Annotation of imach/src/imach.c, revision 1.148

1.148   ! brouard     1: /* $Id: imach.c,v 1.147 2014/06/16 10:33:11 brouard Exp $
1.126     brouard     2:   $State: Exp $
                      3:   $Log: imach.c,v $
1.148   ! brouard     4:   Revision 1.147  2014/06/16 10:33:11  brouard
        !             5:   *** empty log message ***
        !             6: 
1.147     brouard     7:   Revision 1.146  2014/06/16 10:20:28  brouard
                      8:   Summary: Merge
                      9:   Author: Brouard
                     10: 
                     11:   Merge, before building revised version.
                     12: 
1.146     brouard    13:   Revision 1.145  2014/06/10 21:23:15  brouard
                     14:   Summary: Debugging with valgrind
                     15:   Author: Nicolas Brouard
                     16: 
                     17:   Lot of changes in order to output the results with some covariates
                     18:   After the Edimburgh REVES conference 2014, it seems mandatory to
                     19:   improve the code.
                     20:   No more memory valgrind error but a lot has to be done in order to
                     21:   continue the work of splitting the code into subroutines.
                     22:   Also, decodemodel has been improved. Tricode is still not
                     23:   optimal. nbcode should be improved. Documentation has been added in
                     24:   the source code.
                     25: 
1.144     brouard    26:   Revision 1.143  2014/01/26 09:45:38  brouard
                     27:   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
                     28: 
                     29:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                     30:   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
                     31: 
1.143     brouard    32:   Revision 1.142  2014/01/26 03:57:36  brouard
                     33:   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
                     34: 
                     35:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                     36: 
1.142     brouard    37:   Revision 1.141  2014/01/26 02:42:01  brouard
                     38:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                     39: 
1.141     brouard    40:   Revision 1.140  2011/09/02 10:37:54  brouard
                     41:   Summary: times.h is ok with mingw32 now.
                     42: 
1.140     brouard    43:   Revision 1.139  2010/06/14 07:50:17  brouard
                     44:   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
                     45:   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
                     46: 
1.139     brouard    47:   Revision 1.138  2010/04/30 18:19:40  brouard
                     48:   *** empty log message ***
                     49: 
1.138     brouard    50:   Revision 1.137  2010/04/29 18:11:38  brouard
                     51:   (Module): Checking covariates for more complex models
                     52:   than V1+V2. A lot of change to be done. Unstable.
                     53: 
1.137     brouard    54:   Revision 1.136  2010/04/26 20:30:53  brouard
                     55:   (Module): merging some libgsl code. Fixing computation
                     56:   of likelione (using inter/intrapolation if mle = 0) in order to
                     57:   get same likelihood as if mle=1.
                     58:   Some cleaning of code and comments added.
                     59: 
1.136     brouard    60:   Revision 1.135  2009/10/29 15:33:14  brouard
                     61:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                     62: 
1.135     brouard    63:   Revision 1.134  2009/10/29 13:18:53  brouard
                     64:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                     65: 
1.134     brouard    66:   Revision 1.133  2009/07/06 10:21:25  brouard
                     67:   just nforces
                     68: 
1.133     brouard    69:   Revision 1.132  2009/07/06 08:22:05  brouard
                     70:   Many tings
                     71: 
1.132     brouard    72:   Revision 1.131  2009/06/20 16:22:47  brouard
                     73:   Some dimensions resccaled
                     74: 
1.131     brouard    75:   Revision 1.130  2009/05/26 06:44:34  brouard
                     76:   (Module): Max Covariate is now set to 20 instead of 8. A
                     77:   lot of cleaning with variables initialized to 0. Trying to make
                     78:   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
                     79: 
1.130     brouard    80:   Revision 1.129  2007/08/31 13:49:27  lievre
                     81:   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
                     82: 
1.129     lievre     83:   Revision 1.128  2006/06/30 13:02:05  brouard
                     84:   (Module): Clarifications on computing e.j
                     85: 
1.128     brouard    86:   Revision 1.127  2006/04/28 18:11:50  brouard
                     87:   (Module): Yes the sum of survivors was wrong since
                     88:   imach-114 because nhstepm was no more computed in the age
                     89:   loop. Now we define nhstepma in the age loop.
                     90:   (Module): In order to speed up (in case of numerous covariates) we
                     91:   compute health expectancies (without variances) in a first step
                     92:   and then all the health expectancies with variances or standard
                     93:   deviation (needs data from the Hessian matrices) which slows the
                     94:   computation.
                     95:   In the future we should be able to stop the program is only health
                     96:   expectancies and graph are needed without standard deviations.
                     97: 
1.127     brouard    98:   Revision 1.126  2006/04/28 17:23:28  brouard
                     99:   (Module): Yes the sum of survivors was wrong since
                    100:   imach-114 because nhstepm was no more computed in the age
                    101:   loop. Now we define nhstepma in the age loop.
                    102:   Version 0.98h
                    103: 
1.126     brouard   104:   Revision 1.125  2006/04/04 15:20:31  lievre
                    105:   Errors in calculation of health expectancies. Age was not initialized.
                    106:   Forecasting file added.
                    107: 
                    108:   Revision 1.124  2006/03/22 17:13:53  lievre
                    109:   Parameters are printed with %lf instead of %f (more numbers after the comma).
                    110:   The log-likelihood is printed in the log file
                    111: 
                    112:   Revision 1.123  2006/03/20 10:52:43  brouard
                    113:   * imach.c (Module): <title> changed, corresponds to .htm file
                    114:   name. <head> headers where missing.
                    115: 
                    116:   * imach.c (Module): Weights can have a decimal point as for
                    117:   English (a comma might work with a correct LC_NUMERIC environment,
                    118:   otherwise the weight is truncated).
                    119:   Modification of warning when the covariates values are not 0 or
                    120:   1.
                    121:   Version 0.98g
                    122: 
                    123:   Revision 1.122  2006/03/20 09:45:41  brouard
                    124:   (Module): Weights can have a decimal point as for
                    125:   English (a comma might work with a correct LC_NUMERIC environment,
                    126:   otherwise the weight is truncated).
                    127:   Modification of warning when the covariates values are not 0 or
                    128:   1.
                    129:   Version 0.98g
                    130: 
                    131:   Revision 1.121  2006/03/16 17:45:01  lievre
                    132:   * imach.c (Module): Comments concerning covariates added
                    133: 
                    134:   * imach.c (Module): refinements in the computation of lli if
                    135:   status=-2 in order to have more reliable computation if stepm is
                    136:   not 1 month. Version 0.98f
                    137: 
                    138:   Revision 1.120  2006/03/16 15:10:38  lievre
                    139:   (Module): refinements in the computation of lli if
                    140:   status=-2 in order to have more reliable computation if stepm is
                    141:   not 1 month. Version 0.98f
                    142: 
                    143:   Revision 1.119  2006/03/15 17:42:26  brouard
                    144:   (Module): Bug if status = -2, the loglikelihood was
                    145:   computed as likelihood omitting the logarithm. Version O.98e
                    146: 
                    147:   Revision 1.118  2006/03/14 18:20:07  brouard
                    148:   (Module): varevsij Comments added explaining the second
                    149:   table of variances if popbased=1 .
                    150:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    151:   (Module): Function pstamp added
                    152:   (Module): Version 0.98d
                    153: 
                    154:   Revision 1.117  2006/03/14 17:16:22  brouard
                    155:   (Module): varevsij Comments added explaining the second
                    156:   table of variances if popbased=1 .
                    157:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    158:   (Module): Function pstamp added
                    159:   (Module): Version 0.98d
                    160: 
                    161:   Revision 1.116  2006/03/06 10:29:27  brouard
                    162:   (Module): Variance-covariance wrong links and
                    163:   varian-covariance of ej. is needed (Saito).
                    164: 
                    165:   Revision 1.115  2006/02/27 12:17:45  brouard
                    166:   (Module): One freematrix added in mlikeli! 0.98c
                    167: 
                    168:   Revision 1.114  2006/02/26 12:57:58  brouard
                    169:   (Module): Some improvements in processing parameter
                    170:   filename with strsep.
                    171: 
                    172:   Revision 1.113  2006/02/24 14:20:24  brouard
                    173:   (Module): Memory leaks checks with valgrind and:
                    174:   datafile was not closed, some imatrix were not freed and on matrix
                    175:   allocation too.
                    176: 
                    177:   Revision 1.112  2006/01/30 09:55:26  brouard
                    178:   (Module): Back to gnuplot.exe instead of wgnuplot.exe
                    179: 
                    180:   Revision 1.111  2006/01/25 20:38:18  brouard
                    181:   (Module): Lots of cleaning and bugs added (Gompertz)
                    182:   (Module): Comments can be added in data file. Missing date values
                    183:   can be a simple dot '.'.
                    184: 
                    185:   Revision 1.110  2006/01/25 00:51:50  brouard
                    186:   (Module): Lots of cleaning and bugs added (Gompertz)
                    187: 
                    188:   Revision 1.109  2006/01/24 19:37:15  brouard
                    189:   (Module): Comments (lines starting with a #) are allowed in data.
                    190: 
                    191:   Revision 1.108  2006/01/19 18:05:42  lievre
                    192:   Gnuplot problem appeared...
                    193:   To be fixed
                    194: 
                    195:   Revision 1.107  2006/01/19 16:20:37  brouard
                    196:   Test existence of gnuplot in imach path
                    197: 
                    198:   Revision 1.106  2006/01/19 13:24:36  brouard
                    199:   Some cleaning and links added in html output
                    200: 
                    201:   Revision 1.105  2006/01/05 20:23:19  lievre
                    202:   *** empty log message ***
                    203: 
                    204:   Revision 1.104  2005/09/30 16:11:43  lievre
                    205:   (Module): sump fixed, loop imx fixed, and simplifications.
                    206:   (Module): If the status is missing at the last wave but we know
                    207:   that the person is alive, then we can code his/her status as -2
                    208:   (instead of missing=-1 in earlier versions) and his/her
                    209:   contributions to the likelihood is 1 - Prob of dying from last
                    210:   health status (= 1-p13= p11+p12 in the easiest case of somebody in
                    211:   the healthy state at last known wave). Version is 0.98
                    212: 
                    213:   Revision 1.103  2005/09/30 15:54:49  lievre
                    214:   (Module): sump fixed, loop imx fixed, and simplifications.
                    215: 
                    216:   Revision 1.102  2004/09/15 17:31:30  brouard
                    217:   Add the possibility to read data file including tab characters.
                    218: 
                    219:   Revision 1.101  2004/09/15 10:38:38  brouard
                    220:   Fix on curr_time
                    221: 
                    222:   Revision 1.100  2004/07/12 18:29:06  brouard
                    223:   Add version for Mac OS X. Just define UNIX in Makefile
                    224: 
                    225:   Revision 1.99  2004/06/05 08:57:40  brouard
                    226:   *** empty log message ***
                    227: 
                    228:   Revision 1.98  2004/05/16 15:05:56  brouard
                    229:   New version 0.97 . First attempt to estimate force of mortality
                    230:   directly from the data i.e. without the need of knowing the health
                    231:   state at each age, but using a Gompertz model: log u =a + b*age .
                    232:   This is the basic analysis of mortality and should be done before any
                    233:   other analysis, in order to test if the mortality estimated from the
                    234:   cross-longitudinal survey is different from the mortality estimated
                    235:   from other sources like vital statistic data.
                    236: 
                    237:   The same imach parameter file can be used but the option for mle should be -3.
                    238: 
1.133     brouard   239:   Agnès, who wrote this part of the code, tried to keep most of the
1.126     brouard   240:   former routines in order to include the new code within the former code.
                    241: 
                    242:   The output is very simple: only an estimate of the intercept and of
                    243:   the slope with 95% confident intervals.
                    244: 
                    245:   Current limitations:
                    246:   A) Even if you enter covariates, i.e. with the
                    247:   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
                    248:   B) There is no computation of Life Expectancy nor Life Table.
                    249: 
                    250:   Revision 1.97  2004/02/20 13:25:42  lievre
                    251:   Version 0.96d. Population forecasting command line is (temporarily)
                    252:   suppressed.
                    253: 
                    254:   Revision 1.96  2003/07/15 15:38:55  brouard
                    255:   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
                    256:   rewritten within the same printf. Workaround: many printfs.
                    257: 
                    258:   Revision 1.95  2003/07/08 07:54:34  brouard
                    259:   * imach.c (Repository):
                    260:   (Repository): Using imachwizard code to output a more meaningful covariance
                    261:   matrix (cov(a12,c31) instead of numbers.
                    262: 
                    263:   Revision 1.94  2003/06/27 13:00:02  brouard
                    264:   Just cleaning
                    265: 
                    266:   Revision 1.93  2003/06/25 16:33:55  brouard
                    267:   (Module): On windows (cygwin) function asctime_r doesn't
                    268:   exist so I changed back to asctime which exists.
                    269:   (Module): Version 0.96b
                    270: 
                    271:   Revision 1.92  2003/06/25 16:30:45  brouard
                    272:   (Module): On windows (cygwin) function asctime_r doesn't
                    273:   exist so I changed back to asctime which exists.
                    274: 
                    275:   Revision 1.91  2003/06/25 15:30:29  brouard
                    276:   * imach.c (Repository): Duplicated warning errors corrected.
                    277:   (Repository): Elapsed time after each iteration is now output. It
                    278:   helps to forecast when convergence will be reached. Elapsed time
                    279:   is stamped in powell.  We created a new html file for the graphs
                    280:   concerning matrix of covariance. It has extension -cov.htm.
                    281: 
                    282:   Revision 1.90  2003/06/24 12:34:15  brouard
                    283:   (Module): Some bugs corrected for windows. Also, when
                    284:   mle=-1 a template is output in file "or"mypar.txt with the design
                    285:   of the covariance matrix to be input.
                    286: 
                    287:   Revision 1.89  2003/06/24 12:30:52  brouard
                    288:   (Module): Some bugs corrected for windows. Also, when
                    289:   mle=-1 a template is output in file "or"mypar.txt with the design
                    290:   of the covariance matrix to be input.
                    291: 
                    292:   Revision 1.88  2003/06/23 17:54:56  brouard
                    293:   * 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.
                    294: 
                    295:   Revision 1.87  2003/06/18 12:26:01  brouard
                    296:   Version 0.96
                    297: 
                    298:   Revision 1.86  2003/06/17 20:04:08  brouard
                    299:   (Module): Change position of html and gnuplot routines and added
                    300:   routine fileappend.
                    301: 
                    302:   Revision 1.85  2003/06/17 13:12:43  brouard
                    303:   * imach.c (Repository): Check when date of death was earlier that
                    304:   current date of interview. It may happen when the death was just
                    305:   prior to the death. In this case, dh was negative and likelihood
                    306:   was wrong (infinity). We still send an "Error" but patch by
                    307:   assuming that the date of death was just one stepm after the
                    308:   interview.
                    309:   (Repository): Because some people have very long ID (first column)
                    310:   we changed int to long in num[] and we added a new lvector for
                    311:   memory allocation. But we also truncated to 8 characters (left
                    312:   truncation)
                    313:   (Repository): No more line truncation errors.
                    314: 
                    315:   Revision 1.84  2003/06/13 21:44:43  brouard
                    316:   * imach.c (Repository): Replace "freqsummary" at a correct
                    317:   place. It differs from routine "prevalence" which may be called
                    318:   many times. Probs is memory consuming and must be used with
                    319:   parcimony.
                    320:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
                    321: 
                    322:   Revision 1.83  2003/06/10 13:39:11  lievre
                    323:   *** empty log message ***
                    324: 
                    325:   Revision 1.82  2003/06/05 15:57:20  brouard
                    326:   Add log in  imach.c and  fullversion number is now printed.
                    327: 
                    328: */
                    329: /*
                    330:    Interpolated Markov Chain
                    331: 
                    332:   Short summary of the programme:
                    333:   
                    334:   This program computes Healthy Life Expectancies from
                    335:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
                    336:   first survey ("cross") where individuals from different ages are
                    337:   interviewed on their health status or degree of disability (in the
                    338:   case of a health survey which is our main interest) -2- at least a
                    339:   second wave of interviews ("longitudinal") which measure each change
                    340:   (if any) in individual health status.  Health expectancies are
                    341:   computed from the time spent in each health state according to a
                    342:   model. More health states you consider, more time is necessary to reach the
                    343:   Maximum Likelihood of the parameters involved in the model.  The
                    344:   simplest model is the multinomial logistic model where pij is the
                    345:   probability to be observed in state j at the second wave
                    346:   conditional to be observed in state i at the first wave. Therefore
                    347:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
                    348:   'age' is age and 'sex' is a covariate. If you want to have a more
                    349:   complex model than "constant and age", you should modify the program
                    350:   where the markup *Covariates have to be included here again* invites
                    351:   you to do it.  More covariates you add, slower the
                    352:   convergence.
                    353: 
                    354:   The advantage of this computer programme, compared to a simple
                    355:   multinomial logistic model, is clear when the delay between waves is not
                    356:   identical for each individual. Also, if a individual missed an
                    357:   intermediate interview, the information is lost, but taken into
                    358:   account using an interpolation or extrapolation.  
                    359: 
                    360:   hPijx is the probability to be observed in state i at age x+h
                    361:   conditional to the observed state i at age x. The delay 'h' can be
                    362:   split into an exact number (nh*stepm) of unobserved intermediate
                    363:   states. This elementary transition (by month, quarter,
                    364:   semester or year) is modelled as a multinomial logistic.  The hPx
                    365:   matrix is simply the matrix product of nh*stepm elementary matrices
                    366:   and the contribution of each individual to the likelihood is simply
                    367:   hPijx.
                    368: 
                    369:   Also this programme outputs the covariance matrix of the parameters but also
                    370:   of the life expectancies. It also computes the period (stable) prevalence. 
                    371:   
1.133     brouard   372:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                    373:            Institut national d'études démographiques, Paris.
1.126     brouard   374:   This software have been partly granted by Euro-REVES, a concerted action
                    375:   from the European Union.
                    376:   It is copyrighted identically to a GNU software product, ie programme and
                    377:   software can be distributed freely for non commercial use. Latest version
                    378:   can be accessed at http://euroreves.ined.fr/imach .
                    379: 
                    380:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
                    381:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
                    382:   
                    383:   **********************************************************************/
                    384: /*
                    385:   main
                    386:   read parameterfile
                    387:   read datafile
                    388:   concatwav
                    389:   freqsummary
                    390:   if (mle >= 1)
                    391:     mlikeli
                    392:   print results files
                    393:   if mle==1 
                    394:      computes hessian
                    395:   read end of parameter file: agemin, agemax, bage, fage, estepm
                    396:       begin-prev-date,...
                    397:   open gnuplot file
                    398:   open html file
1.145     brouard   399:   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
                    400:    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                    401:                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
                    402:     freexexit2 possible for memory heap.
                    403: 
                    404:   h Pij x                         | pij_nom  ficrestpij
                    405:    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
                    406:        1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
                    407:        1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
                    408: 
                    409:        1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
                    410:        1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
                    411:   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
                    412:    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
                    413:    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
                    414: 
1.126     brouard   415:   forecasting if prevfcast==1 prevforecast call prevalence()
                    416:   health expectancies
                    417:   Variance-covariance of DFLE
                    418:   prevalence()
                    419:    movingaverage()
                    420:   varevsij() 
                    421:   if popbased==1 varevsij(,popbased)
                    422:   total life expectancies
                    423:   Variance of period (stable) prevalence
                    424:  end
                    425: */
                    426: 
                    427: 
                    428: 
                    429:  
                    430: #include <math.h>
                    431: #include <stdio.h>
                    432: #include <stdlib.h>
                    433: #include <string.h>
                    434: #include <unistd.h>
                    435: 
                    436: #include <limits.h>
                    437: #include <sys/types.h>
                    438: #include <sys/stat.h>
                    439: #include <errno.h>
                    440: extern int errno;
                    441: 
1.141     brouard   442: #ifdef LINUX
1.126     brouard   443: #include <time.h>
                    444: #include "timeval.h"
1.141     brouard   445: #else
                    446: #include <sys/time.h>
                    447: #endif
1.126     brouard   448: 
1.136     brouard   449: #ifdef GSL
                    450: #include <gsl/gsl_errno.h>
                    451: #include <gsl/gsl_multimin.h>
                    452: #endif
                    453: 
1.126     brouard   454: /* #include <libintl.h> */
                    455: /* #define _(String) gettext (String) */
                    456: 
1.141     brouard   457: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126     brouard   458: 
                    459: #define GNUPLOTPROGRAM "gnuplot"
                    460: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
                    461: #define FILENAMELENGTH 132
                    462: 
                    463: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
                    464: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
                    465: 
1.144     brouard   466: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
                    467: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126     brouard   468: 
                    469: #define NINTERVMAX 8
1.144     brouard   470: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
                    471: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
                    472: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145     brouard   473: #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
1.126     brouard   474: #define MAXN 20000
1.144     brouard   475: #define YEARM 12. /**< Number of months per year */
1.126     brouard   476: #define AGESUP 130
                    477: #define AGEBASE 40
1.144     brouard   478: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
1.126     brouard   479: #ifdef UNIX
                    480: #define DIRSEPARATOR '/'
                    481: #define CHARSEPARATOR "/"
                    482: #define ODIRSEPARATOR '\\'
                    483: #else
                    484: #define DIRSEPARATOR '\\'
                    485: #define CHARSEPARATOR "\\"
                    486: #define ODIRSEPARATOR '/'
                    487: #endif
                    488: 
1.148   ! brouard   489: /* $Id: imach.c,v 1.147 2014/06/16 10:33:11 brouard Exp $ */
1.126     brouard   490: /* $State: Exp $ */
                    491: 
1.148   ! brouard   492: char version[]="Imach version 0.98nS, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
        !           493: char fullversion[]="$Revision: 1.147 $ $Date: 2014/06/16 10:33:11 $"; 
1.126     brouard   494: char strstart[80];
                    495: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130     brouard   496: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
1.133     brouard   497: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145     brouard   498: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
                    499: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
                    500: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
                    501: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
                    502: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
                    503: int cptcovprodnoage=0; /**< Number of covariate products without age */   
                    504: int cptcoveff=0; /* Total number of covariates to vary for printing results */
                    505: int cptcov=0; /* Working variable */
1.126     brouard   506: int npar=NPARMAX;
                    507: int nlstate=2; /* Number of live states */
                    508: int ndeath=1; /* Number of dead states */
1.130     brouard   509: int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126     brouard   510: int popbased=0;
                    511: 
                    512: int *wav; /* Number of waves for this individuual 0 is possible */
1.130     brouard   513: int maxwav=0; /* Maxim number of waves */
                    514: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
                    515: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
                    516: int gipmx=0, gsw=0; /* Global variables on the number of contributions 
1.126     brouard   517:                   to the likelihood and the sum of weights (done by funcone)*/
1.130     brouard   518: int mle=1, weightopt=0;
1.126     brouard   519: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
                    520: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
                    521: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
                    522:           * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130     brouard   523: double jmean=1; /* Mean space between 2 waves */
1.145     brouard   524: double **matprod2(); /* test */
1.126     brouard   525: double **oldm, **newm, **savm; /* Working pointers to matrices */
                    526: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136     brouard   527: /*FILE *fic ; */ /* Used in readdata only */
                    528: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126     brouard   529: FILE *ficlog, *ficrespow;
1.130     brouard   530: int globpr=0; /* Global variable for printing or not */
1.126     brouard   531: double fretone; /* Only one call to likelihood */
1.130     brouard   532: long ipmx=0; /* Number of contributions */
1.126     brouard   533: double sw; /* Sum of weights */
                    534: char filerespow[FILENAMELENGTH];
                    535: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
                    536: FILE *ficresilk;
                    537: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
                    538: FILE *ficresprobmorprev;
                    539: FILE *fichtm, *fichtmcov; /* Html File */
                    540: FILE *ficreseij;
                    541: char filerese[FILENAMELENGTH];
                    542: FILE *ficresstdeij;
                    543: char fileresstde[FILENAMELENGTH];
                    544: FILE *ficrescveij;
                    545: char filerescve[FILENAMELENGTH];
                    546: FILE  *ficresvij;
                    547: char fileresv[FILENAMELENGTH];
                    548: FILE  *ficresvpl;
                    549: char fileresvpl[FILENAMELENGTH];
                    550: char title[MAXLINE];
                    551: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
                    552: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
                    553: char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
                    554: char command[FILENAMELENGTH];
                    555: int  outcmd=0;
                    556: 
                    557: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
                    558: 
                    559: char filelog[FILENAMELENGTH]; /* Log file */
                    560: char filerest[FILENAMELENGTH];
                    561: char fileregp[FILENAMELENGTH];
                    562: char popfile[FILENAMELENGTH];
                    563: 
                    564: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
                    565: 
                    566: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
                    567: struct timezone tzp;
                    568: extern int gettimeofday();
                    569: struct tm tmg, tm, tmf, *gmtime(), *localtime();
                    570: long time_value;
                    571: extern long time();
                    572: char strcurr[80], strfor[80];
                    573: 
                    574: char *endptr;
                    575: long lval;
                    576: double dval;
                    577: 
                    578: #define NR_END 1
                    579: #define FREE_ARG char*
                    580: #define FTOL 1.0e-10
                    581: 
                    582: #define NRANSI 
                    583: #define ITMAX 200 
                    584: 
                    585: #define TOL 2.0e-4 
                    586: 
                    587: #define CGOLD 0.3819660 
                    588: #define ZEPS 1.0e-10 
                    589: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
                    590: 
                    591: #define GOLD 1.618034 
                    592: #define GLIMIT 100.0 
                    593: #define TINY 1.0e-20 
                    594: 
                    595: static double maxarg1,maxarg2;
                    596: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
                    597: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                    598:   
                    599: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
                    600: #define rint(a) floor(a+0.5)
                    601: 
                    602: static double sqrarg;
                    603: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
                    604: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                    605: int agegomp= AGEGOMP;
                    606: 
                    607: int imx; 
                    608: int stepm=1;
                    609: /* Stepm, step in month: minimum step interpolation*/
                    610: 
                    611: int estepm;
                    612: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                    613: 
                    614: int m,nb;
                    615: long *num;
                    616: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
                    617: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
                    618: double **pmmij, ***probs;
                    619: double *ageexmed,*agecens;
                    620: double dateintmean=0;
                    621: 
                    622: double *weight;
                    623: int **s; /* Status */
1.141     brouard   624: double *agedc;
1.145     brouard   625: double  **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141     brouard   626:                  * covar=matrix(0,NCOVMAX,1,n); 
                    627:                  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
                    628: double  idx; 
                    629: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145     brouard   630: int *Ndum; /** Freq of modality (tricode */
1.141     brouard   631: int **codtab; /**< codtab=imatrix(1,100,1,10); */
                    632: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126     brouard   633: double *lsurv, *lpop, *tpop;
                    634: 
1.143     brouard   635: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
                    636: double ftolhess; /**< Tolerance for computing hessian */
1.126     brouard   637: 
                    638: /**************** split *************************/
                    639: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
                    640: {
                    641:   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
                    642:      the name of the file (name), its extension only (ext) and its first part of the name (finame)
                    643:   */ 
                    644:   char *ss;                            /* pointer */
                    645:   int  l1, l2;                         /* length counters */
                    646: 
                    647:   l1 = strlen(path );                  /* length of path */
                    648:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                    649:   ss= strrchr( path, DIRSEPARATOR );           /* find last / */
                    650:   if ( ss == NULL ) {                  /* no directory, so determine current directory */
                    651:     strcpy( name, path );              /* we got the fullname name because no directory */
                    652:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                    653:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
                    654:     /* get current working directory */
                    655:     /*    extern  char* getcwd ( char *buf , int len);*/
                    656:     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
                    657:       return( GLOCK_ERROR_GETCWD );
                    658:     }
                    659:     /* got dirc from getcwd*/
                    660:     printf(" DIRC = %s \n",dirc);
                    661:   } else {                             /* strip direcotry from path */
                    662:     ss++;                              /* after this, the filename */
                    663:     l2 = strlen( ss );                 /* length of filename */
                    664:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                    665:     strcpy( name, ss );                /* save file name */
                    666:     strncpy( dirc, path, l1 - l2 );    /* now the directory */
                    667:     dirc[l1-l2] = 0;                   /* add zero */
                    668:     printf(" DIRC2 = %s \n",dirc);
                    669:   }
                    670:   /* We add a separator at the end of dirc if not exists */
                    671:   l1 = strlen( dirc );                 /* length of directory */
                    672:   if( dirc[l1-1] != DIRSEPARATOR ){
                    673:     dirc[l1] =  DIRSEPARATOR;
                    674:     dirc[l1+1] = 0; 
                    675:     printf(" DIRC3 = %s \n",dirc);
                    676:   }
                    677:   ss = strrchr( name, '.' );           /* find last / */
                    678:   if (ss >0){
                    679:     ss++;
                    680:     strcpy(ext,ss);                    /* save extension */
                    681:     l1= strlen( name);
                    682:     l2= strlen(ss)+1;
                    683:     strncpy( finame, name, l1-l2);
                    684:     finame[l1-l2]= 0;
                    685:   }
                    686: 
                    687:   return( 0 );                         /* we're done */
                    688: }
                    689: 
                    690: 
                    691: /******************************************/
                    692: 
                    693: void replace_back_to_slash(char *s, char*t)
                    694: {
                    695:   int i;
                    696:   int lg=0;
                    697:   i=0;
                    698:   lg=strlen(t);
                    699:   for(i=0; i<= lg; i++) {
                    700:     (s[i] = t[i]);
                    701:     if (t[i]== '\\') s[i]='/';
                    702:   }
                    703: }
                    704: 
1.132     brouard   705: char *trimbb(char *out, char *in)
1.137     brouard   706: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132     brouard   707:   char *s;
                    708:   s=out;
                    709:   while (*in != '\0'){
1.137     brouard   710:     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132     brouard   711:       in++;
                    712:     }
                    713:     *out++ = *in++;
                    714:   }
                    715:   *out='\0';
                    716:   return s;
                    717: }
                    718: 
1.145     brouard   719: char *cutl(char *blocc, char *alocc, char *in, char occ)
                    720: {
                    721:   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
                    722:      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                    723:      gives blocc="abcdef2ghi" and alocc="j".
                    724:      If occ is not found blocc is null and alocc is equal to in. Returns blocc
                    725:   */
                    726:   char *s, *t, *bl;
                    727:   t=in;s=in;
                    728:   while ((*in != occ) && (*in != '\0')){
                    729:     *alocc++ = *in++;
                    730:   }
                    731:   if( *in == occ){
                    732:     *(alocc)='\0';
                    733:     s=++in;
                    734:   }
                    735:  
                    736:   if (s == t) {/* occ not found */
                    737:     *(alocc-(in-s))='\0';
                    738:     in=s;
                    739:   }
                    740:   while ( *in != '\0'){
                    741:     *blocc++ = *in++;
                    742:   }
                    743: 
                    744:   *blocc='\0';
                    745:   return t;
                    746: }
1.137     brouard   747: char *cutv(char *blocc, char *alocc, char *in, char occ)
                    748: {
                    749:   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
                    750:      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                    751:      gives blocc="abcdef2ghi" and alocc="j".
                    752:      If occ is not found blocc is null and alocc is equal to in. Returns alocc
                    753:   */
                    754:   char *s, *t;
                    755:   t=in;s=in;
                    756:   while (*in != '\0'){
                    757:     while( *in == occ){
                    758:       *blocc++ = *in++;
                    759:       s=in;
                    760:     }
                    761:     *blocc++ = *in++;
                    762:   }
                    763:   if (s == t) /* occ not found */
                    764:     *(blocc-(in-s))='\0';
                    765:   else
                    766:     *(blocc-(in-s)-1)='\0';
                    767:   in=s;
                    768:   while ( *in != '\0'){
                    769:     *alocc++ = *in++;
                    770:   }
                    771: 
                    772:   *alocc='\0';
                    773:   return s;
                    774: }
                    775: 
1.126     brouard   776: int nbocc(char *s, char occ)
                    777: {
                    778:   int i,j=0;
                    779:   int lg=20;
                    780:   i=0;
                    781:   lg=strlen(s);
                    782:   for(i=0; i<= lg; i++) {
                    783:   if  (s[i] == occ ) j++;
                    784:   }
                    785:   return j;
                    786: }
                    787: 
1.137     brouard   788: /* void cutv(char *u,char *v, char*t, char occ) */
                    789: /* { */
                    790: /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
                    791: /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
                    792: /*      gives u="abcdef2ghi" and v="j" *\/ */
                    793: /*   int i,lg,j,p=0; */
                    794: /*   i=0; */
                    795: /*   lg=strlen(t); */
                    796: /*   for(j=0; j<=lg-1; j++) { */
                    797: /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
                    798: /*   } */
1.126     brouard   799: 
1.137     brouard   800: /*   for(j=0; j<p; j++) { */
                    801: /*     (u[j] = t[j]); */
                    802: /*   } */
                    803: /*      u[p]='\0'; */
1.126     brouard   804: 
1.137     brouard   805: /*    for(j=0; j<= lg; j++) { */
                    806: /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
                    807: /*   } */
                    808: /* } */
1.126     brouard   809: 
                    810: /********************** nrerror ********************/
                    811: 
                    812: void nrerror(char error_text[])
                    813: {
                    814:   fprintf(stderr,"ERREUR ...\n");
                    815:   fprintf(stderr,"%s\n",error_text);
                    816:   exit(EXIT_FAILURE);
                    817: }
                    818: /*********************** vector *******************/
                    819: double *vector(int nl, int nh)
                    820: {
                    821:   double *v;
                    822:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                    823:   if (!v) nrerror("allocation failure in vector");
                    824:   return v-nl+NR_END;
                    825: }
                    826: 
                    827: /************************ free vector ******************/
                    828: void free_vector(double*v, int nl, int nh)
                    829: {
                    830:   free((FREE_ARG)(v+nl-NR_END));
                    831: }
                    832: 
                    833: /************************ivector *******************************/
                    834: int *ivector(long nl,long nh)
                    835: {
                    836:   int *v;
                    837:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                    838:   if (!v) nrerror("allocation failure in ivector");
                    839:   return v-nl+NR_END;
                    840: }
                    841: 
                    842: /******************free ivector **************************/
                    843: void free_ivector(int *v, long nl, long nh)
                    844: {
                    845:   free((FREE_ARG)(v+nl-NR_END));
                    846: }
                    847: 
                    848: /************************lvector *******************************/
                    849: long *lvector(long nl,long nh)
                    850: {
                    851:   long *v;
                    852:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
                    853:   if (!v) nrerror("allocation failure in ivector");
                    854:   return v-nl+NR_END;
                    855: }
                    856: 
                    857: /******************free lvector **************************/
                    858: void free_lvector(long *v, long nl, long nh)
                    859: {
                    860:   free((FREE_ARG)(v+nl-NR_END));
                    861: }
                    862: 
                    863: /******************* imatrix *******************************/
                    864: int **imatrix(long nrl, long nrh, long ncl, long nch) 
                    865:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
                    866: { 
                    867:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                    868:   int **m; 
                    869:   
                    870:   /* allocate pointers to rows */ 
                    871:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
                    872:   if (!m) nrerror("allocation failure 1 in matrix()"); 
                    873:   m += NR_END; 
                    874:   m -= nrl; 
                    875:   
                    876:   
                    877:   /* allocate rows and set pointers to them */ 
                    878:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                    879:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
                    880:   m[nrl] += NR_END; 
                    881:   m[nrl] -= ncl; 
                    882:   
                    883:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
                    884:   
                    885:   /* return pointer to array of pointers to rows */ 
                    886:   return m; 
                    887: } 
                    888: 
                    889: /****************** free_imatrix *************************/
                    890: void free_imatrix(m,nrl,nrh,ncl,nch)
                    891:       int **m;
                    892:       long nch,ncl,nrh,nrl; 
                    893:      /* free an int matrix allocated by imatrix() */ 
                    894: { 
                    895:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                    896:   free((FREE_ARG) (m+nrl-NR_END)); 
                    897: } 
                    898: 
                    899: /******************* matrix *******************************/
                    900: double **matrix(long nrl, long nrh, long ncl, long nch)
                    901: {
                    902:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                    903:   double **m;
                    904: 
                    905:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                    906:   if (!m) nrerror("allocation failure 1 in matrix()");
                    907:   m += NR_END;
                    908:   m -= nrl;
                    909: 
                    910:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                    911:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                    912:   m[nrl] += NR_END;
                    913:   m[nrl] -= ncl;
                    914: 
                    915:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                    916:   return m;
1.145     brouard   917:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
                    918: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
                    919: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126     brouard   920:    */
                    921: }
                    922: 
                    923: /*************************free matrix ************************/
                    924: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                    925: {
                    926:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                    927:   free((FREE_ARG)(m+nrl-NR_END));
                    928: }
                    929: 
                    930: /******************* ma3x *******************************/
                    931: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
                    932: {
                    933:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
                    934:   double ***m;
                    935: 
                    936:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                    937:   if (!m) nrerror("allocation failure 1 in matrix()");
                    938:   m += NR_END;
                    939:   m -= nrl;
                    940: 
                    941:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                    942:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                    943:   m[nrl] += NR_END;
                    944:   m[nrl] -= ncl;
                    945: 
                    946:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                    947: 
                    948:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                    949:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                    950:   m[nrl][ncl] += NR_END;
                    951:   m[nrl][ncl] -= nll;
                    952:   for (j=ncl+1; j<=nch; j++) 
                    953:     m[nrl][j]=m[nrl][j-1]+nlay;
                    954:   
                    955:   for (i=nrl+1; i<=nrh; i++) {
                    956:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                    957:     for (j=ncl+1; j<=nch; j++) 
                    958:       m[i][j]=m[i][j-1]+nlay;
                    959:   }
                    960:   return m; 
                    961:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                    962:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
                    963:   */
                    964: }
                    965: 
                    966: /*************************free ma3x ************************/
                    967: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                    968: {
                    969:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                    970:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                    971:   free((FREE_ARG)(m+nrl-NR_END));
                    972: }
                    973: 
                    974: /*************** function subdirf ***********/
                    975: char *subdirf(char fileres[])
                    976: {
                    977:   /* Caution optionfilefiname is hidden */
                    978:   strcpy(tmpout,optionfilefiname);
                    979:   strcat(tmpout,"/"); /* Add to the right */
                    980:   strcat(tmpout,fileres);
                    981:   return tmpout;
                    982: }
                    983: 
                    984: /*************** function subdirf2 ***********/
                    985: char *subdirf2(char fileres[], char *preop)
                    986: {
                    987:   
                    988:   /* Caution optionfilefiname is hidden */
                    989:   strcpy(tmpout,optionfilefiname);
                    990:   strcat(tmpout,"/");
                    991:   strcat(tmpout,preop);
                    992:   strcat(tmpout,fileres);
                    993:   return tmpout;
                    994: }
                    995: 
                    996: /*************** function subdirf3 ***********/
                    997: char *subdirf3(char fileres[], char *preop, char *preop2)
                    998: {
                    999:   
                   1000:   /* Caution optionfilefiname is hidden */
                   1001:   strcpy(tmpout,optionfilefiname);
                   1002:   strcat(tmpout,"/");
                   1003:   strcat(tmpout,preop);
                   1004:   strcat(tmpout,preop2);
                   1005:   strcat(tmpout,fileres);
                   1006:   return tmpout;
                   1007: }
                   1008: 
                   1009: /***************** f1dim *************************/
                   1010: extern int ncom; 
                   1011: extern double *pcom,*xicom;
                   1012: extern double (*nrfunc)(double []); 
                   1013:  
                   1014: double f1dim(double x) 
                   1015: { 
                   1016:   int j; 
                   1017:   double f;
                   1018:   double *xt; 
                   1019:  
                   1020:   xt=vector(1,ncom); 
                   1021:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                   1022:   f=(*nrfunc)(xt); 
                   1023:   free_vector(xt,1,ncom); 
                   1024:   return f; 
                   1025: } 
                   1026: 
                   1027: /*****************brent *************************/
                   1028: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
                   1029: { 
                   1030:   int iter; 
                   1031:   double a,b,d,etemp;
                   1032:   double fu,fv,fw,fx;
                   1033:   double ftemp;
                   1034:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
                   1035:   double e=0.0; 
                   1036:  
                   1037:   a=(ax < cx ? ax : cx); 
                   1038:   b=(ax > cx ? ax : cx); 
                   1039:   x=w=v=bx; 
                   1040:   fw=fv=fx=(*f)(x); 
                   1041:   for (iter=1;iter<=ITMAX;iter++) { 
                   1042:     xm=0.5*(a+b); 
                   1043:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                   1044:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                   1045:     printf(".");fflush(stdout);
                   1046:     fprintf(ficlog,".");fflush(ficlog);
                   1047: #ifdef DEBUG
                   1048:     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);
                   1049:     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);
                   1050:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                   1051: #endif
                   1052:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                   1053:       *xmin=x; 
                   1054:       return fx; 
                   1055:     } 
                   1056:     ftemp=fu;
                   1057:     if (fabs(e) > tol1) { 
                   1058:       r=(x-w)*(fx-fv); 
                   1059:       q=(x-v)*(fx-fw); 
                   1060:       p=(x-v)*q-(x-w)*r; 
                   1061:       q=2.0*(q-r); 
                   1062:       if (q > 0.0) p = -p; 
                   1063:       q=fabs(q); 
                   1064:       etemp=e; 
                   1065:       e=d; 
                   1066:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
                   1067:        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                   1068:       else { 
                   1069:        d=p/q; 
                   1070:        u=x+d; 
                   1071:        if (u-a < tol2 || b-u < tol2) 
                   1072:          d=SIGN(tol1,xm-x); 
                   1073:       } 
                   1074:     } else { 
                   1075:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                   1076:     } 
                   1077:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                   1078:     fu=(*f)(u); 
                   1079:     if (fu <= fx) { 
                   1080:       if (u >= x) a=x; else b=x; 
                   1081:       SHFT(v,w,x,u) 
                   1082:        SHFT(fv,fw,fx,fu) 
                   1083:        } else { 
                   1084:          if (u < x) a=u; else b=u; 
                   1085:          if (fu <= fw || w == x) { 
                   1086:            v=w; 
                   1087:            w=u; 
                   1088:            fv=fw; 
                   1089:            fw=fu; 
                   1090:          } else if (fu <= fv || v == x || v == w) { 
                   1091:            v=u; 
                   1092:            fv=fu; 
                   1093:          } 
                   1094:        } 
                   1095:   } 
                   1096:   nrerror("Too many iterations in brent"); 
                   1097:   *xmin=x; 
                   1098:   return fx; 
                   1099: } 
                   1100: 
                   1101: /****************** mnbrak ***********************/
                   1102: 
                   1103: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                   1104:            double (*func)(double)) 
                   1105: { 
                   1106:   double ulim,u,r,q, dum;
                   1107:   double fu; 
                   1108:  
                   1109:   *fa=(*func)(*ax); 
                   1110:   *fb=(*func)(*bx); 
                   1111:   if (*fb > *fa) { 
                   1112:     SHFT(dum,*ax,*bx,dum) 
                   1113:       SHFT(dum,*fb,*fa,dum) 
                   1114:       } 
                   1115:   *cx=(*bx)+GOLD*(*bx-*ax); 
                   1116:   *fc=(*func)(*cx); 
                   1117:   while (*fb > *fc) { 
                   1118:     r=(*bx-*ax)*(*fb-*fc); 
                   1119:     q=(*bx-*cx)*(*fb-*fa); 
                   1120:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
                   1121:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
                   1122:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
                   1123:     if ((*bx-u)*(u-*cx) > 0.0) { 
                   1124:       fu=(*func)(u); 
                   1125:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
                   1126:       fu=(*func)(u); 
                   1127:       if (fu < *fc) { 
                   1128:        SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                   1129:          SHFT(*fb,*fc,fu,(*func)(u)) 
                   1130:          } 
                   1131:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                   1132:       u=ulim; 
                   1133:       fu=(*func)(u); 
                   1134:     } else { 
                   1135:       u=(*cx)+GOLD*(*cx-*bx); 
                   1136:       fu=(*func)(u); 
                   1137:     } 
                   1138:     SHFT(*ax,*bx,*cx,u) 
                   1139:       SHFT(*fa,*fb,*fc,fu) 
                   1140:       } 
                   1141: } 
                   1142: 
                   1143: /*************** linmin ************************/
                   1144: 
                   1145: int ncom; 
                   1146: double *pcom,*xicom;
                   1147: double (*nrfunc)(double []); 
                   1148:  
                   1149: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                   1150: { 
                   1151:   double brent(double ax, double bx, double cx, 
                   1152:               double (*f)(double), double tol, double *xmin); 
                   1153:   double f1dim(double x); 
                   1154:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                   1155:              double *fc, double (*func)(double)); 
                   1156:   int j; 
                   1157:   double xx,xmin,bx,ax; 
                   1158:   double fx,fb,fa;
                   1159:  
                   1160:   ncom=n; 
                   1161:   pcom=vector(1,n); 
                   1162:   xicom=vector(1,n); 
                   1163:   nrfunc=func; 
                   1164:   for (j=1;j<=n;j++) { 
                   1165:     pcom[j]=p[j]; 
                   1166:     xicom[j]=xi[j]; 
                   1167:   } 
                   1168:   ax=0.0; 
                   1169:   xx=1.0; 
                   1170:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
                   1171:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
                   1172: #ifdef DEBUG
                   1173:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                   1174:   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                   1175: #endif
                   1176:   for (j=1;j<=n;j++) { 
                   1177:     xi[j] *= xmin; 
                   1178:     p[j] += xi[j]; 
                   1179:   } 
                   1180:   free_vector(xicom,1,n); 
                   1181:   free_vector(pcom,1,n); 
                   1182: } 
                   1183: 
                   1184: char *asc_diff_time(long time_sec, char ascdiff[])
                   1185: {
                   1186:   long sec_left, days, hours, minutes;
                   1187:   days = (time_sec) / (60*60*24);
                   1188:   sec_left = (time_sec) % (60*60*24);
                   1189:   hours = (sec_left) / (60*60) ;
                   1190:   sec_left = (sec_left) %(60*60);
                   1191:   minutes = (sec_left) /60;
                   1192:   sec_left = (sec_left) % (60);
1.141     brouard  1193:   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
1.126     brouard  1194:   return ascdiff;
                   1195: }
                   1196: 
                   1197: /*************** powell ************************/
                   1198: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                   1199:            double (*func)(double [])) 
                   1200: { 
                   1201:   void linmin(double p[], double xi[], int n, double *fret, 
                   1202:              double (*func)(double [])); 
                   1203:   int i,ibig,j; 
                   1204:   double del,t,*pt,*ptt,*xit;
                   1205:   double fp,fptt;
                   1206:   double *xits;
                   1207:   int niterf, itmp;
                   1208: 
                   1209:   pt=vector(1,n); 
                   1210:   ptt=vector(1,n); 
                   1211:   xit=vector(1,n); 
                   1212:   xits=vector(1,n); 
                   1213:   *fret=(*func)(p); 
                   1214:   for (j=1;j<=n;j++) pt[j]=p[j]; 
                   1215:   for (*iter=1;;++(*iter)) { 
                   1216:     fp=(*fret); 
                   1217:     ibig=0; 
                   1218:     del=0.0; 
                   1219:     last_time=curr_time;
                   1220:     (void) gettimeofday(&curr_time,&tzp);
                   1221:     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
                   1222:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
                   1223: /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
                   1224:    for (i=1;i<=n;i++) {
                   1225:       printf(" %d %.12f",i, p[i]);
                   1226:       fprintf(ficlog," %d %.12lf",i, p[i]);
                   1227:       fprintf(ficrespow," %.12lf", p[i]);
                   1228:     }
                   1229:     printf("\n");
                   1230:     fprintf(ficlog,"\n");
                   1231:     fprintf(ficrespow,"\n");fflush(ficrespow);
                   1232:     if(*iter <=3){
                   1233:       tm = *localtime(&curr_time.tv_sec);
                   1234:       strcpy(strcurr,asctime(&tm));
                   1235: /*       asctime_r(&tm,strcurr); */
                   1236:       forecast_time=curr_time; 
                   1237:       itmp = strlen(strcurr);
                   1238:       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                   1239:        strcurr[itmp-1]='\0';
                   1240:       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                   1241:       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                   1242:       for(niterf=10;niterf<=30;niterf+=10){
                   1243:        forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                   1244:        tmf = *localtime(&forecast_time.tv_sec);
                   1245: /*     asctime_r(&tmf,strfor); */
                   1246:        strcpy(strfor,asctime(&tmf));
                   1247:        itmp = strlen(strfor);
                   1248:        if(strfor[itmp-1]=='\n')
                   1249:        strfor[itmp-1]='\0';
                   1250:        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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
                   1251:        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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
                   1252:       }
                   1253:     }
                   1254:     for (i=1;i<=n;i++) { 
                   1255:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
                   1256:       fptt=(*fret); 
                   1257: #ifdef DEBUG
                   1258:       printf("fret=%lf \n",*fret);
                   1259:       fprintf(ficlog,"fret=%lf \n",*fret);
                   1260: #endif
                   1261:       printf("%d",i);fflush(stdout);
                   1262:       fprintf(ficlog,"%d",i);fflush(ficlog);
                   1263:       linmin(p,xit,n,fret,func); 
                   1264:       if (fabs(fptt-(*fret)) > del) { 
                   1265:        del=fabs(fptt-(*fret)); 
                   1266:        ibig=i; 
                   1267:       } 
                   1268: #ifdef DEBUG
                   1269:       printf("%d %.12e",i,(*fret));
                   1270:       fprintf(ficlog,"%d %.12e",i,(*fret));
                   1271:       for (j=1;j<=n;j++) {
                   1272:        xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                   1273:        printf(" x(%d)=%.12e",j,xit[j]);
                   1274:        fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
                   1275:       }
                   1276:       for(j=1;j<=n;j++) {
                   1277:        printf(" p=%.12e",p[j]);
                   1278:        fprintf(ficlog," p=%.12e",p[j]);
                   1279:       }
                   1280:       printf("\n");
                   1281:       fprintf(ficlog,"\n");
                   1282: #endif
                   1283:     } 
                   1284:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
                   1285: #ifdef DEBUG
                   1286:       int k[2],l;
                   1287:       k[0]=1;
                   1288:       k[1]=-1;
                   1289:       printf("Max: %.12e",(*func)(p));
                   1290:       fprintf(ficlog,"Max: %.12e",(*func)(p));
                   1291:       for (j=1;j<=n;j++) {
                   1292:        printf(" %.12e",p[j]);
                   1293:        fprintf(ficlog," %.12e",p[j]);
                   1294:       }
                   1295:       printf("\n");
                   1296:       fprintf(ficlog,"\n");
                   1297:       for(l=0;l<=1;l++) {
                   1298:        for (j=1;j<=n;j++) {
                   1299:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                   1300:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   1301:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   1302:        }
                   1303:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   1304:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   1305:       }
                   1306: #endif
                   1307: 
                   1308: 
                   1309:       free_vector(xit,1,n); 
                   1310:       free_vector(xits,1,n); 
                   1311:       free_vector(ptt,1,n); 
                   1312:       free_vector(pt,1,n); 
                   1313:       return; 
                   1314:     } 
                   1315:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
                   1316:     for (j=1;j<=n;j++) { 
                   1317:       ptt[j]=2.0*p[j]-pt[j]; 
                   1318:       xit[j]=p[j]-pt[j]; 
                   1319:       pt[j]=p[j]; 
                   1320:     } 
                   1321:     fptt=(*func)(ptt); 
                   1322:     if (fptt < fp) { 
                   1323:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
                   1324:       if (t < 0.0) { 
                   1325:        linmin(p,xit,n,fret,func); 
                   1326:        for (j=1;j<=n;j++) { 
                   1327:          xi[j][ibig]=xi[j][n]; 
                   1328:          xi[j][n]=xit[j]; 
                   1329:        }
                   1330: #ifdef DEBUG
                   1331:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   1332:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   1333:        for(j=1;j<=n;j++){
                   1334:          printf(" %.12e",xit[j]);
                   1335:          fprintf(ficlog," %.12e",xit[j]);
                   1336:        }
                   1337:        printf("\n");
                   1338:        fprintf(ficlog,"\n");
                   1339: #endif
                   1340:       }
                   1341:     } 
                   1342:   } 
                   1343: } 
                   1344: 
                   1345: /**** Prevalence limit (stable or period prevalence)  ****************/
                   1346: 
                   1347: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
                   1348: {
                   1349:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
                   1350:      matrix by transitions matrix until convergence is reached */
                   1351: 
                   1352:   int i, ii,j,k;
                   1353:   double min, max, maxmin, maxmax,sumnew=0.;
1.145     brouard  1354:   /* double **matprod2(); */ /* test */
1.131     brouard  1355:   double **out, cov[NCOVMAX+1], **pmij();
1.126     brouard  1356:   double **newm;
                   1357:   double agefin, delaymax=50 ; /* Max number of years to converge */
                   1358: 
                   1359:   for (ii=1;ii<=nlstate+ndeath;ii++)
                   1360:     for (j=1;j<=nlstate+ndeath;j++){
                   1361:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1362:     }
                   1363: 
                   1364:    cov[1]=1.;
                   1365:  
                   1366:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   1367:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                   1368:     newm=savm;
                   1369:     /* Covariates have to be included here again */
1.138     brouard  1370:     cov[2]=agefin;
                   1371:     
                   1372:     for (k=1; k<=cptcovn;k++) {
                   1373:       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145     brouard  1374:       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138     brouard  1375:     }
1.145     brouard  1376:     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                   1377:     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
                   1378:     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138     brouard  1379:     
                   1380:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                   1381:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                   1382:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145     brouard  1383:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   1384:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142     brouard  1385:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138     brouard  1386:     
1.126     brouard  1387:     savm=oldm;
                   1388:     oldm=newm;
                   1389:     maxmax=0.;
                   1390:     for(j=1;j<=nlstate;j++){
                   1391:       min=1.;
                   1392:       max=0.;
                   1393:       for(i=1; i<=nlstate; i++) {
                   1394:        sumnew=0;
                   1395:        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                   1396:        prlim[i][j]= newm[i][j]/(1-sumnew);
1.145     brouard  1397:         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126     brouard  1398:        max=FMAX(max,prlim[i][j]);
                   1399:        min=FMIN(min,prlim[i][j]);
                   1400:       }
                   1401:       maxmin=max-min;
                   1402:       maxmax=FMAX(maxmax,maxmin);
                   1403:     }
                   1404:     if(maxmax < ftolpl){
                   1405:       return prlim;
                   1406:     }
                   1407:   }
                   1408: }
                   1409: 
                   1410: /*************** transition probabilities ***************/ 
                   1411: 
                   1412: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                   1413: {
1.138     brouard  1414:   /* According to parameters values stored in x and the covariate's values stored in cov,
                   1415:      computes the probability to be observed in state j being in state i by appying the
                   1416:      model to the ncovmodel covariates (including constant and age).
                   1417:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                   1418:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
                   1419:      ncth covariate in the global vector x is given by the formula:
                   1420:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
                   1421:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
                   1422:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
                   1423:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
                   1424:      Outputs ps[i][j] the probability to be observed in j being in j according to
                   1425:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
                   1426:   */
                   1427:   double s1, lnpijopii;
1.126     brouard  1428:   /*double t34;*/
                   1429:   int i,j,j1, nc, ii, jj;
                   1430: 
                   1431:     for(i=1; i<= nlstate; i++){
                   1432:       for(j=1; j<i;j++){
1.138     brouard  1433:        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   1434:          /*lnpijopii += param[i][j][nc]*cov[nc];*/
                   1435:          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                   1436: /*      printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126     brouard  1437:        }
1.138     brouard  1438:        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   1439: /*     printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126     brouard  1440:       }
                   1441:       for(j=i+1; j<=nlstate+ndeath;j++){
1.138     brouard  1442:        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   1443:          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                   1444:          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                   1445: /*       printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126     brouard  1446:        }
1.138     brouard  1447:        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126     brouard  1448:       }
                   1449:     }
                   1450:     
                   1451:     for(i=1; i<= nlstate; i++){
                   1452:       s1=0;
1.131     brouard  1453:       for(j=1; j<i; j++){
1.138     brouard  1454:        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131     brouard  1455:        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   1456:       }
                   1457:       for(j=i+1; j<=nlstate+ndeath; j++){
1.138     brouard  1458:        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131     brouard  1459:        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   1460:       }
1.138     brouard  1461:       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126     brouard  1462:       ps[i][i]=1./(s1+1.);
1.138     brouard  1463:       /* Computing other pijs */
1.126     brouard  1464:       for(j=1; j<i; j++)
                   1465:        ps[i][j]= exp(ps[i][j])*ps[i][i];
                   1466:       for(j=i+1; j<=nlstate+ndeath; j++)
                   1467:        ps[i][j]= exp(ps[i][j])*ps[i][i];
                   1468:       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   1469:     } /* end i */
                   1470:     
                   1471:     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   1472:       for(jj=1; jj<= nlstate+ndeath; jj++){
                   1473:        ps[ii][jj]=0;
                   1474:        ps[ii][ii]=1;
                   1475:       }
                   1476:     }
                   1477:     
1.145     brouard  1478:     
                   1479:     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
                   1480:     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
                   1481:     /*         printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
                   1482:     /*   } */
                   1483:     /*   printf("\n "); */
                   1484:     /* } */
                   1485:     /* printf("\n ");printf("%lf ",cov[2]);*/
                   1486:     /*
1.126     brouard  1487:       for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   1488:       goto end;*/
                   1489:     return ps;
                   1490: }
                   1491: 
                   1492: /**************** Product of 2 matrices ******************/
                   1493: 
1.145     brouard  1494: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126     brouard  1495: {
                   1496:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                   1497:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                   1498:   /* in, b, out are matrice of pointers which should have been initialized 
                   1499:      before: only the contents of out is modified. The function returns
                   1500:      a pointer to pointers identical to out */
1.145     brouard  1501:   int i, j, k;
1.126     brouard  1502:   for(i=nrl; i<= nrh; i++)
1.145     brouard  1503:     for(k=ncolol; k<=ncoloh; k++){
                   1504:       out[i][k]=0.;
                   1505:       for(j=ncl; j<=nch; j++)
                   1506:        out[i][k] +=in[i][j]*b[j][k];
                   1507:     }
1.126     brouard  1508:   return out;
                   1509: }
                   1510: 
                   1511: 
                   1512: /************* Higher Matrix Product ***************/
                   1513: 
                   1514: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                   1515: {
                   1516:   /* Computes the transition matrix starting at age 'age' over 
                   1517:      'nhstepm*hstepm*stepm' months (i.e. until
                   1518:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                   1519:      nhstepm*hstepm matrices. 
                   1520:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                   1521:      (typically every 2 years instead of every month which is too big 
                   1522:      for the memory).
                   1523:      Model is determined by parameters x and covariates have to be 
                   1524:      included manually here. 
                   1525: 
                   1526:      */
                   1527: 
                   1528:   int i, j, d, h, k;
1.131     brouard  1529:   double **out, cov[NCOVMAX+1];
1.126     brouard  1530:   double **newm;
                   1531: 
                   1532:   /* Hstepm could be zero and should return the unit matrix */
                   1533:   for (i=1;i<=nlstate+ndeath;i++)
                   1534:     for (j=1;j<=nlstate+ndeath;j++){
                   1535:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   1536:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   1537:     }
                   1538:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   1539:   for(h=1; h <=nhstepm; h++){
                   1540:     for(d=1; d <=hstepm; d++){
                   1541:       newm=savm;
                   1542:       /* Covariates have to be included here again */
                   1543:       cov[1]=1.;
                   1544:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131     brouard  1545:       for (k=1; k<=cptcovn;k++) 
                   1546:        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126     brouard  1547:       for (k=1; k<=cptcovage;k++)
                   1548:        cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145     brouard  1549:       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126     brouard  1550:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   1551: 
                   1552: 
                   1553:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   1554:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                   1555:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                   1556:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1557:       savm=oldm;
                   1558:       oldm=newm;
                   1559:     }
                   1560:     for(i=1; i<=nlstate+ndeath; i++)
                   1561:       for(j=1;j<=nlstate+ndeath;j++) {
                   1562:        po[i][j][h]=newm[i][j];
1.128     brouard  1563:        /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126     brouard  1564:       }
1.128     brouard  1565:     /*printf("h=%d ",h);*/
1.126     brouard  1566:   } /* end h */
1.128     brouard  1567: /*     printf("\n H=%d \n",h); */
1.126     brouard  1568:   return po;
                   1569: }
                   1570: 
                   1571: 
                   1572: /*************** log-likelihood *************/
                   1573: double func( double *x)
                   1574: {
                   1575:   int i, ii, j, k, mi, d, kk;
1.131     brouard  1576:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126     brouard  1577:   double **out;
                   1578:   double sw; /* Sum of weights */
                   1579:   double lli; /* Individual log likelihood */
                   1580:   int s1, s2;
                   1581:   double bbh, survp;
                   1582:   long ipmx;
                   1583:   /*extern weight */
                   1584:   /* We are differentiating ll according to initial status */
                   1585:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1586:   /*for(i=1;i<imx;i++) 
                   1587:     printf(" %d\n",s[4][i]);
                   1588:   */
                   1589:   cov[1]=1.;
                   1590: 
                   1591:   for(k=1; k<=nlstate; k++) ll[k]=0.;
                   1592: 
                   1593:   if(mle==1){
                   1594:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138     brouard  1595:       /* Computes the values of the ncovmodel covariates of the model
                   1596:         depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
                   1597:         Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                   1598:         to be observed in j being in i according to the model.
                   1599:        */
1.145     brouard  1600:       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
                   1601:        cov[2+k]=covar[Tvar[k]][i];
                   1602:       }
1.137     brouard  1603:       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
1.138     brouard  1604:         is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
1.137     brouard  1605:         has been calculated etc */
1.126     brouard  1606:       for(mi=1; mi<= wav[i]-1; mi++){
                   1607:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1608:          for (j=1;j<=nlstate+ndeath;j++){
                   1609:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1610:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1611:          }
                   1612:        for(d=0; d<dh[mi][i]; d++){
                   1613:          newm=savm;
                   1614:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1615:          for (kk=1; kk<=cptcovage;kk++) {
1.137     brouard  1616:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126     brouard  1617:          }
                   1618:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1619:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1620:          savm=oldm;
                   1621:          oldm=newm;
                   1622:        } /* end mult */
                   1623:       
                   1624:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   1625:        /* But now since version 0.9 we anticipate for bias at large stepm.
                   1626:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   1627:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   1628:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   1629:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   1630:         * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                   1631:         * probability in order to take into account the bias as a fraction of the way
                   1632:         * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   1633:         * -stepm/2 to stepm/2 .
                   1634:         * For stepm=1 the results are the same as for previous versions of Imach.
                   1635:         * For stepm > 1 the results are less biased than in previous versions. 
                   1636:         */
                   1637:        s1=s[mw[mi][i]][i];
                   1638:        s2=s[mw[mi+1][i]][i];
                   1639:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1640:        /* bias bh is positive if real duration
                   1641:         * is higher than the multiple of stepm and negative otherwise.
                   1642:         */
                   1643:        /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                   1644:        if( s2 > nlstate){ 
                   1645:          /* i.e. if s2 is a death state and if the date of death is known 
                   1646:             then the contribution to the likelihood is the probability to 
                   1647:             die between last step unit time and current  step unit time, 
                   1648:             which is also equal to probability to die before dh 
                   1649:             minus probability to die before dh-stepm . 
                   1650:             In version up to 0.92 likelihood was computed
                   1651:        as if date of death was unknown. Death was treated as any other
                   1652:        health state: the date of the interview describes the actual state
                   1653:        and not the date of a change in health state. The former idea was
                   1654:        to consider that at each interview the state was recorded
                   1655:        (healthy, disable or death) and IMaCh was corrected; but when we
                   1656:        introduced the exact date of death then we should have modified
                   1657:        the contribution of an exact death to the likelihood. This new
                   1658:        contribution is smaller and very dependent of the step unit
                   1659:        stepm. It is no more the probability to die between last interview
                   1660:        and month of death but the probability to survive from last
                   1661:        interview up to one month before death multiplied by the
                   1662:        probability to die within a month. Thanks to Chris
                   1663:        Jackson for correcting this bug.  Former versions increased
                   1664:        mortality artificially. The bad side is that we add another loop
                   1665:        which slows down the processing. The difference can be up to 10%
                   1666:        lower mortality.
                   1667:          */
                   1668:          lli=log(out[s1][s2] - savm[s1][s2]);
                   1669: 
                   1670: 
                   1671:        } else if  (s2==-2) {
                   1672:          for (j=1,survp=0. ; j<=nlstate; j++) 
                   1673:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   1674:          /*survp += out[s1][j]; */
                   1675:          lli= log(survp);
                   1676:        }
                   1677:        
                   1678:        else if  (s2==-4) { 
                   1679:          for (j=3,survp=0. ; j<=nlstate; j++)  
                   1680:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   1681:          lli= log(survp); 
                   1682:        } 
                   1683: 
                   1684:        else if  (s2==-5) { 
                   1685:          for (j=1,survp=0. ; j<=2; j++)  
                   1686:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   1687:          lli= log(survp); 
                   1688:        } 
                   1689:        
                   1690:        else{
                   1691:          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1692:          /*  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 */
                   1693:        } 
                   1694:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   1695:        /*if(lli ==000.0)*/
                   1696:        /*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); */
                   1697:        ipmx +=1;
                   1698:        sw += weight[i];
                   1699:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1700:       } /* end of wave */
                   1701:     } /* end of individual */
                   1702:   }  else if(mle==2){
                   1703:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1704:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1705:       for(mi=1; mi<= wav[i]-1; mi++){
                   1706:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1707:          for (j=1;j<=nlstate+ndeath;j++){
                   1708:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1709:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1710:          }
                   1711:        for(d=0; d<=dh[mi][i]; d++){
                   1712:          newm=savm;
                   1713:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1714:          for (kk=1; kk<=cptcovage;kk++) {
                   1715:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1716:          }
                   1717:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1718:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1719:          savm=oldm;
                   1720:          oldm=newm;
                   1721:        } /* end mult */
                   1722:       
                   1723:        s1=s[mw[mi][i]][i];
                   1724:        s2=s[mw[mi+1][i]][i];
                   1725:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1726:        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 */
                   1727:        ipmx +=1;
                   1728:        sw += weight[i];
                   1729:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1730:       } /* end of wave */
                   1731:     } /* end of individual */
                   1732:   }  else if(mle==3){  /* exponential inter-extrapolation */
                   1733:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1734:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1735:       for(mi=1; mi<= wav[i]-1; mi++){
                   1736:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1737:          for (j=1;j<=nlstate+ndeath;j++){
                   1738:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1739:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1740:          }
                   1741:        for(d=0; d<dh[mi][i]; d++){
                   1742:          newm=savm;
                   1743:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1744:          for (kk=1; kk<=cptcovage;kk++) {
                   1745:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1746:          }
                   1747:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1748:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1749:          savm=oldm;
                   1750:          oldm=newm;
                   1751:        } /* end mult */
                   1752:       
                   1753:        s1=s[mw[mi][i]][i];
                   1754:        s2=s[mw[mi+1][i]][i];
                   1755:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1756:        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 */
                   1757:        ipmx +=1;
                   1758:        sw += weight[i];
                   1759:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1760:       } /* end of wave */
                   1761:     } /* end of individual */
                   1762:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
                   1763:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1764:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1765:       for(mi=1; mi<= wav[i]-1; mi++){
                   1766:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1767:          for (j=1;j<=nlstate+ndeath;j++){
                   1768:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1769:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1770:          }
                   1771:        for(d=0; d<dh[mi][i]; d++){
                   1772:          newm=savm;
                   1773:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1774:          for (kk=1; kk<=cptcovage;kk++) {
                   1775:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1776:          }
                   1777:        
                   1778:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1779:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1780:          savm=oldm;
                   1781:          oldm=newm;
                   1782:        } /* end mult */
                   1783:       
                   1784:        s1=s[mw[mi][i]][i];
                   1785:        s2=s[mw[mi+1][i]][i];
                   1786:        if( s2 > nlstate){ 
                   1787:          lli=log(out[s1][s2] - savm[s1][s2]);
                   1788:        }else{
                   1789:          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   1790:        }
                   1791:        ipmx +=1;
                   1792:        sw += weight[i];
                   1793:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1794: /*     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]); */
                   1795:       } /* end of wave */
                   1796:     } /* end of individual */
                   1797:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   1798:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1799:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1800:       for(mi=1; mi<= wav[i]-1; mi++){
                   1801:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1802:          for (j=1;j<=nlstate+ndeath;j++){
                   1803:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1804:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1805:          }
                   1806:        for(d=0; d<dh[mi][i]; d++){
                   1807:          newm=savm;
                   1808:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1809:          for (kk=1; kk<=cptcovage;kk++) {
                   1810:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1811:          }
                   1812:        
                   1813:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1814:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1815:          savm=oldm;
                   1816:          oldm=newm;
                   1817:        } /* end mult */
                   1818:       
                   1819:        s1=s[mw[mi][i]][i];
                   1820:        s2=s[mw[mi+1][i]][i];
                   1821:        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   1822:        ipmx +=1;
                   1823:        sw += weight[i];
                   1824:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1825:        /*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]);*/
                   1826:       } /* end of wave */
                   1827:     } /* end of individual */
                   1828:   } /* End of if */
                   1829:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   1830:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   1831:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   1832:   return -l;
                   1833: }
                   1834: 
                   1835: /*************** log-likelihood *************/
                   1836: double funcone( double *x)
                   1837: {
                   1838:   /* Same as likeli but slower because of a lot of printf and if */
                   1839:   int i, ii, j, k, mi, d, kk;
1.131     brouard  1840:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126     brouard  1841:   double **out;
                   1842:   double lli; /* Individual log likelihood */
                   1843:   double llt;
                   1844:   int s1, s2;
                   1845:   double bbh, survp;
                   1846:   /*extern weight */
                   1847:   /* We are differentiating ll according to initial status */
                   1848:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1849:   /*for(i=1;i<imx;i++) 
                   1850:     printf(" %d\n",s[4][i]);
                   1851:   */
                   1852:   cov[1]=1.;
                   1853: 
                   1854:   for(k=1; k<=nlstate; k++) ll[k]=0.;
                   1855: 
                   1856:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1857:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1858:     for(mi=1; mi<= wav[i]-1; mi++){
                   1859:       for (ii=1;ii<=nlstate+ndeath;ii++)
                   1860:        for (j=1;j<=nlstate+ndeath;j++){
                   1861:          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1862:          savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1863:        }
                   1864:       for(d=0; d<dh[mi][i]; d++){
                   1865:        newm=savm;
                   1866:        cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1867:        for (kk=1; kk<=cptcovage;kk++) {
                   1868:          cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1869:        }
1.145     brouard  1870:        /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126     brouard  1871:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1872:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145     brouard  1873:        /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                   1874:        /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126     brouard  1875:        savm=oldm;
                   1876:        oldm=newm;
                   1877:       } /* end mult */
                   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 is positive if real duration
                   1883:        * is higher than the multiple of stepm and negative otherwise.
                   1884:        */
                   1885:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
                   1886:        lli=log(out[s1][s2] - savm[s1][s2]);
                   1887:       } else if  (s2==-2) {
                   1888:        for (j=1,survp=0. ; j<=nlstate; j++) 
                   1889:          survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   1890:        lli= log(survp);
                   1891:       }else if (mle==1){
                   1892:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1893:       } else if(mle==2){
                   1894:        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 */
                   1895:       } else if(mle==3){  /* exponential inter-extrapolation */
                   1896:        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 */
                   1897:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
                   1898:        lli=log(out[s1][s2]); /* Original formula */
1.136     brouard  1899:       } else{  /* mle=0 back to 1 */
                   1900:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1901:        /*lli=log(out[s1][s2]); */ /* Original formula */
1.126     brouard  1902:       } /* End of if */
                   1903:       ipmx +=1;
                   1904:       sw += weight[i];
                   1905:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132     brouard  1906:       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126     brouard  1907:       if(globpr){
1.141     brouard  1908:        fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126     brouard  1909:  %11.6f %11.6f %11.6f ", \
                   1910:                num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   1911:                2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                   1912:        for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   1913:          llt +=ll[k]*gipmx/gsw;
                   1914:          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   1915:        }
                   1916:        fprintf(ficresilk," %10.6f\n", -llt);
                   1917:       }
                   1918:     } /* end of wave */
                   1919:   } /* end of individual */
                   1920:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   1921:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   1922:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   1923:   if(globpr==0){ /* First time we count the contributions and weights */
                   1924:     gipmx=ipmx;
                   1925:     gsw=sw;
                   1926:   }
                   1927:   return -l;
                   1928: }
                   1929: 
                   1930: 
                   1931: /*************** function likelione ***********/
                   1932: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
                   1933: {
                   1934:   /* This routine should help understanding what is done with 
                   1935:      the selection of individuals/waves and
                   1936:      to check the exact contribution to the likelihood.
                   1937:      Plotting could be done.
                   1938:    */
                   1939:   int k;
                   1940: 
                   1941:   if(*globpri !=0){ /* Just counts and sums, no printings */
                   1942:     strcpy(fileresilk,"ilk"); 
                   1943:     strcat(fileresilk,fileres);
                   1944:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                   1945:       printf("Problem with resultfile: %s\n", fileresilk);
                   1946:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                   1947:     }
                   1948:     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");
                   1949:     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
                   1950:     /*         i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   1951:     for(k=1; k<=nlstate; k++) 
                   1952:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   1953:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
                   1954:   }
                   1955: 
                   1956:   *fretone=(*funcone)(p);
                   1957:   if(*globpri !=0){
                   1958:     fclose(ficresilk);
                   1959:     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
                   1960:     fflush(fichtm); 
                   1961:   } 
                   1962:   return;
                   1963: }
                   1964: 
                   1965: 
                   1966: /*********** Maximum Likelihood Estimation ***************/
                   1967: 
                   1968: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                   1969: {
                   1970:   int i,j, iter;
                   1971:   double **xi;
                   1972:   double fret;
                   1973:   double fretone; /* Only one call to likelihood */
                   1974:   /*  char filerespow[FILENAMELENGTH];*/
                   1975:   xi=matrix(1,npar,1,npar);
                   1976:   for (i=1;i<=npar;i++)
                   1977:     for (j=1;j<=npar;j++)
                   1978:       xi[i][j]=(i==j ? 1.0 : 0.0);
                   1979:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
                   1980:   strcpy(filerespow,"pow"); 
                   1981:   strcat(filerespow,fileres);
                   1982:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   1983:     printf("Problem with resultfile: %s\n", filerespow);
                   1984:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   1985:   }
                   1986:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   1987:   for (i=1;i<=nlstate;i++)
                   1988:     for(j=1;j<=nlstate+ndeath;j++)
                   1989:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   1990:   fprintf(ficrespow,"\n");
                   1991: 
                   1992:   powell(p,xi,npar,ftol,&iter,&fret,func);
                   1993: 
                   1994:   free_matrix(xi,1,npar,1,npar);
                   1995:   fclose(ficrespow);
                   1996:   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
                   1997:   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                   1998:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                   1999: 
                   2000: }
                   2001: 
                   2002: /**** Computes Hessian and covariance matrix ***/
                   2003: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                   2004: {
                   2005:   double  **a,**y,*x,pd;
                   2006:   double **hess;
                   2007:   int i, j,jk;
                   2008:   int *indx;
                   2009: 
                   2010:   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                   2011:   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                   2012:   void lubksb(double **a, int npar, int *indx, double b[]) ;
                   2013:   void ludcmp(double **a, int npar, int *indx, double *d) ;
                   2014:   double gompertz(double p[]);
                   2015:   hess=matrix(1,npar,1,npar);
                   2016: 
                   2017:   printf("\nCalculation of the hessian matrix. Wait...\n");
                   2018:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                   2019:   for (i=1;i<=npar;i++){
                   2020:     printf("%d",i);fflush(stdout);
                   2021:     fprintf(ficlog,"%d",i);fflush(ficlog);
                   2022:    
                   2023:      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                   2024:     
                   2025:     /*  printf(" %f ",p[i]);
                   2026:        printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
                   2027:   }
                   2028:   
                   2029:   for (i=1;i<=npar;i++) {
                   2030:     for (j=1;j<=npar;j++)  {
                   2031:       if (j>i) { 
                   2032:        printf(".%d%d",i,j);fflush(stdout);
                   2033:        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                   2034:        hess[i][j]=hessij(p,delti,i,j,func,npar);
                   2035:        
                   2036:        hess[j][i]=hess[i][j];    
                   2037:        /*printf(" %lf ",hess[i][j]);*/
                   2038:       }
                   2039:     }
                   2040:   }
                   2041:   printf("\n");
                   2042:   fprintf(ficlog,"\n");
                   2043: 
                   2044:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                   2045:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                   2046:   
                   2047:   a=matrix(1,npar,1,npar);
                   2048:   y=matrix(1,npar,1,npar);
                   2049:   x=vector(1,npar);
                   2050:   indx=ivector(1,npar);
                   2051:   for (i=1;i<=npar;i++)
                   2052:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   2053:   ludcmp(a,npar,indx,&pd);
                   2054: 
                   2055:   for (j=1;j<=npar;j++) {
                   2056:     for (i=1;i<=npar;i++) x[i]=0;
                   2057:     x[j]=1;
                   2058:     lubksb(a,npar,indx,x);
                   2059:     for (i=1;i<=npar;i++){ 
                   2060:       matcov[i][j]=x[i];
                   2061:     }
                   2062:   }
                   2063: 
                   2064:   printf("\n#Hessian matrix#\n");
                   2065:   fprintf(ficlog,"\n#Hessian matrix#\n");
                   2066:   for (i=1;i<=npar;i++) { 
                   2067:     for (j=1;j<=npar;j++) { 
                   2068:       printf("%.3e ",hess[i][j]);
                   2069:       fprintf(ficlog,"%.3e ",hess[i][j]);
                   2070:     }
                   2071:     printf("\n");
                   2072:     fprintf(ficlog,"\n");
                   2073:   }
                   2074: 
                   2075:   /* Recompute Inverse */
                   2076:   for (i=1;i<=npar;i++)
                   2077:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
                   2078:   ludcmp(a,npar,indx,&pd);
                   2079: 
                   2080:   /*  printf("\n#Hessian matrix recomputed#\n");
                   2081: 
                   2082:   for (j=1;j<=npar;j++) {
                   2083:     for (i=1;i<=npar;i++) x[i]=0;
                   2084:     x[j]=1;
                   2085:     lubksb(a,npar,indx,x);
                   2086:     for (i=1;i<=npar;i++){ 
                   2087:       y[i][j]=x[i];
                   2088:       printf("%.3e ",y[i][j]);
                   2089:       fprintf(ficlog,"%.3e ",y[i][j]);
                   2090:     }
                   2091:     printf("\n");
                   2092:     fprintf(ficlog,"\n");
                   2093:   }
                   2094:   */
                   2095: 
                   2096:   free_matrix(a,1,npar,1,npar);
                   2097:   free_matrix(y,1,npar,1,npar);
                   2098:   free_vector(x,1,npar);
                   2099:   free_ivector(indx,1,npar);
                   2100:   free_matrix(hess,1,npar,1,npar);
                   2101: 
                   2102: 
                   2103: }
                   2104: 
                   2105: /*************** hessian matrix ****************/
                   2106: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
                   2107: {
                   2108:   int i;
                   2109:   int l=1, lmax=20;
                   2110:   double k1,k2;
1.132     brouard  2111:   double p2[MAXPARM+1]; /* identical to x */
1.126     brouard  2112:   double res;
                   2113:   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   2114:   double fx;
                   2115:   int k=0,kmax=10;
                   2116:   double l1;
                   2117: 
                   2118:   fx=func(x);
                   2119:   for (i=1;i<=npar;i++) p2[i]=x[i];
1.145     brouard  2120:   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
1.126     brouard  2121:     l1=pow(10,l);
                   2122:     delts=delt;
                   2123:     for(k=1 ; k <kmax; k=k+1){
                   2124:       delt = delta*(l1*k);
                   2125:       p2[theta]=x[theta] +delt;
1.145     brouard  2126:       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
1.126     brouard  2127:       p2[theta]=x[theta]-delt;
                   2128:       k2=func(p2)-fx;
                   2129:       /*res= (k1-2.0*fx+k2)/delt/delt; */
                   2130:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   2131:       
1.132     brouard  2132: #ifdef DEBUGHESS
1.126     brouard  2133:       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);
                   2134:       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);
                   2135: #endif
                   2136:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   2137:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   2138:        k=kmax;
                   2139:       }
                   2140:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                   2141:        k=kmax; l=lmax*10.;
                   2142:       }
                   2143:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   2144:        delts=delt;
                   2145:       }
                   2146:     }
                   2147:   }
                   2148:   delti[theta]=delts;
                   2149:   return res; 
                   2150:   
                   2151: }
                   2152: 
                   2153: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
                   2154: {
                   2155:   int i;
                   2156:   int l=1, l1, lmax=20;
                   2157:   double k1,k2,k3,k4,res,fx;
1.132     brouard  2158:   double p2[MAXPARM+1];
1.126     brouard  2159:   int k;
                   2160: 
                   2161:   fx=func(x);
                   2162:   for (k=1; k<=2; k++) {
                   2163:     for (i=1;i<=npar;i++) p2[i]=x[i];
                   2164:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   2165:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   2166:     k1=func(p2)-fx;
                   2167:   
                   2168:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   2169:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   2170:     k2=func(p2)-fx;
                   2171:   
                   2172:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   2173:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   2174:     k3=func(p2)-fx;
                   2175:   
                   2176:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   2177:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   2178:     k4=func(p2)-fx;
                   2179:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   2180: #ifdef DEBUG
                   2181:     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);
                   2182:     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);
                   2183: #endif
                   2184:   }
                   2185:   return res;
                   2186: }
                   2187: 
                   2188: /************** Inverse of matrix **************/
                   2189: void ludcmp(double **a, int n, int *indx, double *d) 
                   2190: { 
                   2191:   int i,imax,j,k; 
                   2192:   double big,dum,sum,temp; 
                   2193:   double *vv; 
                   2194:  
                   2195:   vv=vector(1,n); 
                   2196:   *d=1.0; 
                   2197:   for (i=1;i<=n;i++) { 
                   2198:     big=0.0; 
                   2199:     for (j=1;j<=n;j++) 
                   2200:       if ((temp=fabs(a[i][j])) > big) big=temp; 
                   2201:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   2202:     vv[i]=1.0/big; 
                   2203:   } 
                   2204:   for (j=1;j<=n;j++) { 
                   2205:     for (i=1;i<j;i++) { 
                   2206:       sum=a[i][j]; 
                   2207:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   2208:       a[i][j]=sum; 
                   2209:     } 
                   2210:     big=0.0; 
                   2211:     for (i=j;i<=n;i++) { 
                   2212:       sum=a[i][j]; 
                   2213:       for (k=1;k<j;k++) 
                   2214:        sum -= a[i][k]*a[k][j]; 
                   2215:       a[i][j]=sum; 
                   2216:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   2217:        big=dum; 
                   2218:        imax=i; 
                   2219:       } 
                   2220:     } 
                   2221:     if (j != imax) { 
                   2222:       for (k=1;k<=n;k++) { 
                   2223:        dum=a[imax][k]; 
                   2224:        a[imax][k]=a[j][k]; 
                   2225:        a[j][k]=dum; 
                   2226:       } 
                   2227:       *d = -(*d); 
                   2228:       vv[imax]=vv[j]; 
                   2229:     } 
                   2230:     indx[j]=imax; 
                   2231:     if (a[j][j] == 0.0) a[j][j]=TINY; 
                   2232:     if (j != n) { 
                   2233:       dum=1.0/(a[j][j]); 
                   2234:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   2235:     } 
                   2236:   } 
                   2237:   free_vector(vv,1,n);  /* Doesn't work */
                   2238: ;
                   2239: } 
                   2240: 
                   2241: void lubksb(double **a, int n, int *indx, double b[]) 
                   2242: { 
                   2243:   int i,ii=0,ip,j; 
                   2244:   double sum; 
                   2245:  
                   2246:   for (i=1;i<=n;i++) { 
                   2247:     ip=indx[i]; 
                   2248:     sum=b[ip]; 
                   2249:     b[ip]=b[i]; 
                   2250:     if (ii) 
                   2251:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   2252:     else if (sum) ii=i; 
                   2253:     b[i]=sum; 
                   2254:   } 
                   2255:   for (i=n;i>=1;i--) { 
                   2256:     sum=b[i]; 
                   2257:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   2258:     b[i]=sum/a[i][i]; 
                   2259:   } 
                   2260: } 
                   2261: 
                   2262: void pstamp(FILE *fichier)
                   2263: {
                   2264:   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
                   2265: }
                   2266: 
                   2267: /************ Frequencies ********************/
                   2268: 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[])
                   2269: {  /* Some frequencies */
                   2270:   
1.130     brouard  2271:   int i, m, jk, k1,i1, j1, bool, z1,j;
1.126     brouard  2272:   int first;
                   2273:   double ***freq; /* Frequencies */
                   2274:   double *pp, **prop;
                   2275:   double pos,posprop, k2, dateintsum=0,k2cpt=0;
                   2276:   char fileresp[FILENAMELENGTH];
                   2277:   
                   2278:   pp=vector(1,nlstate);
                   2279:   prop=matrix(1,nlstate,iagemin,iagemax+3);
                   2280:   strcpy(fileresp,"p");
                   2281:   strcat(fileresp,fileres);
                   2282:   if((ficresp=fopen(fileresp,"w"))==NULL) {
                   2283:     printf("Problem with prevalence resultfile: %s\n", fileresp);
                   2284:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                   2285:     exit(0);
                   2286:   }
                   2287:   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
                   2288:   j1=0;
                   2289:   
                   2290:   j=cptcoveff;
                   2291:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   2292: 
                   2293:   first=1;
                   2294: 
1.145     brouard  2295:   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
                   2296:   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
                   2297:   /*    j1++;
                   2298: */
                   2299:   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126     brouard  2300:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                   2301:        scanf("%d", i);*/
                   2302:       for (i=-5; i<=nlstate+ndeath; i++)  
                   2303:        for (jk=-5; jk<=nlstate+ndeath; jk++)  
                   2304:          for(m=iagemin; m <= iagemax+3; m++)
                   2305:            freq[i][jk][m]=0;
1.143     brouard  2306:       
                   2307:       for (i=1; i<=nlstate; i++)  
                   2308:        for(m=iagemin; m <= iagemax+3; m++)
                   2309:          prop[i][m]=0;
1.126     brouard  2310:       
                   2311:       dateintsum=0;
                   2312:       k2cpt=0;
                   2313:       for (i=1; i<=imx; i++) {
                   2314:        bool=1;
1.144     brouard  2315:        if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                   2316:          for (z1=1; z1<=cptcoveff; z1++)       
                   2317:             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145     brouard  2318:                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144     brouard  2319:               bool=0;
1.145     brouard  2320:               /* 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", 
                   2321:                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   2322:                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144     brouard  2323:               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                   2324:             } 
1.126     brouard  2325:        }
1.144     brouard  2326:  
1.126     brouard  2327:        if (bool==1){
                   2328:          for(m=firstpass; m<=lastpass; m++){
                   2329:            k2=anint[m][i]+(mint[m][i]/12.);
                   2330:            /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                   2331:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   2332:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   2333:              if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   2334:              if (m<lastpass) {
                   2335:                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   2336:                freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                   2337:              }
                   2338:              
                   2339:              if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   2340:                dateintsum=dateintsum+k2;
                   2341:                k2cpt++;
                   2342:              }
                   2343:              /*}*/
                   2344:          }
                   2345:        }
1.145     brouard  2346:       } /* end i */
1.126     brouard  2347:        
                   2348:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                   2349:       pstamp(ficresp);
                   2350:       if  (cptcovn>0) {
                   2351:        fprintf(ficresp, "\n#********** Variable "); 
                   2352:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2353:        fprintf(ficresp, "**********\n#");
1.143     brouard  2354:        fprintf(ficlog, "\n#********** Variable "); 
                   2355:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2356:        fprintf(ficlog, "**********\n#");
1.126     brouard  2357:       }
                   2358:       for(i=1; i<=nlstate;i++) 
                   2359:        fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                   2360:       fprintf(ficresp, "\n");
                   2361:       
                   2362:       for(i=iagemin; i <= iagemax+3; i++){
                   2363:        if(i==iagemax+3){
                   2364:          fprintf(ficlog,"Total");
                   2365:        }else{
                   2366:          if(first==1){
                   2367:            first=0;
                   2368:            printf("See log file for details...\n");
                   2369:          }
                   2370:          fprintf(ficlog,"Age %d", i);
                   2371:        }
                   2372:        for(jk=1; jk <=nlstate ; jk++){
                   2373:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                   2374:            pp[jk] += freq[jk][m][i]; 
                   2375:        }
                   2376:        for(jk=1; jk <=nlstate ; jk++){
                   2377:          for(m=-1, pos=0; m <=0 ; m++)
                   2378:            pos += freq[jk][m][i];
                   2379:          if(pp[jk]>=1.e-10){
                   2380:            if(first==1){
1.132     brouard  2381:              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126     brouard  2382:            }
                   2383:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   2384:          }else{
                   2385:            if(first==1)
                   2386:              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   2387:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   2388:          }
                   2389:        }
                   2390: 
                   2391:        for(jk=1; jk <=nlstate ; jk++){
                   2392:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                   2393:            pp[jk] += freq[jk][m][i];
                   2394:        }       
                   2395:        for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                   2396:          pos += pp[jk];
                   2397:          posprop += prop[jk][i];
                   2398:        }
                   2399:        for(jk=1; jk <=nlstate ; jk++){
                   2400:          if(pos>=1.e-5){
                   2401:            if(first==1)
                   2402:              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   2403:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   2404:          }else{
                   2405:            if(first==1)
                   2406:              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   2407:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   2408:          }
                   2409:          if( i <= iagemax){
                   2410:            if(pos>=1.e-5){
                   2411:              fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                   2412:              /*probs[i][jk][j1]= pp[jk]/pos;*/
                   2413:              /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                   2414:            }
                   2415:            else
                   2416:              fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                   2417:          }
                   2418:        }
                   2419:        
                   2420:        for(jk=-1; jk <=nlstate+ndeath; jk++)
                   2421:          for(m=-1; m <=nlstate+ndeath; m++)
                   2422:            if(freq[jk][m][i] !=0 ) {
                   2423:            if(first==1)
                   2424:              printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                   2425:              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                   2426:            }
                   2427:        if(i <= iagemax)
                   2428:          fprintf(ficresp,"\n");
                   2429:        if(first==1)
                   2430:          printf("Others in log...\n");
                   2431:        fprintf(ficlog,"\n");
                   2432:       }
1.145     brouard  2433:       /*}*/
1.126     brouard  2434:   }
                   2435:   dateintmean=dateintsum/k2cpt; 
                   2436:  
                   2437:   fclose(ficresp);
                   2438:   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
                   2439:   free_vector(pp,1,nlstate);
                   2440:   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
                   2441:   /* End of Freq */
                   2442: }
                   2443: 
                   2444: /************ Prevalence ********************/
                   2445: 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)
                   2446: {  
                   2447:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   2448:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   2449:      We still use firstpass and lastpass as another selection.
                   2450:   */
                   2451:  
1.130     brouard  2452:   int i, m, jk, k1, i1, j1, bool, z1,j;
1.126     brouard  2453:   double ***freq; /* Frequencies */
                   2454:   double *pp, **prop;
                   2455:   double pos,posprop; 
                   2456:   double  y2; /* in fractional years */
                   2457:   int iagemin, iagemax;
1.145     brouard  2458:   int first; /** to stop verbosity which is redirected to log file */
1.126     brouard  2459: 
                   2460:   iagemin= (int) agemin;
                   2461:   iagemax= (int) agemax;
                   2462:   /*pp=vector(1,nlstate);*/
                   2463:   prop=matrix(1,nlstate,iagemin,iagemax+3); 
                   2464:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                   2465:   j1=0;
                   2466:   
1.145     brouard  2467:   /*j=cptcoveff;*/
1.126     brouard  2468:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   2469:   
1.145     brouard  2470:   first=1;
                   2471:   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
                   2472:     /*for(i1=1; i1<=ncodemax[k1];i1++){
                   2473:       j1++;*/
1.126     brouard  2474:       
                   2475:       for (i=1; i<=nlstate; i++)  
                   2476:        for(m=iagemin; m <= iagemax+3; m++)
                   2477:          prop[i][m]=0.0;
                   2478:      
                   2479:       for (i=1; i<=imx; i++) { /* Each individual */
                   2480:        bool=1;
                   2481:        if  (cptcovn>0) {
                   2482:          for (z1=1; z1<=cptcoveff; z1++) 
                   2483:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                   2484:              bool=0;
                   2485:        } 
                   2486:        if (bool==1) { 
                   2487:          for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                   2488:            y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   2489:            if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                   2490:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   2491:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   2492:              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); 
                   2493:              if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   2494:                /*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]]);*/
                   2495:                prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   2496:                prop[s[m][i]][iagemax+3] += weight[i]; 
                   2497:              } 
                   2498:            }
                   2499:          } /* end selection of waves */
                   2500:        }
                   2501:       }
                   2502:       for(i=iagemin; i <= iagemax+3; i++){  
                   2503:        for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   2504:          posprop += prop[jk][i]; 
                   2505:        } 
1.145     brouard  2506:        
1.126     brouard  2507:        for(jk=1; jk <=nlstate ; jk++){     
                   2508:          if( i <=  iagemax){ 
                   2509:            if(posprop>=1.e-5){ 
                   2510:              probs[i][jk][j1]= prop[jk][i]/posprop;
1.145     brouard  2511:            } else{
                   2512:              if(first==1){
                   2513:                first=0;
                   2514:                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]);
                   2515:              }
                   2516:            }
1.126     brouard  2517:          } 
                   2518:        }/* end jk */ 
                   2519:       }/* end i */ 
1.145     brouard  2520:     /*} *//* end i1 */
                   2521:   } /* end j1 */
1.126     brouard  2522:   
                   2523:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   2524:   /*free_vector(pp,1,nlstate);*/
                   2525:   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                   2526: }  /* End of prevalence */
                   2527: 
                   2528: /************* Waves Concatenation ***************/
                   2529: 
                   2530: 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)
                   2531: {
                   2532:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   2533:      Death is a valid wave (if date is known).
                   2534:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                   2535:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   2536:      and mw[mi+1][i]. dh depends on stepm.
                   2537:      */
                   2538: 
                   2539:   int i, mi, m;
                   2540:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   2541:      double sum=0., jmean=0.;*/
                   2542:   int first;
                   2543:   int j, k=0,jk, ju, jl;
                   2544:   double sum=0.;
                   2545:   first=0;
                   2546:   jmin=1e+5;
                   2547:   jmax=-1;
                   2548:   jmean=0.;
                   2549:   for(i=1; i<=imx; i++){
                   2550:     mi=0;
                   2551:     m=firstpass;
                   2552:     while(s[m][i] <= nlstate){
                   2553:       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
                   2554:        mw[++mi][i]=m;
                   2555:       if(m >=lastpass)
                   2556:        break;
                   2557:       else
                   2558:        m++;
                   2559:     }/* end while */
                   2560:     if (s[m][i] > nlstate){
                   2561:       mi++;    /* Death is another wave */
                   2562:       /* if(mi==0)  never been interviewed correctly before death */
                   2563:         /* Only death is a correct wave */
                   2564:       mw[mi][i]=m;
                   2565:     }
                   2566: 
                   2567:     wav[i]=mi;
                   2568:     if(mi==0){
                   2569:       nbwarn++;
                   2570:       if(first==0){
                   2571:        printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                   2572:        first=1;
                   2573:       }
                   2574:       if(first==1){
                   2575:        fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
                   2576:       }
                   2577:     } /* end mi==0 */
                   2578:   } /* End individuals */
                   2579: 
                   2580:   for(i=1; i<=imx; i++){
                   2581:     for(mi=1; mi<wav[i];mi++){
                   2582:       if (stepm <=0)
                   2583:        dh[mi][i]=1;
                   2584:       else{
                   2585:        if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                   2586:          if (agedc[i] < 2*AGESUP) {
                   2587:            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   2588:            if(j==0) j=1;  /* Survives at least one month after exam */
                   2589:            else if(j<0){
                   2590:              nberr++;
                   2591:              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]);
                   2592:              j=1; /* Temporary Dangerous patch */
                   2593:              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);
                   2594:              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]);
                   2595:              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);
                   2596:            }
                   2597:            k=k+1;
                   2598:            if (j >= jmax){
                   2599:              jmax=j;
                   2600:              ijmax=i;
                   2601:            }
                   2602:            if (j <= jmin){
                   2603:              jmin=j;
                   2604:              ijmin=i;
                   2605:            }
                   2606:            sum=sum+j;
                   2607:            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   2608:            /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                   2609:          }
                   2610:        }
                   2611:        else{
                   2612:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                   2613: /*       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]); */
                   2614: 
                   2615:          k=k+1;
                   2616:          if (j >= jmax) {
                   2617:            jmax=j;
                   2618:            ijmax=i;
                   2619:          }
                   2620:          else if (j <= jmin){
                   2621:            jmin=j;
                   2622:            ijmin=i;
                   2623:          }
                   2624:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                   2625:          /*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]);*/
                   2626:          if(j<0){
                   2627:            nberr++;
                   2628:            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]);
                   2629:            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]);
                   2630:          }
                   2631:          sum=sum+j;
                   2632:        }
                   2633:        jk= j/stepm;
                   2634:        jl= j -jk*stepm;
                   2635:        ju= j -(jk+1)*stepm;
                   2636:        if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   2637:          if(jl==0){
                   2638:            dh[mi][i]=jk;
                   2639:            bh[mi][i]=0;
                   2640:          }else{ /* We want a negative bias in order to only have interpolation ie
1.136     brouard  2641:                  * to avoid the price of an extra matrix product in likelihood */
1.126     brouard  2642:            dh[mi][i]=jk+1;
                   2643:            bh[mi][i]=ju;
                   2644:          }
                   2645:        }else{
                   2646:          if(jl <= -ju){
                   2647:            dh[mi][i]=jk;
                   2648:            bh[mi][i]=jl;       /* bias is positive if real duration
                   2649:                                 * is higher than the multiple of stepm and negative otherwise.
                   2650:                                 */
                   2651:          }
                   2652:          else{
                   2653:            dh[mi][i]=jk+1;
                   2654:            bh[mi][i]=ju;
                   2655:          }
                   2656:          if(dh[mi][i]==0){
                   2657:            dh[mi][i]=1; /* At least one step */
                   2658:            bh[mi][i]=ju; /* At least one step */
                   2659:            /*  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);*/
                   2660:          }
                   2661:        } /* end if mle */
                   2662:       }
                   2663:     } /* end wave */
                   2664:   }
                   2665:   jmean=sum/k;
                   2666:   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141     brouard  2667:   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126     brouard  2668:  }
                   2669: 
                   2670: /*********** Tricode ****************************/
1.145     brouard  2671: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126     brouard  2672: {
1.144     brouard  2673:   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
                   2674:   /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
                   2675:   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145     brouard  2676:    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
                   2677:   /* nbcode[Tvar[j]][1]= 
1.144     brouard  2678:   */
1.130     brouard  2679: 
1.145     brouard  2680:   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136     brouard  2681:   int modmaxcovj=0; /* Modality max of covariates j */
1.145     brouard  2682:   int cptcode=0; /* Modality max of covariates j */
                   2683:   int modmincovj=0; /* Modality min of covariates j */
                   2684: 
                   2685: 
1.126     brouard  2686:   cptcoveff=0; 
                   2687:  
1.145     brouard  2688:   for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144     brouard  2689:   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126     brouard  2690: 
1.145     brouard  2691:   /* Loop on covariates without age and products */
                   2692:   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
                   2693:     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
1.136     brouard  2694:                               modality of this covariate Vj*/ 
1.145     brouard  2695:       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                   2696:                                    * If product of Vn*Vm, still boolean *:
                   2697:                                    * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                   2698:                                    * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                   2699:       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136     brouard  2700:                                      modality of the nth covariate of individual i. */
1.145     brouard  2701:       if (ij > modmaxcovj)
                   2702:         modmaxcovj=ij; 
                   2703:       else if (ij < modmincovj) 
                   2704:        modmincovj=ij; 
                   2705:       if ((ij < -1) && (ij > NCOVMAX)){
                   2706:        printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                   2707:        exit(1);
                   2708:       }else
1.136     brouard  2709:       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145     brouard  2710:       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126     brouard  2711:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136     brouard  2712:       /* getting the maximum value of the modality of the covariate
                   2713:         (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                   2714:         female is 1, then modmaxcovj=1.*/
1.126     brouard  2715:     }
1.145     brouard  2716:     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
                   2717:     cptcode=modmaxcovj;
1.137     brouard  2718:     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145     brouard  2719:    /*for (i=0; i<=cptcode; i++) {*/
                   2720:     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
                   2721:       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
                   2722:       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
                   2723:        ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
                   2724:       }
                   2725:       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
                   2726:         historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131     brouard  2727:     } /* Ndum[-1] number of undefined modalities */
1.126     brouard  2728: 
1.136     brouard  2729:     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145     brouard  2730:     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
                   2731:     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
                   2732:        modmincovj=3; modmaxcovj = 7;
                   2733:        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
                   2734:        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
                   2735:        variables V1_1 and V1_2.
                   2736:        nbcode[Tvar[j]][ij]=k;
                   2737:        nbcode[Tvar[j]][1]=0;
                   2738:        nbcode[Tvar[j]][2]=1;
                   2739:        nbcode[Tvar[j]][3]=2;
                   2740:     */
                   2741:     ij=1; /* ij is similar to i but can jumps over null modalities */
                   2742:     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
                   2743:       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
                   2744:        /*recode from 0 */
1.131     brouard  2745:        if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
                   2746:          nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                   2747:                                     k is a modality. If we have model=V1+V1*sex 
                   2748:                                     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126     brouard  2749:          ij++;
                   2750:        }
                   2751:        if (ij > ncodemax[j]) break; 
1.137     brouard  2752:       }  /* end of loop on */
                   2753:     } /* end of loop on modality */ 
                   2754:   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
                   2755:   
1.145     brouard  2756:  for (k=-1; k< maxncov; k++) Ndum[k]=0; 
1.137     brouard  2757:   
1.145     brouard  2758:   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
                   2759:    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
                   2760:    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
                   2761:    Ndum[ij]++; 
                   2762:  } 
1.126     brouard  2763: 
                   2764:  ij=1;
1.145     brouard  2765:  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
                   2766:    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126     brouard  2767:    if((Ndum[i]!=0) && (i<=ncovcol)){
1.145     brouard  2768:      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                   2769:      Tvaraff[ij]=i; /*For printing (unclear) */
1.126     brouard  2770:      ij++;
1.145     brouard  2771:    }else
                   2772:        Tvaraff[ij]=0;
1.126     brouard  2773:  }
1.131     brouard  2774:  ij--;
1.144     brouard  2775:  cptcoveff=ij; /*Number of total covariates*/
1.145     brouard  2776: 
1.126     brouard  2777: }
                   2778: 
1.145     brouard  2779: 
1.126     brouard  2780: /*********** Health Expectancies ****************/
                   2781: 
1.127     brouard  2782: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126     brouard  2783: 
                   2784: {
                   2785:   /* Health expectancies, no variances */
                   2786:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
                   2787:   int nhstepma, nstepma; /* Decreasing with age */
                   2788:   double age, agelim, hf;
                   2789:   double ***p3mat;
                   2790:   double eip;
                   2791: 
                   2792:   pstamp(ficreseij);
                   2793:   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
                   2794:   fprintf(ficreseij,"# Age");
                   2795:   for(i=1; i<=nlstate;i++){
                   2796:     for(j=1; j<=nlstate;j++){
                   2797:       fprintf(ficreseij," e%1d%1d ",i,j);
                   2798:     }
                   2799:     fprintf(ficreseij," e%1d. ",i);
                   2800:   }
                   2801:   fprintf(ficreseij,"\n");
                   2802: 
                   2803:   
                   2804:   if(estepm < stepm){
                   2805:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   2806:   }
                   2807:   else  hstepm=estepm;   
                   2808:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   2809:    * This is mainly to measure the difference between two models: for example
                   2810:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   2811:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   2812:    * progression in between and thus overestimating or underestimating according
                   2813:    * to the curvature of the survival function. If, for the same date, we 
                   2814:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   2815:    * to compare the new estimate of Life expectancy with the same linear 
                   2816:    * hypothesis. A more precise result, taking into account a more precise
                   2817:    * curvature will be obtained if estepm is as small as stepm. */
                   2818: 
                   2819:   /* For example we decided to compute the life expectancy with the smallest unit */
                   2820:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   2821:      nhstepm is the number of hstepm from age to agelim 
                   2822:      nstepm is the number of stepm from age to agelin. 
                   2823:      Look at hpijx to understand the reason of that which relies in memory size
                   2824:      and note for a fixed period like estepm months */
                   2825:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   2826:      survival function given by stepm (the optimization length). Unfortunately it
                   2827:      means that if the survival funtion is printed only each two years of age and if
                   2828:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   2829:      results. So we changed our mind and took the option of the best precision.
                   2830:   */
                   2831:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   2832: 
                   2833:   agelim=AGESUP;
                   2834:   /* If stepm=6 months */
                   2835:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   2836:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   2837:     
                   2838: /* nhstepm age range expressed in number of stepm */
                   2839:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   2840:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   2841:   /* if (stepm >= YEARM) hstepm=1;*/
                   2842:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   2843:   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2844: 
                   2845:   for (age=bage; age<=fage; age ++){ 
                   2846:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   2847:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   2848:     /* if (stepm >= YEARM) hstepm=1;*/
                   2849:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   2850: 
                   2851:     /* If stepm=6 months */
                   2852:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   2853:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   2854:     
                   2855:     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
                   2856:     
                   2857:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   2858:     
                   2859:     printf("%d|",(int)age);fflush(stdout);
                   2860:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   2861:     
                   2862:     /* Computing expectancies */
                   2863:     for(i=1; i<=nlstate;i++)
                   2864:       for(j=1; j<=nlstate;j++)
                   2865:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   2866:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   2867:          
                   2868:          /* 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]);*/
                   2869: 
                   2870:        }
                   2871: 
                   2872:     fprintf(ficreseij,"%3.0f",age );
                   2873:     for(i=1; i<=nlstate;i++){
                   2874:       eip=0;
                   2875:       for(j=1; j<=nlstate;j++){
                   2876:        eip +=eij[i][j][(int)age];
                   2877:        fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                   2878:       }
                   2879:       fprintf(ficreseij,"%9.4f", eip );
                   2880:     }
                   2881:     fprintf(ficreseij,"\n");
                   2882:     
                   2883:   }
                   2884:   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2885:   printf("\n");
                   2886:   fprintf(ficlog,"\n");
                   2887:   
                   2888: }
                   2889: 
1.127     brouard  2890: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126     brouard  2891: 
                   2892: {
                   2893:   /* Covariances of health expectancies eij and of total life expectancies according
                   2894:    to initial status i, ei. .
                   2895:   */
                   2896:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
                   2897:   int nhstepma, nstepma; /* Decreasing with age */
                   2898:   double age, agelim, hf;
                   2899:   double ***p3matp, ***p3matm, ***varhe;
                   2900:   double **dnewm,**doldm;
                   2901:   double *xp, *xm;
                   2902:   double **gp, **gm;
                   2903:   double ***gradg, ***trgradg;
                   2904:   int theta;
                   2905: 
                   2906:   double eip, vip;
                   2907: 
                   2908:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                   2909:   xp=vector(1,npar);
                   2910:   xm=vector(1,npar);
                   2911:   dnewm=matrix(1,nlstate*nlstate,1,npar);
                   2912:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                   2913:   
                   2914:   pstamp(ficresstdeij);
                   2915:   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
                   2916:   fprintf(ficresstdeij,"# Age");
                   2917:   for(i=1; i<=nlstate;i++){
                   2918:     for(j=1; j<=nlstate;j++)
                   2919:       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
                   2920:     fprintf(ficresstdeij," e%1d. ",i);
                   2921:   }
                   2922:   fprintf(ficresstdeij,"\n");
                   2923: 
                   2924:   pstamp(ficrescveij);
                   2925:   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
                   2926:   fprintf(ficrescveij,"# Age");
                   2927:   for(i=1; i<=nlstate;i++)
                   2928:     for(j=1; j<=nlstate;j++){
                   2929:       cptj= (j-1)*nlstate+i;
                   2930:       for(i2=1; i2<=nlstate;i2++)
                   2931:        for(j2=1; j2<=nlstate;j2++){
                   2932:          cptj2= (j2-1)*nlstate+i2;
                   2933:          if(cptj2 <= cptj)
                   2934:            fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
                   2935:        }
                   2936:     }
                   2937:   fprintf(ficrescveij,"\n");
                   2938:   
                   2939:   if(estepm < stepm){
                   2940:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   2941:   }
                   2942:   else  hstepm=estepm;   
                   2943:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   2944:    * This is mainly to measure the difference between two models: for example
                   2945:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   2946:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   2947:    * progression in between and thus overestimating or underestimating according
                   2948:    * to the curvature of the survival function. If, for the same date, we 
                   2949:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   2950:    * to compare the new estimate of Life expectancy with the same linear 
                   2951:    * hypothesis. A more precise result, taking into account a more precise
                   2952:    * curvature will be obtained if estepm is as small as stepm. */
                   2953: 
                   2954:   /* For example we decided to compute the life expectancy with the smallest unit */
                   2955:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   2956:      nhstepm is the number of hstepm from age to agelim 
                   2957:      nstepm is the number of stepm from age to agelin. 
                   2958:      Look at hpijx to understand the reason of that which relies in memory size
                   2959:      and note for a fixed period like estepm months */
                   2960:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   2961:      survival function given by stepm (the optimization length). Unfortunately it
                   2962:      means that if the survival funtion is printed only each two years of age and if
                   2963:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   2964:      results. So we changed our mind and took the option of the best precision.
                   2965:   */
                   2966:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   2967: 
                   2968:   /* If stepm=6 months */
                   2969:   /* nhstepm age range expressed in number of stepm */
                   2970:   agelim=AGESUP;
                   2971:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                   2972:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   2973:   /* if (stepm >= YEARM) hstepm=1;*/
                   2974:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   2975:   
                   2976:   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2977:   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2978:   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   2979:   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                   2980:   gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   2981:   gm=matrix(0,nhstepm,1,nlstate*nlstate);
                   2982: 
                   2983:   for (age=bage; age<=fage; age ++){ 
                   2984:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   2985:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   2986:     /* if (stepm >= YEARM) hstepm=1;*/
                   2987:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   2988: 
                   2989:     /* If stepm=6 months */
                   2990:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   2991:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   2992:     
                   2993:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   2994: 
                   2995:     /* Computing  Variances of health expectancies */
                   2996:     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
                   2997:        decrease memory allocation */
                   2998:     for(theta=1; theta <=npar; theta++){
                   2999:       for(i=1; i<=npar; i++){ 
                   3000:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   3001:        xm[i] = x[i] - (i==theta ?delti[theta]:0);
                   3002:       }
                   3003:       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
                   3004:       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                   3005:   
                   3006:       for(j=1; j<= nlstate; j++){
                   3007:        for(i=1; i<=nlstate; i++){
                   3008:          for(h=0; h<=nhstepm-1; h++){
                   3009:            gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                   3010:            gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                   3011:          }
                   3012:        }
                   3013:       }
                   3014:      
                   3015:       for(ij=1; ij<= nlstate*nlstate; ij++)
                   3016:        for(h=0; h<=nhstepm-1; h++){
                   3017:          gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                   3018:        }
                   3019:     }/* End theta */
                   3020:     
                   3021:     
                   3022:     for(h=0; h<=nhstepm-1; h++)
                   3023:       for(j=1; j<=nlstate*nlstate;j++)
                   3024:        for(theta=1; theta <=npar; theta++)
                   3025:          trgradg[h][j][theta]=gradg[h][theta][j];
                   3026:     
                   3027: 
                   3028:      for(ij=1;ij<=nlstate*nlstate;ij++)
                   3029:       for(ji=1;ji<=nlstate*nlstate;ji++)
                   3030:        varhe[ij][ji][(int)age] =0.;
                   3031: 
                   3032:      printf("%d|",(int)age);fflush(stdout);
                   3033:      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   3034:      for(h=0;h<=nhstepm-1;h++){
                   3035:       for(k=0;k<=nhstepm-1;k++){
                   3036:        matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   3037:        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   3038:        for(ij=1;ij<=nlstate*nlstate;ij++)
                   3039:          for(ji=1;ji<=nlstate*nlstate;ji++)
                   3040:            varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
                   3041:       }
                   3042:     }
                   3043: 
                   3044:     /* Computing expectancies */
                   3045:     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
                   3046:     for(i=1; i<=nlstate;i++)
                   3047:       for(j=1; j<=nlstate;j++)
                   3048:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   3049:          eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                   3050:          
                   3051:          /* 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]);*/
                   3052: 
                   3053:        }
                   3054: 
                   3055:     fprintf(ficresstdeij,"%3.0f",age );
                   3056:     for(i=1; i<=nlstate;i++){
                   3057:       eip=0.;
                   3058:       vip=0.;
                   3059:       for(j=1; j<=nlstate;j++){
                   3060:        eip += eij[i][j][(int)age];
                   3061:        for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                   3062:          vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                   3063:        fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
                   3064:       }
                   3065:       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
                   3066:     }
                   3067:     fprintf(ficresstdeij,"\n");
                   3068: 
                   3069:     fprintf(ficrescveij,"%3.0f",age );
                   3070:     for(i=1; i<=nlstate;i++)
                   3071:       for(j=1; j<=nlstate;j++){
                   3072:        cptj= (j-1)*nlstate+i;
                   3073:        for(i2=1; i2<=nlstate;i2++)
                   3074:          for(j2=1; j2<=nlstate;j2++){
                   3075:            cptj2= (j2-1)*nlstate+i2;
                   3076:            if(cptj2 <= cptj)
                   3077:              fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                   3078:          }
                   3079:       }
                   3080:     fprintf(ficrescveij,"\n");
                   3081:    
                   3082:   }
                   3083:   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   3084:   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   3085:   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   3086:   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   3087:   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3088:   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3089:   printf("\n");
                   3090:   fprintf(ficlog,"\n");
                   3091: 
                   3092:   free_vector(xm,1,npar);
                   3093:   free_vector(xp,1,npar);
                   3094:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   3095:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   3096:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                   3097: }
                   3098: 
                   3099: /************ Variance ******************/
                   3100: 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[])
                   3101: {
                   3102:   /* Variance of health expectancies */
                   3103:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   3104:   /* double **newm;*/
                   3105:   double **dnewm,**doldm;
                   3106:   double **dnewmp,**doldmp;
                   3107:   int i, j, nhstepm, hstepm, h, nstepm ;
                   3108:   int k, cptcode;
                   3109:   double *xp;
                   3110:   double **gp, **gm;  /* for var eij */
                   3111:   double ***gradg, ***trgradg; /*for var eij */
                   3112:   double **gradgp, **trgradgp; /* for var p point j */
                   3113:   double *gpp, *gmp; /* for var p point j */
                   3114:   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   3115:   double ***p3mat;
                   3116:   double age,agelim, hf;
                   3117:   double ***mobaverage;
                   3118:   int theta;
                   3119:   char digit[4];
                   3120:   char digitp[25];
                   3121: 
                   3122:   char fileresprobmorprev[FILENAMELENGTH];
                   3123: 
                   3124:   if(popbased==1){
                   3125:     if(mobilav!=0)
                   3126:       strcpy(digitp,"-populbased-mobilav-");
                   3127:     else strcpy(digitp,"-populbased-nomobil-");
                   3128:   }
                   3129:   else 
                   3130:     strcpy(digitp,"-stablbased-");
                   3131: 
                   3132:   if (mobilav!=0) {
                   3133:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3134:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   3135:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   3136:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   3137:     }
                   3138:   }
                   3139: 
                   3140:   strcpy(fileresprobmorprev,"prmorprev"); 
                   3141:   sprintf(digit,"%-d",ij);
                   3142:   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   3143:   strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   3144:   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   3145:   strcat(fileresprobmorprev,fileres);
                   3146:   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   3147:     printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   3148:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   3149:   }
                   3150:   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   3151:  
                   3152:   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   3153:   pstamp(ficresprobmorprev);
                   3154:   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);
                   3155:   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   3156:   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   3157:     fprintf(ficresprobmorprev," p.%-d SE",j);
                   3158:     for(i=1; i<=nlstate;i++)
                   3159:       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   3160:   }  
                   3161:   fprintf(ficresprobmorprev,"\n");
                   3162:   fprintf(ficgp,"\n# Routine varevsij");
                   3163:   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
                   3164:   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");
                   3165:   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   3166: /*   } */
                   3167:   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3168:   pstamp(ficresvij);
                   3169:   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
                   3170:   if(popbased==1)
1.128     brouard  3171:     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126     brouard  3172:   else
                   3173:     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
                   3174:   fprintf(ficresvij,"# Age");
                   3175:   for(i=1; i<=nlstate;i++)
                   3176:     for(j=1; j<=nlstate;j++)
                   3177:       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
                   3178:   fprintf(ficresvij,"\n");
                   3179: 
                   3180:   xp=vector(1,npar);
                   3181:   dnewm=matrix(1,nlstate,1,npar);
                   3182:   doldm=matrix(1,nlstate,1,nlstate);
                   3183:   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   3184:   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3185: 
                   3186:   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                   3187:   gpp=vector(nlstate+1,nlstate+ndeath);
                   3188:   gmp=vector(nlstate+1,nlstate+ndeath);
                   3189:   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   3190:   
                   3191:   if(estepm < stepm){
                   3192:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   3193:   }
                   3194:   else  hstepm=estepm;   
                   3195:   /* For example we decided to compute the life expectancy with the smallest unit */
                   3196:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   3197:      nhstepm is the number of hstepm from age to agelim 
                   3198:      nstepm is the number of stepm from age to agelin. 
1.128     brouard  3199:      Look at function hpijx to understand why (it is linked to memory size questions) */
1.126     brouard  3200:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   3201:      survival function given by stepm (the optimization length). Unfortunately it
                   3202:      means that if the survival funtion is printed every two years of age and if
                   3203:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   3204:      results. So we changed our mind and took the option of the best precision.
                   3205:   */
                   3206:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   3207:   agelim = AGESUP;
                   3208:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   3209:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   3210:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   3211:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3212:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   3213:     gp=matrix(0,nhstepm,1,nlstate);
                   3214:     gm=matrix(0,nhstepm,1,nlstate);
                   3215: 
                   3216: 
                   3217:     for(theta=1; theta <=npar; theta++){
                   3218:       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                   3219:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   3220:       }
                   3221:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   3222:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3223: 
                   3224:       if (popbased==1) {
                   3225:        if(mobilav ==0){
                   3226:          for(i=1; i<=nlstate;i++)
                   3227:            prlim[i][i]=probs[(int)age][i][ij];
                   3228:        }else{ /* mobilav */ 
                   3229:          for(i=1; i<=nlstate;i++)
                   3230:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   3231:        }
                   3232:       }
                   3233:   
                   3234:       for(j=1; j<= nlstate; j++){
                   3235:        for(h=0; h<=nhstepm; h++){
                   3236:          for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                   3237:            gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   3238:        }
                   3239:       }
                   3240:       /* This for computing probability of death (h=1 means
                   3241:          computed over hstepm matrices product = hstepm*stepm months) 
                   3242:          as a weighted average of prlim.
                   3243:       */
                   3244:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   3245:        for(i=1,gpp[j]=0.; i<= nlstate; i++)
                   3246:          gpp[j] += prlim[i][i]*p3mat[i][j][1];
                   3247:       }    
                   3248:       /* end probability of death */
                   3249: 
                   3250:       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                   3251:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   3252:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   3253:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3254:  
                   3255:       if (popbased==1) {
                   3256:        if(mobilav ==0){
                   3257:          for(i=1; i<=nlstate;i++)
                   3258:            prlim[i][i]=probs[(int)age][i][ij];
                   3259:        }else{ /* mobilav */ 
                   3260:          for(i=1; i<=nlstate;i++)
                   3261:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   3262:        }
                   3263:       }
                   3264: 
1.128     brouard  3265:       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
1.126     brouard  3266:        for(h=0; h<=nhstepm; h++){
                   3267:          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   3268:            gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   3269:        }
                   3270:       }
                   3271:       /* This for computing probability of death (h=1 means
                   3272:          computed over hstepm matrices product = hstepm*stepm months) 
                   3273:          as a weighted average of prlim.
                   3274:       */
                   3275:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   3276:        for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   3277:          gmp[j] += prlim[i][i]*p3mat[i][j][1];
                   3278:       }    
                   3279:       /* end probability of death */
                   3280: 
                   3281:       for(j=1; j<= nlstate; j++) /* vareij */
                   3282:        for(h=0; h<=nhstepm; h++){
                   3283:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   3284:        }
                   3285: 
                   3286:       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                   3287:        gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   3288:       }
                   3289: 
                   3290:     } /* End theta */
                   3291: 
                   3292:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   3293: 
                   3294:     for(h=0; h<=nhstepm; h++) /* veij */
                   3295:       for(j=1; j<=nlstate;j++)
                   3296:        for(theta=1; theta <=npar; theta++)
                   3297:          trgradg[h][j][theta]=gradg[h][theta][j];
                   3298: 
                   3299:     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   3300:       for(theta=1; theta <=npar; theta++)
                   3301:        trgradgp[j][theta]=gradgp[theta][j];
                   3302:   
                   3303: 
                   3304:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   3305:     for(i=1;i<=nlstate;i++)
                   3306:       for(j=1;j<=nlstate;j++)
                   3307:        vareij[i][j][(int)age] =0.;
                   3308: 
                   3309:     for(h=0;h<=nhstepm;h++){
                   3310:       for(k=0;k<=nhstepm;k++){
                   3311:        matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                   3312:        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                   3313:        for(i=1;i<=nlstate;i++)
                   3314:          for(j=1;j<=nlstate;j++)
                   3315:            vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                   3316:       }
                   3317:     }
                   3318:   
                   3319:     /* pptj */
                   3320:     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                   3321:     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                   3322:     for(j=nlstate+1;j<=nlstate+ndeath;j++)
                   3323:       for(i=nlstate+1;i<=nlstate+ndeath;i++)
                   3324:        varppt[j][i]=doldmp[j][i];
                   3325:     /* end ppptj */
                   3326:     /*  x centered again */
                   3327:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                   3328:     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                   3329:  
                   3330:     if (popbased==1) {
                   3331:       if(mobilav ==0){
                   3332:        for(i=1; i<=nlstate;i++)
                   3333:          prlim[i][i]=probs[(int)age][i][ij];
                   3334:       }else{ /* mobilav */ 
                   3335:        for(i=1; i<=nlstate;i++)
                   3336:          prlim[i][i]=mobaverage[(int)age][i][ij];
                   3337:       }
                   3338:     }
                   3339:              
                   3340:     /* This for computing probability of death (h=1 means
                   3341:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   3342:        as a weighted average of prlim.
                   3343:     */
                   3344:     for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   3345:       for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                   3346:        gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   3347:     }    
                   3348:     /* end probability of death */
                   3349: 
                   3350:     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   3351:     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   3352:       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   3353:       for(i=1; i<=nlstate;i++){
                   3354:        fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   3355:       }
                   3356:     } 
                   3357:     fprintf(ficresprobmorprev,"\n");
                   3358: 
                   3359:     fprintf(ficresvij,"%.0f ",age );
                   3360:     for(i=1; i<=nlstate;i++)
                   3361:       for(j=1; j<=nlstate;j++){
                   3362:        fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                   3363:       }
                   3364:     fprintf(ficresvij,"\n");
                   3365:     free_matrix(gp,0,nhstepm,1,nlstate);
                   3366:     free_matrix(gm,0,nhstepm,1,nlstate);
                   3367:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                   3368:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                   3369:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3370:   } /* End age */
                   3371:   free_vector(gpp,nlstate+1,nlstate+ndeath);
                   3372:   free_vector(gmp,nlstate+1,nlstate+ndeath);
                   3373:   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   3374:   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145     brouard  3375:   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126     brouard  3376:   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131     brouard  3377:   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126     brouard  3378: /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                   3379: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   3380: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145     brouard  3381:   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
                   3382:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
                   3383:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126     brouard  3384:   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                   3385:   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);
                   3386:   /*  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);
                   3387: */
                   3388: /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
                   3389:   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
                   3390: 
                   3391:   free_vector(xp,1,npar);
                   3392:   free_matrix(doldm,1,nlstate,1,nlstate);
                   3393:   free_matrix(dnewm,1,nlstate,1,npar);
                   3394:   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3395:   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   3396:   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3397:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3398:   fclose(ficresprobmorprev);
                   3399:   fflush(ficgp);
                   3400:   fflush(fichtm); 
                   3401: }  /* end varevsij */
                   3402: 
                   3403: /************ Variance of prevlim ******************/
                   3404: 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[])
                   3405: {
                   3406:   /* Variance of prevalence limit */
                   3407:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   3408:   double **newm;
                   3409:   double **dnewm,**doldm;
                   3410:   int i, j, nhstepm, hstepm;
                   3411:   int k, cptcode;
                   3412:   double *xp;
                   3413:   double *gp, *gm;
                   3414:   double **gradg, **trgradg;
                   3415:   double age,agelim;
                   3416:   int theta;
                   3417:   
                   3418:   pstamp(ficresvpl);
                   3419:   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
                   3420:   fprintf(ficresvpl,"# Age");
                   3421:   for(i=1; i<=nlstate;i++)
                   3422:       fprintf(ficresvpl," %1d-%1d",i,i);
                   3423:   fprintf(ficresvpl,"\n");
                   3424: 
                   3425:   xp=vector(1,npar);
                   3426:   dnewm=matrix(1,nlstate,1,npar);
                   3427:   doldm=matrix(1,nlstate,1,nlstate);
                   3428:   
                   3429:   hstepm=1*YEARM; /* Every year of age */
                   3430:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   3431:   agelim = AGESUP;
                   3432:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   3433:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   3434:     if (stepm >= YEARM) hstepm=1;
                   3435:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   3436:     gradg=matrix(1,npar,1,nlstate);
                   3437:     gp=vector(1,nlstate);
                   3438:     gm=vector(1,nlstate);
                   3439: 
                   3440:     for(theta=1; theta <=npar; theta++){
                   3441:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   3442:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   3443:       }
                   3444:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3445:       for(i=1;i<=nlstate;i++)
                   3446:        gp[i] = prlim[i][i];
                   3447:     
                   3448:       for(i=1; i<=npar; i++) /* Computes gradient */
                   3449:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   3450:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3451:       for(i=1;i<=nlstate;i++)
                   3452:        gm[i] = prlim[i][i];
                   3453: 
                   3454:       for(i=1;i<=nlstate;i++)
                   3455:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                   3456:     } /* End theta */
                   3457: 
                   3458:     trgradg =matrix(1,nlstate,1,npar);
                   3459: 
                   3460:     for(j=1; j<=nlstate;j++)
                   3461:       for(theta=1; theta <=npar; theta++)
                   3462:        trgradg[j][theta]=gradg[theta][j];
                   3463: 
                   3464:     for(i=1;i<=nlstate;i++)
                   3465:       varpl[i][(int)age] =0.;
                   3466:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   3467:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   3468:     for(i=1;i<=nlstate;i++)
                   3469:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   3470: 
                   3471:     fprintf(ficresvpl,"%.0f ",age );
                   3472:     for(i=1; i<=nlstate;i++)
                   3473:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   3474:     fprintf(ficresvpl,"\n");
                   3475:     free_vector(gp,1,nlstate);
                   3476:     free_vector(gm,1,nlstate);
                   3477:     free_matrix(gradg,1,npar,1,nlstate);
                   3478:     free_matrix(trgradg,1,nlstate,1,npar);
                   3479:   } /* End age */
                   3480: 
                   3481:   free_vector(xp,1,npar);
                   3482:   free_matrix(doldm,1,nlstate,1,npar);
                   3483:   free_matrix(dnewm,1,nlstate,1,nlstate);
                   3484: 
                   3485: }
                   3486: 
                   3487: /************ Variance of one-step probabilities  ******************/
                   3488: 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[])
                   3489: {
                   3490:   int i, j=0,  i1, k1, l1, t, tj;
                   3491:   int k2, l2, j1,  z1;
                   3492:   int k=0,l, cptcode;
1.145     brouard  3493:   int first=1, first1, first2;
1.126     brouard  3494:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                   3495:   double **dnewm,**doldm;
                   3496:   double *xp;
                   3497:   double *gp, *gm;
                   3498:   double **gradg, **trgradg;
                   3499:   double **mu;
1.145     brouard  3500:   double age,agelim, cov[NCOVMAX+1];
1.126     brouard  3501:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   3502:   int theta;
                   3503:   char fileresprob[FILENAMELENGTH];
                   3504:   char fileresprobcov[FILENAMELENGTH];
                   3505:   char fileresprobcor[FILENAMELENGTH];
                   3506:   double ***varpij;
                   3507: 
                   3508:   strcpy(fileresprob,"prob"); 
                   3509:   strcat(fileresprob,fileres);
                   3510:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   3511:     printf("Problem with resultfile: %s\n", fileresprob);
                   3512:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   3513:   }
                   3514:   strcpy(fileresprobcov,"probcov"); 
                   3515:   strcat(fileresprobcov,fileres);
                   3516:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   3517:     printf("Problem with resultfile: %s\n", fileresprobcov);
                   3518:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   3519:   }
                   3520:   strcpy(fileresprobcor,"probcor"); 
                   3521:   strcat(fileresprobcor,fileres);
                   3522:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                   3523:     printf("Problem with resultfile: %s\n", fileresprobcor);
                   3524:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   3525:   }
                   3526:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   3527:   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   3528:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   3529:   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   3530:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   3531:   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   3532:   pstamp(ficresprob);
                   3533:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                   3534:   fprintf(ficresprob,"# Age");
                   3535:   pstamp(ficresprobcov);
                   3536:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                   3537:   fprintf(ficresprobcov,"# Age");
                   3538:   pstamp(ficresprobcor);
                   3539:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                   3540:   fprintf(ficresprobcor,"# Age");
                   3541: 
                   3542: 
                   3543:   for(i=1; i<=nlstate;i++)
                   3544:     for(j=1; j<=(nlstate+ndeath);j++){
                   3545:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   3546:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   3547:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
                   3548:     }  
                   3549:  /* fprintf(ficresprob,"\n");
                   3550:   fprintf(ficresprobcov,"\n");
                   3551:   fprintf(ficresprobcor,"\n");
                   3552:  */
1.131     brouard  3553:   xp=vector(1,npar);
1.126     brouard  3554:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   3555:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   3556:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   3557:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   3558:   first=1;
                   3559:   fprintf(ficgp,"\n# Routine varprob");
                   3560:   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   3561:   fprintf(fichtm,"\n");
                   3562: 
                   3563:   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
                   3564:   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
                   3565:   file %s<br>\n",optionfilehtmcov);
                   3566:   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
                   3567: and drawn. It helps understanding how is the covariance between two incidences.\
                   3568:  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                   3569:   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. \
                   3570: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
                   3571: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
                   3572: standard deviations wide on each axis. <br>\
                   3573:  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
                   3574:  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
                   3575: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
                   3576: 
                   3577:   cov[1]=1;
1.145     brouard  3578:   /* tj=cptcoveff; */
                   3579:   tj = (int) pow(2,cptcoveff);
1.126     brouard  3580:   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   3581:   j1=0;
1.145     brouard  3582:   for(j1=1; j1<=tj;j1++){
                   3583:     /*for(i1=1; i1<=ncodemax[t];i1++){ */
                   3584:     /*j1++;*/
1.126     brouard  3585:       if  (cptcovn>0) {
                   3586:        fprintf(ficresprob, "\n#********** Variable "); 
                   3587:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   3588:        fprintf(ficresprob, "**********\n#\n");
                   3589:        fprintf(ficresprobcov, "\n#********** Variable "); 
                   3590:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   3591:        fprintf(ficresprobcov, "**********\n#\n");
                   3592:        
                   3593:        fprintf(ficgp, "\n#********** Variable "); 
                   3594:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   3595:        fprintf(ficgp, "**********\n#\n");
                   3596:        
                   3597:        
                   3598:        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                   3599:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   3600:        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3601:        
                   3602:        fprintf(ficresprobcor, "\n#********** Variable ");    
                   3603:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   3604:        fprintf(ficresprobcor, "**********\n#");    
                   3605:       }
                   3606:       
1.145     brouard  3607:       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                   3608:       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   3609:       gp=vector(1,(nlstate)*(nlstate+ndeath));
                   3610:       gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126     brouard  3611:       for (age=bage; age<=fage; age ++){ 
                   3612:        cov[2]=age;
                   3613:        for (k=1; k<=cptcovn;k++) {
1.145     brouard  3614:          cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                   3615:                                                         * 1  1 1 1 1
                   3616:                                                         * 2  2 1 1 1
                   3617:                                                         * 3  1 2 1 1
                   3618:                                                         */
                   3619:          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126     brouard  3620:        }
                   3621:        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   3622:        for (k=1; k<=cptcovprod;k++)
                   3623:          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   3624:        
                   3625:     
                   3626:        for(theta=1; theta <=npar; theta++){
                   3627:          for(i=1; i<=npar; i++)
                   3628:            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                   3629:          
                   3630:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   3631:          
                   3632:          k=0;
                   3633:          for(i=1; i<= (nlstate); i++){
                   3634:            for(j=1; j<=(nlstate+ndeath);j++){
                   3635:              k=k+1;
                   3636:              gp[k]=pmmij[i][j];
                   3637:            }
                   3638:          }
                   3639:          
                   3640:          for(i=1; i<=npar; i++)
                   3641:            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                   3642:     
                   3643:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   3644:          k=0;
                   3645:          for(i=1; i<=(nlstate); i++){
                   3646:            for(j=1; j<=(nlstate+ndeath);j++){
                   3647:              k=k+1;
                   3648:              gm[k]=pmmij[i][j];
                   3649:            }
                   3650:          }
                   3651:      
                   3652:          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                   3653:            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                   3654:        }
                   3655: 
                   3656:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   3657:          for(theta=1; theta <=npar; theta++)
                   3658:            trgradg[j][theta]=gradg[theta][j];
                   3659:        
                   3660:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   3661:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   3662: 
                   3663:        pmij(pmmij,cov,ncovmodel,x,nlstate);
                   3664:        
                   3665:        k=0;
                   3666:        for(i=1; i<=(nlstate); i++){
                   3667:          for(j=1; j<=(nlstate+ndeath);j++){
                   3668:            k=k+1;
                   3669:            mu[k][(int) age]=pmmij[i][j];
                   3670:          }
                   3671:        }
                   3672:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   3673:          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   3674:            varpij[i][j][(int)age] = doldm[i][j];
                   3675: 
                   3676:        /*printf("\n%d ",(int)age);
                   3677:          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   3678:          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   3679:          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   3680:          }*/
                   3681: 
                   3682:        fprintf(ficresprob,"\n%d ",(int)age);
                   3683:        fprintf(ficresprobcov,"\n%d ",(int)age);
                   3684:        fprintf(ficresprobcor,"\n%d ",(int)age);
                   3685: 
                   3686:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   3687:          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   3688:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   3689:          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   3690:          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                   3691:        }
                   3692:        i=0;
                   3693:        for (k=1; k<=(nlstate);k++){
                   3694:          for (l=1; l<=(nlstate+ndeath);l++){ 
1.145     brouard  3695:            i++;
1.126     brouard  3696:            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   3697:            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   3698:            for (j=1; j<=i;j++){
1.145     brouard  3699:              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126     brouard  3700:              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   3701:              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   3702:            }
                   3703:          }
                   3704:        }/* end of loop for state */
                   3705:       } /* end of loop for age */
1.145     brouard  3706:       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                   3707:       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   3708:       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   3709:       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   3710:       
1.126     brouard  3711:       /* Confidence intervalle of pij  */
                   3712:       /*
1.131     brouard  3713:        fprintf(ficgp,"\nunset parametric;unset label");
1.126     brouard  3714:        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                   3715:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                   3716:        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);
                   3717:        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                   3718:        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                   3719:        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                   3720:       */
                   3721: 
                   3722:       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145     brouard  3723:       first1=1;first2=2;
1.126     brouard  3724:       for (k2=1; k2<=(nlstate);k2++){
                   3725:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                   3726:          if(l2==k2) continue;
                   3727:          j=(k2-1)*(nlstate+ndeath)+l2;
                   3728:          for (k1=1; k1<=(nlstate);k1++){
                   3729:            for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   3730:              if(l1==k1) continue;
                   3731:              i=(k1-1)*(nlstate+ndeath)+l1;
                   3732:              if(i<=j) continue;
                   3733:              for (age=bage; age<=fage; age ++){ 
                   3734:                if ((int)age %5==0){
                   3735:                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   3736:                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   3737:                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   3738:                  mu1=mu[i][(int) age]/stepm*YEARM ;
                   3739:                  mu2=mu[j][(int) age]/stepm*YEARM;
                   3740:                  c12=cv12/sqrt(v1*v2);
                   3741:                  /* Computing eigen value of matrix of covariance */
                   3742:                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   3743:                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135     brouard  3744:                  if ((lc2 <0) || (lc1 <0) ){
1.145     brouard  3745:                    if(first2==1){
                   3746:                      first1=0;
                   3747:                    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);
                   3748:                    }
                   3749:                    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);
                   3750:                    /* lc1=fabs(lc1); */ /* If we want to have them positive */
                   3751:                    /* lc2=fabs(lc2); */
1.135     brouard  3752:                  }
                   3753: 
1.126     brouard  3754:                  /* Eigen vectors */
                   3755:                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   3756:                  /*v21=sqrt(1.-v11*v11); *//* error */
                   3757:                  v21=(lc1-v1)/cv12*v11;
                   3758:                  v12=-v21;
                   3759:                  v22=v11;
                   3760:                  tnalp=v21/v11;
                   3761:                  if(first1==1){
                   3762:                    first1=0;
                   3763:                    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);
                   3764:                  }
                   3765:                  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);
                   3766:                  /*printf(fignu*/
                   3767:                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                   3768:                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   3769:                  if(first==1){
                   3770:                    first=0;
                   3771:                    fprintf(ficgp,"\nset parametric;unset label");
                   3772:                    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
1.145     brouard  3773:                    fprintf(ficgp,"\nset ter png small size 320, 240");
1.126     brouard  3774:                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
                   3775:  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
                   3776: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                   3777:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                   3778:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   3779:                    fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   3780:                    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                   3781:                    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   3782:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   3783:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   3784:                    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",\
                   3785:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   3786:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   3787:                  }else{
                   3788:                    first=0;
                   3789:                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                   3790:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   3791:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   3792:                    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",\
                   3793:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   3794:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   3795:                  }/* if first */
                   3796:                } /* age mod 5 */
                   3797:              } /* end loop age */
                   3798:              fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   3799:              first=1;
                   3800:            } /*l12 */
                   3801:          } /* k12 */
                   3802:        } /*l1 */
                   3803:       }/* k1 */
1.145     brouard  3804:       /* } /* loop covariates */
1.126     brouard  3805:   }
                   3806:   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
                   3807:   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
                   3808:   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   3809:   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
                   3810:   free_vector(xp,1,npar);
                   3811:   fclose(ficresprob);
                   3812:   fclose(ficresprobcov);
                   3813:   fclose(ficresprobcor);
                   3814:   fflush(ficgp);
                   3815:   fflush(fichtmcov);
                   3816: }
                   3817: 
                   3818: 
                   3819: /******************* Printing html file ***********/
                   3820: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                   3821:                  int lastpass, int stepm, int weightopt, char model[],\
                   3822:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   3823:                  int popforecast, int estepm ,\
                   3824:                  double jprev1, double mprev1,double anprev1, \
                   3825:                  double jprev2, double mprev2,double anprev2){
                   3826:   int jj1, k1, i1, cpt;
                   3827: 
                   3828:    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
                   3829:    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
                   3830: </ul>");
                   3831:    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
                   3832:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
                   3833:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
                   3834:    fprintf(fichtm,"\
                   3835:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
                   3836:           stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
                   3837:    fprintf(fichtm,"\
                   3838:  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
                   3839:           subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
                   3840:    fprintf(fichtm,"\
1.128     brouard  3841:  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126     brouard  3842:    <a href=\"%s\">%s</a> <br>\n",
                   3843:           estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
                   3844:    fprintf(fichtm,"\
                   3845:  - Population projections by age and states: \
                   3846:    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
                   3847: 
                   3848: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
                   3849: 
1.145     brouard  3850:  m=pow(2,cptcoveff);
1.126     brouard  3851:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   3852: 
                   3853:  jj1=0;
                   3854:  for(k1=1; k1<=m;k1++){
                   3855:    for(i1=1; i1<=ncodemax[k1];i1++){
                   3856:      jj1++;
                   3857:      if (cptcovn > 0) {
                   3858:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   3859:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   3860:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   3861:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3862:      }
                   3863:      /* Pij */
1.145     brouard  3864:      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> \
                   3865: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
1.126     brouard  3866:      /* Quasi-incidences */
                   3867:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145     brouard  3868:  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> \
                   3869: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
1.126     brouard  3870:        /* Period (stable) prevalence in each health state */
                   3871:        for(cpt=1; cpt<nlstate;cpt++){
1.145     brouard  3872:         fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
                   3873: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126     brouard  3874:        }
                   3875:      for(cpt=1; cpt<=nlstate;cpt++) {
                   3876:         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
                   3877: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
                   3878:      }
                   3879:    } /* end i1 */
                   3880:  }/* End k1 */
                   3881:  fprintf(fichtm,"</ul>");
                   3882: 
                   3883: 
                   3884:  fprintf(fichtm,"\
                   3885: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
                   3886:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
                   3887: 
                   3888:  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   3889:         subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
                   3890:  fprintf(fichtm,"\
                   3891:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   3892:         subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
                   3893: 
                   3894:  fprintf(fichtm,"\
                   3895:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   3896:         subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
                   3897:  fprintf(fichtm,"\
                   3898:  - 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): \
                   3899:    <a href=\"%s\">%s</a> <br>\n</li>",
                   3900:           estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
                   3901:  fprintf(fichtm,"\
                   3902:  - (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): \
                   3903:    <a href=\"%s\">%s</a> <br>\n</li>",
                   3904:           estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
                   3905:  fprintf(fichtm,"\
1.128     brouard  3906:  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.126     brouard  3907:         estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
                   3908:  fprintf(fichtm,"\
1.128     brouard  3909:  - 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",
                   3910:         estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126     brouard  3911:  fprintf(fichtm,"\
                   3912:  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
                   3913:         subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
                   3914: 
                   3915: /*  if(popforecast==1) fprintf(fichtm,"\n */
                   3916: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   3917: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                   3918: /*     <br>",fileres,fileres,fileres,fileres); */
                   3919: /*  else  */
                   3920: /*    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); */
                   3921:  fflush(fichtm);
                   3922:  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
                   3923: 
1.145     brouard  3924:  m=pow(2,cptcoveff);
1.126     brouard  3925:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   3926: 
                   3927:  jj1=0;
                   3928:  for(k1=1; k1<=m;k1++){
                   3929:    for(i1=1; i1<=ncodemax[k1];i1++){
                   3930:      jj1++;
                   3931:      if (cptcovn > 0) {
                   3932:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   3933:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   3934:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   3935:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3936:      }
                   3937:      for(cpt=1; cpt<=nlstate;cpt++) {
                   3938:        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145     brouard  3939: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
                   3940: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
1.126     brouard  3941:      }
                   3942:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128     brouard  3943: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
                   3944: true period expectancies (those weighted with period prevalences are also\
                   3945:  drawn in addition to the population based expectancies computed using\
                   3946:  observed and cahotic prevalences: %s%d.png<br>\
1.126     brouard  3947: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
                   3948:    } /* end i1 */
                   3949:  }/* End k1 */
                   3950:  fprintf(fichtm,"</ul>");
                   3951:  fflush(fichtm);
                   3952: }
                   3953: 
                   3954: /******************* Gnuplot file **************/
                   3955: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
                   3956: 
                   3957:   char dirfileres[132],optfileres[132];
1.130     brouard  3958:   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
                   3959:   int ng=0;
1.126     brouard  3960: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
                   3961: /*     printf("Problem with file %s",optionfilegnuplot); */
                   3962: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                   3963: /*   } */
                   3964: 
                   3965:   /*#ifdef windows */
                   3966:   fprintf(ficgp,"cd \"%s\" \n",pathc);
                   3967:     /*#endif */
                   3968:   m=pow(2,cptcoveff);
                   3969: 
                   3970:   strcpy(dirfileres,optionfilefiname);
                   3971:   strcpy(optfileres,"vpl");
                   3972:  /* 1eme*/
                   3973:   for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145     brouard  3974:     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
                   3975:      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
                   3976:      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126     brouard  3977:      fprintf(ficgp,"set xlabel \"Age\" \n\
                   3978: set ylabel \"Probability\" \n\
1.145     brouard  3979: set ter png small size 320, 240\n\
1.126     brouard  3980: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
                   3981: 
                   3982:      for (i=1; i<= nlstate ; i ++) {
                   3983:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131     brouard  3984:        else        fprintf(ficgp," \%%*lf (\%%*lf)");
1.126     brouard  3985:      }
1.145     brouard  3986:      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126     brouard  3987:      for (i=1; i<= nlstate ; i ++) {
                   3988:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3989:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3990:      } 
1.145     brouard  3991:      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
1.126     brouard  3992:      for (i=1; i<= nlstate ; i ++) {
                   3993:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3994:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3995:      }  
1.145     brouard  3996:      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126     brouard  3997:    }
                   3998:   }
                   3999:   /*2 eme*/
                   4000:   
                   4001:   for (k1=1; k1<= m ; k1 ++) { 
                   4002:     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145     brouard  4003:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126     brouard  4004:     
                   4005:     for (i=1; i<= nlstate+1 ; i ++) {
                   4006:       k=2*i;
                   4007:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
                   4008:       for (j=1; j<= nlstate+1 ; j ++) {
                   4009:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   4010:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   4011:       }   
                   4012:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                   4013:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
                   4014:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
                   4015:       for (j=1; j<= nlstate+1 ; j ++) {
                   4016:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   4017:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   4018:       }   
1.145     brouard  4019:       fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126     brouard  4020:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
                   4021:       for (j=1; j<= nlstate+1 ; j ++) {
                   4022:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   4023:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   4024:       }   
1.145     brouard  4025:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                   4026:       else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126     brouard  4027:     }
                   4028:   }
                   4029:   
                   4030:   /*3eme*/
                   4031:   
                   4032:   for (k1=1; k1<= m ; k1 ++) { 
                   4033:     for (cpt=1; cpt<= nlstate ; cpt ++) {
                   4034:       /*       k=2+nlstate*(2*cpt-2); */
                   4035:       k=2+(nlstate+1)*(cpt-1);
                   4036:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145     brouard  4037:       fprintf(ficgp,"set ter png small size 320, 240\n\
1.126     brouard  4038: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
                   4039:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   4040:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   4041:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   4042:        fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   4043:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   4044:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   4045:        
                   4046:       */
                   4047:       for (i=1; i< nlstate ; i ++) {
                   4048:        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);
                   4049:        /*      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);*/
                   4050:        
                   4051:       } 
                   4052:       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
                   4053:     }
                   4054:   }
                   4055:   
                   4056:   /* CV preval stable (period) */
                   4057:   for (k1=1; k1<= m ; k1 ++) { 
                   4058:     for (cpt=1; cpt<=nlstate ; cpt ++) {
                   4059:       k=3;
1.145     brouard  4060:       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126     brouard  4061:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145     brouard  4062: set ter png small size 320, 240\n\
1.126     brouard  4063: unset log y\n\
                   4064: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
                   4065:       
                   4066:       for (i=1; i< nlstate ; i ++)
                   4067:        fprintf(ficgp,"+$%d",k+i+1);
                   4068:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
                   4069:       
                   4070:       l=3+(nlstate+ndeath)*cpt;
                   4071:       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
                   4072:       for (i=1; i< nlstate ; i ++) {
                   4073:        l=3+(nlstate+ndeath)*cpt;
                   4074:        fprintf(ficgp,"+$%d",l+i+1);
                   4075:       }
                   4076:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
                   4077:     } 
                   4078:   }  
                   4079:   
                   4080:   /* proba elementaires */
                   4081:   for(i=1,jk=1; i <=nlstate; i++){
                   4082:     for(k=1; k <=(nlstate+ndeath); k++){
                   4083:       if (k != i) {
                   4084:        for(j=1; j <=ncovmodel; j++){
                   4085:          fprintf(ficgp,"p%d=%f ",jk,p[jk]);
                   4086:          jk++; 
                   4087:          fprintf(ficgp,"\n");
                   4088:        }
                   4089:       }
                   4090:     }
                   4091:    }
1.145     brouard  4092:   /*goto avoid;*/
1.126     brouard  4093:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
                   4094:      for(jk=1; jk <=m; jk++) {
1.145     brouard  4095:        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
1.126     brouard  4096:        if (ng==2)
                   4097:         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                   4098:        else
                   4099:         fprintf(ficgp,"\nset title \"Probability\"\n");
1.145     brouard  4100:        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
1.126     brouard  4101:        i=1;
                   4102:        for(k2=1; k2<=nlstate; k2++) {
                   4103:         k3=i;
                   4104:         for(k=1; k<=(nlstate+ndeath); k++) {
                   4105:           if (k != k2){
                   4106:             if(ng==2)
                   4107:               fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   4108:             else
                   4109:               fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141     brouard  4110:             ij=1;/* To be checked else nbcode[0][0] wrong */
1.126     brouard  4111:             for(j=3; j <=ncovmodel; j++) {
1.145     brouard  4112:               /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                   4113:               /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                   4114:               /*        ij++; */
                   4115:               /* } */
                   4116:               /* else */
1.126     brouard  4117:                 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   4118:             }
                   4119:             fprintf(ficgp,")/(1");
                   4120:             
                   4121:             for(k1=1; k1 <=nlstate; k1++){   
                   4122:               fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   4123:               ij=1;
                   4124:               for(j=3; j <=ncovmodel; j++){
1.145     brouard  4125:                 /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                   4126:                 /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                   4127:                 /*   ij++; */
                   4128:                 /* } */
                   4129:                 /* else */
1.126     brouard  4130:                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   4131:               }
                   4132:               fprintf(ficgp,")");
                   4133:             }
                   4134:             fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                   4135:             if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   4136:             i=i+ncovmodel;
                   4137:           }
                   4138:         } /* end k */
                   4139:        } /* end k2 */
                   4140:      } /* end jk */
                   4141:    } /* end ng */
1.145     brouard  4142:  avoid:
1.126     brouard  4143:    fflush(ficgp); 
                   4144: }  /* end gnuplot */
                   4145: 
                   4146: 
                   4147: /*************** Moving average **************/
                   4148: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
                   4149: 
                   4150:   int i, cpt, cptcod;
                   4151:   int modcovmax =1;
                   4152:   int mobilavrange, mob;
                   4153:   double age;
                   4154: 
                   4155:   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                   4156:                           a covariate has 2 modalities */
                   4157:   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
                   4158: 
                   4159:   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   4160:     if(mobilav==1) mobilavrange=5; /* default */
                   4161:     else mobilavrange=mobilav;
                   4162:     for (age=bage; age<=fage; age++)
                   4163:       for (i=1; i<=nlstate;i++)
                   4164:        for (cptcod=1;cptcod<=modcovmax;cptcod++)
                   4165:          mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   4166:     /* We keep the original values on the extreme ages bage, fage and for 
                   4167:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                   4168:        we use a 5 terms etc. until the borders are no more concerned. 
                   4169:     */ 
                   4170:     for (mob=3;mob <=mobilavrange;mob=mob+2){
                   4171:       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                   4172:        for (i=1; i<=nlstate;i++){
                   4173:          for (cptcod=1;cptcod<=modcovmax;cptcod++){
                   4174:            mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                   4175:              for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   4176:                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   4177:                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                   4178:              }
                   4179:            mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                   4180:          }
                   4181:        }
                   4182:       }/* end age */
                   4183:     }/* end mob */
                   4184:   }else return -1;
                   4185:   return 0;
                   4186: }/* End movingaverage */
                   4187: 
                   4188: 
                   4189: /************** Forecasting ******************/
                   4190: 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){
                   4191:   /* proj1, year, month, day of starting projection 
                   4192:      agemin, agemax range of age
                   4193:      dateprev1 dateprev2 range of dates during which prevalence is computed
                   4194:      anproj2 year of en of projection (same day and month as proj1).
                   4195:   */
                   4196:   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
                   4197:   int *popage;
                   4198:   double agec; /* generic age */
                   4199:   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
                   4200:   double *popeffectif,*popcount;
                   4201:   double ***p3mat;
                   4202:   double ***mobaverage;
                   4203:   char fileresf[FILENAMELENGTH];
                   4204: 
                   4205:   agelim=AGESUP;
                   4206:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   4207:  
                   4208:   strcpy(fileresf,"f"); 
                   4209:   strcat(fileresf,fileres);
                   4210:   if((ficresf=fopen(fileresf,"w"))==NULL) {
                   4211:     printf("Problem with forecast resultfile: %s\n", fileresf);
                   4212:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
                   4213:   }
                   4214:   printf("Computing forecasting: result on file '%s' \n", fileresf);
                   4215:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
                   4216: 
                   4217:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   4218: 
                   4219:   if (mobilav!=0) {
                   4220:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4221:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   4222:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   4223:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   4224:     }
                   4225:   }
                   4226: 
                   4227:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   4228:   if (stepm<=12) stepsize=1;
                   4229:   if(estepm < stepm){
                   4230:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   4231:   }
                   4232:   else  hstepm=estepm;   
                   4233: 
                   4234:   hstepm=hstepm/stepm; 
                   4235:   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                   4236:                                fractional in yp1 */
                   4237:   anprojmean=yp;
                   4238:   yp2=modf((yp1*12),&yp);
                   4239:   mprojmean=yp;
                   4240:   yp1=modf((yp2*30.5),&yp);
                   4241:   jprojmean=yp;
                   4242:   if(jprojmean==0) jprojmean=1;
                   4243:   if(mprojmean==0) jprojmean=1;
                   4244: 
                   4245:   i1=cptcoveff;
                   4246:   if (cptcovn < 1){i1=1;}
                   4247:   
                   4248:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
                   4249:   
                   4250:   fprintf(ficresf,"#****** Routine prevforecast **\n");
                   4251: 
                   4252: /*           if (h==(int)(YEARM*yearp)){ */
                   4253:   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
                   4254:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   4255:       k=k+1;
                   4256:       fprintf(ficresf,"\n#******");
                   4257:       for(j=1;j<=cptcoveff;j++) {
                   4258:        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]]);
                   4259:       }
                   4260:       fprintf(ficresf,"******\n");
                   4261:       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
                   4262:       for(j=1; j<=nlstate+ndeath;j++){ 
                   4263:        for(i=1; i<=nlstate;i++)              
                   4264:           fprintf(ficresf," p%d%d",i,j);
                   4265:        fprintf(ficresf," p.%d",j);
                   4266:       }
                   4267:       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
                   4268:        fprintf(ficresf,"\n");
                   4269:        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                   4270: 
                   4271:        for (agec=fage; agec>=(ageminpar-1); agec--){ 
                   4272:          nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                   4273:          nhstepm = nhstepm/hstepm; 
                   4274:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4275:          oldm=oldms;savm=savms;
                   4276:          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   4277:        
                   4278:          for (h=0; h<=nhstepm; h++){
                   4279:            if (h*hstepm/YEARM*stepm ==yearp) {
                   4280:               fprintf(ficresf,"\n");
                   4281:               for(j=1;j<=cptcoveff;j++) 
                   4282:                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4283:              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                   4284:            } 
                   4285:            for(j=1; j<=nlstate+ndeath;j++) {
                   4286:              ppij=0.;
                   4287:              for(i=1; i<=nlstate;i++) {
                   4288:                if (mobilav==1) 
                   4289:                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   4290:                else {
                   4291:                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   4292:                }
                   4293:                if (h*hstepm/YEARM*stepm== yearp) {
                   4294:                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   4295:                }
                   4296:              } /* end i */
                   4297:              if (h*hstepm/YEARM*stepm==yearp) {
                   4298:                fprintf(ficresf," %.3f", ppij);
                   4299:              }
                   4300:            }/* end j */
                   4301:          } /* end h */
                   4302:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4303:        } /* end agec */
                   4304:       } /* end yearp */
                   4305:     } /* end cptcod */
                   4306:   } /* end  cptcov */
                   4307:        
                   4308:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4309: 
                   4310:   fclose(ficresf);
                   4311: }
                   4312: 
                   4313: /************** Forecasting *****not tested NB*************/
                   4314: 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){
                   4315:   
                   4316:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
                   4317:   int *popage;
                   4318:   double calagedatem, agelim, kk1, kk2;
                   4319:   double *popeffectif,*popcount;
                   4320:   double ***p3mat,***tabpop,***tabpopprev;
                   4321:   double ***mobaverage;
                   4322:   char filerespop[FILENAMELENGTH];
                   4323: 
                   4324:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4325:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4326:   agelim=AGESUP;
                   4327:   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
                   4328:   
                   4329:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   4330:   
                   4331:   
                   4332:   strcpy(filerespop,"pop"); 
                   4333:   strcat(filerespop,fileres);
                   4334:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
                   4335:     printf("Problem with forecast resultfile: %s\n", filerespop);
                   4336:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
                   4337:   }
                   4338:   printf("Computing forecasting: result on file '%s' \n", filerespop);
                   4339:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
                   4340: 
                   4341:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   4342: 
                   4343:   if (mobilav!=0) {
                   4344:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4345:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   4346:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   4347:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   4348:     }
                   4349:   }
                   4350: 
                   4351:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   4352:   if (stepm<=12) stepsize=1;
                   4353:   
                   4354:   agelim=AGESUP;
                   4355:   
                   4356:   hstepm=1;
                   4357:   hstepm=hstepm/stepm; 
                   4358:   
                   4359:   if (popforecast==1) {
                   4360:     if((ficpop=fopen(popfile,"r"))==NULL) {
                   4361:       printf("Problem with population file : %s\n",popfile);exit(0);
                   4362:       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
                   4363:     } 
                   4364:     popage=ivector(0,AGESUP);
                   4365:     popeffectif=vector(0,AGESUP);
                   4366:     popcount=vector(0,AGESUP);
                   4367:     
                   4368:     i=1;   
                   4369:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
                   4370:    
                   4371:     imx=i;
                   4372:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
                   4373:   }
                   4374: 
                   4375:   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
                   4376:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   4377:       k=k+1;
                   4378:       fprintf(ficrespop,"\n#******");
                   4379:       for(j=1;j<=cptcoveff;j++) {
                   4380:        fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4381:       }
                   4382:       fprintf(ficrespop,"******\n");
                   4383:       fprintf(ficrespop,"# Age");
                   4384:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
                   4385:       if (popforecast==1)  fprintf(ficrespop," [Population]");
                   4386:       
                   4387:       for (cpt=0; cpt<=0;cpt++) { 
                   4388:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   4389:        
                   4390:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                   4391:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   4392:          nhstepm = nhstepm/hstepm; 
                   4393:          
                   4394:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4395:          oldm=oldms;savm=savms;
                   4396:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   4397:        
                   4398:          for (h=0; h<=nhstepm; h++){
                   4399:            if (h==(int) (calagedatem+YEARM*cpt)) {
                   4400:              fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   4401:            } 
                   4402:            for(j=1; j<=nlstate+ndeath;j++) {
                   4403:              kk1=0.;kk2=0;
                   4404:              for(i=1; i<=nlstate;i++) {              
                   4405:                if (mobilav==1) 
                   4406:                  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   4407:                else {
                   4408:                  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   4409:                }
                   4410:              }
                   4411:              if (h==(int)(calagedatem+12*cpt)){
                   4412:                tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   4413:                  /*fprintf(ficrespop," %.3f", kk1);
                   4414:                    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                   4415:              }
                   4416:            }
                   4417:            for(i=1; i<=nlstate;i++){
                   4418:              kk1=0.;
                   4419:                for(j=1; j<=nlstate;j++){
                   4420:                  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   4421:                }
                   4422:                  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
                   4423:            }
                   4424: 
                   4425:            if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                   4426:              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
                   4427:          }
                   4428:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4429:        }
                   4430:       }
                   4431:  
                   4432:   /******/
                   4433: 
                   4434:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
                   4435:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   4436:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                   4437:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   4438:          nhstepm = nhstepm/hstepm; 
                   4439:          
                   4440:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4441:          oldm=oldms;savm=savms;
                   4442:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   4443:          for (h=0; h<=nhstepm; h++){
                   4444:            if (h==(int) (calagedatem+YEARM*cpt)) {
                   4445:              fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   4446:            } 
                   4447:            for(j=1; j<=nlstate+ndeath;j++) {
                   4448:              kk1=0.;kk2=0;
                   4449:              for(i=1; i<=nlstate;i++) {              
                   4450:                kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                   4451:              }
                   4452:              if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
                   4453:            }
                   4454:          }
                   4455:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4456:        }
                   4457:       }
                   4458:    } 
                   4459:   }
                   4460:  
                   4461:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4462: 
                   4463:   if (popforecast==1) {
                   4464:     free_ivector(popage,0,AGESUP);
                   4465:     free_vector(popeffectif,0,AGESUP);
                   4466:     free_vector(popcount,0,AGESUP);
                   4467:   }
                   4468:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4469:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4470:   fclose(ficrespop);
                   4471: } /* End of popforecast */
                   4472: 
                   4473: int fileappend(FILE *fichier, char *optionfich)
                   4474: {
                   4475:   if((fichier=fopen(optionfich,"a"))==NULL) {
                   4476:     printf("Problem with file: %s\n", optionfich);
                   4477:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
                   4478:     return (0);
                   4479:   }
                   4480:   fflush(fichier);
                   4481:   return (1);
                   4482: }
                   4483: 
                   4484: 
                   4485: /**************** function prwizard **********************/
                   4486: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
                   4487: {
                   4488: 
                   4489:   /* Wizard to print covariance matrix template */
                   4490: 
                   4491:   char ca[32], cb[32], cc[32];
                   4492:   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
                   4493:   int numlinepar;
                   4494: 
                   4495:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4496:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4497:   for(i=1; i <=nlstate; i++){
                   4498:     jj=0;
                   4499:     for(j=1; j <=nlstate+ndeath; j++){
                   4500:       if(j==i) continue;
                   4501:       jj++;
                   4502:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   4503:       printf("%1d%1d",i,j);
                   4504:       fprintf(ficparo,"%1d%1d",i,j);
                   4505:       for(k=1; k<=ncovmodel;k++){
                   4506:        /*        printf(" %lf",param[i][j][k]); */
                   4507:        /*        fprintf(ficparo," %lf",param[i][j][k]); */
                   4508:        printf(" 0.");
                   4509:        fprintf(ficparo," 0.");
                   4510:       }
                   4511:       printf("\n");
                   4512:       fprintf(ficparo,"\n");
                   4513:     }
                   4514:   }
                   4515:   printf("# Scales (for hessian or gradient estimation)\n");
                   4516:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
                   4517:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
                   4518:   for(i=1; i <=nlstate; i++){
                   4519:     jj=0;
                   4520:     for(j=1; j <=nlstate+ndeath; j++){
                   4521:       if(j==i) continue;
                   4522:       jj++;
                   4523:       fprintf(ficparo,"%1d%1d",i,j);
                   4524:       printf("%1d%1d",i,j);
                   4525:       fflush(stdout);
                   4526:       for(k=1; k<=ncovmodel;k++){
                   4527:        /*      printf(" %le",delti3[i][j][k]); */
                   4528:        /*      fprintf(ficparo," %le",delti3[i][j][k]); */
                   4529:        printf(" 0.");
                   4530:        fprintf(ficparo," 0.");
                   4531:       }
                   4532:       numlinepar++;
                   4533:       printf("\n");
                   4534:       fprintf(ficparo,"\n");
                   4535:     }
                   4536:   }
                   4537:   printf("# Covariance matrix\n");
                   4538: /* # 121 Var(a12)\n\ */
                   4539: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   4540: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   4541: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   4542: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   4543: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   4544: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   4545: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   4546:   fflush(stdout);
                   4547:   fprintf(ficparo,"# Covariance matrix\n");
                   4548:   /* # 121 Var(a12)\n\ */
                   4549:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   4550:   /* #   ...\n\ */
                   4551:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
                   4552:   
                   4553:   for(itimes=1;itimes<=2;itimes++){
                   4554:     jj=0;
                   4555:     for(i=1; i <=nlstate; i++){
                   4556:       for(j=1; j <=nlstate+ndeath; j++){
                   4557:        if(j==i) continue;
                   4558:        for(k=1; k<=ncovmodel;k++){
                   4559:          jj++;
                   4560:          ca[0]= k+'a'-1;ca[1]='\0';
                   4561:          if(itimes==1){
                   4562:            printf("#%1d%1d%d",i,j,k);
                   4563:            fprintf(ficparo,"#%1d%1d%d",i,j,k);
                   4564:          }else{
                   4565:            printf("%1d%1d%d",i,j,k);
                   4566:            fprintf(ficparo,"%1d%1d%d",i,j,k);
                   4567:            /*  printf(" %.5le",matcov[i][j]); */
                   4568:          }
                   4569:          ll=0;
                   4570:          for(li=1;li <=nlstate; li++){
                   4571:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   4572:              if(lj==li) continue;
                   4573:              for(lk=1;lk<=ncovmodel;lk++){
                   4574:                ll++;
                   4575:                if(ll<=jj){
                   4576:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   4577:                  if(ll<jj){
                   4578:                    if(itimes==1){
                   4579:                      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4580:                      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4581:                    }else{
                   4582:                      printf(" 0.");
                   4583:                      fprintf(ficparo," 0.");
                   4584:                    }
                   4585:                  }else{
                   4586:                    if(itimes==1){
                   4587:                      printf(" Var(%s%1d%1d)",ca,i,j);
                   4588:                      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                   4589:                    }else{
                   4590:                      printf(" 0.");
                   4591:                      fprintf(ficparo," 0.");
                   4592:                    }
                   4593:                  }
                   4594:                }
                   4595:              } /* end lk */
                   4596:            } /* end lj */
                   4597:          } /* end li */
                   4598:          printf("\n");
                   4599:          fprintf(ficparo,"\n");
                   4600:          numlinepar++;
                   4601:        } /* end k*/
                   4602:       } /*end j */
                   4603:     } /* end i */
                   4604:   } /* end itimes */
                   4605: 
                   4606: } /* end of prwizard */
                   4607: /******************* Gompertz Likelihood ******************************/
                   4608: double gompertz(double x[])
                   4609: { 
                   4610:   double A,B,L=0.0,sump=0.,num=0.;
                   4611:   int i,n=0; /* n is the size of the sample */
                   4612: 
                   4613:   for (i=0;i<=imx-1 ; i++) {
                   4614:     sump=sump+weight[i];
                   4615:     /*    sump=sump+1;*/
                   4616:     num=num+1;
                   4617:   }
                   4618:  
                   4619:  
                   4620:   /* for (i=0; i<=imx; i++) 
                   4621:      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]);*/
                   4622: 
                   4623:   for (i=1;i<=imx ; i++)
                   4624:     {
                   4625:       if (cens[i] == 1 && wav[i]>1)
                   4626:        A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
                   4627:       
                   4628:       if (cens[i] == 0 && wav[i]>1)
                   4629:        A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                   4630:             +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
                   4631:       
                   4632:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   4633:       if (wav[i] > 1 ) { /* ??? */
                   4634:        L=L+A*weight[i];
                   4635:        /*      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]);*/
                   4636:       }
                   4637:     }
                   4638: 
                   4639:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   4640:  
                   4641:   return -2*L*num/sump;
                   4642: }
                   4643: 
1.136     brouard  4644: #ifdef GSL
                   4645: /******************* Gompertz_f Likelihood ******************************/
                   4646: double gompertz_f(const gsl_vector *v, void *params)
                   4647: { 
                   4648:   double A,B,LL=0.0,sump=0.,num=0.;
                   4649:   double *x= (double *) v->data;
                   4650:   int i,n=0; /* n is the size of the sample */
                   4651: 
                   4652:   for (i=0;i<=imx-1 ; i++) {
                   4653:     sump=sump+weight[i];
                   4654:     /*    sump=sump+1;*/
                   4655:     num=num+1;
                   4656:   }
                   4657:  
                   4658:  
                   4659:   /* for (i=0; i<=imx; i++) 
                   4660:      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]);*/
                   4661:   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
                   4662:   for (i=1;i<=imx ; i++)
                   4663:     {
                   4664:       if (cens[i] == 1 && wav[i]>1)
                   4665:        A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
                   4666:       
                   4667:       if (cens[i] == 0 && wav[i]>1)
                   4668:        A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                   4669:             +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
                   4670:       
                   4671:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   4672:       if (wav[i] > 1 ) { /* ??? */
                   4673:        LL=LL+A*weight[i];
                   4674:        /*      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]);*/
                   4675:       }
                   4676:     }
                   4677: 
                   4678:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   4679:   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
                   4680:  
                   4681:   return -2*LL*num/sump;
                   4682: }
                   4683: #endif
                   4684: 
1.126     brouard  4685: /******************* Printing html file ***********/
                   4686: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                   4687:                  int lastpass, int stepm, int weightopt, char model[],\
                   4688:                  int imx,  double p[],double **matcov,double agemortsup){
                   4689:   int i,k;
                   4690: 
                   4691:   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
                   4692:   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
                   4693:   for (i=1;i<=2;i++) 
                   4694:     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]));
                   4695:   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
                   4696:   fprintf(fichtm,"</ul>");
                   4697: 
                   4698: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
                   4699: 
                   4700:  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>");
                   4701: 
                   4702:  for (k=agegomp;k<(agemortsup-2);k++) 
                   4703:    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]);
                   4704: 
                   4705:  
                   4706:   fflush(fichtm);
                   4707: }
                   4708: 
                   4709: /******************* Gnuplot file **************/
                   4710: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
                   4711: 
                   4712:   char dirfileres[132],optfileres[132];
                   4713:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
                   4714:   int ng;
                   4715: 
                   4716: 
                   4717:   /*#ifdef windows */
                   4718:   fprintf(ficgp,"cd \"%s\" \n",pathc);
                   4719:     /*#endif */
                   4720: 
                   4721: 
                   4722:   strcpy(dirfileres,optionfilefiname);
                   4723:   strcpy(optfileres,"vpl");
                   4724:   fprintf(ficgp,"set out \"graphmort.png\"\n "); 
                   4725:   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
1.145     brouard  4726:   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
                   4727:   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126     brouard  4728:   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
                   4729: 
                   4730: } 
                   4731: 
1.136     brouard  4732: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
                   4733: {
1.126     brouard  4734: 
1.136     brouard  4735:   /*-------- data file ----------*/
                   4736:   FILE *fic;
                   4737:   char dummy[]="                         ";
                   4738:   int i, j, n;
                   4739:   int linei, month, year,iout;
                   4740:   char line[MAXLINE], linetmp[MAXLINE];
                   4741:   char stra[80], strb[80];
                   4742:   char *stratrunc;
                   4743:   int lstra;
1.126     brouard  4744: 
                   4745: 
1.136     brouard  4746:   if((fic=fopen(datafile,"r"))==NULL)    {
                   4747:     printf("Problem while opening datafile: %s\n", datafile);return 1;
                   4748:     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
                   4749:   }
1.126     brouard  4750: 
1.136     brouard  4751:   i=1;
                   4752:   linei=0;
                   4753:   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
                   4754:     linei=linei+1;
                   4755:     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
                   4756:       if(line[j] == '\t')
                   4757:        line[j] = ' ';
                   4758:     }
                   4759:     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
                   4760:       ;
                   4761:     };
                   4762:     line[j+1]=0;  /* Trims blanks at end of line */
                   4763:     if(line[0]=='#'){
                   4764:       fprintf(ficlog,"Comment line\n%s\n",line);
                   4765:       printf("Comment line\n%s\n",line);
                   4766:       continue;
                   4767:     }
                   4768:     trimbb(linetmp,line); /* Trims multiple blanks in line */
                   4769:     for (j=0; line[j]!='\0';j++){
                   4770:       line[j]=linetmp[j];
                   4771:     }
                   4772:   
1.126     brouard  4773: 
1.136     brouard  4774:     for (j=maxwav;j>=1;j--){
1.137     brouard  4775:       cutv(stra, strb, line, ' '); 
1.136     brouard  4776:       if(strb[0]=='.') { /* Missing status */
                   4777:        lval=-1;
                   4778:       }else{
                   4779:        errno=0;
                   4780:        lval=strtol(strb,&endptr,10); 
                   4781:       /*       if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                   4782:        if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  4783:          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);
                   4784:          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136     brouard  4785:          return 1;
                   4786:        }
                   4787:       }
                   4788:       s[j][i]=lval;
                   4789:       
                   4790:       strcpy(line,stra);
                   4791:       cutv(stra, strb,line,' ');
                   4792:       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
                   4793:       }
1.145     brouard  4794:       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
1.136     brouard  4795:        month=99;
                   4796:        year=9999;
                   4797:       }else{
1.141     brouard  4798:        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);
                   4799:        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136     brouard  4800:        return 1;
                   4801:       }
                   4802:       anint[j][i]= (double) year; 
                   4803:       mint[j][i]= (double)month; 
                   4804:       strcpy(line,stra);
                   4805:     } /* ENd Waves */
                   4806:     
                   4807:     cutv(stra, strb,line,' '); 
                   4808:     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
                   4809:     }
                   4810:     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
                   4811:       month=99;
                   4812:       year=9999;
                   4813:     }else{
1.141     brouard  4814:       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);
                   4815:        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136     brouard  4816:        return 1;
                   4817:     }
                   4818:     andc[i]=(double) year; 
                   4819:     moisdc[i]=(double) month; 
                   4820:     strcpy(line,stra);
                   4821:     
                   4822:     cutv(stra, strb,line,' '); 
                   4823:     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
                   4824:     }
1.145     brouard  4825:     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
1.136     brouard  4826:       month=99;
                   4827:       year=9999;
                   4828:     }else{
1.141     brouard  4829:       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);
                   4830:       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136     brouard  4831:        return 1;
                   4832:     }
                   4833:     if (year==9999) {
1.141     brouard  4834:       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);
                   4835:       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136     brouard  4836:        return 1;
1.126     brouard  4837: 
1.136     brouard  4838:     }
                   4839:     annais[i]=(double)(year);
                   4840:     moisnais[i]=(double)(month); 
                   4841:     strcpy(line,stra);
                   4842:     
                   4843:     cutv(stra, strb,line,' '); 
                   4844:     errno=0;
                   4845:     dval=strtod(strb,&endptr); 
                   4846:     if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  4847:       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
                   4848:       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
1.136     brouard  4849:       fflush(ficlog);
                   4850:       return 1;
                   4851:     }
                   4852:     weight[i]=dval; 
                   4853:     strcpy(line,stra);
                   4854:     
                   4855:     for (j=ncovcol;j>=1;j--){
                   4856:       cutv(stra, strb,line,' '); 
                   4857:       if(strb[0]=='.') { /* Missing status */
                   4858:        lval=-1;
                   4859:       }else{
                   4860:        errno=0;
                   4861:        lval=strtol(strb,&endptr,10); 
                   4862:        if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  4863:          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);
                   4864:          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136     brouard  4865:          return 1;
                   4866:        }
                   4867:       }
                   4868:       if(lval <-1 || lval >1){
1.141     brouard  4869:        printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  4870:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   4871:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
                   4872:  For example, for multinomial values like 1, 2 and 3,\n \
                   4873:  build V1=0 V2=0 for the reference value (1),\n \
                   4874:         V1=1 V2=0 for (2) \n \
                   4875:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
                   4876:  output of IMaCh is often meaningless.\n \
                   4877:  Exiting.\n",lval,linei, i,line,j);
1.141     brouard  4878:        fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  4879:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   4880:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
                   4881:  For example, for multinomial values like 1, 2 and 3,\n \
                   4882:  build V1=0 V2=0 for the reference value (1),\n \
                   4883:         V1=1 V2=0 for (2) \n \
                   4884:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
                   4885:  output of IMaCh is often meaningless.\n \
                   4886:  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
                   4887:        return 1;
                   4888:       }
                   4889:       covar[j][i]=(double)(lval);
                   4890:       strcpy(line,stra);
                   4891:     }  
                   4892:     lstra=strlen(stra);
                   4893:      
                   4894:     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
                   4895:       stratrunc = &(stra[lstra-9]);
                   4896:       num[i]=atol(stratrunc);
                   4897:     }
                   4898:     else
                   4899:       num[i]=atol(stra);
                   4900:     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
                   4901:       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;}*/
                   4902:     
                   4903:     i=i+1;
                   4904:   } /* End loop reading  data */
1.126     brouard  4905: 
1.136     brouard  4906:   *imax=i-1; /* Number of individuals */
                   4907:   fclose(fic);
                   4908:  
                   4909:   return (0);
                   4910:   endread:
                   4911:     printf("Exiting readdata: ");
                   4912:     fclose(fic);
                   4913:     return (1);
1.126     brouard  4914: 
                   4915: 
                   4916: 
1.136     brouard  4917: }
1.145     brouard  4918: void removespace(char *str) {
                   4919:   char *p1 = str, *p2 = str;
                   4920:   do
                   4921:     while (*p2 == ' ')
                   4922:       p2++;
                   4923:   while (*p1++ = *p2++);
                   4924: }
                   4925: 
                   4926: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
                   4927:    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
                   4928:    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
                   4929:    * - cptcovn or number of covariates k of the models excluding age*products =6
                   4930:    * - cptcovage number of covariates with age*products =2
                   4931:    * - cptcovs number of simple covariates
                   4932:    * - 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
                   4933:    *     which is a new column after the 9 (ncovcol) variables. 
                   4934:    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
                   4935:    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
                   4936:    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
                   4937:    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
                   4938:  */
1.136     brouard  4939: {
1.145     brouard  4940:   int i, j, k, ks;
1.136     brouard  4941:   int i1, j1, k1, k2;
                   4942:   char modelsav[80];
1.145     brouard  4943:   char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136     brouard  4944: 
1.145     brouard  4945:   /*removespace(model);*/
1.136     brouard  4946:   if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145     brouard  4947:     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
                   4948:     j=nbocc(model,'+'); /**< j=Number of '+' */
                   4949:     j1=nbocc(model,'*'); /**< j1=Number of '*' */
                   4950:     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
                   4951:     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                   4952:                   /* including age products which are counted in cptcovage.
                   4953:                  /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
                   4954:     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
                   4955:     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
1.136     brouard  4956:     strcpy(modelsav,model); 
1.137     brouard  4957:     if (strstr(model,"AGE") !=0){
                   4958:       printf("Error. AGE must be in lower case 'age' model=%s ",model);
                   4959:       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136     brouard  4960:       return 1;
                   4961:     }
1.141     brouard  4962:     if (strstr(model,"v") !=0){
                   4963:       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
                   4964:       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
                   4965:       return 1;
                   4966:     }
1.136     brouard  4967:     
1.145     brouard  4968:     /*   Design
                   4969:      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
                   4970:      *  <          ncovcol=8                >
                   4971:      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
                   4972:      *   k=  1    2      3       4     5       6      7        8
                   4973:      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
                   4974:      *  covar[k,i], value of kth covariate if not including age for individual i:
                   4975:      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
                   4976:      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
                   4977:      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
                   4978:      *  Tage[++cptcovage]=k
                   4979:      *       if products, new covar are created after ncovcol with k1
                   4980:      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
                   4981:      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
                   4982:      *  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
                   4983:      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
                   4984:      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
                   4985:      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
                   4986:      *  <          ncovcol=8                >
                   4987:      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
                   4988:      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
                   4989:      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
                   4990:      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   4991:      * p Tprod[1]@2={                         6, 5}
                   4992:      *p Tvard[1][1]@4= {7, 8, 5, 6}
                   4993:      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
                   4994:      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   4995:      *How to reorganize?
                   4996:      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
                   4997:      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   4998:      *       {2,   1,     4,      8,    5,      6,     3,       7}
                   4999:      * Struct []
                   5000:      */
                   5001: 
1.136     brouard  5002:     /* This loop fills the array Tvar from the string 'model'.*/
                   5003:     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137     brouard  5004:     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
                   5005:     /*         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
                   5006:     /*         k=3 V4 Tvar[k=3]= 4 (from V4) */
                   5007:     /*         k=2 V1 Tvar[k=2]= 1 (from V1) */
                   5008:     /*         k=1 Tvar[1]=2 (from V2) */
                   5009:     /*         k=5 Tvar[5] */
                   5010:     /* for (k=1; k<=cptcovn;k++) { */
                   5011:     /*         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
                   5012:     /*         } */
                   5013:     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145     brouard  5014:     /*
                   5015:      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
                   5016:     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
                   5017:         Tvar[k]=0;
                   5018:     cptcovage=0;
                   5019:     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
                   5020:       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                   5021:                                     modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
1.137     brouard  5022:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136     brouard  5023:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
                   5024:       /*scanf("%d",i);*/
1.145     brouard  5025:       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
                   5026:        cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
                   5027:        if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
                   5028:          /* covar is not filled and then is empty */
1.136     brouard  5029:          cptcovprod--;
1.145     brouard  5030:          cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
                   5031:          Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136     brouard  5032:          cptcovage++; /* Sums the number of covariates which include age as a product */
1.137     brouard  5033:          Tage[cptcovage]=k;  /* Tage[1] = 4 */
1.136     brouard  5034:          /*printf("stre=%s ", stre);*/
1.137     brouard  5035:        } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136     brouard  5036:          cptcovprod--;
1.145     brouard  5037:          cutl(stre,strb,strc,'V');
1.136     brouard  5038:          Tvar[k]=atoi(stre);
                   5039:          cptcovage++;
                   5040:          Tage[cptcovage]=k;
1.137     brouard  5041:        } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
                   5042:          /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145     brouard  5043:          cptcovn++;
                   5044:          cptcovprodnoage++;k1++;
                   5045:          cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                   5046:          Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137     brouard  5047:                                  because this model-covariate is a construction we invent a new column
                   5048:                                  ncovcol + k1
                   5049:                                  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                   5050:                                  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145     brouard  5051:          cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137     brouard  5052:          Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
1.145     brouard  5053:          Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
                   5054:          Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
                   5055:          k2=k2+2;
                   5056:          Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
                   5057:          Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137     brouard  5058:          for (i=1; i<=lastobs;i++){
                   5059:            /* Computes the new covariate which is a product of
1.145     brouard  5060:               covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136     brouard  5061:            covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137     brouard  5062:          }
                   5063:        } /* End age is not in the model */
                   5064:       } /* End if model includes a product */
1.136     brouard  5065:       else { /* no more sum */
                   5066:        /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
                   5067:        /*  scanf("%d",i);*/
1.145     brouard  5068:        cutl(strd,strc,strb,'V');
                   5069:        ks++; /**< Number of simple covariates */
                   5070:        cptcovn++;
                   5071:        Tvar[k]=atoi(strd);
1.136     brouard  5072:       }
1.137     brouard  5073:       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
1.136     brouard  5074:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                   5075:        scanf("%d",i);*/
                   5076:     } /* end of loop + */
                   5077:   } /* end model */
                   5078:   
                   5079:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
                   5080:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
                   5081: 
                   5082:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
                   5083:   printf("cptcovprod=%d ", cptcovprod);
                   5084:   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
                   5085: 
                   5086:   scanf("%d ",i);*/
                   5087: 
                   5088: 
1.137     brouard  5089:   return (0); /* with covar[new additional covariate if product] and Tage if age */ 
1.136     brouard  5090:   endread:
                   5091:     printf("Exiting decodemodel: ");
                   5092:     return (1);
                   5093: }
                   5094: 
                   5095: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
                   5096: {
                   5097:   int i, m;
                   5098: 
                   5099:   for (i=1; i<=imx; i++) {
                   5100:     for(m=2; (m<= maxwav); m++) {
                   5101:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
                   5102:        anint[m][i]=9999;
                   5103:        s[m][i]=-1;
                   5104:       }
                   5105:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
                   5106:        *nberr++;
                   5107:        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\n",(int)moisdc[i],(int)andc[i],num[i],i);
                   5108:        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\n",(int)moisdc[i],(int)andc[i],num[i],i);
                   5109:        s[m][i]=-1;
                   5110:       }
                   5111:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
                   5112:        *nberr++;
                   5113:        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]); 
                   5114:        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]); 
                   5115:        s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
                   5116:       }
                   5117:     }
                   5118:   }
                   5119: 
                   5120:   for (i=1; i<=imx; i++)  {
                   5121:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
                   5122:     for(m=firstpass; (m<= lastpass); m++){
                   5123:       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
                   5124:        if (s[m][i] >= nlstate+1) {
                   5125:          if(agedc[i]>0)
                   5126:            if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                   5127:              agev[m][i]=agedc[i];
                   5128:          /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
                   5129:            else {
                   5130:              if ((int)andc[i]!=9999){
                   5131:                nbwarn++;
                   5132:                printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   5133:                fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   5134:                agev[m][i]=-1;
                   5135:              }
                   5136:            }
                   5137:        }
                   5138:        else if(s[m][i] !=9){ /* Standard case, age in fractional
                   5139:                                 years but with the precision of a month */
                   5140:          agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
                   5141:          if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
                   5142:            agev[m][i]=1;
                   5143:          else if(agev[m][i] < *agemin){ 
                   5144:            *agemin=agev[m][i];
                   5145:            printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
                   5146:          }
                   5147:          else if(agev[m][i] >*agemax){
                   5148:            *agemax=agev[m][i];
1.139     brouard  5149:            printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
1.136     brouard  5150:          }
                   5151:          /*agev[m][i]=anint[m][i]-annais[i];*/
                   5152:          /*     agev[m][i] = age[i]+2*m;*/
                   5153:        }
                   5154:        else { /* =9 */
                   5155:          agev[m][i]=1;
                   5156:          s[m][i]=-1;
                   5157:        }
                   5158:       }
                   5159:       else /*= 0 Unknown */
                   5160:        agev[m][i]=1;
                   5161:     }
                   5162:     
                   5163:   }
                   5164:   for (i=1; i<=imx; i++)  {
                   5165:     for(m=firstpass; (m<=lastpass); m++){
                   5166:       if (s[m][i] > (nlstate+ndeath)) {
                   5167:        *nberr++;
                   5168:        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);     
                   5169:        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);     
                   5170:        return 1;
                   5171:       }
                   5172:     }
                   5173:   }
                   5174: 
                   5175:   /*for (i=1; i<=imx; i++){
                   5176:   for (m=firstpass; (m<lastpass); m++){
                   5177:      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
                   5178: }
                   5179: 
                   5180: }*/
                   5181: 
                   5182: 
1.139     brouard  5183:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
                   5184:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
1.136     brouard  5185: 
                   5186:   return (0);
                   5187:   endread:
                   5188:     printf("Exiting calandcheckages: ");
                   5189:     return (1);
                   5190: }
                   5191: 
                   5192: 
                   5193: /***********************************************/
                   5194: /**************** Main Program *****************/
                   5195: /***********************************************/
                   5196: 
                   5197: int main(int argc, char *argv[])
                   5198: {
                   5199: #ifdef GSL
                   5200:   const gsl_multimin_fminimizer_type *T;
                   5201:   size_t iteri = 0, it;
                   5202:   int rval = GSL_CONTINUE;
                   5203:   int status = GSL_SUCCESS;
                   5204:   double ssval;
                   5205: #endif
                   5206:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
                   5207:   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
                   5208:   int linei, month, year,iout;
                   5209:   int jj, ll, li, lj, lk, imk;
                   5210:   int numlinepar=0; /* Current linenumber of parameter file */
                   5211:   int itimes;
                   5212:   int NDIM=2;
                   5213:   int vpopbased=0;
                   5214: 
                   5215:   char ca[32], cb[32], cc[32];
                   5216:   /*  FILE *fichtm; *//* Html File */
                   5217:   /* FILE *ficgp;*/ /*Gnuplot File */
                   5218:   struct stat info;
                   5219:   double agedeb, agefin,hf;
                   5220:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
                   5221: 
                   5222:   double fret;
                   5223:   double **xi,tmp,delta;
                   5224: 
                   5225:   double dum; /* Dummy variable */
                   5226:   double ***p3mat;
                   5227:   double ***mobaverage;
                   5228:   int *indx;
                   5229:   char line[MAXLINE], linepar[MAXLINE];
                   5230:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
                   5231:   char pathr[MAXLINE], pathimach[MAXLINE]; 
                   5232:   char **bp, *tok, *val; /* pathtot */
                   5233:   int firstobs=1, lastobs=10;
                   5234:   int sdeb, sfin; /* Status at beginning and end */
                   5235:   int c,  h , cpt,l;
                   5236:   int ju,jl, mi;
                   5237:   int i1,j1, jk,aa,bb, stepsize, ij;
                   5238:   int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
                   5239:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
                   5240:   int mobilav=0,popforecast=0;
                   5241:   int hstepm, nhstepm;
                   5242:   int agemortsup;
                   5243:   float  sumlpop=0.;
                   5244:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
                   5245:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
                   5246: 
                   5247:   double bage, fage, age, agelim, agebase;
                   5248:   double ftolpl=FTOL;
                   5249:   double **prlim;
                   5250:   double ***param; /* Matrix of parameters */
                   5251:   double  *p;
                   5252:   double **matcov; /* Matrix of covariance */
                   5253:   double ***delti3; /* Scale */
                   5254:   double *delti; /* Scale */
                   5255:   double ***eij, ***vareij;
                   5256:   double **varpl; /* Variances of prevalence limits by age */
                   5257:   double *epj, vepp;
                   5258:   double kk1, kk2;
                   5259:   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
                   5260:   double **ximort;
1.145     brouard  5261:   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136     brouard  5262:   int *dcwave;
                   5263: 
                   5264:   char z[1]="c", occ;
                   5265: 
                   5266:   /*char  *strt;*/
                   5267:   char strtend[80];
1.126     brouard  5268: 
                   5269:   long total_usecs;
                   5270:  
                   5271: /*   setlocale (LC_ALL, ""); */
                   5272: /*   bindtextdomain (PACKAGE, LOCALEDIR); */
                   5273: /*   textdomain (PACKAGE); */
                   5274: /*   setlocale (LC_CTYPE, ""); */
                   5275: /*   setlocale (LC_MESSAGES, ""); */
                   5276: 
                   5277:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
                   5278:   (void) gettimeofday(&start_time,&tzp);
                   5279:   curr_time=start_time;
                   5280:   tm = *localtime(&start_time.tv_sec);
                   5281:   tmg = *gmtime(&start_time.tv_sec);
                   5282:   strcpy(strstart,asctime(&tm));
                   5283: 
                   5284: /*  printf("Localtime (at start)=%s",strstart); */
                   5285: /*  tp.tv_sec = tp.tv_sec +86400; */
                   5286: /*  tm = *localtime(&start_time.tv_sec); */
                   5287: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
                   5288: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
                   5289: /*   tmg.tm_hour=tmg.tm_hour + 1; */
                   5290: /*   tp.tv_sec = mktime(&tmg); */
                   5291: /*   strt=asctime(&tmg); */
                   5292: /*   printf("Time(after) =%s",strstart);  */
                   5293: /*  (void) time (&time_value);
                   5294: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
                   5295: *  tm = *localtime(&time_value);
                   5296: *  strstart=asctime(&tm);
                   5297: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
                   5298: */
                   5299: 
                   5300:   nberr=0; /* Number of errors and warnings */
                   5301:   nbwarn=0;
                   5302:   getcwd(pathcd, size);
                   5303: 
                   5304:   printf("\n%s\n%s",version,fullversion);
                   5305:   if(argc <=1){
                   5306:     printf("\nEnter the parameter file name: ");
                   5307:     fgets(pathr,FILENAMELENGTH,stdin);
                   5308:     i=strlen(pathr);
                   5309:     if(pathr[i-1]=='\n')
                   5310:       pathr[i-1]='\0';
                   5311:    for (tok = pathr; tok != NULL; ){
                   5312:       printf("Pathr |%s|\n",pathr);
                   5313:       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
                   5314:       printf("val= |%s| pathr=%s\n",val,pathr);
                   5315:       strcpy (pathtot, val);
                   5316:       if(pathr[0] == '\0') break; /* Dirty */
                   5317:     }
                   5318:   }
                   5319:   else{
                   5320:     strcpy(pathtot,argv[1]);
                   5321:   }
                   5322:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
                   5323:   /*cygwin_split_path(pathtot,path,optionfile);
                   5324:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
                   5325:   /* cutv(path,optionfile,pathtot,'\\');*/
                   5326: 
                   5327:   /* Split argv[0], imach program to get pathimach */
                   5328:   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
                   5329:   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   5330:   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   5331:  /*   strcpy(pathimach,argv[0]); */
                   5332:   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
                   5333:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
                   5334:   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
                   5335:   chdir(path); /* Can be a relative path */
                   5336:   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
                   5337:     printf("Current directory %s!\n",pathcd);
                   5338:   strcpy(command,"mkdir ");
                   5339:   strcat(command,optionfilefiname);
                   5340:   if((outcmd=system(command)) != 0){
                   5341:     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
                   5342:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
                   5343:     /* fclose(ficlog); */
                   5344: /*     exit(1); */
                   5345:   }
                   5346: /*   if((imk=mkdir(optionfilefiname))<0){ */
                   5347: /*     perror("mkdir"); */
                   5348: /*   } */
                   5349: 
                   5350:   /*-------- arguments in the command line --------*/
                   5351: 
                   5352:   /* Log file */
                   5353:   strcat(filelog, optionfilefiname);
                   5354:   strcat(filelog,".log");    /* */
                   5355:   if((ficlog=fopen(filelog,"w"))==NULL)    {
                   5356:     printf("Problem with logfile %s\n",filelog);
                   5357:     goto end;
                   5358:   }
                   5359:   fprintf(ficlog,"Log filename:%s\n",filelog);
                   5360:   fprintf(ficlog,"\n%s\n%s",version,fullversion);
                   5361:   fprintf(ficlog,"\nEnter the parameter file name: \n");
                   5362:   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
                   5363:  path=%s \n\
                   5364:  optionfile=%s\n\
                   5365:  optionfilext=%s\n\
                   5366:  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
                   5367: 
                   5368:   printf("Local time (at start):%s",strstart);
                   5369:   fprintf(ficlog,"Local time (at start): %s",strstart);
                   5370:   fflush(ficlog);
                   5371: /*   (void) gettimeofday(&curr_time,&tzp); */
                   5372: /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
                   5373: 
                   5374:   /* */
                   5375:   strcpy(fileres,"r");
                   5376:   strcat(fileres, optionfilefiname);
                   5377:   strcat(fileres,".txt");    /* Other files have txt extension */
                   5378: 
                   5379:   /*---------arguments file --------*/
                   5380: 
                   5381:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
                   5382:     printf("Problem with optionfile %s\n",optionfile);
                   5383:     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
                   5384:     fflush(ficlog);
                   5385:     goto end;
                   5386:   }
                   5387: 
                   5388: 
                   5389: 
                   5390:   strcpy(filereso,"o");
                   5391:   strcat(filereso,fileres);
                   5392:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
                   5393:     printf("Problem with Output resultfile: %s\n", filereso);
                   5394:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
                   5395:     fflush(ficlog);
                   5396:     goto end;
                   5397:   }
                   5398: 
                   5399:   /* Reads comments: lines beginning with '#' */
                   5400:   numlinepar=0;
                   5401:   while((c=getc(ficpar))=='#' && c!= EOF){
                   5402:     ungetc(c,ficpar);
                   5403:     fgets(line, MAXLINE, ficpar);
                   5404:     numlinepar++;
1.141     brouard  5405:     fputs(line,stdout);
1.126     brouard  5406:     fputs(line,ficparo);
                   5407:     fputs(line,ficlog);
                   5408:   }
                   5409:   ungetc(c,ficpar);
                   5410: 
                   5411:   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);
                   5412:   numlinepar++;
                   5413:   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);
                   5414:   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);
                   5415:   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);
                   5416:   fflush(ficlog);
                   5417:   while((c=getc(ficpar))=='#' && c!= EOF){
                   5418:     ungetc(c,ficpar);
                   5419:     fgets(line, MAXLINE, ficpar);
                   5420:     numlinepar++;
1.141     brouard  5421:     fputs(line, stdout);
                   5422:     //puts(line);
1.126     brouard  5423:     fputs(line,ficparo);
                   5424:     fputs(line,ficlog);
                   5425:   }
                   5426:   ungetc(c,ficpar);
                   5427: 
                   5428:    
1.145     brouard  5429:   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
1.136     brouard  5430:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
                   5431:   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
                   5432:      v1+v2*age+v2*v3 makes cptcovn = 3
                   5433:   */
                   5434:   if (strlen(model)>1) 
1.145     brouard  5435:     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*/
                   5436:   else
                   5437:     ncovmodel=2;
1.126     brouard  5438:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133     brouard  5439:   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
                   5440:   npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131     brouard  5441:   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
                   5442:     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);
                   5443:     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);
                   5444:     fflush(stdout);
                   5445:     fclose (ficlog);
                   5446:     goto end;
                   5447:   }
1.126     brouard  5448:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   5449:   delti=delti3[1][1];
                   5450:   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
                   5451:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
                   5452:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
                   5453:     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   5454:     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   5455:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   5456:     fclose (ficparo);
                   5457:     fclose (ficlog);
                   5458:     goto end;
                   5459:     exit(0);
                   5460:   }
                   5461:   else if(mle==-3) {
                   5462:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
                   5463:     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
                   5464:     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
                   5465:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   5466:     matcov=matrix(1,npar,1,npar);
                   5467:   }
                   5468:   else{
1.145     brouard  5469:     /* Read guessed parameters */
1.126     brouard  5470:     /* Reads comments: lines beginning with '#' */
                   5471:     while((c=getc(ficpar))=='#' && c!= EOF){
                   5472:       ungetc(c,ficpar);
                   5473:       fgets(line, MAXLINE, ficpar);
                   5474:       numlinepar++;
1.141     brouard  5475:       fputs(line,stdout);
1.126     brouard  5476:       fputs(line,ficparo);
                   5477:       fputs(line,ficlog);
                   5478:     }
                   5479:     ungetc(c,ficpar);
                   5480:     
                   5481:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   5482:     for(i=1; i <=nlstate; i++){
                   5483:       j=0;
                   5484:       for(jj=1; jj <=nlstate+ndeath; jj++){
                   5485:        if(jj==i) continue;
                   5486:        j++;
                   5487:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   5488:        if ((i1 != i) && (j1 != j)){
                   5489:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
                   5490: It might be a problem of design; if ncovcol and the model are correct\n \
                   5491: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
                   5492:          exit(1);
                   5493:        }
                   5494:        fprintf(ficparo,"%1d%1d",i1,j1);
                   5495:        if(mle==1)
                   5496:          printf("%1d%1d",i,j);
                   5497:        fprintf(ficlog,"%1d%1d",i,j);
                   5498:        for(k=1; k<=ncovmodel;k++){
                   5499:          fscanf(ficpar," %lf",&param[i][j][k]);
                   5500:          if(mle==1){
                   5501:            printf(" %lf",param[i][j][k]);
                   5502:            fprintf(ficlog," %lf",param[i][j][k]);
                   5503:          }
                   5504:          else
                   5505:            fprintf(ficlog," %lf",param[i][j][k]);
                   5506:          fprintf(ficparo," %lf",param[i][j][k]);
                   5507:        }
                   5508:        fscanf(ficpar,"\n");
                   5509:        numlinepar++;
                   5510:        if(mle==1)
                   5511:          printf("\n");
                   5512:        fprintf(ficlog,"\n");
                   5513:        fprintf(ficparo,"\n");
                   5514:       }
                   5515:     }  
                   5516:     fflush(ficlog);
                   5517: 
1.145     brouard  5518:     /* Reads scales values */
1.126     brouard  5519:     p=param[1][1];
                   5520:     
                   5521:     /* Reads comments: lines beginning with '#' */
                   5522:     while((c=getc(ficpar))=='#' && c!= EOF){
                   5523:       ungetc(c,ficpar);
                   5524:       fgets(line, MAXLINE, ficpar);
                   5525:       numlinepar++;
1.141     brouard  5526:       fputs(line,stdout);
1.126     brouard  5527:       fputs(line,ficparo);
                   5528:       fputs(line,ficlog);
                   5529:     }
                   5530:     ungetc(c,ficpar);
                   5531: 
                   5532:     for(i=1; i <=nlstate; i++){
                   5533:       for(j=1; j <=nlstate+ndeath-1; j++){
                   5534:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   5535:        if ((i1-i)*(j1-j)!=0){
                   5536:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   5537:          exit(1);
                   5538:        }
                   5539:        printf("%1d%1d",i,j);
                   5540:        fprintf(ficparo,"%1d%1d",i1,j1);
                   5541:        fprintf(ficlog,"%1d%1d",i1,j1);
                   5542:        for(k=1; k<=ncovmodel;k++){
                   5543:          fscanf(ficpar,"%le",&delti3[i][j][k]);
                   5544:          printf(" %le",delti3[i][j][k]);
                   5545:          fprintf(ficparo," %le",delti3[i][j][k]);
                   5546:          fprintf(ficlog," %le",delti3[i][j][k]);
                   5547:        }
                   5548:        fscanf(ficpar,"\n");
                   5549:        numlinepar++;
                   5550:        printf("\n");
                   5551:        fprintf(ficparo,"\n");
                   5552:        fprintf(ficlog,"\n");
                   5553:       }
                   5554:     }
                   5555:     fflush(ficlog);
                   5556: 
1.145     brouard  5557:     /* Reads covariance matrix */
1.126     brouard  5558:     delti=delti3[1][1];
                   5559: 
                   5560: 
                   5561:     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
                   5562:   
                   5563:     /* Reads comments: lines beginning with '#' */
                   5564:     while((c=getc(ficpar))=='#' && c!= EOF){
                   5565:       ungetc(c,ficpar);
                   5566:       fgets(line, MAXLINE, ficpar);
                   5567:       numlinepar++;
1.141     brouard  5568:       fputs(line,stdout);
1.126     brouard  5569:       fputs(line,ficparo);
                   5570:       fputs(line,ficlog);
                   5571:     }
                   5572:     ungetc(c,ficpar);
                   5573:   
                   5574:     matcov=matrix(1,npar,1,npar);
1.131     brouard  5575:     for(i=1; i <=npar; i++)
                   5576:       for(j=1; j <=npar; j++) matcov[i][j]=0.;
                   5577:       
1.126     brouard  5578:     for(i=1; i <=npar; i++){
1.145     brouard  5579:       fscanf(ficpar,"%s",str);
1.126     brouard  5580:       if(mle==1)
                   5581:        printf("%s",str);
                   5582:       fprintf(ficlog,"%s",str);
                   5583:       fprintf(ficparo,"%s",str);
                   5584:       for(j=1; j <=i; j++){
                   5585:        fscanf(ficpar," %le",&matcov[i][j]);
                   5586:        if(mle==1){
                   5587:          printf(" %.5le",matcov[i][j]);
                   5588:        }
                   5589:        fprintf(ficlog," %.5le",matcov[i][j]);
                   5590:        fprintf(ficparo," %.5le",matcov[i][j]);
                   5591:       }
                   5592:       fscanf(ficpar,"\n");
                   5593:       numlinepar++;
                   5594:       if(mle==1)
                   5595:        printf("\n");
                   5596:       fprintf(ficlog,"\n");
                   5597:       fprintf(ficparo,"\n");
                   5598:     }
                   5599:     for(i=1; i <=npar; i++)
                   5600:       for(j=i+1;j<=npar;j++)
                   5601:        matcov[i][j]=matcov[j][i];
                   5602:     
                   5603:     if(mle==1)
                   5604:       printf("\n");
                   5605:     fprintf(ficlog,"\n");
                   5606:     
                   5607:     fflush(ficlog);
                   5608:     
                   5609:     /*-------- Rewriting parameter file ----------*/
                   5610:     strcpy(rfileres,"r");    /* "Rparameterfile */
                   5611:     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
                   5612:     strcat(rfileres,".");    /* */
                   5613:     strcat(rfileres,optionfilext);    /* Other files have txt extension */
                   5614:     if((ficres =fopen(rfileres,"w"))==NULL) {
                   5615:       printf("Problem writing new parameter file: %s\n", fileres);goto end;
                   5616:       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
                   5617:     }
                   5618:     fprintf(ficres,"#%s\n",version);
                   5619:   }    /* End of mle != -3 */
                   5620: 
                   5621: 
                   5622:   n= lastobs;
                   5623:   num=lvector(1,n);
                   5624:   moisnais=vector(1,n);
                   5625:   annais=vector(1,n);
                   5626:   moisdc=vector(1,n);
                   5627:   andc=vector(1,n);
                   5628:   agedc=vector(1,n);
                   5629:   cod=ivector(1,n);
                   5630:   weight=vector(1,n);
                   5631:   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
                   5632:   mint=matrix(1,maxwav,1,n);
                   5633:   anint=matrix(1,maxwav,1,n);
1.131     brouard  5634:   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
1.126     brouard  5635:   tab=ivector(1,NCOVMAX);
1.144     brouard  5636:   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126     brouard  5637: 
1.136     brouard  5638:   /* Reads data from file datafile */
                   5639:   if (readdata(datafile, firstobs, lastobs, &imx)==1)
                   5640:     goto end;
                   5641: 
                   5642:   /* Calculation of the number of parameters from char model */
1.137     brouard  5643:     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
                   5644:        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
                   5645:        k=3 V4 Tvar[k=3]= 4 (from V4)
                   5646:        k=2 V1 Tvar[k=2]= 1 (from V1)
                   5647:        k=1 Tvar[1]=2 (from V2)
                   5648:     */
                   5649:   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
                   5650:   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
                   5651:       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
                   5652:       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
                   5653:   */
                   5654:   /* For model-covariate k tells which data-covariate to use but
                   5655:     because this model-covariate is a construction we invent a new column
                   5656:     ncovcol + k1
                   5657:     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
                   5658:     Tvar[3=V1*V4]=4+1 etc */
1.145     brouard  5659:   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137     brouard  5660:   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
                   5661:      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
                   5662:   */
1.145     brouard  5663:   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
                   5664:   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141     brouard  5665:                            * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                   5666:                            * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145     brouard  5667:   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137     brouard  5668:                         4 covariates (3 plus signs)
                   5669:                         Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                   5670:                      */  
1.136     brouard  5671: 
                   5672:   if(decodemodel(model, lastobs) == 1)
                   5673:     goto end;
                   5674: 
1.137     brouard  5675:   if((double)(lastobs-imx)/(double)imx > 1.10){
                   5676:     nbwarn++;
                   5677:     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); 
                   5678:     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); 
                   5679:   }
1.136     brouard  5680:     /*  if(mle==1){*/
1.137     brouard  5681:   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
                   5682:     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136     brouard  5683:   }
                   5684: 
                   5685:     /*-calculation of age at interview from date of interview and age at death -*/
                   5686:   agev=matrix(1,maxwav,1,imx);
                   5687: 
                   5688:   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
                   5689:     goto end;
                   5690: 
1.126     brouard  5691: 
1.136     brouard  5692:   agegomp=(int)agemin;
                   5693:   free_vector(moisnais,1,n);
                   5694:   free_vector(annais,1,n);
1.126     brouard  5695:   /* free_matrix(mint,1,maxwav,1,n);
                   5696:      free_matrix(anint,1,maxwav,1,n);*/
                   5697:   free_vector(moisdc,1,n);
                   5698:   free_vector(andc,1,n);
1.145     brouard  5699:   /* */
                   5700:   
1.126     brouard  5701:   wav=ivector(1,imx);
                   5702:   dh=imatrix(1,lastpass-firstpass+1,1,imx);
                   5703:   bh=imatrix(1,lastpass-firstpass+1,1,imx);
                   5704:   mw=imatrix(1,lastpass-firstpass+1,1,imx);
                   5705:    
                   5706:   /* Concatenates waves */
                   5707:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
1.145     brouard  5708:   /* */
                   5709:  
1.126     brouard  5710:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
                   5711: 
                   5712:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
                   5713:   ncodemax[1]=1;
1.145     brouard  5714:   Ndum =ivector(-1,NCOVMAX);  
                   5715:   if (ncovmodel > 2)
                   5716:     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
                   5717: 
                   5718:   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
                   5719:   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
                   5720:   h=0;
                   5721: 
                   5722: 
                   5723:   /*if (cptcovn > 0) */
1.126     brouard  5724:       
1.145     brouard  5725:  
1.126     brouard  5726:   m=pow(2,cptcoveff);
                   5727:  
1.131     brouard  5728:   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143     brouard  5729:     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 */ 
                   5730:       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
                   5731:        for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
1.126     brouard  5732:          h++;
1.141     brouard  5733:          if (h>m) 
1.136     brouard  5734:            h=1;
1.144     brouard  5735:          /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143     brouard  5736:           *     h     1     2     3     4
                   5737:           *______________________________  
                   5738:           *     1 i=1 1 i=1 1 i=1 1 i=1 1
                   5739:           *     2     2     1     1     1
                   5740:           *     3 i=2 1     2     1     1
                   5741:           *     4     2     2     1     1
                   5742:           *     5 i=3 1 i=2 1     2     1
                   5743:           *     6     2     1     2     1
                   5744:           *     7 i=4 1     2     2     1
                   5745:           *     8     2     2     2     1
                   5746:           *     9 i=5 1 i=3 1 i=2 1     1
                   5747:           *    10     2     1     1     1
                   5748:           *    11 i=6 1     2     1     1
                   5749:           *    12     2     2     1     1
                   5750:           *    13 i=7 1 i=4 1     2     1    
                   5751:           *    14     2     1     2     1
                   5752:           *    15 i=8 1     2     2     1
                   5753:           *    16     2     2     2     1
                   5754:           */
1.141     brouard  5755:          codtab[h][k]=j;
1.145     brouard  5756:          /*codtab[h][Tvar[k]]=j;*/
1.130     brouard  5757:          printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
1.126     brouard  5758:        } 
                   5759:       }
                   5760:     }
                   5761:   } 
                   5762:   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
                   5763:      codtab[1][2]=1;codtab[2][2]=2; */
                   5764:   /* for(i=1; i <=m ;i++){ 
                   5765:      for(k=1; k <=cptcovn; k++){
1.131     brouard  5766:        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126     brouard  5767:      }
                   5768:      printf("\n");
                   5769:      }
                   5770:      scanf("%d",i);*/
1.145     brouard  5771: 
                   5772:  free_ivector(Ndum,-1,NCOVMAX);
                   5773: 
                   5774: 
1.126     brouard  5775:     
                   5776:   /*------------ gnuplot -------------*/
                   5777:   strcpy(optionfilegnuplot,optionfilefiname);
                   5778:   if(mle==-3)
                   5779:     strcat(optionfilegnuplot,"-mort");
                   5780:   strcat(optionfilegnuplot,".gp");
                   5781: 
                   5782:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
                   5783:     printf("Problem with file %s",optionfilegnuplot);
                   5784:   }
                   5785:   else{
                   5786:     fprintf(ficgp,"\n# %s\n", version); 
                   5787:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
1.141     brouard  5788:     //fprintf(ficgp,"set missing 'NaNq'\n");
                   5789:     fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126     brouard  5790:   }
                   5791:   /*  fclose(ficgp);*/
                   5792:   /*--------- index.htm --------*/
                   5793: 
                   5794:   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
                   5795:   if(mle==-3)
                   5796:     strcat(optionfilehtm,"-mort");
                   5797:   strcat(optionfilehtm,".htm");
                   5798:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
1.131     brouard  5799:     printf("Problem with %s \n",optionfilehtm);
                   5800:     exit(0);
1.126     brouard  5801:   }
                   5802: 
                   5803:   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
                   5804:   strcat(optionfilehtmcov,"-cov.htm");
                   5805:   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
                   5806:     printf("Problem with %s \n",optionfilehtmcov), exit(0);
                   5807:   }
                   5808:   else{
                   5809:   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   5810: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   5811: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
                   5812:          optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   5813:   }
                   5814: 
                   5815:   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   5816: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   5817: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
                   5818: \n\
                   5819: <hr  size=\"2\" color=\"#EC5E5E\">\
                   5820:  <ul><li><h4>Parameter files</h4>\n\
                   5821:  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
                   5822:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
                   5823:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
                   5824:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
                   5825:  - Date and time at start: %s</ul>\n",\
                   5826:          optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
                   5827:          optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
                   5828:          fileres,fileres,\
                   5829:          filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
                   5830:   fflush(fichtm);
                   5831: 
                   5832:   strcpy(pathr,path);
                   5833:   strcat(pathr,optionfilefiname);
                   5834:   chdir(optionfilefiname); /* Move to directory named optionfile */
                   5835:   
                   5836:   /* Calculates basic frequencies. Computes observed prevalence at single age
                   5837:      and prints on file fileres'p'. */
                   5838:   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
                   5839: 
                   5840:   fprintf(fichtm,"\n");
                   5841:   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
                   5842: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
                   5843: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
                   5844:          imx,agemin,agemax,jmin,jmax,jmean);
                   5845:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   5846:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   5847:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   5848:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   5849:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
                   5850:     
                   5851:    
                   5852:   /* For Powell, parameters are in a vector p[] starting at p[1]
                   5853:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
                   5854:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
                   5855: 
                   5856:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
                   5857: 
                   5858:   if (mle==-3){
1.136     brouard  5859:     ximort=matrix(1,NDIM,1,NDIM); 
                   5860: /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126     brouard  5861:     cens=ivector(1,n);
                   5862:     ageexmed=vector(1,n);
                   5863:     agecens=vector(1,n);
                   5864:     dcwave=ivector(1,n);
                   5865:  
                   5866:     for (i=1; i<=imx; i++){
                   5867:       dcwave[i]=-1;
                   5868:       for (m=firstpass; m<=lastpass; m++)
                   5869:        if (s[m][i]>nlstate) {
                   5870:          dcwave[i]=m;
                   5871:          /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                   5872:          break;
                   5873:        }
                   5874:     }
                   5875: 
                   5876:     for (i=1; i<=imx; i++) {
                   5877:       if (wav[i]>0){
                   5878:        ageexmed[i]=agev[mw[1][i]][i];
                   5879:        j=wav[i];
                   5880:        agecens[i]=1.; 
                   5881: 
                   5882:        if (ageexmed[i]> 1 && wav[i] > 0){
                   5883:          agecens[i]=agev[mw[j][i]][i];
                   5884:          cens[i]= 1;
                   5885:        }else if (ageexmed[i]< 1) 
                   5886:          cens[i]= -1;
                   5887:        if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                   5888:          cens[i]=0 ;
                   5889:       }
                   5890:       else cens[i]=-1;
                   5891:     }
                   5892:     
                   5893:     for (i=1;i<=NDIM;i++) {
                   5894:       for (j=1;j<=NDIM;j++)
                   5895:        ximort[i][j]=(i == j ? 1.0 : 0.0);
                   5896:     }
                   5897:     
1.145     brouard  5898:     /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126     brouard  5899:     /*printf("%lf %lf", p[1], p[2]);*/
                   5900:     
                   5901:     
1.136     brouard  5902: #ifdef GSL
                   5903:     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
                   5904: #elsedef
1.126     brouard  5905:     printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.136     brouard  5906: #endif
1.126     brouard  5907:     strcpy(filerespow,"pow-mort"); 
                   5908:     strcat(filerespow,fileres);
                   5909:     if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   5910:       printf("Problem with resultfile: %s\n", filerespow);
                   5911:       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   5912:     }
1.136     brouard  5913: #ifdef GSL
                   5914:     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
                   5915: #elsedef
1.126     brouard  5916:     fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136     brouard  5917: #endif
1.126     brouard  5918:     /*  for (i=1;i<=nlstate;i++)
                   5919:        for(j=1;j<=nlstate+ndeath;j++)
                   5920:        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   5921:     */
                   5922:     fprintf(ficrespow,"\n");
1.136     brouard  5923: #ifdef GSL
                   5924:     /* gsl starts here */ 
                   5925:     T = gsl_multimin_fminimizer_nmsimplex;
                   5926:     gsl_multimin_fminimizer *sfm = NULL;
                   5927:     gsl_vector *ss, *x;
                   5928:     gsl_multimin_function minex_func;
                   5929: 
                   5930:     /* Initial vertex size vector */
                   5931:     ss = gsl_vector_alloc (NDIM);
                   5932:     
                   5933:     if (ss == NULL){
                   5934:       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
                   5935:     }
                   5936:     /* Set all step sizes to 1 */
                   5937:     gsl_vector_set_all (ss, 0.001);
                   5938: 
                   5939:     /* Starting point */
1.126     brouard  5940:     
1.136     brouard  5941:     x = gsl_vector_alloc (NDIM);
                   5942:     
                   5943:     if (x == NULL){
                   5944:       gsl_vector_free(ss);
                   5945:       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
                   5946:     }
                   5947:   
                   5948:     /* Initialize method and iterate */
                   5949:     /*     p[1]=0.0268; p[NDIM]=0.083; */
                   5950: /*     gsl_vector_set(x, 0, 0.0268); */
                   5951: /*     gsl_vector_set(x, 1, 0.083); */
                   5952:     gsl_vector_set(x, 0, p[1]);
                   5953:     gsl_vector_set(x, 1, p[2]);
                   5954: 
                   5955:     minex_func.f = &gompertz_f;
                   5956:     minex_func.n = NDIM;
                   5957:     minex_func.params = (void *)&p; /* ??? */
                   5958:     
                   5959:     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
                   5960:     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
                   5961:     
                   5962:     printf("Iterations beginning .....\n\n");
                   5963:     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
                   5964: 
                   5965:     iteri=0;
                   5966:     while (rval == GSL_CONTINUE){
                   5967:       iteri++;
                   5968:       status = gsl_multimin_fminimizer_iterate(sfm);
                   5969:       
                   5970:       if (status) printf("error: %s\n", gsl_strerror (status));
                   5971:       fflush(0);
                   5972:       
                   5973:       if (status) 
                   5974:         break;
                   5975:       
                   5976:       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
                   5977:       ssval = gsl_multimin_fminimizer_size (sfm);
                   5978:       
                   5979:       if (rval == GSL_SUCCESS)
                   5980:         printf ("converged to a local maximum at\n");
                   5981:       
                   5982:       printf("%5d ", iteri);
                   5983:       for (it = 0; it < NDIM; it++){
                   5984:        printf ("%10.5f ", gsl_vector_get (sfm->x, it));
                   5985:       }
                   5986:       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
                   5987:     }
                   5988:     
                   5989:     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
                   5990:     
                   5991:     gsl_vector_free(x); /* initial values */
                   5992:     gsl_vector_free(ss); /* inital step size */
                   5993:     for (it=0; it<NDIM; it++){
                   5994:       p[it+1]=gsl_vector_get(sfm->x,it);
                   5995:       fprintf(ficrespow," %.12lf", p[it]);
                   5996:     }
                   5997:     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
                   5998: #endif
                   5999: #ifdef POWELL
                   6000:      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
                   6001: #endif  
1.126     brouard  6002:     fclose(ficrespow);
                   6003:     
                   6004:     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
                   6005: 
                   6006:     for(i=1; i <=NDIM; i++)
                   6007:       for(j=i+1;j<=NDIM;j++)
                   6008:        matcov[i][j]=matcov[j][i];
                   6009:     
                   6010:     printf("\nCovariance matrix\n ");
                   6011:     for(i=1; i <=NDIM; i++) {
                   6012:       for(j=1;j<=NDIM;j++){ 
                   6013:        printf("%f ",matcov[i][j]);
                   6014:       }
                   6015:       printf("\n ");
                   6016:     }
                   6017:     
                   6018:     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
                   6019:     for (i=1;i<=NDIM;i++) 
                   6020:       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
                   6021: 
                   6022:     lsurv=vector(1,AGESUP);
                   6023:     lpop=vector(1,AGESUP);
                   6024:     tpop=vector(1,AGESUP);
                   6025:     lsurv[agegomp]=100000;
                   6026:     
                   6027:     for (k=agegomp;k<=AGESUP;k++) {
                   6028:       agemortsup=k;
                   6029:       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
                   6030:     }
                   6031:     
                   6032:     for (k=agegomp;k<agemortsup;k++)
                   6033:       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
                   6034:     
                   6035:     for (k=agegomp;k<agemortsup;k++){
                   6036:       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
                   6037:       sumlpop=sumlpop+lpop[k];
                   6038:     }
                   6039:     
                   6040:     tpop[agegomp]=sumlpop;
                   6041:     for (k=agegomp;k<(agemortsup-3);k++){
                   6042:       /*  tpop[k+1]=2;*/
                   6043:       tpop[k+1]=tpop[k]-lpop[k];
                   6044:     }
                   6045:     
                   6046:     
                   6047:     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
                   6048:     for (k=agegomp;k<(agemortsup-2);k++) 
                   6049:       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]);
                   6050:     
                   6051:     
                   6052:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   6053:     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   6054:     
                   6055:     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                   6056:                     stepm, weightopt,\
                   6057:                     model,imx,p,matcov,agemortsup);
                   6058:     
                   6059:     free_vector(lsurv,1,AGESUP);
                   6060:     free_vector(lpop,1,AGESUP);
                   6061:     free_vector(tpop,1,AGESUP);
1.136     brouard  6062: #ifdef GSL
                   6063:     free_ivector(cens,1,n);
                   6064:     free_vector(agecens,1,n);
                   6065:     free_ivector(dcwave,1,n);
                   6066:     free_matrix(ximort,1,NDIM,1,NDIM);
                   6067: #endif
1.126     brouard  6068:   } /* Endof if mle==-3 */
                   6069:   
                   6070:   else{ /* For mle >=1 */
1.132     brouard  6071:     globpr=0;/* debug */
                   6072:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126     brouard  6073:     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   6074:     for (k=1; k<=npar;k++)
                   6075:       printf(" %d %8.5f",k,p[k]);
                   6076:     printf("\n");
                   6077:     globpr=1; /* to print the contributions */
                   6078:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   6079:     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   6080:     for (k=1; k<=npar;k++)
                   6081:       printf(" %d %8.5f",k,p[k]);
                   6082:     printf("\n");
                   6083:     if(mle>=1){ /* Could be 1 or 2 */
                   6084:       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
                   6085:     }
                   6086:     
                   6087:     /*--------- results files --------------*/
                   6088:     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);
                   6089:     
                   6090:     
                   6091:     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   6092:     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   6093:     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   6094:     for(i=1,jk=1; i <=nlstate; i++){
                   6095:       for(k=1; k <=(nlstate+ndeath); k++){
                   6096:        if (k != i) {
                   6097:          printf("%d%d ",i,k);
                   6098:          fprintf(ficlog,"%d%d ",i,k);
                   6099:          fprintf(ficres,"%1d%1d ",i,k);
                   6100:          for(j=1; j <=ncovmodel; j++){
                   6101:            printf("%lf ",p[jk]);
                   6102:            fprintf(ficlog,"%lf ",p[jk]);
                   6103:            fprintf(ficres,"%lf ",p[jk]);
                   6104:            jk++; 
                   6105:          }
                   6106:          printf("\n");
                   6107:          fprintf(ficlog,"\n");
                   6108:          fprintf(ficres,"\n");
                   6109:        }
                   6110:       }
                   6111:     }
                   6112:     if(mle!=0){
                   6113:       /* Computing hessian and covariance matrix */
                   6114:       ftolhess=ftol; /* Usually correct */
                   6115:       hesscov(matcov, p, npar, delti, ftolhess, func);
                   6116:     }
                   6117:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
                   6118:     printf("# Scales (for hessian or gradient estimation)\n");
                   6119:     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
                   6120:     for(i=1,jk=1; i <=nlstate; i++){
                   6121:       for(j=1; j <=nlstate+ndeath; j++){
                   6122:        if (j!=i) {
                   6123:          fprintf(ficres,"%1d%1d",i,j);
                   6124:          printf("%1d%1d",i,j);
                   6125:          fprintf(ficlog,"%1d%1d",i,j);
                   6126:          for(k=1; k<=ncovmodel;k++){
                   6127:            printf(" %.5e",delti[jk]);
                   6128:            fprintf(ficlog," %.5e",delti[jk]);
                   6129:            fprintf(ficres," %.5e",delti[jk]);
                   6130:            jk++;
                   6131:          }
                   6132:          printf("\n");
                   6133:          fprintf(ficlog,"\n");
                   6134:          fprintf(ficres,"\n");
                   6135:        }
                   6136:       }
                   6137:     }
                   6138:     
                   6139:     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");
                   6140:     if(mle>=1)
                   6141:       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");
                   6142:     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");
                   6143:     /* # 121 Var(a12)\n\ */
                   6144:     /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   6145:     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   6146:     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   6147:     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   6148:     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   6149:     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   6150:     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   6151:     
                   6152:     
                   6153:     /* Just to have a covariance matrix which will be more understandable
                   6154:        even is we still don't want to manage dictionary of variables
                   6155:     */
                   6156:     for(itimes=1;itimes<=2;itimes++){
                   6157:       jj=0;
                   6158:       for(i=1; i <=nlstate; i++){
                   6159:        for(j=1; j <=nlstate+ndeath; j++){
                   6160:          if(j==i) continue;
                   6161:          for(k=1; k<=ncovmodel;k++){
                   6162:            jj++;
                   6163:            ca[0]= k+'a'-1;ca[1]='\0';
                   6164:            if(itimes==1){
                   6165:              if(mle>=1)
                   6166:                printf("#%1d%1d%d",i,j,k);
                   6167:              fprintf(ficlog,"#%1d%1d%d",i,j,k);
                   6168:              fprintf(ficres,"#%1d%1d%d",i,j,k);
                   6169:            }else{
                   6170:              if(mle>=1)
                   6171:                printf("%1d%1d%d",i,j,k);
                   6172:              fprintf(ficlog,"%1d%1d%d",i,j,k);
                   6173:              fprintf(ficres,"%1d%1d%d",i,j,k);
                   6174:            }
                   6175:            ll=0;
                   6176:            for(li=1;li <=nlstate; li++){
                   6177:              for(lj=1;lj <=nlstate+ndeath; lj++){
                   6178:                if(lj==li) continue;
                   6179:                for(lk=1;lk<=ncovmodel;lk++){
                   6180:                  ll++;
                   6181:                  if(ll<=jj){
                   6182:                    cb[0]= lk +'a'-1;cb[1]='\0';
                   6183:                    if(ll<jj){
                   6184:                      if(itimes==1){
                   6185:                        if(mle>=1)
                   6186:                          printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   6187:                        fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   6188:                        fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   6189:                      }else{
                   6190:                        if(mle>=1)
                   6191:                          printf(" %.5e",matcov[jj][ll]); 
                   6192:                        fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   6193:                        fprintf(ficres," %.5e",matcov[jj][ll]); 
                   6194:                      }
                   6195:                    }else{
                   6196:                      if(itimes==1){
                   6197:                        if(mle>=1)
                   6198:                          printf(" Var(%s%1d%1d)",ca,i,j);
                   6199:                        fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                   6200:                        fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                   6201:                      }else{
                   6202:                        if(mle>=1)
                   6203:                          printf(" %.5e",matcov[jj][ll]); 
                   6204:                        fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   6205:                        fprintf(ficres," %.5e",matcov[jj][ll]); 
                   6206:                      }
                   6207:                    }
                   6208:                  }
                   6209:                } /* end lk */
                   6210:              } /* end lj */
                   6211:            } /* end li */
                   6212:            if(mle>=1)
                   6213:              printf("\n");
                   6214:            fprintf(ficlog,"\n");
                   6215:            fprintf(ficres,"\n");
                   6216:            numlinepar++;
                   6217:          } /* end k*/
                   6218:        } /*end j */
                   6219:       } /* end i */
                   6220:     } /* end itimes */
                   6221:     
                   6222:     fflush(ficlog);
                   6223:     fflush(ficres);
                   6224:     
                   6225:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6226:       ungetc(c,ficpar);
                   6227:       fgets(line, MAXLINE, ficpar);
1.141     brouard  6228:       fputs(line,stdout);
1.126     brouard  6229:       fputs(line,ficparo);
                   6230:     }
                   6231:     ungetc(c,ficpar);
                   6232:     
                   6233:     estepm=0;
                   6234:     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
                   6235:     if (estepm==0 || estepm < stepm) estepm=stepm;
                   6236:     if (fage <= 2) {
                   6237:       bage = ageminpar;
                   6238:       fage = agemaxpar;
                   6239:     }
                   6240:     
                   6241:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
                   6242:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
                   6243:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
                   6244:     
                   6245:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6246:       ungetc(c,ficpar);
                   6247:       fgets(line, MAXLINE, ficpar);
1.141     brouard  6248:       fputs(line,stdout);
1.126     brouard  6249:       fputs(line,ficparo);
                   6250:     }
                   6251:     ungetc(c,ficpar);
                   6252:     
                   6253:     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);
                   6254:     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);
                   6255:     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);
                   6256:     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   6257:     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);
                   6258:     
                   6259:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6260:       ungetc(c,ficpar);
                   6261:       fgets(line, MAXLINE, ficpar);
1.141     brouard  6262:       fputs(line,stdout);
1.126     brouard  6263:       fputs(line,ficparo);
                   6264:     }
                   6265:     ungetc(c,ficpar);
                   6266:     
                   6267:     
                   6268:     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
                   6269:     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
                   6270:     
                   6271:     fscanf(ficpar,"pop_based=%d\n",&popbased);
                   6272:     fprintf(ficparo,"pop_based=%d\n",popbased);   
                   6273:     fprintf(ficres,"pop_based=%d\n",popbased);   
                   6274:     
                   6275:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6276:       ungetc(c,ficpar);
                   6277:       fgets(line, MAXLINE, ficpar);
1.141     brouard  6278:       fputs(line,stdout);
1.126     brouard  6279:       fputs(line,ficparo);
                   6280:     }
                   6281:     ungetc(c,ficpar);
                   6282:     
                   6283:     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);
                   6284:     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);
                   6285:     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);
                   6286:     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);
                   6287:     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);
                   6288:     /* day and month of proj2 are not used but only year anproj2.*/
                   6289:     
                   6290:     
                   6291:     
1.145     brouard  6292:      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
                   6293:     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126     brouard  6294:     
                   6295:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   6296:     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   6297:     
                   6298:     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                   6299:                 model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                   6300:                 jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
                   6301:       
                   6302:    /*------------ free_vector  -------------*/
                   6303:    /*  chdir(path); */
                   6304:  
                   6305:     free_ivector(wav,1,imx);
                   6306:     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
                   6307:     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
                   6308:     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
                   6309:     free_lvector(num,1,n);
                   6310:     free_vector(agedc,1,n);
                   6311:     /*free_matrix(covar,0,NCOVMAX,1,n);*/
                   6312:     /*free_matrix(covar,1,NCOVMAX,1,n);*/
                   6313:     fclose(ficparo);
                   6314:     fclose(ficres);
                   6315: 
                   6316: 
                   6317:     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
1.145     brouard  6318: #include "prevlim.h"  /* Use ficrespl, ficlog */
1.126     brouard  6319:     fclose(ficrespl);
                   6320: 
1.145     brouard  6321: #ifdef FREEEXIT2
                   6322: #include "freeexit2.h"
                   6323: #endif
                   6324: 
1.126     brouard  6325:     /*------------- h Pij x at various ages ------------*/
1.145     brouard  6326: #include "hpijx.h"
                   6327:     fclose(ficrespij);
1.126     brouard  6328: 
1.145     brouard  6329:   /*-------------- Variance of one-step probabilities---*/
                   6330:     k=1;
1.126     brouard  6331:     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
                   6332: 
                   6333: 
                   6334:     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   6335:     for(i=1;i<=AGESUP;i++)
                   6336:       for(j=1;j<=NCOVMAX;j++)
                   6337:        for(k=1;k<=NCOVMAX;k++)
                   6338:          probs[i][j][k]=0.;
                   6339: 
                   6340:     /*---------- Forecasting ------------------*/
                   6341:     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
                   6342:     if(prevfcast==1){
                   6343:       /*    if(stepm ==1){*/
                   6344:       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
                   6345:       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
                   6346:       /*      }  */
                   6347:       /*      else{ */
                   6348:       /*        erreur=108; */
                   6349:       /*        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); */
                   6350:       /*        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); */
                   6351:       /*      } */
                   6352:     }
                   6353:   
                   6354: 
1.127     brouard  6355:     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
                   6356: 
                   6357:     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   6358:     /*  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",\
                   6359:        ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
                   6360:     */
1.126     brouard  6361: 
1.127     brouard  6362:     if (mobilav!=0) {
                   6363:       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   6364:       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   6365:        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   6366:        printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   6367:       }
1.126     brouard  6368:     }
                   6369: 
                   6370: 
1.127     brouard  6371:     /*---------- Health expectancies, no variances ------------*/
                   6372: 
1.126     brouard  6373:     strcpy(filerese,"e");
                   6374:     strcat(filerese,fileres);
                   6375:     if((ficreseij=fopen(filerese,"w"))==NULL) {
                   6376:       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   6377:       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   6378:     }
                   6379:     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
                   6380:     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145     brouard  6381:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   6382:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   6383:           
                   6384:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127     brouard  6385:        fprintf(ficreseij,"\n#****** ");
                   6386:        for(j=1;j<=cptcoveff;j++) {
                   6387:          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   6388:        }
                   6389:        fprintf(ficreseij,"******\n");
                   6390: 
                   6391:        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   6392:        oldm=oldms;savm=savms;
                   6393:        evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
                   6394:       
                   6395:        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145     brouard  6396:       /*}*/
1.127     brouard  6397:     }
                   6398:     fclose(ficreseij);
                   6399: 
                   6400: 
                   6401:     /*---------- Health expectancies and variances ------------*/
                   6402: 
                   6403: 
                   6404:     strcpy(filerest,"t");
                   6405:     strcat(filerest,fileres);
                   6406:     if((ficrest=fopen(filerest,"w"))==NULL) {
                   6407:       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
                   6408:       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
                   6409:     }
                   6410:     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
                   6411:     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
                   6412: 
1.126     brouard  6413: 
                   6414:     strcpy(fileresstde,"stde");
                   6415:     strcat(fileresstde,fileres);
                   6416:     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
                   6417:       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
                   6418:       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
                   6419:     }
                   6420:     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
                   6421:     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
                   6422: 
                   6423:     strcpy(filerescve,"cve");
                   6424:     strcat(filerescve,fileres);
                   6425:     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
                   6426:       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
                   6427:       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
                   6428:     }
                   6429:     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
                   6430:     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
                   6431: 
                   6432:     strcpy(fileresv,"v");
                   6433:     strcat(fileresv,fileres);
                   6434:     if((ficresvij=fopen(fileresv,"w"))==NULL) {
                   6435:       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
                   6436:       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
                   6437:     }
                   6438:     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
                   6439:     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
                   6440: 
1.145     brouard  6441:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   6442:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   6443:           
                   6444:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
                   6445:        fprintf(ficrest,"\n#****** ");
1.126     brouard  6446:        for(j=1;j<=cptcoveff;j++) 
                   6447:          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   6448:        fprintf(ficrest,"******\n");
                   6449: 
                   6450:        fprintf(ficresstdeij,"\n#****** ");
                   6451:        fprintf(ficrescveij,"\n#****** ");
                   6452:        for(j=1;j<=cptcoveff;j++) {
                   6453:          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   6454:          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   6455:        }
                   6456:        fprintf(ficresstdeij,"******\n");
                   6457:        fprintf(ficrescveij,"******\n");
                   6458: 
                   6459:        fprintf(ficresvij,"\n#****** ");
                   6460:        for(j=1;j<=cptcoveff;j++) 
                   6461:          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   6462:        fprintf(ficresvij,"******\n");
                   6463: 
                   6464:        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   6465:        oldm=oldms;savm=savms;
1.127     brouard  6466:        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
1.145     brouard  6467:        /*
                   6468:         */
                   6469:        /* goto endfree; */
1.126     brouard  6470:  
                   6471:        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   6472:        pstamp(ficrest);
1.145     brouard  6473: 
                   6474: 
1.128     brouard  6475:        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145     brouard  6476:          oldm=oldms;savm=savms; /* Segmentation fault */
                   6477:          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
                   6478:          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
1.128     brouard  6479:          if(vpopbased==1)
                   6480:            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);
                   6481:          else
                   6482:            fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
                   6483:          fprintf(ficrest,"# Age e.. (std) ");
                   6484:          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   6485:          fprintf(ficrest,"\n");
1.126     brouard  6486: 
1.128     brouard  6487:          epj=vector(1,nlstate+1);
                   6488:          for(age=bage; age <=fage ;age++){
                   6489:            prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
                   6490:            if (vpopbased==1) {
                   6491:              if(mobilav ==0){
                   6492:                for(i=1; i<=nlstate;i++)
                   6493:                  prlim[i][i]=probs[(int)age][i][k];
                   6494:              }else{ /* mobilav */ 
                   6495:                for(i=1; i<=nlstate;i++)
                   6496:                  prlim[i][i]=mobaverage[(int)age][i][k];
                   6497:              }
1.126     brouard  6498:            }
                   6499:        
1.128     brouard  6500:            fprintf(ficrest," %4.0f",age);
                   6501:            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                   6502:              for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   6503:                epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   6504:                /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   6505:              }
                   6506:              epj[nlstate+1] +=epj[j];
1.126     brouard  6507:            }
                   6508: 
1.128     brouard  6509:            for(i=1, vepp=0.;i <=nlstate;i++)
                   6510:              for(j=1;j <=nlstate;j++)
                   6511:                vepp += vareij[i][j][(int)age];
                   6512:            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                   6513:            for(j=1;j <=nlstate;j++){
                   6514:              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                   6515:            }
                   6516:            fprintf(ficrest,"\n");
1.126     brouard  6517:          }
                   6518:        }
                   6519:        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   6520:        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   6521:        free_vector(epj,1,nlstate+1);
1.145     brouard  6522:       /*}*/
1.126     brouard  6523:     }
                   6524:     free_vector(weight,1,n);
1.145     brouard  6525:     free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126     brouard  6526:     free_imatrix(s,1,maxwav+1,1,n);
                   6527:     free_matrix(anint,1,maxwav,1,n); 
                   6528:     free_matrix(mint,1,maxwav,1,n);
                   6529:     free_ivector(cod,1,n);
                   6530:     free_ivector(tab,1,NCOVMAX);
                   6531:     fclose(ficresstdeij);
                   6532:     fclose(ficrescveij);
                   6533:     fclose(ficresvij);
                   6534:     fclose(ficrest);
                   6535:     fclose(ficpar);
                   6536:   
                   6537:     /*------- Variance of period (stable) prevalence------*/   
                   6538: 
                   6539:     strcpy(fileresvpl,"vpl");
                   6540:     strcat(fileresvpl,fileres);
                   6541:     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
                   6542:       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
                   6543:       exit(0);
                   6544:     }
                   6545:     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
                   6546: 
1.145     brouard  6547:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   6548:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   6549:           
                   6550:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
                   6551:        fprintf(ficresvpl,"\n#****** ");
1.126     brouard  6552:        for(j=1;j<=cptcoveff;j++) 
                   6553:          fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   6554:        fprintf(ficresvpl,"******\n");
                   6555:       
                   6556:        varpl=matrix(1,nlstate,(int) bage, (int) fage);
                   6557:        oldm=oldms;savm=savms;
                   6558:        varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
                   6559:        free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145     brouard  6560:       /*}*/
1.126     brouard  6561:     }
                   6562: 
                   6563:     fclose(ficresvpl);
                   6564: 
                   6565:     /*---------- End : free ----------------*/
                   6566:     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   6567:     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   6568:   }  /* mle==-3 arrives here for freeing */
1.131     brouard  6569:  endfree:
1.141     brouard  6570:     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126     brouard  6571:     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
                   6572:     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   6573:     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   6574:     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   6575:     free_matrix(covar,0,NCOVMAX,1,n);
                   6576:     free_matrix(matcov,1,npar,1,npar);
                   6577:     /*free_vector(delti,1,npar);*/
                   6578:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   6579:     free_matrix(agev,1,maxwav,1,imx);
                   6580:     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
                   6581: 
1.145     brouard  6582:     free_ivector(ncodemax,1,NCOVMAX);
                   6583:     free_ivector(Tvar,1,NCOVMAX);
                   6584:     free_ivector(Tprod,1,NCOVMAX);
                   6585:     free_ivector(Tvaraff,1,NCOVMAX);
                   6586:     free_ivector(Tage,1,NCOVMAX);
1.126     brouard  6587: 
                   6588:     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
                   6589:     free_imatrix(codtab,1,100,1,10);
                   6590:   fflush(fichtm);
                   6591:   fflush(ficgp);
                   6592:   
                   6593: 
                   6594:   if((nberr >0) || (nbwarn>0)){
                   6595:     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
                   6596:     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
                   6597:   }else{
                   6598:     printf("End of Imach\n");
                   6599:     fprintf(ficlog,"End of Imach\n");
                   6600:   }
                   6601:   printf("See log file on %s\n",filelog);
                   6602:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
                   6603:   (void) gettimeofday(&end_time,&tzp);
                   6604:   tm = *localtime(&end_time.tv_sec);
                   6605:   tmg = *gmtime(&end_time.tv_sec);
                   6606:   strcpy(strtend,asctime(&tm));
                   6607:   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
                   6608:   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
                   6609:   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
                   6610: 
1.141     brouard  6611:   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126     brouard  6612:   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.141     brouard  6613:   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126     brouard  6614:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
                   6615: /*   if(fileappend(fichtm,optionfilehtm)){ */
                   6616:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   6617:   fclose(fichtm);
                   6618:   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   6619:   fclose(fichtmcov);
                   6620:   fclose(ficgp);
                   6621:   fclose(ficlog);
                   6622:   /*------ End -----------*/
                   6623: 
                   6624: 
                   6625:    printf("Before Current directory %s!\n",pathcd);
                   6626:    if(chdir(pathcd) != 0)
                   6627:     printf("Can't move to directory %s!\n",path);
                   6628:   if(getcwd(pathcd,MAXLINE) > 0)
                   6629:     printf("Current directory %s!\n",pathcd);
                   6630:   /*strcat(plotcmd,CHARSEPARATOR);*/
                   6631:   sprintf(plotcmd,"gnuplot");
                   6632: #ifndef UNIX
                   6633:   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
                   6634: #endif
                   6635:   if(!stat(plotcmd,&info)){
                   6636:     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
                   6637:     if(!stat(getenv("GNUPLOTBIN"),&info)){
                   6638:       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
                   6639:     }else
                   6640:       strcpy(pplotcmd,plotcmd);
                   6641: #ifdef UNIX
                   6642:     strcpy(plotcmd,GNUPLOTPROGRAM);
                   6643:     if(!stat(plotcmd,&info)){
                   6644:       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
                   6645:     }else
                   6646:       strcpy(pplotcmd,plotcmd);
                   6647: #endif
                   6648:   }else
                   6649:     strcpy(pplotcmd,plotcmd);
                   6650:   
                   6651:   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
                   6652:   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
                   6653: 
                   6654:   if((outcmd=system(plotcmd)) != 0){
                   6655:     printf("\n Problem with gnuplot\n");
                   6656:   }
                   6657:   printf(" Wait...");
                   6658:   while (z[0] != 'q') {
                   6659:     /* chdir(path); */
                   6660:     printf("\nType e to edit output files, g to graph again and q for exiting: ");
                   6661:     scanf("%s",z);
                   6662: /*     if (z[0] == 'c') system("./imach"); */
                   6663:     if (z[0] == 'e') {
                   6664:       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
                   6665:       system(optionfilehtm);
                   6666:     }
                   6667:     else if (z[0] == 'g') system(plotcmd);
                   6668:     else if (z[0] == 'q') exit(0);
                   6669:   }
                   6670:   end:
                   6671:   while (z[0] != 'q') {
                   6672:     printf("\nType  q for exiting: ");
                   6673:     scanf("%s",z);
                   6674:   }
                   6675: }
                   6676: 
                   6677: 
                   6678: 

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