
3594: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3595: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3596: for(i=1;i<=nlstate;i++)
3597: for(j=1;j<=nlstate;j++)
3598: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3599: }
3600: }
3601:
3602: /* pptj */
3603: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3604: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3605: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3606: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3607: varppt[j][i]=doldmp[j][i];
3608: /* end ppptj */
3609: /* x centered again */
3610: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3611: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3612:
3613: if (popbased==1) {
3614: if(mobilav ==0){
3615: for(i=1; i<=nlstate;i++)
3616: prlim[i][i]=probs[(int)age][i][ij];
3617: }else{ /* mobilav */
3618: for(i=1; i<=nlstate;i++)
3619: prlim[i][i]=mobaverage[(int)age][i][ij];
3620: }
3621: }
3622:
3623: /* This for computing probability of death (h=1 means
3624: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3625: as a weighted average of prlim.
3626: */
3627: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3628: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3629: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3630: }
3631: /* end probability of death */
3632:
3633: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3634: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3635: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3636: for(i=1; i<=nlstate;i++){
3637: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3638: }
3639: }
3640: fprintf(ficresprobmorprev,"\n");
3641:
3642: fprintf(ficresvij,"%.0f ",age );
3643: for(i=1; i<=nlstate;i++)
3644: for(j=1; j<=nlstate;j++){
3645: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3646: }
3647: fprintf(ficresvij,"\n");
3648: free_matrix(gp,0,nhstepm,1,nlstate);
3649: free_matrix(gm,0,nhstepm,1,nlstate);
3650: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3651: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3652: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3653: } /* End age */
3654: free_vector(gpp,nlstate+1,nlstate+ndeath);
3655: free_vector(gmp,nlstate+1,nlstate+ndeath);
3656: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3657: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3658: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3659: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3660: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3661: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3662: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3663: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3664: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3665: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3666: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3667: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3668: 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);
3669: /* 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);
3670: */
3671: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3672: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3673:
3674: free_vector(xp,1,npar);
3675: free_matrix(doldm,1,nlstate,1,nlstate);
3676: free_matrix(dnewm,1,nlstate,1,npar);
3677: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3678: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3679: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3680: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3681: fclose(ficresprobmorprev);
3682: fflush(ficgp);
3683: fflush(fichtm);
3684: } /* end varevsij */
3685:
3686: /************ Variance of prevlim ******************/
3687: 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[])
3688: {
3689: /* Variance of prevalence limit */
3690: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3691:
3692: double **dnewm,**doldm;
3693: int i, j, nhstepm, hstepm;
3694: double *xp;
3695: double *gp, *gm;
3696: double **gradg, **trgradg;
3697: double age,agelim;
3698: int theta;
3699:
3700: pstamp(ficresvpl);
3701: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3702: fprintf(ficresvpl,"# Age");
3703: for(i=1; i<=nlstate;i++)
3704: fprintf(ficresvpl," %1d-%1d",i,i);
3705: fprintf(ficresvpl,"\n");
3706:
3707: xp=vector(1,npar);
3708: dnewm=matrix(1,nlstate,1,npar);
3709: doldm=matrix(1,nlstate,1,nlstate);
3710:
3711: hstepm=1*YEARM; /* Every year of age */
3712: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3713: agelim = AGESUP;
3714: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3715: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3716: if (stepm >= YEARM) hstepm=1;
3717: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3718: gradg=matrix(1,npar,1,nlstate);
3719: gp=vector(1,nlstate);
3720: gm=vector(1,nlstate);
3721:
3722: for(theta=1; theta <=npar; theta++){
3723: for(i=1; i<=npar; i++){ /* Computes gradient */
3724: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3725: }
3726: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3727: for(i=1;i<=nlstate;i++)
3728: gp[i] = prlim[i][i];
3729:
3730: for(i=1; i<=npar; i++) /* Computes gradient */
3731: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3732: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3733: for(i=1;i<=nlstate;i++)
3734: gm[i] = prlim[i][i];
3735:
3736: for(i=1;i<=nlstate;i++)
3737: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3738: } /* End theta */
3739:
3740: trgradg =matrix(1,nlstate,1,npar);
3741:
3742: for(j=1; j<=nlstate;j++)
3743: for(theta=1; theta <=npar; theta++)
3744: trgradg[j][theta]=gradg[theta][j];
3745:
3746: for(i=1;i<=nlstate;i++)
3747: varpl[i][(int)age] =0.;
3748: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3749: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3750: for(i=1;i<=nlstate;i++)
3751: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3752:
3753: fprintf(ficresvpl,"%.0f ",age );
3754: for(i=1; i<=nlstate;i++)
3755: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3756: fprintf(ficresvpl,"\n");
3757: free_vector(gp,1,nlstate);
3758: free_vector(gm,1,nlstate);
3759: free_matrix(gradg,1,npar,1,nlstate);
3760: free_matrix(trgradg,1,nlstate,1,npar);
3761: } /* End age */
3762:
3763: free_vector(xp,1,npar);
3764: free_matrix(doldm,1,nlstate,1,npar);
3765: free_matrix(dnewm,1,nlstate,1,nlstate);
3766:
3767: }
3768:
3769: /************ Variance of one-step probabilities ******************/
3770: 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[])
3771: {
3772: int i, j=0, k1, l1, tj;
3773: int k2, l2, j1, z1;
3774: int k=0, l;
3775: int first=1, first1, first2;
3776: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3777: double **dnewm,**doldm;
3778: double *xp;
3779: double *gp, *gm;
3780: double **gradg, **trgradg;
3781: double **mu;
3782: double age, cov[NCOVMAX+1];
3783: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3784: int theta;
3785: char fileresprob[FILENAMELENGTH];
3786: char fileresprobcov[FILENAMELENGTH];
3787: char fileresprobcor[FILENAMELENGTH];
3788: double ***varpij;
3789:
3790: strcpy(fileresprob,"prob");
3791: strcat(fileresprob,fileres);
3792: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3793: printf("Problem with resultfile: %s\n", fileresprob);
3794: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3795: }
3796: strcpy(fileresprobcov,"probcov");
3797: strcat(fileresprobcov,fileres);
3798: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3799: printf("Problem with resultfile: %s\n", fileresprobcov);
3800: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3801: }
3802: strcpy(fileresprobcor,"probcor");
3803: strcat(fileresprobcor,fileres);
3804: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3805: printf("Problem with resultfile: %s\n", fileresprobcor);
3806: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3807: }
3808: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3809: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3810: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3811: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3812: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3813: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3814: pstamp(ficresprob);
3815: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3816: fprintf(ficresprob,"# Age");
3817: pstamp(ficresprobcov);
3818: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3819: fprintf(ficresprobcov,"# Age");
3820: pstamp(ficresprobcor);
3821: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3822: fprintf(ficresprobcor,"# Age");
3823:
3824:
3825: for(i=1; i<=nlstate;i++)
3826: for(j=1; j<=(nlstate+ndeath);j++){
3827: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3828: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3829: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3830: }
3831: /* fprintf(ficresprob,"\n");
3832: fprintf(ficresprobcov,"\n");
3833: fprintf(ficresprobcor,"\n");
3834: */
3835: xp=vector(1,npar);
3836: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3837: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3838: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3839: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3840: first=1;
3841: fprintf(ficgp,"\n# Routine varprob");
3842: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3843: fprintf(fichtm,"\n");
3844:
3845: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3846: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3847: file %s<br>\n",optionfilehtmcov);
3848: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3849: and drawn. It helps understanding how is the covariance between two incidences.\
3850: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3851: 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. \
3852: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3853: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3854: standard deviations wide on each axis. <br>\
3855: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3856: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3857: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3858:
3859: cov[1]=1;
3860: /* tj=cptcoveff; */
3861: tj = (int) pow(2,cptcoveff);
3862: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3863: j1=0;
3864: for(j1=1; j1<=tj;j1++){
3865: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3866: /*j1++;*/
3867: if (cptcovn>0) {
3868: fprintf(ficresprob, "\n#********** Variable ");
3869: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3870: fprintf(ficresprob, "**********\n#\n");
3871: fprintf(ficresprobcov, "\n#********** Variable ");
3872: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3873: fprintf(ficresprobcov, "**********\n#\n");
3874:
3875: fprintf(ficgp, "\n#********** Variable ");
3876: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3877: fprintf(ficgp, "**********\n#\n");
3878:
3879:
3880: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3881: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3882: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3883:
3884: fprintf(ficresprobcor, "\n#********** Variable ");
3885: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3886: fprintf(ficresprobcor, "**********\n#");
3887: }
3888:
3889: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3890: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3891: gp=vector(1,(nlstate)*(nlstate+ndeath));
3892: gm=vector(1,(nlstate)*(nlstate+ndeath));
3893: for (age=bage; age<=fage; age ++){
3894: cov[2]=age;
3895: for (k=1; k<=cptcovn;k++) {
3896: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3897: * 1 1 1 1 1
3898: * 2 2 1 1 1
3899: * 3 1 2 1 1
3900: */
3901: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3902: }
3903: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3904: for (k=1; k<=cptcovprod;k++)
3905: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3906:
3907:
3908: for(theta=1; theta <=npar; theta++){
3909: for(i=1; i<=npar; i++)
3910: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3911:
3912: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3913:
3914: k=0;
3915: for(i=1; i<= (nlstate); i++){
3916: for(j=1; j<=(nlstate+ndeath);j++){
3917: k=k+1;
3918: gp[k]=pmmij[i][j];
3919: }
3920: }
3921:
3922: for(i=1; i<=npar; i++)
3923: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3924:
3925: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3926: k=0;
3927: for(i=1; i<=(nlstate); i++){
3928: for(j=1; j<=(nlstate+ndeath);j++){
3929: k=k+1;
3930: gm[k]=pmmij[i][j];
3931: }
3932: }
3933:
3934: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3935: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3936: }
3937:
3938: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3939: for(theta=1; theta <=npar; theta++)
3940: trgradg[j][theta]=gradg[theta][j];
3941:
3942: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3943: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3944:
3945: pmij(pmmij,cov,ncovmodel,x,nlstate);
3946:
3947: k=0;
3948: for(i=1; i<=(nlstate); i++){
3949: for(j=1; j<=(nlstate+ndeath);j++){
3950: k=k+1;
3951: mu[k][(int) age]=pmmij[i][j];
3952: }
3953: }
3954: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3955: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3956: varpij[i][j][(int)age] = doldm[i][j];
3957:
3958: /*printf("\n%d ",(int)age);
3959: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3960: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3961: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3962: }*/
3963:
3964: fprintf(ficresprob,"\n%d ",(int)age);
3965: fprintf(ficresprobcov,"\n%d ",(int)age);
3966: fprintf(ficresprobcor,"\n%d ",(int)age);
3967:
3968: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3969: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3970: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3971: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3972: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3973: }
3974: i=0;
3975: for (k=1; k<=(nlstate);k++){
3976: for (l=1; l<=(nlstate+ndeath);l++){
3977: i++;
3978: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3979: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3980: for (j=1; j<=i;j++){
3981: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3982: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3983: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3984: }
3985: }
3986: }/* end of loop for state */
3987: } /* end of loop for age */
3988: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3989: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3990: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3991: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3992:
3993: /* Confidence intervalle of pij */
3994: /*
3995: fprintf(ficgp,"\nunset parametric;unset label");
3996: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3997: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3998: 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);
3999: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4000: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4001: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4002: */
4003:
4004: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4005: first1=1;first2=2;
4006: for (k2=1; k2<=(nlstate);k2++){
4007: for (l2=1; l2<=(nlstate+ndeath);l2++){
4008: if(l2==k2) continue;
4009: j=(k2-1)*(nlstate+ndeath)+l2;
4010: for (k1=1; k1<=(nlstate);k1++){
4011: for (l1=1; l1<=(nlstate+ndeath);l1++){
4012: if(l1==k1) continue;
4013: i=(k1-1)*(nlstate+ndeath)+l1;
4014: if(i<=j) continue;
4015: for (age=bage; age<=fage; age ++){
4016: if ((int)age %5==0){
4017: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4018: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4019: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4020: mu1=mu[i][(int) age]/stepm*YEARM ;
4021: mu2=mu[j][(int) age]/stepm*YEARM;
4022: c12=cv12/sqrt(v1*v2);
4023: /* Computing eigen value of matrix of covariance */
4024: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4025: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4026: if ((lc2 <0) || (lc1 <0) ){
4027: if(first2==1){
4028: first1=0;
4029: 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);
4030: }
4031: 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);
4032: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4033: /* lc2=fabs(lc2); */
4034: }
4035:
4036: /* Eigen vectors */
4037: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4038: /*v21=sqrt(1.-v11*v11); *//* error */
4039: v21=(lc1-v1)/cv12*v11;
4040: v12=-v21;
4041: v22=v11;
4042: tnalp=v21/v11;
4043: if(first1==1){
4044: first1=0;
4045: 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);
4046: }
4047: 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);
4048: /*printf(fignu*/
4049: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4050: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4051: if(first==1){
4052: first=0;
4053: fprintf(ficgp,"\nset parametric;unset label");
4054: 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);
4055: fprintf(ficgp,"\nset ter png small size 320, 240");
4056: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4057: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4058: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4059: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4060: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4061: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4062: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4063: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4064: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4065: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4066: 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",\
4067: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4068: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4069: }else{
4070: first=0;
4071: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4072: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4073: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4074: 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",\
4075: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4076: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4077: }/* if first */
4078: } /* age mod 5 */
4079: } /* end loop age */
4080: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4081: first=1;
4082: } /*l12 */
4083: } /* k12 */
4084: } /*l1 */
4085: }/* k1 */
4086: /* } */ /* loop covariates */
4087: }
4088: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4089: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4090: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4091: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4092: free_vector(xp,1,npar);
4093: fclose(ficresprob);
4094: fclose(ficresprobcov);
4095: fclose(ficresprobcor);
4096: fflush(ficgp);
4097: fflush(fichtmcov);
4098: }
4099:
4100:
4101: /******************* Printing html file ***********/
4102: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4103: int lastpass, int stepm, int weightopt, char model[],\
4104: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4105: int popforecast, int estepm ,\
4106: double jprev1, double mprev1,double anprev1, \
4107: double jprev2, double mprev2,double anprev2){
4108: int jj1, k1, i1, cpt;
4109:
4110: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4111: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4112: </ul>");
4113: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4114: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4115: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4116: fprintf(fichtm,"\
4117: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4118: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4119: fprintf(fichtm,"\
4120: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4121: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4122: fprintf(fichtm,"\
4123: - (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): \
4124: <a href=\"%s\">%s</a> <br>\n",
4125: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4126: fprintf(fichtm,"\
4127: - Population projections by age and states: \
4128: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4129:
4130: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4131:
4132: m=pow(2,cptcoveff);
4133: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4134:
4135: jj1=0;
4136: for(k1=1; k1<=m;k1++){
4137: for(i1=1; i1<=ncodemax[k1];i1++){
4138: jj1++;
4139: if (cptcovn > 0) {
4140: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4141: for (cpt=1; cpt<=cptcoveff;cpt++)
4142: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4143: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4144: }
4145: /* Pij */
4146: 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> \
4147: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4148: /* Quasi-incidences */
4149: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4150: 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> \
4151: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4152: /* Period (stable) prevalence in each health state */
4153: for(cpt=1; cpt<=nlstate;cpt++){
4154: 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> \
4155: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4156: }
4157: for(cpt=1; cpt<=nlstate;cpt++) {
4158: 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> \
4159: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4160: }
4161: } /* end i1 */
4162: }/* End k1 */
4163: fprintf(fichtm,"</ul>");
4164:
4165:
4166: fprintf(fichtm,"\
4167: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4168: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4169:
4170: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4171: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4172: fprintf(fichtm,"\
4173: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4174: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4175:
4176: fprintf(fichtm,"\
4177: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4178: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4179: fprintf(fichtm,"\
4180: - 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): \
4181: <a href=\"%s\">%s</a> <br>\n</li>",
4182: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4183: fprintf(fichtm,"\
4184: - (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): \
4185: <a href=\"%s\">%s</a> <br>\n</li>",
4186: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4187: fprintf(fichtm,"\
4188: - 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",
4189: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4190: fprintf(fichtm,"\
4191: - 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",
4192: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4193: fprintf(fichtm,"\
4194: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4195: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4196:
4197: /* if(popforecast==1) fprintf(fichtm,"\n */
4198: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4199: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4200: /* <br>",fileres,fileres,fileres,fileres); */
4201: /* else */
4202: /* 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); */
4203: fflush(fichtm);
4204: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4205:
4206: m=pow(2,cptcoveff);
4207: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4208:
4209: jj1=0;
4210: for(k1=1; k1<=m;k1++){
4211: for(i1=1; i1<=ncodemax[k1];i1++){
4212: jj1++;
4213: if (cptcovn > 0) {
4214: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4215: for (cpt=1; cpt<=cptcoveff;cpt++)
4216: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4217: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4218: }
4219: for(cpt=1; cpt<=nlstate;cpt++) {
4220: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4221: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4222: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4223: }
4224: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4225: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4226: true period expectancies (those weighted with period prevalences are also\
4227: drawn in addition to the population based expectancies computed using\
4228: observed and cahotic prevalences: %s%d.png<br>\
4229: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4230: } /* end i1 */
4231: }/* End k1 */
4232: fprintf(fichtm,"</ul>");
4233: fflush(fichtm);
4234: }
4235:
4236: /******************* Gnuplot file **************/
4237: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4238:
4239: char dirfileres[132],optfileres[132];
4240: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4241: int ng=0;
4242: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4243: /* printf("Problem with file %s",optionfilegnuplot); */
4244: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4245: /* } */
4246:
4247: /*#ifdef windows */
4248: fprintf(ficgp,"cd \"%s\" \n",pathc);
4249: /*#endif */
4250: m=pow(2,cptcoveff);
4251:
4252: strcpy(dirfileres,optionfilefiname);
4253: strcpy(optfileres,"vpl");
4254: /* 1eme*/
4255: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4256: for (cpt=1; cpt<= nlstate ; cpt ++) {
4257: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4258: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4259: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4260: fprintf(ficgp,"set xlabel \"Age\" \n\
4261: set ylabel \"Probability\" \n\
4262: set ter png small size 320, 240\n\
4263: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4264:
4265: for (i=1; i<= nlstate ; i ++) {
4266: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4267: else fprintf(ficgp," %%*lf (%%*lf)");
4268: }
4269: 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);
4270: for (i=1; i<= nlstate ; i ++) {
4271: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4272: else fprintf(ficgp," %%*lf (%%*lf)");
4273: }
4274: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4275: for (i=1; i<= nlstate ; i ++) {
4276: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4277: else fprintf(ficgp," %%*lf (%%*lf)");
4278: }
4279: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4280: }
4281: }
4282: /*2 eme*/
4283: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4284: for (k1=1; k1<= m ; k1 ++) {
4285: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4286: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4287:
4288: for (i=1; i<= nlstate+1 ; i ++) {
4289: k=2*i;
4290: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4291: for (j=1; j<= nlstate+1 ; j ++) {
4292: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4293: else fprintf(ficgp," %%*lf (%%*lf)");
4294: }
4295: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4296: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4297: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4298: for (j=1; j<= nlstate+1 ; j ++) {
4299: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4300: else fprintf(ficgp," %%*lf (%%*lf)");
4301: }
4302: fprintf(ficgp,"\" t\"\" w l lt 0,");
4303: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4304: for (j=1; j<= nlstate+1 ; j ++) {
4305: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4306: else fprintf(ficgp," %%*lf (%%*lf)");
4307: }
4308: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4309: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4310: }
4311: }
4312:
4313: /*3eme*/
4314:
4315: for (k1=1; k1<= m ; k1 ++) {
4316: for (cpt=1; cpt<= nlstate ; cpt ++) {
4317: /* k=2+nlstate*(2*cpt-2); */
4318: k=2+(nlstate+1)*(cpt-1);
4319: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4320: fprintf(ficgp,"set ter png small size 320, 240\n\
4321: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4322: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4323: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4324: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4325: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4326: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4327: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4328:
4329: */
4330: for (i=1; i< nlstate ; i ++) {
4331: 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);
4332: /* 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);*/
4333:
4334: }
4335: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4336: }
4337: }
4338:
4339: /* CV preval stable (period) */
4340: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4341: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4342: k=3;
4343: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4344: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4345: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4346: set ter png small size 320, 240\n\
4347: unset log y\n\
4348: plot [%.f:%.f] ", ageminpar, agemaxpar);
4349: for (i=1; i<= nlstate ; i ++){
4350: if(i==1)
4351: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4352: else
4353: fprintf(ficgp,", '' ");
4354: l=(nlstate+ndeath)*(i-1)+1;
4355: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4356: for (j=1; j<= (nlstate-1) ; j ++)
4357: fprintf(ficgp,"+$%d",k+l+j);
4358: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4359: } /* nlstate */
4360: fprintf(ficgp,"\n");
4361: } /* end cpt state*/
4362: } /* end covariate */
4363:
4364: /* proba elementaires */
4365: for(i=1,jk=1; i <=nlstate; i++){
4366: for(k=1; k <=(nlstate+ndeath); k++){
4367: if (k != i) {
4368: for(j=1; j <=ncovmodel; j++){
4369: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4370: jk++;
4371: fprintf(ficgp,"\n");
4372: }
4373: }
4374: }
4375: }
4376: /*goto avoid;*/
4377: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4378: for(jk=1; jk <=m; jk++) {
4379: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4380: if (ng==2)
4381: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4382: else
4383: fprintf(ficgp,"\nset title \"Probability\"\n");
4384: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4385: i=1;
4386: for(k2=1; k2<=nlstate; k2++) {
4387: k3=i;
4388: for(k=1; k<=(nlstate+ndeath); k++) {
4389: if (k != k2){
4390: if(ng==2)
4391: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4392: else
4393: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4394: ij=1;/* To be checked else nbcode[0][0] wrong */
4395: for(j=3; j <=ncovmodel; j++) {
4396: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4397: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4398: /* ij++; */
4399: /* } */
4400: /* else */
4401: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4402: }
4403: fprintf(ficgp,")/(1");
4404:
4405: for(k1=1; k1 <=nlstate; k1++){
4406: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4407: ij=1;
4408: for(j=3; j <=ncovmodel; j++){
4409: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4410: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4411: /* ij++; */
4412: /* } */
4413: /* else */
4414: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4415: }
4416: fprintf(ficgp,")");
4417: }
4418: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4419: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4420: i=i+ncovmodel;
4421: }
4422: } /* end k */
4423: } /* end k2 */
4424: } /* end jk */
4425: } /* end ng */
4426: /* avoid: */
4427: fflush(ficgp);
4428: } /* end gnuplot */
4429:
4430:
4431: /*************** Moving average **************/
4432: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4433:
4434: int i, cpt, cptcod;
4435: int modcovmax =1;
4436: int mobilavrange, mob;
4437: double age;
4438:
4439: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4440: a covariate has 2 modalities */
4441: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4442:
4443: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4444: if(mobilav==1) mobilavrange=5; /* default */
4445: else mobilavrange=mobilav;
4446: for (age=bage; age<=fage; age++)
4447: for (i=1; i<=nlstate;i++)
4448: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4449: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4450: /* We keep the original values on the extreme ages bage, fage and for
4451: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4452: we use a 5 terms etc. until the borders are no more concerned.
4453: */
4454: for (mob=3;mob <=mobilavrange;mob=mob+2){
4455: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4456: for (i=1; i<=nlstate;i++){
4457: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4458: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4459: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4460: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4461: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4462: }
4463: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4464: }
4465: }
4466: }/* end age */
4467: }/* end mob */
4468: }else return -1;
4469: return 0;
4470: }/* End movingaverage */
4471:
4472:
4473: /************** Forecasting ******************/
4474: 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){
4475: /* proj1, year, month, day of starting projection
4476: agemin, agemax range of age
4477: dateprev1 dateprev2 range of dates during which prevalence is computed
4478: anproj2 year of en of projection (same day and month as proj1).
4479: */
4480: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4481: double agec; /* generic age */
4482: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4483: double *popeffectif,*popcount;
4484: double ***p3mat;
4485: double ***mobaverage;
4486: char fileresf[FILENAMELENGTH];
4487:
4488: agelim=AGESUP;
4489: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4490:
4491: strcpy(fileresf,"f");
4492: strcat(fileresf,fileres);
4493: if((ficresf=fopen(fileresf,"w"))==NULL) {
4494: printf("Problem with forecast resultfile: %s\n", fileresf);
4495: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4496: }
4497: printf("Computing forecasting: result on file '%s' \n", fileresf);
4498: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4499:
4500: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4501:
4502: if (mobilav!=0) {
4503: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4504: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4505: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4506: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4507: }
4508: }
4509:
4510: stepsize=(int) (stepm+YEARM-1)/YEARM;
4511: if (stepm<=12) stepsize=1;
4512: if(estepm < stepm){
4513: printf ("Problem %d lower than %d\n",estepm, stepm);
4514: }
4515: else hstepm=estepm;
4516:
4517: hstepm=hstepm/stepm;
4518: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4519: fractional in yp1 */
4520: anprojmean=yp;
4521: yp2=modf((yp1*12),&yp);
4522: mprojmean=yp;
4523: yp1=modf((yp2*30.5),&yp);
4524: jprojmean=yp;
4525: if(jprojmean==0) jprojmean=1;
4526: if(mprojmean==0) jprojmean=1;
4527:
4528: i1=cptcoveff;
4529: if (cptcovn < 1){i1=1;}
4530:
4531: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4532:
4533: fprintf(ficresf,"#****** Routine prevforecast **\n");
4534:
4535: /* if (h==(int)(YEARM*yearp)){ */
4536: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4537: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4538: k=k+1;
4539: fprintf(ficresf,"\n#******");
4540: for(j=1;j<=cptcoveff;j++) {
4541: 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]]);
4542: }
4543: fprintf(ficresf,"******\n");
4544: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4545: for(j=1; j<=nlstate+ndeath;j++){
4546: for(i=1; i<=nlstate;i++)
4547: fprintf(ficresf," p%d%d",i,j);
4548: fprintf(ficresf," p.%d",j);
4549: }
4550: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4551: fprintf(ficresf,"\n");
4552: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4553:
4554: for (agec=fage; agec>=(ageminpar-1); agec--){
4555: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4556: nhstepm = nhstepm/hstepm;
4557: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4558: oldm=oldms;savm=savms;
4559: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4560:
4561: for (h=0; h<=nhstepm; h++){
4562: if (h*hstepm/YEARM*stepm ==yearp) {
4563: fprintf(ficresf,"\n");
4564: for(j=1;j<=cptcoveff;j++)
4565: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4566: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4567: }
4568: for(j=1; j<=nlstate+ndeath;j++) {
4569: ppij=0.;
4570: for(i=1; i<=nlstate;i++) {
4571: if (mobilav==1)
4572: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4573: else {
4574: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4575: }
4576: if (h*hstepm/YEARM*stepm== yearp) {
4577: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4578: }
4579: } /* end i */
4580: if (h*hstepm/YEARM*stepm==yearp) {
4581: fprintf(ficresf," %.3f", ppij);
4582: }
4583: }/* end j */
4584: } /* end h */
4585: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4586: } /* end agec */
4587: } /* end yearp */
4588: } /* end cptcod */
4589: } /* end cptcov */
4590:
4591: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4592:
4593: fclose(ficresf);
4594: }
4595:
4596: /************** Forecasting *****not tested NB*************/
4597: 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){
4598:
4599: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4600: int *popage;
4601: double calagedatem, agelim, kk1, kk2;
4602: double *popeffectif,*popcount;
4603: double ***p3mat,***tabpop,***tabpopprev;
4604: double ***mobaverage;
4605: char filerespop[FILENAMELENGTH];
4606:
4607: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4608: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4609: agelim=AGESUP;
4610: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4611:
4612: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4613:
4614:
4615: strcpy(filerespop,"pop");
4616: strcat(filerespop,fileres);
4617: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4618: printf("Problem with forecast resultfile: %s\n", filerespop);
4619: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4620: }
4621: printf("Computing forecasting: result on file '%s' \n", filerespop);
4622: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4623:
4624: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4625:
4626: if (mobilav!=0) {
4627: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4628: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4629: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4630: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4631: }
4632: }
4633:
4634: stepsize=(int) (stepm+YEARM-1)/YEARM;
4635: if (stepm<=12) stepsize=1;
4636:
4637: agelim=AGESUP;
4638:
4639: hstepm=1;
4640: hstepm=hstepm/stepm;
4641:
4642: if (popforecast==1) {
4643: if((ficpop=fopen(popfile,"r"))==NULL) {
4644: printf("Problem with population file : %s\n",popfile);exit(0);
4645: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4646: }
4647: popage=ivector(0,AGESUP);
4648: popeffectif=vector(0,AGESUP);
4649: popcount=vector(0,AGESUP);
4650:
4651: i=1;
4652: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4653:
4654: imx=i;
4655: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4656: }
4657:
4658: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4659: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4660: k=k+1;
4661: fprintf(ficrespop,"\n#******");
4662: for(j=1;j<=cptcoveff;j++) {
4663: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4664: }
4665: fprintf(ficrespop,"******\n");
4666: fprintf(ficrespop,"# Age");
4667: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4668: if (popforecast==1) fprintf(ficrespop," [Population]");
4669:
4670: for (cpt=0; cpt<=0;cpt++) {
4671: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4672:
4673: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4674: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4675: nhstepm = nhstepm/hstepm;
4676:
4677: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4678: oldm=oldms;savm=savms;
4679: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4680:
4681: for (h=0; h<=nhstepm; h++){
4682: if (h==(int) (calagedatem+YEARM*cpt)) {
4683: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4684: }
4685: for(j=1; j<=nlstate+ndeath;j++) {
4686: kk1=0.;kk2=0;
4687: for(i=1; i<=nlstate;i++) {
4688: if (mobilav==1)
4689: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4690: else {
4691: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4692: }
4693: }
4694: if (h==(int)(calagedatem+12*cpt)){
4695: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4696: /*fprintf(ficrespop," %.3f", kk1);
4697: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4698: }
4699: }
4700: for(i=1; i<=nlstate;i++){
4701: kk1=0.;
4702: for(j=1; j<=nlstate;j++){
4703: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4704: }
4705: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4706: }
4707:
4708: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4709: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4710: }
4711: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4712: }
4713: }
4714:
4715: /******/
4716:
4717: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4718: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4719: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4720: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4721: nhstepm = nhstepm/hstepm;
4722:
4723: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4724: oldm=oldms;savm=savms;
4725: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4726: for (h=0; h<=nhstepm; h++){
4727: if (h==(int) (calagedatem+YEARM*cpt)) {
4728: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4729: }
4730: for(j=1; j<=nlstate+ndeath;j++) {
4731: kk1=0.;kk2=0;
4732: for(i=1; i<=nlstate;i++) {
4733: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4734: }
4735: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4736: }
4737: }
4738: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4739: }
4740: }
4741: }
4742: }
4743:
4744: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4745:
4746: if (popforecast==1) {
4747: free_ivector(popage,0,AGESUP);
4748: free_vector(popeffectif,0,AGESUP);
4749: free_vector(popcount,0,AGESUP);
4750: }
4751: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4752: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4753: fclose(ficrespop);
4754: } /* End of popforecast */
4755:
4756: int fileappend(FILE *fichier, char *optionfich)
4757: {
4758: if((fichier=fopen(optionfich,"a"))==NULL) {
4759: printf("Problem with file: %s\n", optionfich);
4760: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4761: return (0);
4762: }
4763: fflush(fichier);
4764: return (1);
4765: }
4766:
4767:
4768: /**************** function prwizard **********************/
4769: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4770: {
4771:
4772: /* Wizard to print covariance matrix template */
4773:
4774: char ca[32], cb[32];
4775: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4776: int numlinepar;
4777:
4778: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4779: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4780: for(i=1; i <=nlstate; i++){
4781: jj=0;
4782: for(j=1; j <=nlstate+ndeath; j++){
4783: if(j==i) continue;
4784: jj++;
4785: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4786: printf("%1d%1d",i,j);
4787: fprintf(ficparo,"%1d%1d",i,j);
4788: for(k=1; k<=ncovmodel;k++){
4789: /* printf(" %lf",param[i][j][k]); */
4790: /* fprintf(ficparo," %lf",param[i][j][k]); */
4791: printf(" 0.");
4792: fprintf(ficparo," 0.");
4793: }
4794: printf("\n");
4795: fprintf(ficparo,"\n");
4796: }
4797: }
4798: printf("# Scales (for hessian or gradient estimation)\n");
4799: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4800: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4801: for(i=1; i <=nlstate; i++){
4802: jj=0;
4803: for(j=1; j <=nlstate+ndeath; j++){
4804: if(j==i) continue;
4805: jj++;
4806: fprintf(ficparo,"%1d%1d",i,j);
4807: printf("%1d%1d",i,j);
4808: fflush(stdout);
4809: for(k=1; k<=ncovmodel;k++){
4810: /* printf(" %le",delti3[i][j][k]); */
4811: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4812: printf(" 0.");
4813: fprintf(ficparo," 0.");
4814: }
4815: numlinepar++;
4816: printf("\n");
4817: fprintf(ficparo,"\n");
4818: }
4819: }
4820: printf("# Covariance matrix\n");
4821: /* # 121 Var(a12)\n\ */
4822: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4823: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4824: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4825: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4826: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4827: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4828: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4829: fflush(stdout);
4830: fprintf(ficparo,"# Covariance matrix\n");
4831: /* # 121 Var(a12)\n\ */
4832: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4833: /* # ...\n\ */
4834: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4835:
4836: for(itimes=1;itimes<=2;itimes++){
4837: jj=0;
4838: for(i=1; i <=nlstate; i++){
4839: for(j=1; j <=nlstate+ndeath; j++){
4840: if(j==i) continue;
4841: for(k=1; k<=ncovmodel;k++){
4842: jj++;
4843: ca[0]= k+'a'-1;ca[1]='\0';
4844: if(itimes==1){
4845: printf("#%1d%1d%d",i,j,k);
4846: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4847: }else{
4848: printf("%1d%1d%d",i,j,k);
4849: fprintf(ficparo,"%1d%1d%d",i,j,k);
4850: /* printf(" %.5le",matcov[i][j]); */
4851: }
4852: ll=0;
4853: for(li=1;li <=nlstate; li++){
4854: for(lj=1;lj <=nlstate+ndeath; lj++){
4855: if(lj==li) continue;
4856: for(lk=1;lk<=ncovmodel;lk++){
4857: ll++;
4858: if(ll<=jj){
4859: cb[0]= lk +'a'-1;cb[1]='\0';
4860: if(ll<jj){
4861: if(itimes==1){
4862: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4863: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4864: }else{
4865: printf(" 0.");
4866: fprintf(ficparo," 0.");
4867: }
4868: }else{
4869: if(itimes==1){
4870: printf(" Var(%s%1d%1d)",ca,i,j);
4871: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4872: }else{
4873: printf(" 0.");
4874: fprintf(ficparo," 0.");
4875: }
4876: }
4877: }
4878: } /* end lk */
4879: } /* end lj */
4880: } /* end li */
4881: printf("\n");
4882: fprintf(ficparo,"\n");
4883: numlinepar++;
4884: } /* end k*/
4885: } /*end j */
4886: } /* end i */
4887: } /* end itimes */
4888:
4889: } /* end of prwizard */
4890: /******************* Gompertz Likelihood ******************************/
4891: double gompertz(double x[])
4892: {
4893: double A,B,L=0.0,sump=0.,num=0.;
4894: int i,n=0; /* n is the size of the sample */
4895:
4896: for (i=0;i<=imx-1 ; i++) {
4897: sump=sump+weight[i];
4898: /* sump=sump+1;*/
4899: num=num+1;
4900: }
4901:
4902:
4903: /* for (i=0; i<=imx; i++)
4904: 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]);*/
4905:
4906: for (i=1;i<=imx ; i++)
4907: {
4908: if (cens[i] == 1 && wav[i]>1)
4909: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4910:
4911: if (cens[i] == 0 && wav[i]>1)
4912: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4913: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4914:
4915: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4916: if (wav[i] > 1 ) { /* ??? */
4917: L=L+A*weight[i];
4918: /* 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]);*/
4919: }
4920: }
4921:
4922: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4923:
4924: return -2*L*num/sump;
4925: }
4926:
4927: #ifdef GSL
4928: /******************* Gompertz_f Likelihood ******************************/
4929: double gompertz_f(const gsl_vector *v, void *params)
4930: {
4931: double A,B,LL=0.0,sump=0.,num=0.;
4932: double *x= (double *) v->data;
4933: int i,n=0; /* n is the size of the sample */
4934:
4935: for (i=0;i<=imx-1 ; i++) {
4936: sump=sump+weight[i];
4937: /* sump=sump+1;*/
4938: num=num+1;
4939: }
4940:
4941:
4942: /* for (i=0; i<=imx; i++)
4943: 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]);*/
4944: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4945: for (i=1;i<=imx ; i++)
4946: {
4947: if (cens[i] == 1 && wav[i]>1)
4948: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4949:
4950: if (cens[i] == 0 && wav[i]>1)
4951: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4952: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4953:
4954: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4955: if (wav[i] > 1 ) { /* ??? */
4956: LL=LL+A*weight[i];
4957: /* 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]);*/
4958: }
4959: }
4960:
4961: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4962: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4963:
4964: return -2*LL*num/sump;
4965: }
4966: #endif
4967:
4968: /******************* Printing html file ***********/
4969: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4970: int lastpass, int stepm, int weightopt, char model[],\
4971: int imx, double p[],double **matcov,double agemortsup){
4972: int i,k;
4973:
4974: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4975: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4976: for (i=1;i<=2;i++)
4977: 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]));
4978: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4979: fprintf(fichtm,"</ul>");
4980:
4981: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4982:
4983: 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>");
4984:
4985: for (k=agegomp;k<(agemortsup-2);k++)
4986: 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]);
4987:
4988:
4989: fflush(fichtm);
4990: }
4991:
4992: /******************* Gnuplot file **************/
4993: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4994:
4995: char dirfileres[132],optfileres[132];
4996:
4997: int ng;
4998:
4999:
5000: /*#ifdef windows */
5001: fprintf(ficgp,"cd \"%s\" \n",pathc);
5002: /*#endif */
5003:
5004:
5005: strcpy(dirfileres,optionfilefiname);
5006: strcpy(optfileres,"vpl");
5007: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5008: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5009: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5010: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5011: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5012:
5013: }
5014:
5015: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5016: {
5017:
5018: /*-------- data file ----------*/
5019: FILE *fic;
5020: char dummy[]=" ";
5021: int i=0, j=0, n=0;
5022: int linei, month, year,iout;
5023: char line[MAXLINE], linetmp[MAXLINE];
5024: char stra[MAXLINE], strb[MAXLINE];
5025: char *stratrunc;
5026: int lstra;
5027:
5028:
5029: if((fic=fopen(datafile,"r"))==NULL) {
5030: printf("Problem while opening datafile: %s\n", datafile);return 1;
5031: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5032: }
5033:
5034: i=1;
5035: linei=0;
5036: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5037: linei=linei+1;
5038: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5039: if(line[j] == '\t')
5040: line[j] = ' ';
5041: }
5042: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5043: ;
5044: };
5045: line[j+1]=0; /* Trims blanks at end of line */
5046: if(line[0]=='#'){
5047: fprintf(ficlog,"Comment line\n%s\n",line);
5048: printf("Comment line\n%s\n",line);
5049: continue;
5050: }
5051: trimbb(linetmp,line); /* Trims multiple blanks in line */
5052: strcpy(line, linetmp);
5053:
5054:
5055: for (j=maxwav;j>=1;j--){
5056: cutv(stra, strb, line, ' ');
5057: if(strb[0]=='.') { /* Missing status */
5058: lval=-1;
5059: }else{
5060: errno=0;
5061: lval=strtol(strb,&endptr,10);
5062: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5063: if( strb[0]=='\0' || (*endptr != '\0')){
5064: 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);
5065: 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);
5066: return 1;
5067: }
5068: }
5069: s[j][i]=lval;
5070:
5071: strcpy(line,stra);
5072: cutv(stra, strb,line,' ');
5073: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5074: }
5075: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5076: month=99;
5077: year=9999;
5078: }else{
5079: 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);
5080: 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);
5081: return 1;
5082: }
5083: anint[j][i]= (double) year;
5084: mint[j][i]= (double)month;
5085: strcpy(line,stra);
5086: } /* ENd Waves */
5087:
5088: cutv(stra, strb,line,' ');
5089: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5090: }
5091: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5092: month=99;
5093: year=9999;
5094: }else{
5095: 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);
5096: 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);
5097: return 1;
5098: }
5099: andc[i]=(double) year;
5100: moisdc[i]=(double) month;
5101: strcpy(line,stra);
5102:
5103: cutv(stra, strb,line,' ');
5104: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5105: }
5106: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5107: month=99;
5108: year=9999;
5109: }else{
5110: 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);
5111: 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);
5112: return 1;
5113: }
5114: if (year==9999) {
5115: 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);
5116: 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);
5117: return 1;
5118:
5119: }
5120: annais[i]=(double)(year);
5121: moisnais[i]=(double)(month);
5122: strcpy(line,stra);
5123:
5124: cutv(stra, strb,line,' ');
5125: errno=0;
5126: dval=strtod(strb,&endptr);
5127: if( strb[0]=='\0' || (*endptr != '\0')){
5128: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5129: 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);
5130: fflush(ficlog);
5131: return 1;
5132: }
5133: weight[i]=dval;
5134: strcpy(line,stra);
5135:
5136: for (j=ncovcol;j>=1;j--){
5137: cutv(stra, strb,line,' ');
5138: if(strb[0]=='.') { /* Missing status */
5139: lval=-1;
5140: }else{
5141: errno=0;
5142: lval=strtol(strb,&endptr,10);
5143: if( strb[0]=='\0' || (*endptr != '\0')){
5144: 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);
5145: 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);
5146: return 1;
5147: }
5148: }
5149: if(lval <-1 || lval >1){
5150: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5151: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5152: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5153: For example, for multinomial values like 1, 2 and 3,\n \
5154: build V1=0 V2=0 for the reference value (1),\n \
5155: V1=1 V2=0 for (2) \n \
5156: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5157: output of IMaCh is often meaningless.\n \
5158: Exiting.\n",lval,linei, i,line,j);
5159: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5160: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5161: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5162: For example, for multinomial values like 1, 2 and 3,\n \
5163: build V1=0 V2=0 for the reference value (1),\n \
5164: V1=1 V2=0 for (2) \n \
5165: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5166: output of IMaCh is often meaningless.\n \
5167: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5168: return 1;
5169: }
5170: covar[j][i]=(double)(lval);
5171: strcpy(line,stra);
5172: }
5173: lstra=strlen(stra);
5174:
5175: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5176: stratrunc = &(stra[lstra-9]);
5177: num[i]=atol(stratrunc);
5178: }
5179: else
5180: num[i]=atol(stra);
5181: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5182: 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;}*/
5183:
5184: i=i+1;
5185: } /* End loop reading data */
5186:
5187: *imax=i-1; /* Number of individuals */
5188: fclose(fic);
5189:
5190: return (0);
5191: /* endread: */
5192: printf("Exiting readdata: ");
5193: fclose(fic);
5194: return (1);
5195:
5196:
5197:
5198: }
5199: void removespace(char *str) {
5200: char *p1 = str, *p2 = str;
5201: do
5202: while (*p2 == ' ')
5203: p2++;
5204: while (*p1++ == *p2++);
5205: }
5206:
5207: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5208: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5209: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5210: * - cptcovn or number of covariates k of the models excluding age*products =6
5211: * - cptcovage number of covariates with age*products =2
5212: * - cptcovs number of simple covariates
5213: * - 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
5214: * which is a new column after the 9 (ncovcol) variables.
5215: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5216: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5217: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5218: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5219: */
5220: {
5221: int i, j, k, ks;
5222: int j1, k1, k2;
5223: char modelsav[80];
5224: char stra[80], strb[80], strc[80], strd[80],stre[80];
5225:
5226: /*removespace(model);*/
5227: if (strlen(model) >1){ /* If there is at least 1 covariate */
5228: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5229: j=nbocc(model,'+'); /**< j=Number of '+' */
5230: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5231: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5232: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5233: /* including age products which are counted in cptcovage.
5234: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5235: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5236: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5237: strcpy(modelsav,model);
5238: if (strstr(model,"AGE") !=0){
5239: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5240: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5241: return 1;
5242: }
5243: if (strstr(model,"v") !=0){
5244: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5245: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5246: return 1;
5247: }
5248:
5249: /* Design
5250: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5251: * < ncovcol=8 >
5252: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5253: * k= 1 2 3 4 5 6 7 8
5254: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5255: * covar[k,i], value of kth covariate if not including age for individual i:
5256: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5257: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5258: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5259: * Tage[++cptcovage]=k
5260: * if products, new covar are created after ncovcol with k1
5261: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5262: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5263: * 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
5264: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5265: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5266: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5267: * < ncovcol=8 >
5268: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5269: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5270: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5271: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5272: * p Tprod[1]@2={ 6, 5}
5273: *p Tvard[1][1]@4= {7, 8, 5, 6}
5274: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5275: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5276: *How to reorganize?
5277: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5278: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5279: * {2, 1, 4, 8, 5, 6, 3, 7}
5280: * Struct []
5281: */
5282:
5283: /* This loop fills the array Tvar from the string 'model'.*/
5284: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5285: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5286: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5287: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5288: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5289: /* k=1 Tvar[1]=2 (from V2) */
5290: /* k=5 Tvar[5] */
5291: /* for (k=1; k<=cptcovn;k++) { */
5292: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5293: /* } */
5294: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5295: /*
5296: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5297: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5298: Tvar[k]=0;
5299: cptcovage=0;
5300: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5301: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5302: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5303: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5304: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5305: /*scanf("%d",i);*/
5306: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5307: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5308: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5309: /* covar is not filled and then is empty */
5310: cptcovprod--;
5311: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5312: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5313: cptcovage++; /* Sums the number of covariates which include age as a product */
5314: Tage[cptcovage]=k; /* Tage[1] = 4 */
5315: /*printf("stre=%s ", stre);*/
5316: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5317: cptcovprod--;
5318: cutl(stre,strb,strc,'V');
5319: Tvar[k]=atoi(stre);
5320: cptcovage++;
5321: Tage[cptcovage]=k;
5322: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5323: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5324: cptcovn++;
5325: cptcovprodnoage++;k1++;
5326: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5327: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5328: because this model-covariate is a construction we invent a new column
5329: ncovcol + k1
5330: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5331: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5332: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5333: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5334: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5335: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5336: k2=k2+2;
5337: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5338: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5339: for (i=1; i<=lastobs;i++){
5340: /* Computes the new covariate which is a product of
5341: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5342: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5343: }
5344: } /* End age is not in the model */
5345: } /* End if model includes a product */
5346: else { /* no more sum */
5347: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5348: /* scanf("%d",i);*/
5349: cutl(strd,strc,strb,'V');
5350: ks++; /**< Number of simple covariates */
5351: cptcovn++;
5352: Tvar[k]=atoi(strd);
5353: }
5354: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5355: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5356: scanf("%d",i);*/
5357: } /* end of loop + */
5358: } /* end model */
5359:
5360: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5361: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5362:
5363: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5364: printf("cptcovprod=%d ", cptcovprod);
5365: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5366:
5367: scanf("%d ",i);*/
5368:
5369:
5370: return (0); /* with covar[new additional covariate if product] and Tage if age */
5371: /*endread:*/
5372: printf("Exiting decodemodel: ");
5373: return (1);
5374: }
5375:
5376: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5377: {
5378: int i, m;
5379:
5380: for (i=1; i<=imx; i++) {
5381: for(m=2; (m<= maxwav); m++) {
5382: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5383: anint[m][i]=9999;
5384: s[m][i]=-1;
5385: }
5386: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5387: *nberr = *nberr + 1;
5388: 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);
5389: 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);
5390: s[m][i]=-1;
5391: }
5392: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5393: (*nberr)++;
5394: 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]);
5395: 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]);
5396: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5397: }
5398: }
5399: }
5400:
5401: for (i=1; i<=imx; i++) {
5402: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5403: for(m=firstpass; (m<= lastpass); m++){
5404: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5405: if (s[m][i] >= nlstate+1) {
5406: if(agedc[i]>0){
5407: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5408: agev[m][i]=agedc[i];
5409: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5410: }else {
5411: if ((int)andc[i]!=9999){
5412: nbwarn++;
5413: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5414: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5415: agev[m][i]=-1;
5416: }
5417: }
5418: } /* agedc > 0 */
5419: }
5420: else if(s[m][i] !=9){ /* Standard case, age in fractional
5421: years but with the precision of a month */
5422: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5423: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5424: agev[m][i]=1;
5425: else if(agev[m][i] < *agemin){
5426: *agemin=agev[m][i];
5427: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5428: }
5429: else if(agev[m][i] >*agemax){
5430: *agemax=agev[m][i];
5431: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5432: }
5433: /*agev[m][i]=anint[m][i]-annais[i];*/
5434: /* agev[m][i] = age[i]+2*m;*/
5435: }
5436: else { /* =9 */
5437: agev[m][i]=1;
5438: s[m][i]=-1;
5439: }
5440: }
5441: else /*= 0 Unknown */
5442: agev[m][i]=1;
5443: }
5444:
5445: }
5446: for (i=1; i<=imx; i++) {
5447: for(m=firstpass; (m<=lastpass); m++){
5448: if (s[m][i] > (nlstate+ndeath)) {
5449: (*nberr)++;
5450: 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);
5451: 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);
5452: return 1;
5453: }
5454: }
5455: }
5456:
5457: /*for (i=1; i<=imx; i++){
5458: for (m=firstpass; (m<lastpass); m++){
5459: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5460: }
5461:
5462: }*/
5463:
5464:
5465: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5466: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5467:
5468: return (0);
5469: /* endread:*/
5470: printf("Exiting calandcheckages: ");
5471: return (1);
5472: }
5473:
5474: #if defined(_MSC_VER)
5475: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5476: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5477: //#include "stdafx.h"
5478: //#include <stdio.h>
5479: //#include <tchar.h>
5480: //#include <windows.h>
5481: //#include <iostream>
5482: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5483:
5484: LPFN_ISWOW64PROCESS fnIsWow64Process;
5485:
5486: BOOL IsWow64()
5487: {
5488: BOOL bIsWow64 = FALSE;
5489:
5490: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5491: // (HANDLE, PBOOL);
5492:
5493: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5494:
5495: HMODULE module = GetModuleHandle(_T("kernel32"));
5496: const char funcName[] = "IsWow64Process";
5497: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5498: GetProcAddress(module, funcName);
5499:
5500: if (NULL != fnIsWow64Process)
5501: {
5502: if (!fnIsWow64Process(GetCurrentProcess(),
5503: &bIsWow64))
5504: //throw std::exception("Unknown error");
5505: printf("Unknown error\n");
5506: }
5507: return bIsWow64 != FALSE;
5508: }
5509: #endif
5510:
5511: void syscompilerinfo()
5512: {
5513: /* #include "syscompilerinfo.h"*/
5514:
5515: #if defined __INTEL_COMPILER
5516: struct utsname sysInfo;
5517: #elif defined(__GNUC__)
5518: #include <gnu/libc-version.h> /* Only on gnu */
5519: struct utsname sysInfo;
5520: #endif
5521:
5522: #include <stdint.h>
5523: int cross = CROSS;
5524: if (cross){
5525: printf("Cross-");
5526: fprintf(ficlog,"Cross-");
5527: }
5528: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5529: #if defined(__clang__)
5530: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5531: #endif
5532: #if defined(__ICC) || defined(__INTEL_COMPILER)
5533: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5534: #endif
5535: #if defined(__GNUC__) || defined(__GNUG__)
5536: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5537: #endif
5538: #if defined(__HP_cc) || defined(__HP_aCC)
5539: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5540: #endif
5541: #if defined(__IBMC__) || defined(__IBMCPP__)
5542: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5543: #endif
5544: #if defined(_MSC_VER)
5545: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5546: #endif
5547: #if defined(__PGI)
5548: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5549: #endif
5550: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5551: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5552: #endif
5553: printf(" for ");fprintf(ficlog," for ");
5554:
5555: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5556: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5557: // Windows (x64 and x86)
5558: printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
5559: #elif __unix__ // all unices, not all compilers
5560: // Unix
5561: printf("Unix ");fprintf(ficlog,"Unix ");
5562: #elif __linux__
5563: // linux
5564: printf("linux ");fprintf(ficlog,"linux ");
5565: #elif __APPLE__
5566: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
5567: printf("Mac OS ");fprintf(ficlog,"Mac OS ");
5568: #endif
5569:
5570: /* __MINGW32__ */
5571: /* __CYGWIN__ */
5572: /* __MINGW64__ */
5573: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5574: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5575: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5576: /* _WIN64 // Defined for applications for Win64. */
5577: /* _M_X64 // Defined for compilations that target x64 processors. */
5578: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5579:
5580: #if UINTPTR_MAX == 0xffffffff
5581: printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
5582: #elif UINTPTR_MAX == 0xffffffffffffffff
5583: printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
5584: #else
5585: printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
5586: #endif
5587:
5588: #if defined(__GNUC__)
5589: # if defined(__GNUC_PATCHLEVEL__)
5590: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5591: + __GNUC_MINOR__ * 100 \
5592: + __GNUC_PATCHLEVEL__)
5593: # else
5594: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5595: + __GNUC_MINOR__ * 100)
5596: # endif
5597: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
5598: fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
5599:
5600: if (uname(&sysInfo) != -1) {
5601: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5602: fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5603: }
5604: else
5605: perror("uname() error");
5606: #ifndef __INTEL_COMPILER
5607: printf("GNU libc version: %s\n", gnu_get_libc_version());
5608: fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
5609: #endif
5610: #endif
5611:
5612: // void main()
5613: // {
5614: #if defined(_MSC_VER)
5615: if (IsWow64()){
5616: printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5617: fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
5618: }
5619: else{
5620: printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5621: frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
5622: }
5623: // printf("\nPress Enter to continue...");
5624: // getchar();
5625: // }
5626:
5627: #endif
5628:
5629:
5630: }
5631:
5632: /***********************************************/
5633: /**************** Main Program *****************/
5634: /***********************************************/
5635:
5636: int main(int argc, char *argv[])
5637: {
5638: #ifdef GSL
5639: const gsl_multimin_fminimizer_type *T;
5640: size_t iteri = 0, it;
5641: int rval = GSL_CONTINUE;
5642: int status = GSL_SUCCESS;
5643: double ssval;
5644: #endif
5645: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5646: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5647:
5648: int jj, ll, li, lj, lk;
5649: int numlinepar=0; /* Current linenumber of parameter file */
5650: int itimes;
5651: int NDIM=2;
5652: int vpopbased=0;
5653:
5654: char ca[32], cb[32];
5655: /* FILE *fichtm; *//* Html File */
5656: /* FILE *ficgp;*/ /*Gnuplot File */
5657: struct stat info;
5658: double agedeb;
5659: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5660:
5661: double fret;
5662: double dum; /* Dummy variable */
5663: double ***p3mat;
5664: double ***mobaverage;
5665:
5666: char line[MAXLINE];
5667: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5668: char pathr[MAXLINE], pathimach[MAXLINE];
5669: char *tok, *val; /* pathtot */
5670: int firstobs=1, lastobs=10;
5671: int c, h , cpt;
5672: int jl;
5673: int i1, j1, jk, stepsize;
5674: int *tab;
5675: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5676: int mobilav=0,popforecast=0;
5677: int hstepm, nhstepm;
5678: int agemortsup;
5679: float sumlpop=0.;
5680: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5681: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5682:
5683: double bage=0, fage=110, age, agelim, agebase;
5684: double ftolpl=FTOL;
5685: double **prlim;
5686: double ***param; /* Matrix of parameters */
5687: double *p;
5688: double **matcov; /* Matrix of covariance */
5689: double ***delti3; /* Scale */
5690: double *delti; /* Scale */
5691: double ***eij, ***vareij;
5692: double **varpl; /* Variances of prevalence limits by age */
5693: double *epj, vepp;
5694:
5695: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5696: double **ximort;
5697: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5698: int *dcwave;
5699:
5700: char z[1]="c";
5701:
5702: /*char *strt;*/
5703: char strtend[80];
5704:
5705:
5706: /* setlocale (LC_ALL, ""); */
5707: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5708: /* textdomain (PACKAGE); */
5709: /* setlocale (LC_CTYPE, ""); */
5710: /* setlocale (LC_MESSAGES, ""); */
5711:
5712: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5713: rstart_time = time(NULL);
5714: /* (void) gettimeofday(&start_time,&tzp);*/
5715: start_time = *localtime(&rstart_time);
5716: curr_time=start_time;
5717: /*tml = *localtime(&start_time.tm_sec);*/
5718: /* strcpy(strstart,asctime(&tml)); */
5719: strcpy(strstart,asctime(&start_time));
5720:
5721: /* printf("Localtime (at start)=%s",strstart); */
5722: /* tp.tm_sec = tp.tm_sec +86400; */
5723: /* tm = *localtime(&start_time.tm_sec); */
5724: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5725: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5726: /* tmg.tm_hour=tmg.tm_hour + 1; */
5727: /* tp.tm_sec = mktime(&tmg); */
5728: /* strt=asctime(&tmg); */
5729: /* printf("Time(after) =%s",strstart); */
5730: /* (void) time (&time_value);
5731: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5732: * tm = *localtime(&time_value);
5733: * strstart=asctime(&tm);
5734: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5735: */
5736:
5737: nberr=0; /* Number of errors and warnings */
5738: nbwarn=0;
5739: getcwd(pathcd, size);
5740:
5741: printf("\n%s\n%s",version,fullversion);
5742: if(argc <=1){
5743: printf("\nEnter the parameter file name: ");
5744: fgets(pathr,FILENAMELENGTH,stdin);
5745: i=strlen(pathr);
5746: if(pathr[i-1]=='\n')
5747: pathr[i-1]='\0';
5748: i=strlen(pathr);
5749: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5750: pathr[i-1]='\0';
5751: for (tok = pathr; tok != NULL; ){
5752: printf("Pathr |%s|\n",pathr);
5753: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5754: printf("val= |%s| pathr=%s\n",val,pathr);
5755: strcpy (pathtot, val);
5756: if(pathr[0] == '\0') break; /* Dirty */
5757: }
5758: }
5759: else{
5760: strcpy(pathtot,argv[1]);
5761: }
5762: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5763: /*cygwin_split_path(pathtot,path,optionfile);
5764: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5765: /* cutv(path,optionfile,pathtot,'\\');*/
5766:
5767: /* Split argv[0], imach program to get pathimach */
5768: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5769: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5770: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5771: /* strcpy(pathimach,argv[0]); */
5772: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5773: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5774: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5775: chdir(path); /* Can be a relative path */
5776: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5777: printf("Current directory %s!\n",pathcd);
5778: strcpy(command,"mkdir ");
5779: strcat(command,optionfilefiname);
5780: if((outcmd=system(command)) != 0){
5781: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5782: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5783: /* fclose(ficlog); */
5784: /* exit(1); */
5785: }
5786: /* if((imk=mkdir(optionfilefiname))<0){ */
5787: /* perror("mkdir"); */
5788: /* } */
5789:
5790: /*-------- arguments in the command line --------*/
5791:
5792: /* Log file */
5793: strcat(filelog, optionfilefiname);
5794: strcat(filelog,".log"); /* */
5795: if((ficlog=fopen(filelog,"w"))==NULL) {
5796: printf("Problem with logfile %s\n",filelog);
5797: goto end;
5798: }
5799: fprintf(ficlog,"Log filename:%s\n",filelog);
5800: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5801: fprintf(ficlog,"\nEnter the parameter file name: \n");
5802: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5803: path=%s \n\
5804: optionfile=%s\n\
5805: optionfilext=%s\n\
5806: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5807:
5808: syscompilerinfo();
5809:
5810: printf("Local time (at start):%s",strstart);
5811: fprintf(ficlog,"Local time (at start): %s",strstart);
5812: fflush(ficlog);
5813: /* (void) gettimeofday(&curr_time,&tzp); */
5814: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5815:
5816: /* */
5817: strcpy(fileres,"r");
5818: strcat(fileres, optionfilefiname);
5819: strcat(fileres,".txt"); /* Other files have txt extension */
5820:
5821: /*---------arguments file --------*/
5822:
5823: if((ficpar=fopen(optionfile,"r"))==NULL) {
5824: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5825: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5826: fflush(ficlog);
5827: /* goto end; */
5828: exit(70);
5829: }
5830:
5831:
5832:
5833: strcpy(filereso,"o");
5834: strcat(filereso,fileres);
5835: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5836: printf("Problem with Output resultfile: %s\n", filereso);
5837: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5838: fflush(ficlog);
5839: goto end;
5840: }
5841:
5842: /* Reads comments: lines beginning with '#' */
5843: numlinepar=0;
5844: while((c=getc(ficpar))=='#' && c!= EOF){
5845: ungetc(c,ficpar);
5846: fgets(line, MAXLINE, ficpar);
5847: numlinepar++;
5848: fputs(line,stdout);
5849: fputs(line,ficparo);
5850: fputs(line,ficlog);
5851: }
5852: ungetc(c,ficpar);
5853:
5854: 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);
5855: numlinepar++;
5856: 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);
5857: 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);
5858: 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);
5859: fflush(ficlog);
5860: while((c=getc(ficpar))=='#' && c!= EOF){
5861: ungetc(c,ficpar);
5862: fgets(line, MAXLINE, ficpar);
5863: numlinepar++;
5864: fputs(line, stdout);
5865: //puts(line);
5866: fputs(line,ficparo);
5867: fputs(line,ficlog);
5868: }
5869: ungetc(c,ficpar);
5870:
5871:
5872: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5873: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5874: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5875: v1+v2*age+v2*v3 makes cptcovn = 3
5876: */
5877: if (strlen(model)>1)
5878: 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*/
5879: else
5880: ncovmodel=2;
5881: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5882: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5883: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5884: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5885: 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);
5886: 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);
5887: fflush(stdout);
5888: fclose (ficlog);
5889: goto end;
5890: }
5891: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5892: delti=delti3[1][1];
5893: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5894: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5895: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5896: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5897: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5898: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5899: fclose (ficparo);
5900: fclose (ficlog);
5901: goto end;
5902: exit(0);
5903: }
5904: else if(mle==-3) {
5905: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5906: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5907: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5908: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5909: matcov=matrix(1,npar,1,npar);
5910: }
5911: else{
5912: /* Read guessed parameters */
5913: /* Reads comments: lines beginning with '#' */
5914: while((c=getc(ficpar))=='#' && c!= EOF){
5915: ungetc(c,ficpar);
5916: fgets(line, MAXLINE, ficpar);
5917: numlinepar++;
5918: fputs(line,stdout);
5919: fputs(line,ficparo);
5920: fputs(line,ficlog);
5921: }
5922: ungetc(c,ficpar);
5923:
5924: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5925: for(i=1; i <=nlstate; i++){
5926: j=0;
5927: for(jj=1; jj <=nlstate+ndeath; jj++){
5928: if(jj==i) continue;
5929: j++;
5930: fscanf(ficpar,"%1d%1d",&i1,&j1);
5931: if ((i1 != i) && (j1 != j)){
5932: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5933: It might be a problem of design; if ncovcol and the model are correct\n \
5934: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5935: exit(1);
5936: }
5937: fprintf(ficparo,"%1d%1d",i1,j1);
5938: if(mle==1)
5939: printf("%1d%1d",i,j);
5940: fprintf(ficlog,"%1d%1d",i,j);
5941: for(k=1; k<=ncovmodel;k++){
5942: fscanf(ficpar," %lf",¶m[i][j][k]);
5943: if(mle==1){
5944: printf(" %lf",param[i][j][k]);
5945: fprintf(ficlog," %lf",param[i][j][k]);
5946: }
5947: else
5948: fprintf(ficlog," %lf",param[i][j][k]);
5949: fprintf(ficparo," %lf",param[i][j][k]);
5950: }
5951: fscanf(ficpar,"\n");
5952: numlinepar++;
5953: if(mle==1)
5954: printf("\n");
5955: fprintf(ficlog,"\n");
5956: fprintf(ficparo,"\n");
5957: }
5958: }
5959: fflush(ficlog);
5960:
5961: /* Reads scales values */
5962: p=param[1][1];
5963:
5964: /* Reads comments: lines beginning with '#' */
5965: while((c=getc(ficpar))=='#' && c!= EOF){
5966: ungetc(c,ficpar);
5967: fgets(line, MAXLINE, ficpar);
5968: numlinepar++;
5969: fputs(line,stdout);
5970: fputs(line,ficparo);
5971: fputs(line,ficlog);
5972: }
5973: ungetc(c,ficpar);
5974:
5975: for(i=1; i <=nlstate; i++){
5976: for(j=1; j <=nlstate+ndeath-1; j++){
5977: fscanf(ficpar,"%1d%1d",&i1,&j1);
5978: if ( (i1-i) * (j1-j) != 0){
5979: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5980: exit(1);
5981: }
5982: printf("%1d%1d",i,j);
5983: fprintf(ficparo,"%1d%1d",i1,j1);
5984: fprintf(ficlog,"%1d%1d",i1,j1);
5985: for(k=1; k<=ncovmodel;k++){
5986: fscanf(ficpar,"%le",&delti3[i][j][k]);
5987: printf(" %le",delti3[i][j][k]);
5988: fprintf(ficparo," %le",delti3[i][j][k]);
5989: fprintf(ficlog," %le",delti3[i][j][k]);
5990: }
5991: fscanf(ficpar,"\n");
5992: numlinepar++;
5993: printf("\n");
5994: fprintf(ficparo,"\n");
5995: fprintf(ficlog,"\n");
5996: }
5997: }
5998: fflush(ficlog);
5999:
6000: /* Reads covariance matrix */
6001: delti=delti3[1][1];
6002:
6003:
6004: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6005:
6006: /* Reads comments: lines beginning with '#' */
6007: while((c=getc(ficpar))=='#' && c!= EOF){
6008: ungetc(c,ficpar);
6009: fgets(line, MAXLINE, ficpar);
6010: numlinepar++;
6011: fputs(line,stdout);
6012: fputs(line,ficparo);
6013: fputs(line,ficlog);
6014: }
6015: ungetc(c,ficpar);
6016:
6017: matcov=matrix(1,npar,1,npar);
6018: for(i=1; i <=npar; i++)
6019: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6020:
6021: for(i=1; i <=npar; i++){
6022: fscanf(ficpar,"%s",str);
6023: if(mle==1)
6024: printf("%s",str);
6025: fprintf(ficlog,"%s",str);
6026: fprintf(ficparo,"%s",str);
6027: for(j=1; j <=i; j++){
6028: fscanf(ficpar," %le",&matcov[i][j]);
6029: if(mle==1){
6030: printf(" %.5le",matcov[i][j]);
6031: }
6032: fprintf(ficlog," %.5le",matcov[i][j]);
6033: fprintf(ficparo," %.5le",matcov[i][j]);
6034: }
6035: fscanf(ficpar,"\n");
6036: numlinepar++;
6037: if(mle==1)
6038: printf("\n");
6039: fprintf(ficlog,"\n");
6040: fprintf(ficparo,"\n");
6041: }
6042: for(i=1; i <=npar; i++)
6043: for(j=i+1;j<=npar;j++)
6044: matcov[i][j]=matcov[j][i];
6045:
6046: if(mle==1)
6047: printf("\n");
6048: fprintf(ficlog,"\n");
6049:
6050: fflush(ficlog);
6051:
6052: /*-------- Rewriting parameter file ----------*/
6053: strcpy(rfileres,"r"); /* "Rparameterfile */
6054: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6055: strcat(rfileres,"."); /* */
6056: strcat(rfileres,optionfilext); /* Other files have txt extension */
6057: if((ficres =fopen(rfileres,"w"))==NULL) {
6058: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6059: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6060: }
6061: fprintf(ficres,"#%s\n",version);
6062: } /* End of mle != -3 */
6063:
6064:
6065: n= lastobs;
6066: num=lvector(1,n);
6067: moisnais=vector(1,n);
6068: annais=vector(1,n);
6069: moisdc=vector(1,n);
6070: andc=vector(1,n);
6071: agedc=vector(1,n);
6072: cod=ivector(1,n);
6073: weight=vector(1,n);
6074: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6075: mint=matrix(1,maxwav,1,n);
6076: anint=matrix(1,maxwav,1,n);
6077: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6078: tab=ivector(1,NCOVMAX);
6079: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6080:
6081: /* Reads data from file datafile */
6082: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6083: goto end;
6084:
6085: /* Calculation of the number of parameters from char model */
6086: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6087: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6088: k=3 V4 Tvar[k=3]= 4 (from V4)
6089: k=2 V1 Tvar[k=2]= 1 (from V1)
6090: k=1 Tvar[1]=2 (from V2)
6091: */
6092: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6093: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6094: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6095: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6096: */
6097: /* For model-covariate k tells which data-covariate to use but
6098: because this model-covariate is a construction we invent a new column
6099: ncovcol + k1
6100: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6101: Tvar[3=V1*V4]=4+1 etc */
6102: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6103: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6104: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6105: */
6106: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6107: 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
6108: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6109: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6110: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6111: 4 covariates (3 plus signs)
6112: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6113: */
6114:
6115: if(decodemodel(model, lastobs) == 1)
6116: goto end;
6117:
6118: if((double)(lastobs-imx)/(double)imx > 1.10){
6119: nbwarn++;
6120: 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);
6121: 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);
6122: }
6123: /* if(mle==1){*/
6124: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6125: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6126: }
6127:
6128: /*-calculation of age at interview from date of interview and age at death -*/
6129: agev=matrix(1,maxwav,1,imx);
6130:
6131: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6132: goto end;
6133:
6134:
6135: agegomp=(int)agemin;
6136: free_vector(moisnais,1,n);
6137: free_vector(annais,1,n);
6138: /* free_matrix(mint,1,maxwav,1,n);
6139: free_matrix(anint,1,maxwav,1,n);*/
6140: free_vector(moisdc,1,n);
6141: free_vector(andc,1,n);
6142: /* */
6143:
6144: wav=ivector(1,imx);
6145: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6146: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6147: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6148:
6149: /* Concatenates waves */
6150: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6151: /* */
6152:
6153: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6154:
6155: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6156: ncodemax[1]=1;
6157: Ndum =ivector(-1,NCOVMAX);
6158: if (ncovmodel > 2)
6159: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6160:
6161: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6162: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6163: h=0;
6164:
6165:
6166: /*if (cptcovn > 0) */
6167:
6168:
6169: m=pow(2,cptcoveff);
6170:
6171: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6172: 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 */
6173: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6174: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6175: h++;
6176: if (h>m)
6177: h=1;
6178: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6179: * h 1 2 3 4
6180: *______________________________
6181: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6182: * 2 2 1 1 1
6183: * 3 i=2 1 2 1 1
6184: * 4 2 2 1 1
6185: * 5 i=3 1 i=2 1 2 1
6186: * 6 2 1 2 1
6187: * 7 i=4 1 2 2 1
6188: * 8 2 2 2 1
6189: * 9 i=5 1 i=3 1 i=2 1 1
6190: * 10 2 1 1 1
6191: * 11 i=6 1 2 1 1
6192: * 12 2 2 1 1
6193: * 13 i=7 1 i=4 1 2 1
6194: * 14 2 1 2 1
6195: * 15 i=8 1 2 2 1
6196: * 16 2 2 2 1
6197: */
6198: codtab[h][k]=j;
6199: /*codtab[h][Tvar[k]]=j;*/
6200: 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]]);
6201: }
6202: }
6203: }
6204: }
6205: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6206: codtab[1][2]=1;codtab[2][2]=2; */
6207: /* for(i=1; i <=m ;i++){
6208: for(k=1; k <=cptcovn; k++){
6209: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6210: }
6211: printf("\n");
6212: }
6213: scanf("%d",i);*/
6214:
6215: free_ivector(Ndum,-1,NCOVMAX);
6216:
6217:
6218:
6219: /*------------ gnuplot -------------*/
6220: strcpy(optionfilegnuplot,optionfilefiname);
6221: if(mle==-3)
6222: strcat(optionfilegnuplot,"-mort");
6223: strcat(optionfilegnuplot,".gp");
6224:
6225: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6226: printf("Problem with file %s",optionfilegnuplot);
6227: }
6228: else{
6229: fprintf(ficgp,"\n# %s\n", version);
6230: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6231: //fprintf(ficgp,"set missing 'NaNq'\n");
6232: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6233: }
6234: /* fclose(ficgp);*/
6235: /*--------- index.htm --------*/
6236:
6237: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6238: if(mle==-3)
6239: strcat(optionfilehtm,"-mort");
6240: strcat(optionfilehtm,".htm");
6241: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6242: printf("Problem with %s \n",optionfilehtm);
6243: exit(0);
6244: }
6245:
6246: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6247: strcat(optionfilehtmcov,"-cov.htm");
6248: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6249: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6250: }
6251: else{
6252: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6253: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6254: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6255: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6256: }
6257:
6258: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6259: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6260: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6261: \n\
6262: <hr size=\"2\" color=\"#EC5E5E\">\
6263: <ul><li><h4>Parameter files</h4>\n\
6264: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6265: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6266: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6267: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6268: - Date and time at start: %s</ul>\n",\
6269: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6270: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6271: fileres,fileres,\
6272: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6273: fflush(fichtm);
6274:
6275: strcpy(pathr,path);
6276: strcat(pathr,optionfilefiname);
6277: chdir(optionfilefiname); /* Move to directory named optionfile */
6278:
6279: /* Calculates basic frequencies. Computes observed prevalence at single age
6280: and prints on file fileres'p'. */
6281: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6282:
6283: fprintf(fichtm,"\n");
6284: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6285: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6286: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6287: imx,agemin,agemax,jmin,jmax,jmean);
6288: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6289: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6290: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6291: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6292: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6293:
6294:
6295: /* For Powell, parameters are in a vector p[] starting at p[1]
6296: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6297: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6298:
6299: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6300:
6301: if (mle==-3){
6302: ximort=matrix(1,NDIM,1,NDIM);
6303: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6304: cens=ivector(1,n);
6305: ageexmed=vector(1,n);
6306: agecens=vector(1,n);
6307: dcwave=ivector(1,n);
6308:
6309: for (i=1; i<=imx; i++){
6310: dcwave[i]=-1;
6311: for (m=firstpass; m<=lastpass; m++)
6312: if (s[m][i]>nlstate) {
6313: dcwave[i]=m;
6314: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6315: break;
6316: }
6317: }
6318:
6319: for (i=1; i<=imx; i++) {
6320: if (wav[i]>0){
6321: ageexmed[i]=agev[mw[1][i]][i];
6322: j=wav[i];
6323: agecens[i]=1.;
6324:
6325: if (ageexmed[i]> 1 && wav[i] > 0){
6326: agecens[i]=agev[mw[j][i]][i];
6327: cens[i]= 1;
6328: }else if (ageexmed[i]< 1)
6329: cens[i]= -1;
6330: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6331: cens[i]=0 ;
6332: }
6333: else cens[i]=-1;
6334: }
6335:
6336: for (i=1;i<=NDIM;i++) {
6337: for (j=1;j<=NDIM;j++)
6338: ximort[i][j]=(i == j ? 1.0 : 0.0);
6339: }
6340:
6341: /*p[1]=0.0268; p[NDIM]=0.083;*/
6342: /*printf("%lf %lf", p[1], p[2]);*/
6343:
6344:
6345: #ifdef GSL
6346: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6347: #else
6348: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6349: #endif
6350: strcpy(filerespow,"pow-mort");
6351: strcat(filerespow,fileres);
6352: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6353: printf("Problem with resultfile: %s\n", filerespow);
6354: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6355: }
6356: #ifdef GSL
6357: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6358: #else
6359: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6360: #endif
6361: /* for (i=1;i<=nlstate;i++)
6362: for(j=1;j<=nlstate+ndeath;j++)
6363: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6364: */
6365: fprintf(ficrespow,"\n");
6366: #ifdef GSL
6367: /* gsl starts here */
6368: T = gsl_multimin_fminimizer_nmsimplex;
6369: gsl_multimin_fminimizer *sfm = NULL;
6370: gsl_vector *ss, *x;
6371: gsl_multimin_function minex_func;
6372:
6373: /* Initial vertex size vector */
6374: ss = gsl_vector_alloc (NDIM);
6375:
6376: if (ss == NULL){
6377: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6378: }
6379: /* Set all step sizes to 1 */
6380: gsl_vector_set_all (ss, 0.001);
6381:
6382: /* Starting point */
6383:
6384: x = gsl_vector_alloc (NDIM);
6385:
6386: if (x == NULL){
6387: gsl_vector_free(ss);
6388: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6389: }
6390:
6391: /* Initialize method and iterate */
6392: /* p[1]=0.0268; p[NDIM]=0.083; */
6393: /* gsl_vector_set(x, 0, 0.0268); */
6394: /* gsl_vector_set(x, 1, 0.083); */
6395: gsl_vector_set(x, 0, p[1]);
6396: gsl_vector_set(x, 1, p[2]);
6397:
6398: minex_func.f = &gompertz_f;
6399: minex_func.n = NDIM;
6400: minex_func.params = (void *)&p; /* ??? */
6401:
6402: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6403: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6404:
6405: printf("Iterations beginning .....\n\n");
6406: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6407:
6408: iteri=0;
6409: while (rval == GSL_CONTINUE){
6410: iteri++;
6411: status = gsl_multimin_fminimizer_iterate(sfm);
6412:
6413: if (status) printf("error: %s\n", gsl_strerror (status));
6414: fflush(0);
6415:
6416: if (status)
6417: break;
6418:
6419: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6420: ssval = gsl_multimin_fminimizer_size (sfm);
6421:
6422: if (rval == GSL_SUCCESS)
6423: printf ("converged to a local maximum at\n");
6424:
6425: printf("%5d ", iteri);
6426: for (it = 0; it < NDIM; it++){
6427: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6428: }
6429: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6430: }
6431:
6432: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6433:
6434: gsl_vector_free(x); /* initial values */
6435: gsl_vector_free(ss); /* inital step size */
6436: for (it=0; it<NDIM; it++){
6437: p[it+1]=gsl_vector_get(sfm->x,it);
6438: fprintf(ficrespow," %.12lf", p[it]);
6439: }
6440: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6441: #endif
6442: #ifdef POWELL
6443: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6444: #endif
6445: fclose(ficrespow);
6446:
6447: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6448:
6449: for(i=1; i <=NDIM; i++)
6450: for(j=i+1;j<=NDIM;j++)
6451: matcov[i][j]=matcov[j][i];
6452:
6453: printf("\nCovariance matrix\n ");
6454: for(i=1; i <=NDIM; i++) {
6455: for(j=1;j<=NDIM;j++){
6456: printf("%f ",matcov[i][j]);
6457: }
6458: printf("\n ");
6459: }
6460:
6461: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6462: for (i=1;i<=NDIM;i++)
6463: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6464:
6465: lsurv=vector(1,AGESUP);
6466: lpop=vector(1,AGESUP);
6467: tpop=vector(1,AGESUP);
6468: lsurv[agegomp]=100000;
6469:
6470: for (k=agegomp;k<=AGESUP;k++) {
6471: agemortsup=k;
6472: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6473: }
6474:
6475: for (k=agegomp;k<agemortsup;k++)
6476: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6477:
6478: for (k=agegomp;k<agemortsup;k++){
6479: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6480: sumlpop=sumlpop+lpop[k];
6481: }
6482:
6483: tpop[agegomp]=sumlpop;
6484: for (k=agegomp;k<(agemortsup-3);k++){
6485: /* tpop[k+1]=2;*/
6486: tpop[k+1]=tpop[k]-lpop[k];
6487: }
6488:
6489:
6490: printf("\nAge lx qx dx Lx Tx e(x)\n");
6491: for (k=agegomp;k<(agemortsup-2);k++)
6492: 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]);
6493:
6494:
6495: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6496: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6497:
6498: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6499: stepm, weightopt,\
6500: model,imx,p,matcov,agemortsup);
6501:
6502: free_vector(lsurv,1,AGESUP);
6503: free_vector(lpop,1,AGESUP);
6504: free_vector(tpop,1,AGESUP);
6505: #ifdef GSL
6506: free_ivector(cens,1,n);
6507: free_vector(agecens,1,n);
6508: free_ivector(dcwave,1,n);
6509: free_matrix(ximort,1,NDIM,1,NDIM);
6510: #endif
6511: } /* Endof if mle==-3 */
6512:
6513: else{ /* For mle >=1 */
6514: globpr=0;/* debug */
6515: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6516: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6517: for (k=1; k<=npar;k++)
6518: printf(" %d %8.5f",k,p[k]);
6519: printf("\n");
6520: globpr=1; /* to print the contributions */
6521: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6522: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6523: for (k=1; k<=npar;k++)
6524: printf(" %d %8.5f",k,p[k]);
6525: printf("\n");
6526: if(mle>=1){ /* Could be 1 or 2 */
6527: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6528: }
6529:
6530: /*--------- results files --------------*/
6531: 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);
6532:
6533:
6534: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6535: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6536: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6537: for(i=1,jk=1; i <=nlstate; i++){
6538: for(k=1; k <=(nlstate+ndeath); k++){
6539: if (k != i) {
6540: printf("%d%d ",i,k);
6541: fprintf(ficlog,"%d%d ",i,k);
6542: fprintf(ficres,"%1d%1d ",i,k);
6543: for(j=1; j <=ncovmodel; j++){
6544: printf("%lf ",p[jk]);
6545: fprintf(ficlog,"%lf ",p[jk]);
6546: fprintf(ficres,"%lf ",p[jk]);
6547: jk++;
6548: }
6549: printf("\n");
6550: fprintf(ficlog,"\n");
6551: fprintf(ficres,"\n");
6552: }
6553: }
6554: }
6555: if(mle!=0){
6556: /* Computing hessian and covariance matrix */
6557: ftolhess=ftol; /* Usually correct */
6558: hesscov(matcov, p, npar, delti, ftolhess, func);
6559: }
6560: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6561: printf("# Scales (for hessian or gradient estimation)\n");
6562: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6563: for(i=1,jk=1; i <=nlstate; i++){
6564: for(j=1; j <=nlstate+ndeath; j++){
6565: if (j!=i) {
6566: fprintf(ficres,"%1d%1d",i,j);
6567: printf("%1d%1d",i,j);
6568: fprintf(ficlog,"%1d%1d",i,j);
6569: for(k=1; k<=ncovmodel;k++){
6570: printf(" %.5e",delti[jk]);
6571: fprintf(ficlog," %.5e",delti[jk]);
6572: fprintf(ficres," %.5e",delti[jk]);
6573: jk++;
6574: }
6575: printf("\n");
6576: fprintf(ficlog,"\n");
6577: fprintf(ficres,"\n");
6578: }
6579: }
6580: }
6581:
6582: 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");
6583: if(mle>=1)
6584: 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");
6585: 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");
6586: /* # 121 Var(a12)\n\ */
6587: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6588: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6589: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6590: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6591: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6592: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6593: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6594:
6595:
6596: /* Just to have a covariance matrix which will be more understandable
6597: even is we still don't want to manage dictionary of variables
6598: */
6599: for(itimes=1;itimes<=2;itimes++){
6600: jj=0;
6601: for(i=1; i <=nlstate; i++){
6602: for(j=1; j <=nlstate+ndeath; j++){
6603: if(j==i) continue;
6604: for(k=1; k<=ncovmodel;k++){
6605: jj++;
6606: ca[0]= k+'a'-1;ca[1]='\0';
6607: if(itimes==1){
6608: if(mle>=1)
6609: printf("#%1d%1d%d",i,j,k);
6610: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6611: fprintf(ficres,"#%1d%1d%d",i,j,k);
6612: }else{
6613: if(mle>=1)
6614: printf("%1d%1d%d",i,j,k);
6615: fprintf(ficlog,"%1d%1d%d",i,j,k);
6616: fprintf(ficres,"%1d%1d%d",i,j,k);
6617: }
6618: ll=0;
6619: for(li=1;li <=nlstate; li++){
6620: for(lj=1;lj <=nlstate+ndeath; lj++){
6621: if(lj==li) continue;
6622: for(lk=1;lk<=ncovmodel;lk++){
6623: ll++;
6624: if(ll<=jj){
6625: cb[0]= lk +'a'-1;cb[1]='\0';
6626: if(ll<jj){
6627: if(itimes==1){
6628: if(mle>=1)
6629: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6630: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6631: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6632: }else{
6633: if(mle>=1)
6634: printf(" %.5e",matcov[jj][ll]);
6635: fprintf(ficlog," %.5e",matcov[jj][ll]);
6636: fprintf(ficres," %.5e",matcov[jj][ll]);
6637: }
6638: }else{
6639: if(itimes==1){
6640: if(mle>=1)
6641: printf(" Var(%s%1d%1d)",ca,i,j);
6642: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6643: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6644: }else{
6645: if(mle>=1)
6646: printf(" %.5e",matcov[jj][ll]);
6647: fprintf(ficlog," %.5e",matcov[jj][ll]);
6648: fprintf(ficres," %.5e",matcov[jj][ll]);
6649: }
6650: }
6651: }
6652: } /* end lk */
6653: } /* end lj */
6654: } /* end li */
6655: if(mle>=1)
6656: printf("\n");
6657: fprintf(ficlog,"\n");
6658: fprintf(ficres,"\n");
6659: numlinepar++;
6660: } /* end k*/
6661: } /*end j */
6662: } /* end i */
6663: } /* end itimes */
6664:
6665: fflush(ficlog);
6666: fflush(ficres);
6667:
6668: while((c=getc(ficpar))=='#' && c!= EOF){
6669: ungetc(c,ficpar);
6670: fgets(line, MAXLINE, ficpar);
6671: fputs(line,stdout);
6672: fputs(line,ficparo);
6673: }
6674: ungetc(c,ficpar);
6675:
6676: estepm=0;
6677: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6678: if (estepm==0 || estepm < stepm) estepm=stepm;
6679: if (fage <= 2) {
6680: bage = ageminpar;
6681: fage = agemaxpar;
6682: }
6683:
6684: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6685: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6686: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6687:
6688: while((c=getc(ficpar))=='#' && c!= EOF){
6689: ungetc(c,ficpar);
6690: fgets(line, MAXLINE, ficpar);
6691: fputs(line,stdout);
6692: fputs(line,ficparo);
6693: }
6694: ungetc(c,ficpar);
6695:
6696: 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);
6697: 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);
6698: 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);
6699: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6700: 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);
6701:
6702: while((c=getc(ficpar))=='#' && c!= EOF){
6703: ungetc(c,ficpar);
6704: fgets(line, MAXLINE, ficpar);
6705: fputs(line,stdout);
6706: fputs(line,ficparo);
6707: }
6708: ungetc(c,ficpar);
6709:
6710:
6711: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6712: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6713:
6714: fscanf(ficpar,"pop_based=%d\n",&popbased);
6715: fprintf(ficparo,"pop_based=%d\n",popbased);
6716: fprintf(ficres,"pop_based=%d\n",popbased);
6717:
6718: while((c=getc(ficpar))=='#' && c!= EOF){
6719: ungetc(c,ficpar);
6720: fgets(line, MAXLINE, ficpar);
6721: fputs(line,stdout);
6722: fputs(line,ficparo);
6723: }
6724: ungetc(c,ficpar);
6725:
6726: 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);
6727: 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);
6728: 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);
6729: 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);
6730: 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);
6731: /* day and month of proj2 are not used but only year anproj2.*/
6732:
6733:
6734:
6735: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6736: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6737:
6738: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6739: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6740:
6741: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6742: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6743: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6744:
6745: /*------------ free_vector -------------*/
6746: /* chdir(path); */
6747:
6748: free_ivector(wav,1,imx);
6749: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6750: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6751: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6752: free_lvector(num,1,n);
6753: free_vector(agedc,1,n);
6754: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6755: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6756: fclose(ficparo);
6757: fclose(ficres);
6758:
6759:
6760: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6761: #include "prevlim.h" /* Use ficrespl, ficlog */
6762: fclose(ficrespl);
6763:
6764: #ifdef FREEEXIT2
6765: #include "freeexit2.h"
6766: #endif
6767:
6768: /*------------- h Pij x at various ages ------------*/
6769: #include "hpijx.h"
6770: fclose(ficrespij);
6771:
6772: /*-------------- Variance of one-step probabilities---*/
6773: k=1;
6774: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6775:
6776:
6777: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6778: for(i=1;i<=AGESUP;i++)
6779: for(j=1;j<=NCOVMAX;j++)
6780: for(k=1;k<=NCOVMAX;k++)
6781: probs[i][j][k]=0.;
6782:
6783: /*---------- Forecasting ------------------*/
6784: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6785: if(prevfcast==1){
6786: /* if(stepm ==1){*/
6787: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6788: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6789: /* } */
6790: /* else{ */
6791: /* erreur=108; */
6792: /* 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); */
6793: /* 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); */
6794: /* } */
6795: }
6796:
6797:
6798: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6799:
6800: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6801: /* 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",\
6802: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6803: */
6804:
6805: if (mobilav!=0) {
6806: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6807: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6808: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6809: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6810: }
6811: }
6812:
6813:
6814: /*---------- Health expectancies, no variances ------------*/
6815:
6816: strcpy(filerese,"e");
6817: strcat(filerese,fileres);
6818: if((ficreseij=fopen(filerese,"w"))==NULL) {
6819: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6820: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6821: }
6822: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6823: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6824: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6825: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6826:
6827: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6828: fprintf(ficreseij,"\n#****** ");
6829: for(j=1;j<=cptcoveff;j++) {
6830: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6831: }
6832: fprintf(ficreseij,"******\n");
6833:
6834: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6835: oldm=oldms;savm=savms;
6836: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6837:
6838: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6839: /*}*/
6840: }
6841: fclose(ficreseij);
6842:
6843:
6844: /*---------- Health expectancies and variances ------------*/
6845:
6846:
6847: strcpy(filerest,"t");
6848: strcat(filerest,fileres);
6849: if((ficrest=fopen(filerest,"w"))==NULL) {
6850: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6851: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6852: }
6853: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6854: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6855:
6856:
6857: strcpy(fileresstde,"stde");
6858: strcat(fileresstde,fileres);
6859: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6860: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6861: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6862: }
6863: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6864: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6865:
6866: strcpy(filerescve,"cve");
6867: strcat(filerescve,fileres);
6868: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6869: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6870: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6871: }
6872: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6873: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6874:
6875: strcpy(fileresv,"v");
6876: strcat(fileresv,fileres);
6877: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6878: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6879: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6880: }
6881: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6882: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6883:
6884: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6885: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6886:
6887: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6888: fprintf(ficrest,"\n#****** ");
6889: for(j=1;j<=cptcoveff;j++)
6890: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6891: fprintf(ficrest,"******\n");
6892:
6893: fprintf(ficresstdeij,"\n#****** ");
6894: fprintf(ficrescveij,"\n#****** ");
6895: for(j=1;j<=cptcoveff;j++) {
6896: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6897: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6898: }
6899: fprintf(ficresstdeij,"******\n");
6900: fprintf(ficrescveij,"******\n");
6901:
6902: fprintf(ficresvij,"\n#****** ");
6903: for(j=1;j<=cptcoveff;j++)
6904: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6905: fprintf(ficresvij,"******\n");
6906:
6907: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6908: oldm=oldms;savm=savms;
6909: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6910: /*
6911: */
6912: /* goto endfree; */
6913:
6914: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6915: pstamp(ficrest);
6916:
6917:
6918: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6919: oldm=oldms;savm=savms; /* Segmentation fault */
6920: cptcod= 0; /* To be deleted */
6921: 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 */
6922: 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 ");
6923: if(vpopbased==1)
6924: 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);
6925: else
6926: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6927: fprintf(ficrest,"# Age e.. (std) ");
6928: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6929: fprintf(ficrest,"\n");
6930:
6931: epj=vector(1,nlstate+1);
6932: for(age=bage; age <=fage ;age++){
6933: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6934: if (vpopbased==1) {
6935: if(mobilav ==0){
6936: for(i=1; i<=nlstate;i++)
6937: prlim[i][i]=probs[(int)age][i][k];
6938: }else{ /* mobilav */
6939: for(i=1; i<=nlstate;i++)
6940: prlim[i][i]=mobaverage[(int)age][i][k];
6941: }
6942: }
6943:
6944: fprintf(ficrest," %4.0f",age);
6945: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6946: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6947: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6948: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6949: }
6950: epj[nlstate+1] +=epj[j];
6951: }
6952:
6953: for(i=1, vepp=0.;i <=nlstate;i++)
6954: for(j=1;j <=nlstate;j++)
6955: vepp += vareij[i][j][(int)age];
6956: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6957: for(j=1;j <=nlstate;j++){
6958: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6959: }
6960: fprintf(ficrest,"\n");
6961: }
6962: }
6963: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6964: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6965: free_vector(epj,1,nlstate+1);
6966: /*}*/
6967: }
6968: free_vector(weight,1,n);
6969: free_imatrix(Tvard,1,NCOVMAX,1,2);
6970: free_imatrix(s,1,maxwav+1,1,n);
6971: free_matrix(anint,1,maxwav,1,n);
6972: free_matrix(mint,1,maxwav,1,n);
6973: free_ivector(cod,1,n);
6974: free_ivector(tab,1,NCOVMAX);
6975: fclose(ficresstdeij);
6976: fclose(ficrescveij);
6977: fclose(ficresvij);
6978: fclose(ficrest);
6979: fclose(ficpar);
6980:
6981: /*------- Variance of period (stable) prevalence------*/
6982:
6983: strcpy(fileresvpl,"vpl");
6984: strcat(fileresvpl,fileres);
6985: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6986: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6987: exit(0);
6988: }
6989: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6990:
6991: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6992: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6993:
6994: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6995: fprintf(ficresvpl,"\n#****** ");
6996: for(j=1;j<=cptcoveff;j++)
6997: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6998: fprintf(ficresvpl,"******\n");
6999:
7000: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7001: oldm=oldms;savm=savms;
7002: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7003: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7004: /*}*/
7005: }
7006:
7007: fclose(ficresvpl);
7008:
7009: /*---------- End : free ----------------*/
7010: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7011: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7012: } /* mle==-3 arrives here for freeing */
7013: /* endfree:*/
7014: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7015: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7016: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7017: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7018: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7019: free_matrix(covar,0,NCOVMAX,1,n);
7020: free_matrix(matcov,1,npar,1,npar);
7021: /*free_vector(delti,1,npar);*/
7022: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7023: free_matrix(agev,1,maxwav,1,imx);
7024: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7025:
7026: free_ivector(ncodemax,1,NCOVMAX);
7027: free_ivector(Tvar,1,NCOVMAX);
7028: free_ivector(Tprod,1,NCOVMAX);
7029: free_ivector(Tvaraff,1,NCOVMAX);
7030: free_ivector(Tage,1,NCOVMAX);
7031:
7032: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7033: free_imatrix(codtab,1,100,1,10);
7034: fflush(fichtm);
7035: fflush(ficgp);
7036:
7037:
7038: if((nberr >0) || (nbwarn>0)){
7039: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7040: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7041: }else{
7042: printf("End of Imach\n");
7043: fprintf(ficlog,"End of Imach\n");
7044: }
7045: printf("See log file on %s\n",filelog);
7046: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7047: /*(void) gettimeofday(&end_time,&tzp);*/
7048: rend_time = time(NULL);
7049: end_time = *localtime(&rend_time);
7050: /* tml = *localtime(&end_time.tm_sec); */
7051: strcpy(strtend,asctime(&end_time));
7052: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7053: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7054: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7055:
7056: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7057: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7058: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7059: /* printf("Total time was %d uSec.\n", total_usecs);*/
7060: /* if(fileappend(fichtm,optionfilehtm)){ */
7061: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7062: fclose(fichtm);
7063: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7064: fclose(fichtmcov);
7065: fclose(ficgp);
7066: fclose(ficlog);
7067: /*------ End -----------*/
7068:
7069:
7070: printf("Before Current directory %s!\n",pathcd);
7071: if(chdir(pathcd) != 0)
7072: printf("Can't move to directory %s!\n",path);
7073: if(getcwd(pathcd,MAXLINE) > 0)
7074: printf("Current directory %s!\n",pathcd);
7075: /*strcat(plotcmd,CHARSEPARATOR);*/
7076: sprintf(plotcmd,"gnuplot");
7077: #ifdef _WIN32
7078: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7079: #endif
7080: if(!stat(plotcmd,&info)){
7081: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7082: if(!stat(getenv("GNUPLOTBIN"),&info)){
7083: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7084: }else
7085: strcpy(pplotcmd,plotcmd);
7086: #ifdef __unix
7087: strcpy(plotcmd,GNUPLOTPROGRAM);
7088: if(!stat(plotcmd,&info)){
7089: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7090: }else
7091: strcpy(pplotcmd,plotcmd);
7092: #endif
7093: }else
7094: strcpy(pplotcmd,plotcmd);
7095:
7096: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7097: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7098:
7099: if((outcmd=system(plotcmd)) != 0){
7100: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7101: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7102: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7103: if((outcmd=system(plotcmd)) != 0)
7104: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7105: }
7106: printf(" Successful, please wait...");
7107: while (z[0] != 'q') {
7108: /* chdir(path); */
7109: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7110: scanf("%s",z);
7111: /* if (z[0] == 'c') system("./imach"); */
7112: if (z[0] == 'e') {
7113: #ifdef __APPLE__
7114: sprintf(pplotcmd, "open %s", optionfilehtm);
7115: #elif __linux
7116: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7117: #else
7118: sprintf(pplotcmd, "%s", optionfilehtm);
7119: #endif
7120: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7121: system(pplotcmd);
7122: }
7123: else if (z[0] == 'g') system(plotcmd);
7124: else if (z[0] == 'q') exit(0);
7125: }
7126: end:
7127: while (z[0] != 'q') {
7128: printf("\nType q for exiting: ");
7129: scanf("%s",z);
7130: }
7131: }
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