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Diff for /imach/src/imach.c between versions 1.142 and 1.237

-version 1.142, 2014/01/26 03:57:36
+version 1.237, 2016/08/26 09:20:19
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.237  2016/08/26 09:20:19  brouard
+   Summary: to valgrind
+   Revision 1.236  2016/08/25 10:50:18  brouard
+   *** empty log message ***
+   Revision 1.235  2016/08/25 06:59:23  brouard
+   *** empty log message ***
+   Revision 1.234  2016/08/23 16:51:20  brouard
+   *** empty log message ***
+   Revision 1.233  2016/08/23 07:40:50  brouard
+   Summary: not working
+   Revision 1.232  2016/08/22 14:20:21  brouard
+   Summary: not working
+   Revision 1.231  2016/08/22 07:17:15  brouard
+   Summary: not working
+   Revision 1.230  2016/08/22 06:55:53  brouard
+   Summary: Not working
+   Revision 1.229  2016/07/23 09:45:53  brouard
+   Summary: Completing for func too
+   Revision 1.228  2016/07/22 17:45:30  brouard
+   Summary: Fixing some arrays, still debugging
+   Revision 1.226  2016/07/12 18:42:34  brouard
+   Summary: temp
+   Revision 1.225  2016/07/12 08:40:03  brouard
+   Summary: saving but not running
+   Revision 1.224  2016/07/01 13:16:01  brouard
+   Summary: Fixes
+   Revision 1.223  2016/02/19 09:23:35  brouard
+   Summary: temporary
+   Revision 1.222  2016/02/17 08:14:50  brouard
+   Summary: Probably last 0.98 stable version 0.98r6
+   Revision 1.221  2016/02/15 23:35:36  brouard
+   Summary: minor bug
+   Revision 1.219  2016/02/15 00:48:12  brouard
+   *** empty log message ***
+   Revision 1.218  2016/02/12 11:29:23  brouard
+   Summary: 0.99 Back projections
+   Revision 1.217  2015/12/23 17:18:31  brouard
+   Summary: Experimental backcast
+   Revision 1.216  2015/12/18 17:32:11  brouard
+   Summary: 0.98r4 Warning and status=-2
+   Version 0.98r4 is now:
+    - displaying an error when status is -1, date of interview unknown and date of death known;
+    - permitting a status -2 when the vital status is unknown at a known date of right truncation.
+   Older changes concerning s=-2, dating from 2005 have been supersed.
+   Revision 1.215  2015/12/16 08:52:24  brouard
+   Summary: 0.98r4 working
+   Revision 1.214  2015/12/16 06:57:54  brouard
+   Summary: temporary not working
+   Revision 1.213  2015/12/11 18:22:17  brouard
+   Summary: 0.98r4
+   Revision 1.212  2015/11/21 12:47:24  brouard
+   Summary: minor typo
+   Revision 1.211  2015/11/21 12:41:11  brouard
+   Summary: 0.98r3 with some graph of projected cross-sectional
+   Author: Nicolas Brouard
+   Revision 1.210  2015/11/18 17:41:20  brouard
+   Summary: Start working on projected prevalences
+   Revision 1.209  2015/11/17 22:12:03  brouard
+   Summary: Adding ftolpl parameter
+   Author: N Brouard
+   We had difficulties to get smoothed confidence intervals. It was due
+   to the period prevalence which wasn't computed accurately. The inner
+   parameter ftolpl is now an outer parameter of the .imach parameter
+   file after estepm. If ftolpl is small 1.e-4 and estepm too,
+   computation are long.
+   Revision 1.208  2015/11/17 14:31:57  brouard
+   Summary: temporary
+   Revision 1.207  2015/10/27 17:36:57  brouard
+   *** empty log message ***
+   Revision 1.206  2015/10/24 07:14:11  brouard
+   *** empty log message ***
+   Revision 1.205  2015/10/23 15:50:53  brouard
+   Summary: 0.98r3 some clarification for graphs on likelihood contributions
+   Revision 1.204  2015/10/01 16:20:26  brouard
+   Summary: Some new graphs of contribution to likelihood
+   Revision 1.203  2015/09/30 17:45:14  brouard
+   Summary: looking at better estimation of the hessian
+   Also a better criteria for convergence to the period prevalence And
+   therefore adding the number of years needed to converge. (The
+   prevalence in any alive state shold sum to one
+   Revision 1.202  2015/09/22 19:45:16  brouard
+   Summary: Adding some overall graph on contribution to likelihood. Might change
+   Revision 1.201  2015/09/15 17:34:58  brouard
+   Summary: 0.98r0
+   - Some new graphs like suvival functions
+   - Some bugs fixed like model=1+age+V2.
+   Revision 1.200  2015/09/09 16:53:55  brouard
+   Summary: Big bug thanks to Flavia
+   Even model=1+age+V2. did not work anymore
+   Revision 1.199  2015/09/07 14:09:23  brouard
+   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
+   Revision 1.198  2015/09/03 07:14:39  brouard
+   Summary: 0.98q5 Flavia
+   Revision 1.197  2015/09/01 18:24:39  brouard
+   *** empty log message ***
+   Revision 1.196  2015/08/18 23:17:52  brouard
+   Summary: 0.98q5
+   Revision 1.195  2015/08/18 16:28:39  brouard
+   Summary: Adding a hack for testing purpose
+   After reading the title, ftol and model lines, if the comment line has
+   a q, starting with #q, the answer at the end of the run is quit. It
+   permits to run test files in batch with ctest. The former workaround was
+   $ echo q | imach foo.imach
+   Revision 1.194  2015/08/18 13:32:00  brouard
+   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+   Revision 1.193  2015/08/04 07:17:42  brouard
+   Summary: 0.98q4
+   Revision 1.192  2015/07/16 16:49:02  brouard
+   Summary: Fixing some outputs
+   Revision 1.191  2015/07/14 10:00:33  brouard
+   Summary: Some fixes
+   Revision 1.190  2015/05/05 08:51:13  brouard
+   Summary: Adding digits in output parameters (7 digits instead of 6)
+   Fix 1+age+.
+   Revision 1.189  2015/04/30 14:45:16  brouard
+   Summary: 0.98q2
+   Revision 1.188  2015/04/30 08:27:53  brouard
+   *** empty log message ***
+   Revision 1.187  2015/04/29 09:11:15  brouard
+   *** empty log message ***
+   Revision 1.186  2015/04/23 12:01:52  brouard
+   Summary: V1*age is working now, version 0.98q1
+   Some codes had been disabled in order to simplify and Vn*age was
+   working in the optimization phase, ie, giving correct MLE parameters,
+   but, as usual, outputs were not correct and program core dumped.
+   Revision 1.185  2015/03/11 13:26:42  brouard
+   Summary: Inclusion of compile and links command line for Intel Compiler
+   Revision 1.184  2015/03/11 11:52:39  brouard
+   Summary: Back from Windows 8. Intel Compiler
+   Revision 1.183  2015/03/10 20:34:32  brouard
+   Summary: 0.98q0, trying with directest, mnbrak fixed
+   We use directest instead of original Powell test; probably no
+   incidence on the results, but better justifications;
+   We fixed Numerical Recipes mnbrak routine which was wrong and gave
+   wrong results.
+   Revision 1.182  2015/02/12 08:19:57  brouard
+   Summary: Trying to keep directest which seems simpler and more general
+   Author: Nicolas Brouard
+   Revision 1.181  2015/02/11 23:22:24  brouard
+   Summary: Comments on Powell added
+   Author:
+   Revision 1.180  2015/02/11 17:33:45  brouard
+   Summary: Finishing move from main to function (hpijx and prevalence_limit)
+   Revision 1.179  2015/01/04 09:57:06  brouard
+   Summary: back to OS/X
+   Revision 1.178  2015/01/04 09:35:48  brouard
+   *** empty log message ***
+   Revision 1.177  2015/01/03 18:40:56  brouard
+   Summary: Still testing ilc32 on OSX
+   Revision 1.176  2015/01/03 16:45:04  brouard
+   *** empty log message ***
+   Revision 1.175  2015/01/03 16:33:42  brouard
+   *** empty log message ***
+   Revision 1.174  2015/01/03 16:15:49  brouard
+   Summary: Still in cross-compilation
+   Revision 1.173  2015/01/03 12:06:26  brouard
+   Summary: trying to detect cross-compilation
+   Revision 1.172  2014/12/27 12:07:47  brouard
+   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
+   Revision 1.171  2014/12/23 13:26:59  brouard
+   Summary: Back from Visual C
+   Still problem with utsname.h on Windows
+   Revision 1.170  2014/12/23 11:17:12  brouard
+   Summary: Cleaning some \%% back to %%
+   The escape was mandatory for a specific compiler (which one?), but too many warnings.
+   Revision 1.169  2014/12/22 23:08:31  brouard
+   Summary: 0.98p
+   Outputs some informations on compiler used, OS etc. Testing on different platforms.
+   Revision 1.168  2014/12/22 15:17:42  brouard
+   Summary: update
+   Revision 1.167  2014/12/22 13:50:56  brouard
+   Summary: Testing uname and compiler version and if compiled 32 or 64
+   Testing on Linux 64
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
+   Revision 1.143  2014/01/26 09:45:38  brouard
+   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
    Revision 1.142  2014/01/26 03:57:36  brouard
    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
- Line 303
+ Line 669
    Short summary of the programme:
-   This program computes Healthy Life Expectancies from
+   This program computes Healthy Life Expectancies or State-specific
-   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
+   (if states aren't health statuses) Expectancies from
-   first survey ("cross") where individuals from different ages are
+   cross-longitudinal data. Cross-longitudinal data consist in:
-   interviewed on their health status or degree of disability (in the
-   case of a health survey which is our main interest) -2- at least a
+   -1- a first survey ("cross") where individuals from different ages
-   second wave of interviews ("longitudinal") which measure each change
+   are interviewed on their health status or degree of disability (in
-   (if any) in individual health status.  Health expectancies are
+   the case of a health survey which is our main interest)
-   computed from the time spent in each health state according to a
-   model. More health states you consider, more time is necessary to reach the
+   -2- at least a second wave of interviews ("longitudinal") which
-   Maximum Likelihood of the parameters involved in the model.  The
+   measure each change (if any) in individual health status.  Health
-   simplest model is the multinomial logistic model where pij is the
+   expectancies are computed from the time spent in each health state
-   probability to be observed in state j at the second wave
+   according to a model. More health states you consider, more time is
-   conditional to be observed in state i at the first wave. Therefore
+   necessary to reach the Maximum Likelihood of the parameters involved
-   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
+   in the model.  The simplest model is the multinomial logistic model
-   'age' is age and 'sex' is a covariate. If you want to have a more
+   where pij is the probability to be observed in state j at the second
-   complex model than "constant and age", you should modify the program
+   wave conditional to be observed in state i at the first
-   where the markup *Covariates have to be included here again* invites
+   wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
-   you to do it.  More covariates you add, slower the
+   etc , where 'age' is age and 'sex' is a covariate. If you want to
+   have a more complex model than "constant and age", you should modify
+   the program where the markup *Covariates have to be included here
+   again* invites you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
- Line 339
+ Line 708
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
+ Back prevalence and projections:
+  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
+    double agemaxpar, double ftolpl, int *ncvyearp, double
+    dateprev1,double dateprev2, int firstpass, int lastpass, int
+    mobilavproj)
+     Computes the back prevalence limit for any combination of
+     covariate values k at any age between ageminpar and agemaxpar and
+     returns it in **bprlim. In the loops,
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
+        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+    - hBijx Back Probability to be in state i at age x-h being in j at x
+    Computes for any combination of covariates k and any age between bage and fage
+    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                         oldm=oldms;savm=savms;
+    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+      Computes the transition matrix starting at age 'age' over
+      'nhstepm*hstepm*stepm' months (i.e. until
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
+      Returns p3mat[i][j][h] after calling
+      p3mat[i][j][h]=matprod2(newm,
+      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
+      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+      oldm);
+ Important routines
+ - func (or funcone), computes logit (pij) distinguishing
+   o fixed variables (single or product dummies or quantitative);
+   o varying variables by:
+    (1) wave (single, product dummies, quantitative),
+    (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
+        % fixed dummy (treated) or quantitative (not done because time-consuming);
+        % varying dummy (not done) or quantitative (not done);
+ - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
+   and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
+ - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
+   o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
+     race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
             Institut national d'études démographiques, Paris.
- Line 368
+ Line 785
        begin-prev-date,...
    open gnuplot file
    open html file
-   period (stable) prevalence
+   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
-    for age prevalim()
+    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
-   h Pij x
+                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
-   variance of p varprob
+     freexexit2 possible for memory heap.
+   h Pij x                         | pij_nom  ficrestpij
+    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
+ 65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
+   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
+    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
+    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
    forecasting if prevfcast==1 prevforecast call prevalence()
    health expectancies
    Variance-covariance of DFLE
- Line 384
+ Line 813
   end
  */
+ /* #define DEBUG */
+ /* #define DEBUGBRENT */
+ /* #define DEBUGLINMIN */
+ /* #define DEBUGHESS */
+ #define DEBUGHESSIJ
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
+ #define POWELL /* Instead of NLOPT */
+ #define POWELLNOF3INFF1TEST /* Skip test */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
+ #include <ctype.h>
+ #ifdef _WIN32
+ #include <io.h>
+ #include <windows.h>
+ #include <tchar.h>
+ #else
  #include <unistd.h>
+ #endif
  #include <limits.h>
  #include <sys/types.h>
+ #if defined(__GNUC__)
+ #include <sys/utsname.h> /* Doesn't work on Windows */
+ #endif
  #include <sys/stat.h>
  #include <errno.h>
- extern int errno;
+ /* extern int errno; */
+ /* #ifdef LINUX */
+ /* #include <time.h> */
+ /* #include "timeval.h" */
+ /* #else */
+ /* #include <sys/time.h> */
+ /* #endif */
- #ifdef LINUX
  #include <time.h>
- #include "timeval.h"
- #else
- #include <sys/time.h>
- #endif
  #ifdef GSL
  #include <gsl/gsl_errno.h>
  #include <gsl/gsl_multimin.h>
  #endif
+ #ifdef NLOPT
+ #include <nlopt.h>
+ typedef struct {
+   double (* function)(double [] );
+ } myfunc_data ;
+ #endif
  /* #include <libintl.h> */
  /* #define _(String) gettext (String) */
- Line 423  extern int errno;
+ Line 883  extern int errno;
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define MAXPARM 128 /* Maximum number of parameters for the optimization */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- #define NCOVMAX 20 /* Maximum number of covariates */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+ /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
+ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
  #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #define YEARM 12. /**< Number of months per year */
- #define AGESUP 130
+ /* #define AGESUP 130 */
+ #define AGESUP 150
+ #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
  #define AGEBASE 40
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #define AGEOVERFLOW 1.e20
- #ifdef UNIX
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- #define DIRSEPARATOR '/'
+ #ifdef _WIN32
- #define CHARSEPARATOR "/"
- #define ODIRSEPARATOR '\\'
- #else
  #define DIRSEPARATOR '\\'
  #define CHARSEPARATOR "\\"
  #define ODIRSEPARATOR '/'
+ #else
+ #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
+ #define ODIRSEPARATOR '\\'
  #endif
  /* $Id$ */
  /* $State$ */
+ #include "version.h"
- char version[]="Imach version 0.98nR, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+ char version[]=__IMACH_VERSION__;
+ char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
  char fullversion[]="$Revision$ $Date$";
  char strstart[80];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar=0, nforce=0; /* Number of variables, number of forces */
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
+ int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
+ int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
+ int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
+ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
+ int nsd=0; /**< Total number of single dummy variables (output) */
+ int nsq=0; /**< Total number of single quantitative variables (output) */
+ int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
+ int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
+ int ntveff=0; /**< ntveff number of effective time varying variables */
+ int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
+ int cptcov=0; /* Working variable */
+ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- Line 472  int **mw; /* mw[mi][i] is number of the
+ Line 958  int **mw; /* mw[mi][i] is number of the
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ int countcallfunc=0;  /* Count the number of calls to func */
+ int selected(int kvar); /* Is covariate kvar selected for printing results */
  double jmean=1; /* Mean space between 2 waves */
+ double **matprod2(); /* test */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
  /*FILE *fic ; */ /* Used in readdata only */
- FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
  FILE *ficlog, *ficrespow;
  int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- Line 499  char fileresv[FILENAMELENGTH];
+ Line 991  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char model[MAXLINE]; /**< The model line */
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
- Line 514  char popfile[FILENAMELENGTH];
+ Line 1007  char popfile[FILENAMELENGTH];
  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- struct timezone tzp;
+ /* struct timezone tzp; */
- extern int gettimeofday();
+ /* extern int gettimeofday(); */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ struct tm tml, *gmtime(), *localtime();
- long time_value;
- extern long time();
+ extern time_t time();
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
+ struct tm tm;
  char strcurr[80], strfor[80];
  char *endptr;
- Line 549  static double maxarg1,maxarg2;
+ Line 1047  static double maxarg1,maxarg2;
  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  #define rint(a) floor(a+0.5)
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
+ #define mytinydouble 1.0e-16
+ /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
+ /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
+ /* static double dsqrarg; */
+ /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- Line 564  int estepm;
+ Line 1067  int estepm;
  int m,nb;
  long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ int firstpass=0, lastpass=4,*cod, *cens;
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
+                    covariate for which somebody answered excluding
+                    undefined. Usually 2: 0 and 1. */
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered including
+                              undefined. Usually 3: -1, 0 and 1. */
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs;
+ double **pmmij, ***probs; /* Global pointer */
+ double ***mobaverage, ***mobaverages; /* New global variable */
  double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc;
- double  **covar; /**< covar[i,j], value of jth covariate for individual i,
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                    * covar=matrix(0,NCOVMAX,1,n);
-                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
+ double **coqvar; /* Fixed quantitative covariate iqv */
+ double ***cotvar; /* Time varying covariate itv */
+ double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
- int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ /*k          1  2   3   4     5    6    7     8    9 */
+ /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
+ /* Tndvar[k]    1   2   3               4          5 */
+ /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
+ /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
+ /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
+ /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
+ /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
+ /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
+ /* Tprod[i]=k           4               7            */
+ /* Tage[i]=k                  5               8      */
+ /* */
+ /* Type                    */
+ /* V         1  2  3  4  5 */
+ /*           F  F  V  V  V */
+ /*           D  Q  D  D  Q */
+ /*                         */
+ int *TvarsD;
+ int *TvarsDind;
+ int *TvarsQ;
+ int *TvarsQind;
+ #define MAXRESULTLINES 10
+ int nresult=0;
+ int TKresult[MAXRESULTLINES];
+ int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
+ double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
+ /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *Tvarsel; /**< Selected covariates for output */
+ double *Tvalsel; /**< Selected modality value of covariate for output */
+ int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
+ int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
+ int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *Tage;
+ int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
+ int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
+ int *Ndum; /** Freq of modality (tricode */
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
+ int **Tvard;
+ int *Tprod;/**< Gives the k position of the k1 product */
+ int *Tposprod; /**< Gives the k1 product from the k position */
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+    if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+    Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
+ */
+ int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ #define FD 1; /* Fixed dummy covariate */
- double ftolhess; /* Tolerance for computing hessian */
+ #define FQ 2; /* Fixed quantitative covariate */
+ #define FP 3; /* Fixed product covariate */
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
+ #define VD 10; /* Varying dummy covariate */
+ #define VQ 11; /* Varying quantitative covariate */
+ #define VP 12; /* Varying product covariate */
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
+ #define APFD 16; /* Age product * fixed dummy covariate */
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
+ #define APVD 18; /* Age product * varying dummy covariate */
+ #define APVQ 19; /* Age product * varying quantitative covariate */
+ #define FTYPE 1; /* Fixed covariate */
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
+ struct kmodel{
+         int maintype; /* main type */
+         int subtype; /* subtype */
+ };
+ struct kmodel modell[NCOVMAX];
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
+ double ftolhess; /**< Tolerance for computing hessian */
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
- Line 592  static int split( char *path, char *dirc
+ Line 1199  static int split( char *path, char *dirc
       the name of the file (name), its extension only (ext) and its first part of the name (finame)
    */
    char  *ss;                            /* pointer */
-   int   l1, l2;                         /* length counters */
+   int   l1=0, l2=0;                             /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- Line 603  static int split( char *path, char *dirc
+ Line 1210  static int split( char *path, char *dirc
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
      /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #ifdef WIN32
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #else
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
+ #endif
        return( GLOCK_ERROR_GETCWD );
      }
      /* got dirc from getcwd*/
      printf(" DIRC = %s \n",dirc);
-   } else {                              /* strip direcotry from path */
+   } else {                              /* strip directory from path */
      ss++;                               /* after this, the filename */
      l2 = strlen( ss );                  /* length of filename */
      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
-     dirc[l1-l2] = 0;                    /* add zero */
+     dirc[l1-l2] = '\0';                 /* add zero */
      printf(" DIRC2 = %s \n",dirc);
    }
    /* We add a separator at the end of dirc if not exists */
- Line 666  char *trimbb(char *out, char *in)
+ Line 1277  char *trimbb(char *out, char *in)
    return s;
  }
+ /* char *substrchaine(char *out, char *in, char *chain) */
+ /* { */
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
+ /*   char *s, *t; */
+ /*   t=in;s=out; */
+ /*   while ((*in != *chain) && (*in != '\0')){ */
+ /*     *out++ = *in++; */
+ /*   } */
+ /*   /\* *in matches *chain *\/ */
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*   } */
+ /*   in--; chain--; */
+ /*   while ( (*in != '\0')){ */
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*     *out++ = *in++; */
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*   } */
+ /*   *out='\0'; */
+ /*   out=s; */
+ /*   return out; */
+ /* } */
+ char *substrchaine(char *out, char *in, char *chain)
+ {
+   /* Substract chain 'chain' from 'in', return and output 'out' */
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
+   char *strloc;
+   strcpy (out, in);
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
+   if(strloc != NULL){
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
+     /* strcpy (strloc, strloc +strlen(chain));*/
+   }
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+   return out;
+ }
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
+ {
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef" and alocc="ghi2j".
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
+   */
+   char *s, *t;
+   t=in;s=in;
+   while ((*in != occ) && (*in != '\0')){
+     *alocc++ = *in++;
+   }
+   if( *in == occ){
+     *(alocc)='\0';
+     s=++in;
+   }
+   if (s == t) {/* occ not found */
+     *(alocc-(in-s))='\0';
+     in=s;
+   }
+   while ( *in != '\0'){
+     *blocc++ = *in++;
+   }
+   *blocc='\0';
+   return t;
+ }
  char *cutv(char *blocc, char *alocc, char *in, char occ)
  {
-   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
+   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       gives blocc="abcdef2ghi" and alocc="j".
       If occ is not found blocc is null and alocc is equal to in. Returns alocc
- Line 702  int nbocc(char *s, char occ)
+ Line 1384  int nbocc(char *s, char occ)
    i=0;
    lg=strlen(s);
    for(i=0; i<= lg; i++) {
-   if  (s[i] == occ ) j++;
+     if  (s[i] == occ ) j++;
    }
    return j;
  }
- Line 729  int nbocc(char *s, char occ)
+ Line 1411  int nbocc(char *s, char occ)
  /*   } */
  /* } */
+ #ifdef _WIN32
+ char * strsep(char **pp, const char *delim)
+ {
+   char *p, *q;
+   if ((p = *pp) == NULL)
+     return 0;
+   if ((q = strpbrk (p, delim)) != NULL)
+   {
+     *pp = q + 1;
+     *q = '\0';
+   }
+   else
+     *pp = 0;
+   return p;
+ }
+ #endif
  /********************** nrerror ********************/
  void nrerror(char error_text[])
- Line 836  double **matrix(long nrl, long nrh, long
+ Line 1536  double **matrix(long nrl, long nrh, long
    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    return m;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     */
  }
- Line 925  char *subdirf3(char fileres[], char *pre
+ Line 1627  char *subdirf3(char fileres[], char *pre
    strcat(tmpout,fileres);
    return tmpout;
  }
+ /*************** function subdirfext ***********/
+ char *subdirfext(char fileres[], char *preop, char *postop)
+ {
+   strcpy(tmpout,preop);
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
+   return tmpout;
+ }
+ /*************** function subdirfext3 ***********/
+ char *subdirfext3(char fileres[], char *preop, char *postop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
+   return tmpout;
+ }
+ char *asc_diff_time(long time_sec, char ascdiff[])
+ {
+   long sec_left, days, hours, minutes;
+   days = (time_sec) / (60*60*24);
+   sec_left = (time_sec) % (60*60*24);
+   hours = (sec_left) / (60*60) ;
+   sec_left = (sec_left) %(60*60);
+   minutes = (sec_left) /60;
+   sec_left = (sec_left) % (60);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
+   return ascdiff;
+ }
  /***************** f1dim *************************/
  extern int ncom;
- Line 946  double f1dim(double x)
+ Line 1684  double f1dim(double x)
  /*****************brent *************************/
  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
  {
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
+    * returned function value.
+   */
    int iter;
    double a,b,d,etemp;
-   double fu,fv,fw,fx;
+   double fu=0,fv,fw,fx;
-   double ftemp;
+   double ftemp=0.;
    double p,q,r,tol1,tol2,u,v,w,x,xm;
    double e=0.0;
- Line 964  double brent(double ax, double bx, doubl
+ Line 1708  double brent(double ax, double bx, doubl
      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      printf(".");fflush(stdout);
      fprintf(ficlog,".");fflush(ficlog);
- #ifdef DEBUG
+ #ifdef DEBUGBRENT
      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);
      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);
      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
- Line 984  double brent(double ax, double bx, doubl
+ Line 1728  double brent(double ax, double bx, doubl
        etemp=e;
        e=d;
        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+                                 d=CGOLD*(e=(x >= xm ? a-x : b-x));
        else {
-         d=p/q;
+                                 d=p/q;
-         u=x+d;
+                                 u=x+d;
-         if (u-a < tol2 || b-u < tol2)
+                                 if (u-a < tol2 || b-u < tol2)
-           d=SIGN(tol1,xm-x);
+                                         d=SIGN(tol1,xm-x);
        }
      } else {
        d=CGOLD*(e=(x >= xm ? a-x : b-x));
- Line 999  double brent(double ax, double bx, doubl
+ Line 1743  double brent(double ax, double bx, doubl
      if (fu <= fx) {
        if (u >= x) a=x; else b=x;
        SHFT(v,w,x,u)
-         SHFT(fv,fw,fx,fu)
+       SHFT(fv,fw,fx,fu)
-         } else {
+     } else {
-           if (u < x) a=u; else b=u;
+       if (u < x) a=u; else b=u;
-           if (fu <= fw || w == x) {
+       if (fu <= fw || w == x) {
-             v=w;
+                                 v=w;
-             w=u;
+                                 w=u;
-             fv=fw;
+                                 fv=fw;
-             fw=fu;
+                                 fw=fu;
-           } else if (fu <= fv || v == x || v == w) {
+       } else if (fu <= fv || v == x || v == w) {
-             v=u;
+                                 v=u;
-             fv=fu;
+                                 fv=fu;
-           }
+       }
-         }
+     }
    }
    nrerror("Too many iterations in brent");
    *xmin=x;
- Line 1022  double brent(double ax, double bx, doubl
+ Line 1766  double brent(double ax, double bx, doubl
  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
              double (*func)(double))
- {
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
+ new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
+    */
    double ulim,u,r,q, dum;
    double fu;
-   *fa=(*func)(*ax);
+   double scale=10.;
-   *fb=(*func)(*bx);
+   int iterscale=0;
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
+   /*   *bx = *ax - (*ax - *bx)/scale; */
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
+   /* } */
    if (*fb > *fa) {
      SHFT(dum,*ax,*bx,dum)
-       SHFT(dum,*fb,*fa,dum)
+     SHFT(dum,*fb,*fa,dum)
-       }
+   }
    *cx=(*bx)+GOLD*(*bx-*ax);
    *fc=(*func)(*cx);
-   while (*fb > *fc) {
+ #ifdef DEBUG
+   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
+   fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
+ #endif
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
      r=(*bx-*ax)*(*fb-*fc);
-     q=(*bx-*cx)*(*fb-*fa);
+     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-     if ((*bx-u)*(u-*cx) > 0.0) {
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
        fu=(*func)(u);
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ #ifdef DEBUG
+       /* f(x)=A(x-u)**2+f(u) */
+       double A, fparabu;
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
+       printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
+       fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
+ #endif
+ #ifdef MNBRAKORIGINAL
+ #else
+ /*       if (fu > *fc) { */
+ /* #ifdef DEBUG */
+ /*       printf("mnbrak4  fu > fc \n"); */
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
+ /* #endif */
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
+ /*      *cx = dum; */
+ /*      dum = fu; */
+ /*      fu = *fc; */
+ /*      *fc =dum; */
+ /*       } else { /\* end *\/ */
+ /* #ifdef DEBUG */
+ /*       printf("mnbrak3  fu < fc \n"); */
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
+ /* #endif */
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
+ /*      *cx = dum; */
+ /*      dum = fu; */
+ /*      fu = *fc; */
+ /*      *fc =dum; */
+ /*       } */
+ #ifdef DEBUGMNBRAK
+                  double A, fparabu;
+      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+      fparabu= *fa - A*(*ax-u)*(*ax-u);
+      printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
+      fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
+ #endif
+       dum=u; /* Shifting c and u */
+       u = *cx;
+       *cx = dum;
+       dum = fu;
+       fu = *fc;
+       *fc =dum;
+ #endif
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
+ #ifdef DEBUG
+       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
+       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
+ #endif
        fu=(*func)(u);
        if (fu < *fc) {
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ #ifdef DEBUG
-           SHFT(*fb,*fc,fu,(*func)(u))
+                                 printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-           }
+                           fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+ #endif
+                           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+                                 SHFT(*fb,*fc,fu,(*func)(u))
+ #ifdef DEBUG
+                                         printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
+ #endif
+       }
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
+ #ifdef DEBUG
+       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
+       fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
+ #endif
        u=ulim;
        fu=(*func)(u);
-     } else {
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
+ #ifdef DEBUG
+       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
+       fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
+ #endif
        u=(*cx)+GOLD*(*cx-*bx);
        fu=(*func)(u);
-     }
+ #ifdef DEBUG
+       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
+       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
+ #endif
+     } /* end tests */
      SHFT(*ax,*bx,*cx,u)
-       SHFT(*fa,*fb,*fc,fu)
+     SHFT(*fa,*fb,*fc,fu)
-       }
+ #ifdef DEBUG
+       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
+       fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
+ #endif
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
  }
  /*************** linmin ************************/
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
+ the value of func at the returned location p . This is actually all accomplished by calling the
+ routines mnbrak and brent .*/
  int ncom;
  double *pcom,*xicom;
  double (*nrfunc)(double []);
+ #ifdef LINMINORIGINAL
  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ #else
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
+ #endif
  {
    double brent(double ax, double bx, double cx,
                 double (*f)(double), double tol, double *xmin);
- Line 1076  void linmin(double p[], double xi[], int
+ Line 1927  void linmin(double p[], double xi[], int
    int j;
    double xx,xmin,bx,ax;
    double fx,fb,fa;
+ #ifdef LINMINORIGINAL
+ #else
+   double scale=10., axs, xxs; /* Scale added for infinity */
+ #endif
    ncom=n;
    pcom=vector(1,n);
    xicom=vector(1,n);
    nrfunc=func;
    for (j=1;j<=n;j++) {
      pcom[j]=p[j];
-     xicom[j]=xi[j];
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
    }
-   ax=0.0;
-   xx=1.0;
+ #ifdef LINMINORIGINAL
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   xx=1.;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ #else
+   axs=0.0;
+   xxs=1.;
+   do{
+     xx= xxs;
+ #endif
+     ax=0.;
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
+     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
+     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
+ #ifdef LINMINORIGINAL
+ #else
+     if (fx != fx){
+                         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+                         printf("|");
+                         fprintf(ficlog,"|");
+ #ifdef DEBUGLINMIN
+                         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
+ #endif
+     }
+   }while(fx != fx && xxs > 1.e-5);
+ #endif
+ #ifdef DEBUGLINMIN
+   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+   fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+ #endif
+ #ifdef LINMINORIGINAL
+ #else
+         if(fb == fx){ /* Flat function in the direction */
+                 xmin=xx;
+     *flat=1;
+         }else{
+     *flat=0;
+ #endif
+                 /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
+   /* fmin = f(p[j] + xmin * xi[j]) */
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
  #ifdef DEBUG
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
+ #endif
+ #ifdef LINMINORIGINAL
+ #else
+                         }
+ #endif
+ #ifdef DEBUGLINMIN
+   printf("linmin end ");
+   fprintf(ficlog,"linmin end ");
  #endif
    for (j=1;j<=n;j++) {
+ #ifdef LINMINORIGINAL
      xi[j] *= xmin;
-     p[j] += xi[j];
+ #else
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
+ #endif
+     xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
+       printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
+ #endif
+ #endif
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
    }
+ #ifdef DEBUGLINMIN
+   printf("\n");
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   for (j=1;j<=n;j++) {
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+     if(j % ncovmodel == 0){
+       printf("\n");
+       fprintf(ficlog,"\n");
+     }
+   }
+ #else
+ #endif
    free_vector(xicom,1,n);
    free_vector(pcom,1,n);
  }
- char *asc_diff_time(long time_sec, char ascdiff[])
- {
-   long sec_left, days, hours, minutes;
-   days = (time_sec) / (60*60*24);
-   sec_left = (time_sec) % (60*60*24);
-   hours = (sec_left) / (60*60) ;
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
-   sec_left = (sec_left) % (60);
-   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-   return ascdiff;
- }
  /*************** powell ************************/
+ /*
+ Minimization of a function func of n variables. Input consists of an initial starting point
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
+  */
+ #ifdef LINMINORIGINAL
+ #else
+         int *flatdir; /* Function is vanishing in that direction */
+         int flat=0, flatd=0; /* Function is vanishing in that direction */
+ #endif
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
  {
-   void linmin(double p[], double xi[], int n, double *fret,
+ #ifdef LINMINORIGINAL
+  void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []));
+ #else
+  void linmin(double p[], double xi[], int n, double *fret,
+                                                  double (*func)(double []),int *flat);
+ #endif
    int i,ibig,j;
    double del,t,*pt,*ptt,*xit;
+   double directest;
    double fp,fptt;
    double *xits;
    int niterf, itmp;
+ #ifdef LINMINORIGINAL
+ #else
+   flatdir=ivector(1,n);
+   for (j=1;j<=n;j++) flatdir[j]=0;
+ #endif
    pt=vector(1,n);
    ptt=vector(1,n);
- Line 1132  void powell(double p[], double **xi, int
+ Line 2079  void powell(double p[], double **xi, int
    xits=vector(1,n);
    *fret=(*func)(p);
    for (j=1;j<=n;j++) pt[j]=p[j];
+   rcurr_time = time(NULL);
    for (*iter=1;;++(*iter)) {
-     fp=(*fret);
+     fp=(*fret); /* From former iteration or initial value */
      ibig=0;
      del=0.0;
-     last_time=curr_time;
+     rlast_time=rcurr_time;
-     (void) gettimeofday(&curr_time,&tzp);
+     /* (void) gettimeofday(&curr_time,&tzp); */
-     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);
+     rcurr_time = time(NULL);
-     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);
+     curr_time = *localtime(&rcurr_time);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-    for (i=1;i<=n;i++) {
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
+     for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
- Line 1150  void powell(double p[], double **xi, int
+ Line 2100  void powell(double p[], double **xi, int
      fprintf(ficlog,"\n");
      fprintf(ficrespow,"\n");fflush(ficrespow);
      if(*iter <=3){
-       tm = *localtime(&curr_time.tv_sec);
+       tml = *localtime(&rcurr_time);
-       strcpy(strcurr,asctime(&tm));
+       strcpy(strcurr,asctime(&tml));
- /*       asctime_r(&tm,strcurr); */
+       rforecast_time=rcurr_time;
-       forecast_time=curr_time;
        itmp = strlen(strcurr);
        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-         strcurr[itmp-1]='\0';
+                                 strcurr[itmp-1]='\0';
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
        for(niterf=10;niterf<=30;niterf+=10){
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-         tmf = *localtime(&forecast_time.tv_sec);
+                                 forecast_time = *localtime(&rforecast_time);
- /*      asctime_r(&tmf,strfor); */
+                                 strcpy(strfor,asctime(&forecast_time));
-         strcpy(strfor,asctime(&tmf));
+                                 itmp = strlen(strfor);
-         itmp = strlen(strfor);
+                                 if(strfor[itmp-1]=='\n')
-         if(strfor[itmp-1]=='\n')
+                                         strfor[itmp-1]='\0';
-         strfor[itmp-1]='\0';
+                                 printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-         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);
+                                 fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-         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);
        }
      }
-     for (i=1;i<=n;i++) {
+     for (i=1;i<=n;i++) { /* For each direction i */
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
        fptt=(*fret);
  #ifdef DEBUG
-       printf("fret=%lf \n",*fret);
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
  #endif
-       printf("%d",i);fflush(stdout);
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
        fprintf(ficlog,"%d",i);fflush(ficlog);
-       linmin(p,xit,n,fret,func);
+ #ifdef LINMINORIGINAL
-       if (fabs(fptt-(*fret)) > del) {
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-         del=fabs(fptt-(*fret));
+ #else
-         ibig=i;
+       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
+                         flatdir[i]=flat; /* Function is vanishing in that direction i */
+ #endif
+                         /* Outputs are fret(new point p) p is updated and xit rescaled */
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
+                                 /* because that direction will be replaced unless the gain del is small */
+                                 /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
+                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */
+                                 /* with the new direction. */
+                                 del=fabs(fptt-(*fret));
+                                 ibig=i;
        }
  #ifdef DEBUG
        printf("%d %.12e",i,(*fret));
        fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+                                 xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         printf(" x(%d)=%.12e",j,xit[j]);
+                                 printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+                                 fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        }
        for(j=1;j<=n;j++) {
-         printf(" p=%.12e",p[j]);
+                                 printf(" p(%d)=%.12e",j,p[j]);
-         fprintf(ficlog," p=%.12e",p[j]);
+                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);
        }
        printf("\n");
        fprintf(ficlog,"\n");
  #endif
-     }
+     } /* end loop on each direction i */
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
+     /* New value of last point Pn is not computed, P(n-1) */
+       for(j=1;j<=n;j++) {
+                                 if(flatdir[j] >0){
+                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+                                 }
+                                 /* printf("\n"); */
+                                 /* fprintf(ficlog,"\n"); */
+                         }
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
+       /* decreased of more than 3.84  */
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
+       /* By adding 10 parameters more the gain should be 18.31 */
+       /* Starting the program with initial values given by a former maximization will simply change */
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
  #ifdef DEBUG
        int k[2],l;
        k[0]=1;
- Line 1225  void powell(double p[], double **xi, int
+ Line 2206  void powell(double p[], double **xi, int
        }
  #endif
+ #ifdef LINMINORIGINAL
+ #else
+       free_ivector(flatdir,1,n);
+ #endif
        free_vector(xit,1,n);
        free_vector(xits,1,n);
        free_vector(ptt,1,n);
        free_vector(pt,1,n);
        return;
-     }
+     } /* enough precision */
      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-     for (j=1;j<=n;j++) {
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
        ptt[j]=2.0*p[j]-pt[j];
        xit[j]=p[j]-pt[j];
        pt[j]=p[j];
      }
-     fptt=(*func)(ptt);
+     fptt=(*func)(ptt); /* f_3 */
-     if (fptt < fp) {
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+                 if (*iter <=4) {
-       if (t < 0.0) {
+ #else
-         linmin(p,xit,n,fret,func);
+ #endif
+ #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
+ #else
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
+ #endif
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
+       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
+       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+       /*  Even if f3 <f1, directest can be negative and t >0 */
+       /* mu² and del² are equal when f3=f1 */
+                         /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
+                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
+                         /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
+                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
+ #ifdef NRCORIGINAL
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
+ #else
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
+       t= t- del*SQR(fp-fptt);
+ #endif
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
+ #ifdef DEBUG
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+ #endif
+ #ifdef POWELLORIGINAL
+       if (t < 0.0) { /* Then we use it for new direction */
+ #else
+       if (directest*t < 0.0) { /* Contradiction between both tests */
+                                 printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+         fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+       }
+       if (directest < 0.0) { /* Then we use it for new direction */
+ #endif
+ #ifdef DEBUGLINMIN
+         printf("Before linmin in direction P%d-P0\n",n);
+         for (j=1;j<=n;j++) {
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           if(j % ncovmodel == 0){
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+ #endif
+ #ifdef LINMINORIGINAL
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+ #else
+         linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+         flatdir[i]=flat; /* Function is vanishing in that direction i */
+ #endif
+ #ifdef DEBUGLINMIN
+         for (j=1;j<=n;j++) {
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           if(j % ncovmodel == 0){
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+ #endif
          for (j=1;j<=n;j++) {
-           xi[j][ibig]=xi[j][n];
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-           xi[j][n]=xit[j];
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
+         }
+ #ifdef LINMINORIGINAL
+ #else
+         for (j=1, flatd=0;j<=n;j++) {
+           if(flatdir[j]>0)
+             flatd++;
+         }
+         if(flatd >0){
+           printf("%d flat directions\n",flatd);
+           fprintf(ficlog,"%d flat directions\n",flatd);
+           for (j=1;j<=n;j++) {
+             if(flatdir[j]>0){
+               printf("%d ",j);
+               fprintf(ficlog,"%d ",j);
+             }
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
          }
+ #endif
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          for(j=1;j<=n;j++){
-           printf(" %.12e",xit[j]);
+           printf(" %lf",xit[j]);
-           fprintf(ficlog," %.12e",xit[j]);
+           fprintf(ficlog," %lf",xit[j]);
          }
          printf("\n");
          fprintf(ficlog,"\n");
  #endif
-       }
+       } /* end of t or directest negative */
-     }
+ #ifdef POWELLNOF3INFF1TEST
-   }
+ #else
+       } /* end if (fptt < fp)  */
+ #endif
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
+ #else
+ #endif
+                 } /* loop iteration */
  }
  /**** Prevalence limit (stable or period prevalence)  ****************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
- {
+   {
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+     /* Computes the prevalence limit in each live state at age x and for covariate combination ij
-      matrix by transitions matrix until convergence is reached */
+        (and selected quantitative values in nres)
+        by left multiplying the unit
+        matrix by transitions matrix until convergence is reached with precision ftolpl */
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
+   /* or prevalence in state 1, prevalence in state 2, 0 */
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
+   /* Initial matrix pimij */
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
+   /*  0,                   0                  , 1} */
+   /*
+    * and after some iteration: */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
+   /*  0,                   0                  , 1} */
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
    int i, ii,j,k;
-   double min, max, maxmin, maxmax,sumnew=0.;
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-   double **matprod2();
+   /* double **matprod2(); */ /* test */
-   double **out, cov[NCOVMAX+1], **pmij();
+   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
    double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
+   int ncvloop=0;
+   min=vector(1,nlstate);
+   max=vector(1,nlstate);
+   meandiff=vector(1,nlstate);
+         /* Starting with matrix unity */
    for (ii=1;ii<=nlstate+ndeath;ii++)
      for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }
-    cov[1]=1.;
+   cov[1]=1.;
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     ncvloop++;
      newm=savm;
      /* Covariates have to be included here again */
      cov[2]=agefin;
+     if(nagesqr==1)
-     for (k=1; k<=cptcovn;k++) {
+       cov[3]= agefin*agefin;;
-       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-       /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
+       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
+     }
+     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
+     }
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
+       if(Dummy[Tvar[Tage[k]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       } else{
+         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+       }
+       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+     }
+     for (k=1; k<=cptcovprod;k++){ /* For product without age */
+       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
+       if(Dummy[Tvard[k][1]==0]){
+         if(Dummy[Tvard[k][2]==0]){
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
+         }
+       }else{
+         if(Dummy[Tvard[k][2]==0]){
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
+         }
+       }
      }
-     for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-     for (k=1; k<=cptcovprod;k++)
-       cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+                 /* age and covariate values of ij are in 'cov' */
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
      oldm=newm;
-     maxmax=0.;
-     for(j=1;j<=nlstate;j++){
+     for(j=1; j<=nlstate; j++){
-       min=1.;
+       max[j]=0.;
-       max=0.;
+       min[j]=1.;
-       for(i=1; i<=nlstate; i++) {
+     }
-         sumnew=0;
+     for(i=1;i<=nlstate;i++){
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       sumnew=0;
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       for(j=1; j<=nlstate; j++){
          prlim[i][j]= newm[i][j]/(1-sumnew);
-         max=FMAX(max,prlim[i][j]);
+         max[j]=FMAX(max[j],prlim[i][j]);
-         min=FMIN(min,prlim[i][j]);
+         min[j]=FMIN(min[j],prlim[i][j]);
        }
-       maxmin=max-min;
-       maxmax=FMAX(maxmax,maxmin);
      }
+     maxmax=0.;
+     for(j=1; j<=nlstate; j++){
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
+       maxmax=FMAX(maxmax,meandiff[j]);
+       /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
+     } /* j loop */
+     *ncvyear= (int)age- (int)agefin;
+     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
      if(maxmax < ftolpl){
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+       free_vector(min,1,nlstate);
+       free_vector(max,1,nlstate);
+       free_vector(meandiff,1,nlstate);
        return prlim;
      }
-   }
+   } /* age loop */
+     /* After some age loop it doesn't converge */
+   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+ Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
+   free_vector(min,1,nlstate);
+   free_vector(max,1,nlstate);
+   free_vector(meandiff,1,nlstate);
+   return prlim; /* should not reach here */
+ }
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
+  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
+ {
+   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
+   /* or prevalence in state 1, prevalence in state 2, 0 */
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
+   /* Initial matrix pimij */
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
+   /*  0,                   0                  , 1} */
+   /*
+    * and after some iteration: */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
+   /*  0,                   0                  , 1} */
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
+   int i, ii,j,k;
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
+   /* double **matprod2(); */ /* test */
+   double **out, cov[NCOVMAX+1], **bmij();
+   double **newm;
+   double         **dnewm, **doldm, **dsavm;  /* for use */
+   double         **oldm, **savm;  /* for use */
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
+   int ncvloop=0;
+   min=vector(1,nlstate);
+   max=vector(1,nlstate);
+   meandiff=vector(1,nlstate);
+         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+         oldm=oldms; savm=savms;
+         /* Starting with matrix unity */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+                 for (j=1;j<=nlstate+ndeath;j++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     }
+   cov[1]=1.;
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
+   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
+   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
+     ncvloop++;
+     newm=savm; /* oldm should be kept from previous iteration or unity at start */
+                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
+     /* Covariates have to be included here again */
+     cov[2]=agefin;
+     if(nagesqr==1)
+       cov[3]= agefin*agefin;;
+     for (k=1; k<=cptcovn;k++) {
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
+     }
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+     for (k=1; k<=cptcovprod;k++) /* Useless */
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+                 /* ij should be linked to the correct index of cov */
+                 /* age and covariate values ij are in 'cov', but we need to pass
+                  * ij for the observed prevalence at age and status and covariate
+                  * number:  prevacurrent[(int)agefin][ii][ij]
+                  */
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
+     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
+     savm=oldm;
+     oldm=newm;
+     for(j=1; j<=nlstate; j++){
+       max[j]=0.;
+       min[j]=1.;
+     }
+     for(j=1; j<=nlstate; j++){
+       for(i=1;i<=nlstate;i++){
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
+         bprlim[i][j]= newm[i][j];
+         max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
+         min[i]=FMIN(min[i],bprlim[i][j]);
+       }
+     }
+     maxmax=0.;
+     for(i=1; i<=nlstate; i++){
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
+       maxmax=FMAX(maxmax,meandiff[i]);
+       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
+     } /* j loop */
+     *ncvyear= -( (int)age- (int)agefin);
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
+     if(maxmax < ftolpl){
+       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+       free_vector(min,1,nlstate);
+       free_vector(max,1,nlstate);
+       free_vector(meandiff,1,nlstate);
+       return bprlim;
+     }
+   } /* age loop */
+     /* After some age loop it doesn't converge */
+   printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+ Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
+   free_vector(min,1,nlstate);
+   free_vector(max,1,nlstate);
+   free_vector(meandiff,1,nlstate);
+   return bprlim; /* should not reach here */
  }
  /*************** transition probabilities ***************/
- Line 1343  double **pmij(double **ps, double *cov,
+ Line 2639  double **pmij(double **ps, double *cov,
    */
    double s1, lnpijopii;
    /*double t34;*/
-   int i,j,j1, nc, ii, jj;
+   int i,j, nc, ii, jj;
-     for(i=1; i<= nlstate; i++){
+   for(i=1; i<= nlstate; i++){
-       for(j=1; j<i;j++){
+     for(j=1; j<i;j++){
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
-           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
- /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
- /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-       }
-       for(j=i+1; j<=nlstate+ndeath;j++){
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
- /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-         }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
        }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
      }
+     for(j=i+1; j<=nlstate+ndeath;j++){
-     for(i=1; i<= nlstate; i++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-       s1=0;
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-       for(j=1; j<i; j++){
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-       }
-       for(j=i+1; j<=nlstate+ndeath; j++){
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-       }
-       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-       ps[i][i]=1./(s1+1.);
-       /* Computing other pijs */
-       for(j=1; j<i; j++)
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       for(j=i+1; j<=nlstate+ndeath; j++)
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-     } /* end i */
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-       for(jj=1; jj<= nlstate+ndeath; jj++){
-         ps[ii][jj]=0;
-         ps[ii][ii]=1;
        }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      }
+   }
+   for(i=1; i<= nlstate; i++){
+     s1=0;
+     for(j=1; j<i; j++){
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     }
+     for(j=i+1; j<=nlstate+ndeath; j++){
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     }
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+     ps[i][i]=1./(s1+1.);
+     /* Computing other pijs */
+     for(j=1; j<i; j++)
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
+     for(j=i+1; j<=nlstate+ndeath; j++)
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+   } /* end i */
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
+       ps[ii][jj]=0;
+       ps[ii][ii]=1;
+     }
+   }
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+   /*   } */
+   /*   printf("\n "); */
+   /* } */
+   /* printf("\n ");printf("%lf ",cov[2]);*/
+   /*
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
+                 goto end;*/
+   return ps;
+ }
+ /*************** backward transition probabilities ***************/
+  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
+ /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
+  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
+ {
+   /* Computes the backward probability at age agefin and covariate ij
+    * and returns in **ps as well as **bmij.
+    */
+   int i, ii, j,k;
+   double **out, **pmij();
+   double sumnew=0.;
+   double agefin;
+   double **dnewm, **dsavm, **doldm;
+   double **bbmij;
+   doldm=ddoldms; /* global pointers */
+   dnewm=ddnewms;
+   dsavm=ddsavms;
+   agefin=cov[2];
+   /* bmij *//* age is cov[2], ij is included in cov, but we need for
+      the observed prevalence (with this covariate ij) */
+   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
+   /* We do have the matrix Px in savm  and we need pij */
+   for (j=1;j<=nlstate+ndeath;j++){
+     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
+     for (ii=1;ii<=nlstate;ii++){
+       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
+     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       if(sumnew >= 1.e-10){
+         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else */
+         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
+       }else{
+         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
+       }
+     } /*End ii */
+   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
+   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
+   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
+   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
+   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
+   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
+   /* left Product of this matrix by diag matrix of prevalences (savm) */
+   for (j=1;j<=nlstate+ndeath;j++){
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
+     }
+   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
+   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
+   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
+   /* end bmij */
+   return ps;
+ }
+ /*************** transition probabilities ***************/
+ double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ {
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   for(i=1; i<= nlstate; i++){
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     for(j=1; j<i;j++){
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- /*       } */
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
- /*       printf("\n "); */
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
- /*        } */
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
- /*        printf("\n ");printf("%lf ",cov[2]); */
+       }
-        /*
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-       goto end;*/
+     }
-     return ps;
+     for(j=i+1; j<=nlstate+ndeath;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+       }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+     }
+   }
+   for(i=1; i<= nlstate; i++){
+     s1=0;
+     for(j=1; j<i; j++){
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     }
+     for(j=i+1; j<=nlstate+ndeath; j++){
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+     }
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+     ps[i][i]=1./(s1+1.);
+     /* Computing other pijs */
+     for(j=1; j<i; j++)
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
+     for(j=i+1; j<=nlstate+ndeath; j++)
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+   } /* end i */
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
+       ps[ii][jj]=0;
+       ps[ii][ii]=1;
+     }
+   }
+   /* Added for backcast */ /* Transposed matrix too */
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     s1=0.;
+     for(ii=1; ii<= nlstate+ndeath; ii++){
+       s1+=ps[ii][jj];
+     }
+     for(ii=1; ii<= nlstate; ii++){
+       ps[ii][jj]=ps[ii][jj]/s1;
+     }
+   }
+   /* Transposition */
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     for(ii=jj; ii<= nlstate+ndeath; ii++){
+       s1=ps[ii][jj];
+       ps[ii][jj]=ps[jj][ii];
+       ps[jj][ii]=s1;
+     }
+   }
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+   /*   } */
+   /*   printf("\n "); */
+   /* } */
+   /* printf("\n ");printf("%lf ",cov[2]);*/
+   /*
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     goto end;*/
+   return ps;
  }
  /**************** Product of 2 matrices ******************/
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
  {
    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
    /* in, b, out are matrice of pointers which should have been initialized
       before: only the contents of out is modified. The function returns
       a pointer to pointers identical to out */
-   long i, j, k;
+   int i, j, k;
    for(i=nrl; i<= nrh; i++)
-     for(k=ncolol; k<=ncoloh; k++)
+     for(k=ncolol; k<=ncoloh; k++){
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       out[i][k]=0.;
-         out[i][k] +=in[i][j]*b[j][k];
+       for(j=ncl; j<=nch; j++)
+         out[i][k] +=in[i][j]*b[j][k];
+     }
    return out;
  }
  /************* Higher Matrix Product ***************/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
  {
-   /* Computes the transition matrix starting at age 'age' over
+   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 1444  double ***hpxij(double ***po, int nhstep
+ Line 2901  double ***hpxij(double ***po, int nhstep
    int i, j, d, h, k;
    double **out, cov[NCOVMAX+1];
    double **newm;
+   double agexact;
+   double agebegin, ageend;
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
- Line 1457  double ***hpxij(double ***po, int nhstep
+ Line 2916  double ***hpxij(double ***po, int nhstep
        newm=savm;
        /* Covariates have to be included here again */
        cov[1]=1.;
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
-       for (k=1; k<=cptcovn;k++)
+       cov[2]=agexact;
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       if(nagesqr==1)
-       for (k=1; k<=cptcovage;k++)
+         cov[3]= agexact*agexact;
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-       for (k=1; k<=cptcovprod;k++)
+                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+         /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
+       }
+       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
+       }
+       for (k=1; k<=cptcovage;k++){
+         if(Dummy[Tvar[Tage[k]]]){
+           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+         } else{
+           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+         }
+         /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+       }
+       for (k=1; k<=cptcovprod;k++){ /*  */
+         /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+       }
+       /* for (k=1; k<=cptcovn;k++)  */
+       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
+       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
+       /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
+       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+                         /* right multiplication of oldm by the current matrix */
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                     pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* if((int)age == 70){ */
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
        savm=oldm;
        oldm=newm;
      }
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
-         po[i][j][h]=newm[i][j];
+                                 po[i][j][h]=newm[i][j];
-         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
        }
      /*printf("h=%d ",h);*/
    } /* end h */
- /*     printf("\n H=%d \n",h); */
+         /*     printf("\n H=%d \n",h); */
    return po;
  }
+ /************* Higher Back Matrix Product ***************/
- /*************** log-likelihood *************/
+ /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
- double func( double *x)
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
  {
-   int i, ii, j, k, mi, d, kk;
+   /* Computes the transition matrix starting at age 'age' over
-   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+      'nhstepm*hstepm*stepm' months (i.e. until
-   double **out;
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   double sw; /* Sum of weights */
+      nhstepm*hstepm matrices.
-   double lli; /* Individual log likelihood */
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   int s1, s2;
+      (typically every 2 years instead of every month which is too big
-   double bbh, survp;
+      for the memory).
-   long ipmx;
+      Model is determined by parameters x and covariates have to be
-   /*extern weight */
+      included manually here.
-   /* We are differentiating ll according to initial status */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*for(i=1;i<imx;i++)
-     printf(" %d\n",s[4][i]);
    */
-   cov[1]=1.;
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   int i, j, d, h, k;
+   double **out, cov[NCOVMAX+1];
+   double **newm;
+   double agexact;
+   double agebegin, ageend;
+   double **oldm, **savm;
+   oldm=oldms;savm=savms;
+   /* Hstepm could be zero and should return the unit matrix */
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
+     }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(h=1; h <=nhstepm; h++){
+     for(d=1; d <=hstepm; d++){
+       newm=savm;
+       /* Covariates have to be included here again */
+       cov[1]=1.;
+       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
+       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
+       cov[2]=agexact;
+       if(nagesqr==1)
+         cov[3]= agexact*agexact;
+       for (k=1; k<=cptcovn;k++)
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       /* Careful transposed matrix */
+       /* age is in cov[2] */
+       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
+       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+       /* if((int)age == 70){ */
+       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
+       savm=oldm;
+       oldm=newm;
+     }
+     for(i=1; i<=nlstate+ndeath; i++)
+       for(j=1;j<=nlstate+ndeath;j++) {
+         po[i][j][h]=newm[i][j];
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
+     /*printf("h=%d ",h);*/
+   } /* end h */
+   /*     printf("\n H=%d \n",h); */
+   return po;
+ }
+ #ifdef NLOPT
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
+   double fret;
+   double *xt;
+   int j;
+   myfunc_data *d2 = (myfunc_data *) pd;
+ /* xt = (p1-1); */
+   xt=vector(1,n);
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
+   printf("Function = %.12lf ",fret);
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
+   printf("\n");
+  free_vector(xt,1,n);
+   return fret;
+ }
+ #endif
+ /*************** log-likelihood *************/
+ double func( double *x)
+ {
+   int i, ii, j, k, mi, d, kk;
+   int ioffset=0;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+   double **out;
+   double lli; /* Individual log likelihood */
+   int s1, s2;
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
+   double bbh, survp;
+   long ipmx;
+   double agexact;
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
+   */
+   ++countcallfunc;
+   cov[1]=1.;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        /* Computes the values of the ncovmodel covariates of the model
-          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
           to be observed in j being in i according to the model.
-        */
+       */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       ioffset=2+nagesqr+cptcovage;
+    /* Fixed */
+       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
+       }
        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
           has been calculated etc */
+       /* For an individual i, wav[i] gives the number of effective waves */
+       /* We compute the contribution to Likelihood of each effective transition
+          mw[mi][i] is real wave of the mi th effectve wave */
+       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
+          s2=s[mw[mi+1][i]][i];
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
+          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
+          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
+       */
        for(mi=1; mi<= wav[i]-1; mi++){
+         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+         }
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 1525  double func( double *x)
+ Line 3154  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;  /* Should be changed here */
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            savm=oldm;
            oldm=newm;
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
- Line 1543  double func( double *x)
+ Line 3175  double func( double *x)
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
+                                  * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
+                                  * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
+                                  * For stepm > 1 the results are less biased than in previous versions.
-          */
+                                  */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
- Line 1562  double func( double *x)
+ Line 3194  double func( double *x)
               which is also equal to probability to die before dh
               minus probability to die before dh-stepm .
               In version up to 0.92 likelihood was computed
-         as if date of death was unknown. Death was treated as any other
+              as if date of death was unknown. Death was treated as any other
-         health state: the date of the interview describes the actual state
+              health state: the date of the interview describes the actual state
-         and not the date of a change in health state. The former idea was
+              and not the date of a change in health state. The former idea was
-         to consider that at each interview the state was recorded
+              to consider that at each interview the state was recorded
-         (healthy, disable or death) and IMaCh was corrected; but when we
+              (healthy, disable or death) and IMaCh was corrected; but when we
-         introduced the exact date of death then we should have modified
+              introduced the exact date of death then we should have modified
-         the contribution of an exact death to the likelihood. This new
+              the contribution of an exact death to the likelihood. This new
-         contribution is smaller and very dependent of the step unit
+              contribution is smaller and very dependent of the step unit
-         stepm. It is no more the probability to die between last interview
+              stepm. It is no more the probability to die between last interview
-         and month of death but the probability to survive from last
+              and month of death but the probability to survive from last
-         interview up to one month before death multiplied by the
+              interview up to one month before death multiplied by the
-         probability to die within a month. Thanks to Chris
+              probability to die within a month. Thanks to Chris
-         Jackson for correcting this bug.  Former versions increased
+              Jackson for correcting this bug.  Former versions increased
-         mortality artificially. The bad side is that we add another loop
+              mortality artificially. The bad side is that we add another loop
-         which slows down the processing. The difference can be up to 10%
+              which slows down the processing. The difference can be up to 10%
-         lower mortality.
+              lower mortality.
+           */
+           /* If, at the beginning of the maximization mostly, the
+              cumulative probability or probability to be dead is
+              constant (ie = 1) over time d, the difference is equal to
+.  out[s1][3] = savm[s1][3]: probability, being at state
+              s1 at precedent wave, to be dead a month before current
+              wave is equal to probability, being at state s1 at
+              precedent wave, to be dead at mont of the current
+              wave. Then the observed probability (that this person died)
+              is null according to current estimated parameter. In fact,
+              it should be very low but not zero otherwise the log go to
+              infinity.
            */
+ /* #ifdef INFINITYORIGINAL */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
+ /* #else */
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
+ /*          lli=log(mytinydouble); */
+ /*        else */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
+ /* #endif */
            lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  ( s2==-1 ) { /* alive */
-         } else if  (s2==-2) {
            for (j=1,survp=0. ; j<=nlstate; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            /*survp += out[s1][j]; */
            lli= log(survp);
          }
+         else if  (s2==-4) {
-         else if  (s2==-4) {
            for (j=3,survp=0. ; j<=nlstate; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
          }
+         else if  (s2==-5) {
-         else if  (s2==-5) {
+           for (j=1,survp=0. ; j<=2; j++)
-           for (j=1,survp=0. ; j<=2; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
          }
          else{
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            /*  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 */
- Line 1608  double func( double *x)
+ Line 3256  double func( double *x)
          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          /*if(lli ==000.0)*/
          /*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); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         /* if (lli < log(mytinydouble)){ */
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
+         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
+         /* } */
        } /* end of wave */
      } /* end of individual */
    }  else if(mle==2){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1624  double func( double *x)
+ Line 3276  double func( double *x)
            }
          for(d=0; d<=dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1645  double func( double *x)
+ Line 3300  double func( double *x)
      } /* end of individual */
    }  else if(mle==3){  /* exponential inter-extrapolation */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1654  double func( double *x)
+ Line 3309  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1675  double func( double *x)
+ Line 3333  double func( double *x)
      } /* end of individual */
    }else if (mle==4){  /* ml=4 no inter-extrapolation */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1684  double func( double *x)
+ Line 3342  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 1699  double func( double *x)
+ Line 3360  double func( double *x)
          s2=s[mw[mi+1][i]][i];
          if( s2 > nlstate){
            lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  ( s2==-1 ) { /* alive */
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += out[s1][j];
+           lli= log(survp);
          }else{
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          }
- Line 1710  double func( double *x)
+ Line 3375  double func( double *x)
      } /* end of individual */
    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1719  double func( double *x)
+ Line 3384  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 1749  double func( double *x)
+ Line 3417  double func( double *x)
  /*************** log-likelihood *************/
  double funcone( double *x)
  {
-   /* Same as likeli but slower because of a lot of printf and if */
+   /* Same as func but slower because of a lot of printf and if */
    int i, ii, j, k, mi, d, kk;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
    int s1, s2;
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
+   double agexact;
+   double agebegin, ageend;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- Line 1766  double funcone( double *x)
+ Line 3439  double funcone( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     ioffset=2+nagesqr+cptcovage;
-     for(mi=1; mi<= wav[i]-1; mi++){
+     /* Fixed */
+     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
+     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
+     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+       cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
+ /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
+ /*    cov[2+6]=covar[Tvar[6]][i];  */
+ /*    cov[2+6]=covar[2][i]; V2  */
+ /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
+ /*    cov[2+7]=covar[Tvar[7]][i];  */
+ /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
+ /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
+ /*    cov[2+9]=covar[Tvar[9]][i];  */
+ /*    cov[2+9]=covar[1][i]; V1  */
+     }
+     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
+     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
+     /* } */
+     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
+     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
+     /* } */
+     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
+     /* Wave varying (but not age varying) */
+       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+                                 cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+                         }
+       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
+                                 /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+                                 /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+                                 /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+                                 /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
+                                 /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
+       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
+                         /*      iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+                         /*      /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
+                         /*      cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
+       /* } */
        for (ii=1;ii<=nlstate+ndeath;ii++)
-         for (j=1;j<=nlstate+ndeath;j++){
+                                 for (j=1;j<=nlstate+ndeath;j++){
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+                                         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+                                         savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }
+                                 }
-       for(d=0; d<dh[mi][i]; d++){
-         newm=savm;
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
-         for (kk=1; kk<=cptcovage;kk++) {
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+                                 /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-         }
+                                         and mw[mi+1][i]. dh depends on stepm.*/
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+                                 newm=savm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+                                 agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         savm=oldm;
+                                 cov[2]=agexact;
-         oldm=newm;
+                                 if(nagesqr==1)
+                                         cov[3]= agexact*agexact;
+                                 for (kk=1; kk<=cptcovage;kk++) {
+                                         cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+                                 }
+                                 /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
+                                 /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+                                 out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+                                 /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+                                 /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+                                 savm=oldm;
+                                 oldm=newm;
        } /* end mult */
        s1=s[mw[mi][i]][i];
        s2=s[mw[mi+1][i]][i];
+       /* if(s2==-1){ */
+       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
+       /*        /\* exit(1); *\/ */
+       /* } */
        bbh=(double)bh[mi][i]/(double)stepm;
        /* bias is positive if real duration
         * is higher than the multiple of stepm and negative otherwise.
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
-         lli=log(out[s1][s2] - savm[s1][s2]);
+                                 lli=log(out[s1][s2] - savm[s1][s2]);
-       } else if  (s2==-2) {
+       } else if  ( s2==-1 ) { /* alive */
-         for (j=1,survp=0. ; j<=nlstate; j++)
+                                 for (j=1,survp=0. ; j<=nlstate; j++)
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+                                         survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         lli= log(survp);
+                                 lli= log(survp);
        }else if (mle==1){
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        } else if(mle==2){
-         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 */
+                                 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 */
        } else if(mle==3){  /* exponential inter-extrapolation */
-         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 */
+                                 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 */
        } else if (mle==4){  /* mle=4 no inter-extrapolation */
-         lli=log(out[s1][s2]); /* Original formula */
+                                 lli=log(out[s1][s2]); /* Original formula */
        } else{  /* mle=0 back to 1 */
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-         /*lli=log(out[s1][s2]); */ /* Original formula */
+                                 /*lli=log(out[s1][s2]); */ /* Original formula */
        } /* End of if */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        /*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]); */
        if(globpr){
-         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+                                 fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
   %11.6f %11.6f %11.6f ", \
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+                                                                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
 *weight[i]*lli,out[s1][s2],savm[s1][s2]);
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+                                 for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-           llt +=ll[k]*gipmx/gsw;
+                                         llt +=ll[k]*gipmx/gsw;
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+                                         fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-         }
+                                 }
-         fprintf(ficresilk," %10.6f\n", -llt);
+                                 fprintf(ficresilk," %10.6f\n", -llt);
        }
-     } /* end of wave */
+         } /* end of wave */
-   } /* end of individual */
+ } /* end of individual */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   if(globpr==0){ /* First time we count the contributions and weights */
+ if(globpr==0){ /* First time we count the contributions and weights */
-     gipmx=ipmx;
+         gipmx=ipmx;
-     gsw=sw;
+         gsw=sw;
-   }
+ }
-   return -l;
+ return -l;
  }
- Line 1850  void likelione(FILE *ficres,double p[],
+ Line 3577  void likelione(FILE *ficres,double p[],
    int k;
    if(*globpri !=0){ /* Just counts and sums, no printings */
-     strcpy(fileresilk,"ilk");
+     strcpy(fileresilk,"ILK_");
-     strcat(fileresilk,fileres);
+     strcat(fileresilk,fileresu);
      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresilk);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      }
-     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");
+     fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
      for(k=1; k<=nlstate; k++)
        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
- Line 1867  void likelione(FILE *ficres,double p[],
+ Line 3594  void likelione(FILE *ficres,double p[],
    *fretone=(*funcone)(p);
    if(*globpri !=0){
      fclose(ficresilk);
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     if (mle ==0)
-     fflush(fichtm);
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-   }
+     else if(mle >=1)
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
+     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     for (k=1; k<= nlstate ; k++) {
+       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
+     }
+     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fflush(fichtm);
+   }
    return;
  }
- Line 1878  void likelione(FILE *ficres,double p[],
+ Line 3619  void likelione(FILE *ficres,double p[],
  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
-   int i,j, iter;
+   int i,j, iter=0;
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
    /*  char filerespow[FILENAMELENGTH];*/
+ #ifdef NLOPT
+   int creturn;
+   nlopt_opt opt;
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
+   double *lb;
+   double minf; /* the minimum objective value, upon return */
+   double * p1; /* Shifted parameters from 0 instead of 1 */
+   myfunc_data dinst, *d = &dinst;
+ #endif
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
    printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   strcpy(filerespow,"pow");
+   strcpy(filerespow,"POW_");
    strcat(filerespow,fileres);
    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", filerespow);
- Line 1899  void mlikeli(FILE *ficres,double p[], in
+ Line 3652  void mlikeli(FILE *ficres,double p[], in
      for(j=1;j<=nlstate+ndeath;j++)
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
+ #ifdef POWELL
    powell(p,xi,npar,ftol,&iter,&fret,func);
+ #endif
+ #ifdef NLOPT
+ #ifdef NEWUOA
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
+ #endif
+   lb=vector(0,npar-1);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+   nlopt_set_lower_bounds(opt, lb);
+   nlopt_set_initial_step1(opt, 0.1);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
+   d->function = func;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
+   nlopt_set_min_objective(opt, myfunc, d);
+   nlopt_set_xtol_rel(opt, ftol);
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
+     printf("nlopt failed! %d\n",creturn);
+   }
+   else {
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
+     iter=1; /* not equal */
+   }
+   nlopt_destroy(opt);
+ #endif
    free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  }
  /**** Computes Hessian and covariance matrix ***/
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  {
    double  **a,**y,*x,pd;
-   double **hess;
+   /* double **hess; */
-   int i, j,jk;
+   int i, j;
    int *indx;
    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
    double gompertz(double p[]);
-   hess=matrix(1,npar,1,npar);
+   /* hess=matrix(1,npar,1,npar); */
    printf("\nCalculation of the hessian matrix. Wait...\n");
    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    for (i=1;i<=npar;i++){
-     printf("%d",i);fflush(stdout);
+     printf("%d-",i);fflush(stdout);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
- Line 1940  void hesscov(double **matcov, double p[]
+ Line 3720  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++)  {
        if (j>i) {
-         printf(".%d%d",i,j);fflush(stdout);
+         printf(".%d-%d",i,j);fflush(stdout);
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
- Line 1976  void hesscov(double **matcov, double p[]
+ Line 3756  void hesscov(double **matcov, double p[]
    fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
-       printf("%.3e ",hess[i][j]);
+       printf("%.6e ",hess[i][j]);
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.6e ",hess[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
+   /* printf("\n#Covariance matrix#\n"); */
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+   /* for (i=1;i<=npar;i++) {  */
+   /*   for (j=1;j<=npar;j++) {  */
+   /*     printf("%.6e ",matcov[i][j]); */
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
    /* Recompute Inverse */
-   for (i=1;i<=npar;i++)
+   /* for (i=1;i<=npar;i++) */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-   ludcmp(a,npar,indx,&pd);
+   /* ludcmp(a,npar,indx,&pd); */
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
+   /* for (j=1;j<=npar;j++) { */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
+   /*   lubksb(a,npar,indx,x); */
+   /*   for (i=1;i<=npar;i++){  */
+   /*     y[i][j]=x[i]; */
+   /*     printf("%.3e ",y[i][j]); */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
-   /*  printf("\n#Hessian matrix recomputed#\n");
+   /* Verifying the inverse matrix */
+ #ifdef DEBUGHESS
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
    for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
-     x[j]=1;
-     lubksb(a,npar,indx,x);
      for (i=1;i<=npar;i++){
-       y[i][j]=x[i];
+       printf("%.2f ",y[i][j]);
-       printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
-   */
+ #endif
    free_matrix(a,1,npar,1,npar);
    free_matrix(y,1,npar,1,npar);
    free_vector(x,1,npar);
    free_ivector(indx,1,npar);
-   free_matrix(hess,1,npar,1,npar);
+   /* free_matrix(hess,1,npar,1,npar); */
  }
  /*************** hessian matrix ****************/
  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- {
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
    int i;
    int l=1, lmax=20;
-   double k1,k2;
+   double k1,k2, res, fx;
    double p2[MAXPARM+1]; /* identical to x */
-   double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
    int k=0,kmax=10;
    double l1;
    fx=func(x);
    for (i=1;i<=npar;i++) p2[i]=x[i];
-   for(l=0 ; l <=lmax; l++){
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
      l1=pow(10,l);
      delts=delt;
      for(k=1 ; k <kmax; k=k+1){
        delt = delta*(l1*k);
        p2[theta]=x[theta] +delt;
-       k1=func(p2)-fx;
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
        p2[theta]=x[theta]-delt;
        k2=func(p2)-fx;
        /*res= (k1-2.0*fx+k2)/delt/delt; */
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
- #ifdef DEBUGHESS
+ #ifdef DEBUGHESSII
        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);
        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);
  #endif
- Line 2049  double hessii(double x[], double delta,
+ Line 3854  double hessii(double x[], double delta,
          k=kmax;
        }
        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-         k=kmax; l=lmax*10.;
+         k=kmax; l=lmax*10;
        }
        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
          delts=delt;
        }
-     }
+     } /* End loop k */
    }
    delti[theta]=delts;
    return res;
  }
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
-   int l=1, l1, lmax=20;
+   int l=1, lmax=20;
    double k1,k2,k3,k4,res,fx;
    double p2[MAXPARM+1];
-   int k;
+   int k, kmax=1;
+   double v1, v2, cv12, lc1, lc2;
+   int firstime=0;
    fx=func(x);
-   for (k=1; k<=2; k++) {
+   for (k=1; k<=kmax; k=k+10) {
      for (i=1;i<=npar;i++) p2[i]=x[i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
      k1=func(p2)-fx;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
      k2=func(p2)-fx;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
      k3=func(p2)-fx;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
      k4=func(p2)-fx;
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
- #ifdef DEBUG
+     if(k1*k2*k3*k4 <0.){
-     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);
+       firstime=1;
-     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);
+       kmax=kmax+10;
+     }
+     if(kmax >=10 || firstime ==1){
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       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);
+       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);
+     }
+ #ifdef DEBUGHESSIJ
+     v1=hess[thetai][thetai];
+     v2=hess[thetaj][thetaj];
+     cv12=res;
+     /* Computing eigen value of Hessian matrix */
+     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+     if ((lc2 <0) || (lc1 <0) ){
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       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);
+       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);
+     }
  #endif
    }
    return res;
  }
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
+ /* { */
+ /*   int i; */
+ /*   int l=1, lmax=20; */
+ /*   double k1,k2,k3,k4,res,fx; */
+ /*   double p2[MAXPARM+1]; */
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
+ /*   int k=0,kmax=10; */
+ /*   double l1; */
+ /*   fx=func(x); */
+ /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
+ /*     l1=pow(10,l); */
+ /*     delts=delt; */
+ /*     for(k=1 ; k <kmax; k=k+1){ */
+ /*       delt = delti*(l1*k); */
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k1=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+ /*       k2=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k3=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+ /*       k4=func(p2)-fx; */
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
+ /* #ifdef DEBUGHESSIJ */
+ /*       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); */
+ /*       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); */
+ /* #endif */
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
+ /*      k=kmax; */
+ /*       } */
+ /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
+ /*      k=kmax; l=lmax*10; */
+ /*       } */
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
+ /*      delts=delt; */
+ /*       } */
+ /*     } /\* End loop k *\/ */
+ /*   } */
+ /*   delti[theta]=delts; */
+ /*   return res;  */
+ /* } */
  /************** Inverse of matrix **************/
  void ludcmp(double **a, int n, int *indx, double *d)
  {
- Line 2172  void lubksb(double **a, int n, int *indx
+ Line 4054  void lubksb(double **a, int n, int *indx
  void pstamp(FILE *fichier)
  {
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
  }
  /************ Frequencies ********************/
- 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[])
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
+                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
  {  /* Some frequencies */
-   int i, m, jk, k1,i1, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, k, iv;
+   int iind=0, iage=0;
+   int mi; /* Effective wave */
    int first;
    double ***freq; /* Frequencies */
-   double *pp, **prop;
+   double *meanq;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   double **meanqt;
-   char fileresp[FILENAMELENGTH];
+   double *pp, **prop, *posprop, *pospropt;
+   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
+   double agebegin, ageend;
    pp=vector(1,nlstate);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-   strcpy(fileresp,"p");
+   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
-   strcat(fileresp,fileres);
+   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
+   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
+   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   meanqt=matrix(1,lastpass,1,nqtveff);
+   strcpy(fileresp,"P_");
+   strcat(fileresp,fileresu);
+   /*strcat(fileresphtm,fileresu);*/
    if((ficresp=fopen(fileresp,"w"))==NULL) {
      printf("Problem with prevalence resultfile: %s\n", fileresp);
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
+     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fflush(ficlog);
+     exit(70);
+   }
+   else{
+     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
+             fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
+     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     fflush(ficlog);
+     exit(70);
+   }
+   else{
+     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
+             fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
    j1=0;
-   j=cptcoveff;
+   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
+   j=cptcoveff;  /* Only dummy covariates of the model */
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    first=1;
-   for(k1=1; k1<=j;k1++){
+   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
-     for(i1=1; i1<=ncodemax[k1];i1++){
+      reference=low_education V1=0,V2=0
-       j1++;
+      med_educ                V1=1 V2=0,
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+      high_educ               V1=0 V2=1
-         scanf("%d", i);*/
+      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
-       for (i=-5; i<=nlstate+ndeath; i++)
+   */
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           for(m=iagemin; m <= iagemax+3; m++)
-             freq[i][jk][m]=0;
-     for (i=1; i<=nlstate; i++)
+   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
+     posproptt=0.;
+     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+       scanf("%d", i);*/
+     for (i=-5; i<=nlstate+ndeath; i++)
+       for (jk=-5; jk<=nlstate+ndeath; jk++)
+                                 for(m=iagemin; m <= iagemax+3; m++)
+                                         freq[i][jk][m]=0;
+     for (i=1; i<=nlstate; i++)  {
        for(m=iagemin; m <= iagemax+3; m++)
-         prop[i][m]=0;
+                                 prop[i][m]=0;
+       posprop[i]=0;
-       dateintsum=0;
+       pospropt[i]=0;
-       k2cpt=0;
+     }
-       for (i=1; i<=imx; i++) {
+     /* for (z1=1; z1<= nqfveff; z1++) {   */
-         bool=1;
+     /*   meanq[z1]+=0.; */
-         if  (cptcovn>0) {
+     /*   for(m=1;m<=lastpass;m++){ */
-           for (z1=1; z1<=cptcoveff; z1++)
+     /*  meanqt[m][z1]=0.; */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     /*   } */
+     /* } */
+     dateintsum=0;
+     k2cpt=0;
+     /* For that combination of covariate j1, we count and print the frequencies in one pass */
+     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+       bool=1;
+       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
+         if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+           /* for (z1=1; z1<= nqfveff; z1++) {   */
+           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
+           /* } */
+           for (z1=1; z1<=cptcoveff; z1++) {
+             /* if(Tvaraff[z1] ==-20){ */
+             /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
+             /* }else  if(Tvaraff[z1] ==-10){ */
+             /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
+             /* }else  */
+             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
+               /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
                bool=0;
-         }
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
-         if (bool==1){
+                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-           for(m=firstpass; m<=lastpass; m++){
+                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-             k2=anint[m][i]+(mint[m][i]/12.);
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+             } /* Onlyf fixed */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+           } /* end z1 */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+         } /* cptcovn > 0 */
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+       } /* end any */
-               if (m<lastpass) {
+       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+         /* for(m=firstpass; m<=lastpass; m++){ */
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+         for(mi=1; mi<wav[iind];mi++){ /* For that wave */
-               }
+           m=mw[mi][iind];
+           if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+             for (z1=1; z1<=cptcoveff; z1++) {
-                 dateintsum=dateintsum+k2;
+               if( Fixed[Tmodelind[z1]]==1){
-                 k2cpt++;
+                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
+                   bool=0;
+               }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+                   bool=0;
+                 }
                }
-               /*}*/
-           }
-         }
-       }
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
-       if  (cptcovn>0) {
-         fprintf(ficresp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresp, "**********\n#");
-       }
-       for(i=1; i<=nlstate;i++)
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresp, "\n");
-       for(i=iagemin; i <= iagemax+3; i++){
-         if(i==iagemax+3){
-           fprintf(ficlog,"Total");
-         }else{
-           if(first==1){
-             first=0;
-             printf("See log file for details...\n");
-           }
-           fprintf(ficlog,"Age %d", i);
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
-           if(pp[jk]>=1.e-10){
-             if(first==1){
-               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-             }
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           }else{
-             if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-           }
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-           pos += pp[jk];
-           posprop += prop[jk][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5){
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-           }else{
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-           }
-           if( i <= iagemax){
-             if(pos>=1.e-5){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
              }
-             else
+           }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+           /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-           }
+           if(bool==1){
-         }
+             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+                and mw[mi+1][iind]. dh depends on stepm. */
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-           for(m=-1; m <=nlstate+ndeath; m++)
+             ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
-             if(freq[jk][m][i] !=0 ) {
+             if(m >=firstpass && m <=lastpass){
-             if(first==1)
+               k2=anint[m][iind]+(mint[m][iind]/12.);
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+               if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+               if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+               if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+               if (m<lastpass) {
+                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+                 /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
+                 if(s[m][iind]==-1)
+                   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
+               }
+             } /* end if between passes */
+             if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+               dateintsum=dateintsum+k2;
+               k2cpt++;
+               /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
              }
-         if(i <= iagemax)
+           } /* end bool 2 */
-           fprintf(ficresp,"\n");
+         } /* end m */
-         if(first==1)
+       } /* end bool */
-           printf("Others in log...\n");
+     } /* end iind = 1 to imx */
-         fprintf(ficlog,"\n");
+     /* prop[s][age] is feeded for any initial and valid live state as well as
+        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     pstamp(ficresp);
+     /* if  (ncoveff>0) { */
+     if  (cptcoveff>0) {
+       fprintf(ficresp, "\n#********** Variable ");
+       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+       for (z1=1; z1<=cptcoveff; z1++){
+         fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       }
+       fprintf(ficresp, "**********\n#");
+       fprintf(ficresphtm, "**********</h3>\n");
+       fprintf(ficresphtmfr, "**********</h3>\n");
+       fprintf(ficlog, "\n#********** Variable ");
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       fprintf(ficlog, "**********\n");
+     }
+     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
+     for(i=1; i<=nlstate;i++) {
+       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
+     }
+     fprintf(ficresp, "\n");
+     fprintf(ficresphtm, "\n");
+     /* Header of frequency table by age */
+     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
+     fprintf(ficresphtmfr,"<th>Age</th> ");
+     for(jk=-1; jk <=nlstate+ndeath; jk++){
+       for(m=-1; m <=nlstate+ndeath; m++){
+         if(jk!=0 && m!=0)
+           fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
+       }
+     }
+     fprintf(ficresphtmfr, "\n");
+     /* For each age */
+     for(iage=iagemin; iage <= iagemax+3; iage++){
+       fprintf(ficresphtm,"<tr>");
+       if(iage==iagemax+1){
+                                 fprintf(ficlog,"1");
+                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");
+       }else if(iage==iagemax+2){
+                                 fprintf(ficlog,"0");
+                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+       }else if(iage==iagemax+3){
+                                 fprintf(ficlog,"Total");
+                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");
+       }else{
+                                 if(first==1){
+                                         first=0;
+                                         printf("See log file for details...\n");
+                                 }
+                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+                                 fprintf(ficlog,"Age %d", iage);
+       }
+       for(jk=1; jk <=nlstate ; jk++){
+                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+                                         pp[jk] += freq[jk][m][iage];
+       }
+       for(jk=1; jk <=nlstate ; jk++){
+                                 for(m=-1, pos=0; m <=0 ; m++)
+                                         pos += freq[jk][m][iage];
+                                 if(pp[jk]>=1.e-10){
+                                         if(first==1){
+                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                                         }
+                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                                 }else{
+                                         if(first==1)
+                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                                 }
+       }
+       for(jk=1; jk <=nlstate ; jk++){
+                                 /* posprop[jk]=0; */
+                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+                                         pp[jk] += freq[jk][m][iage];
+       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
+       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
+                                 pos += pp[jk]; /* pos is the total number of transitions until this age */
+                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
+                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
+                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+       }
+       for(jk=1; jk <=nlstate ; jk++){
+                                 if(pos>=1.e-5){
+                                         if(first==1)
+                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                 }else{
+                                         if(first==1)
+                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                 }
+                                 if( iage <= iagemax){
+                                         if(pos>=1.e-5){
+                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
+                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
+                                         }
+                                         else{
+                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
+                                         }
+                                 }
+                                 pospropt[jk] +=posprop[jk];
+       } /* end loop jk */
+       /* pospropt=0.; */
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
+                                 for(m=-1; m <=nlstate+ndeath; m++){
+                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+                                                 if(first==1){
+                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                                                 }
+                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                                         }
+                                         if(jk!=0 && m!=0)
+                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
+                                 }
+       } /* end loop jk */
+       posproptt=0.;
+       for(jk=1; jk <=nlstate; jk++){
+                                 posproptt += pospropt[jk];
+       }
+       fprintf(ficresphtmfr,"</tr>\n ");
+       if(iage <= iagemax){
+                                 fprintf(ficresp,"\n");
+                                 fprintf(ficresphtm,"</tr>\n");
+       }
+       if(first==1)
+                                 printf("Others in log...\n");
+       fprintf(ficlog,"\n");
+     } /* end loop age iage */
+     fprintf(ficresphtm,"<tr><th>Tot</th>");
+     for(jk=1; jk <=nlstate ; jk++){
+       if(posproptt < 1.e-5){
+                                 fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+       }else{
+                                 fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
        }
      }
-   }
+     fprintf(ficresphtm,"</tr>\n");
+     fprintf(ficresphtm,"</table>\n");
+     fprintf(ficresphtmfr,"</table>\n");
+     if(posproptt < 1.e-5){
+       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+       invalidvarcomb[j1]=1;
+     }else{
+       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+       invalidvarcomb[j1]=0;
+     }
+     fprintf(ficresphtmfr,"</table>\n");
+   } /* end selected combination of covariate j1 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   fclose(ficresphtm);
+   fclose(ficresphtmfr);
+   free_vector(meanq,1,nqfveff);
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+   free_vector(pospropt,1,nlstate);
+   free_vector(posprop,1,nlstate);
+   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
    free_vector(pp,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   /* End of freqsummary */
-   /* End of Freq */
  }
  /************ Prevalence ********************/
- Line 2348  void prevalence(double ***probs, double
+ Line 4424  void prevalence(double ***probs, double
       We still use firstpass and lastpass as another selection.
    */
-   int i, m, jk, k1, i1, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, iv;
-   double ***freq; /* Frequencies */
+   int mi; /* Effective wave */
-   double *pp, **prop;
+   int iage;
-   double pos,posprop;
+   double agebegin, ageend;
+   double **prop;
+   double posprop;
    double  y2; /* in fractional years */
    int iagemin, iagemax;
+   int first; /** to stop verbosity which is redirected to log file */
    iagemin= (int) agemin;
    iagemax= (int) agemax;
    /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
-   j=cptcoveff;
+   /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   for(k1=1; k1<=j;k1++){
+   first=1;
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
-       j1++;
+     for (i=1; i<=nlstate; i++)
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
-       for (i=1; i<=nlstate; i++)
+         prop[i][iage]=0.0;
-         for(m=iagemin; m <= iagemax+3; m++)
+     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
-           prop[i][m]=0.0;
+     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
-       for (i=1; i<=imx; i++) { /* Each individual */
-         bool=1;
+     for (i=1; i<=imx; i++) { /* Each individual */
-         if  (cptcovn>0) {
+       bool=1;
-           for (z1=1; z1<=cptcoveff; z1++)
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
+         m=mw[mi][i];
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
+         for (z1=1; z1<=cptcoveff; z1++){
+           if( Fixed[Tmodelind[z1]]==1){
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                bool=0;
-         }
+           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-         if (bool==1) {
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+               bool=0;
+             }
+         }
+         if(bool==1){ /* Otherwise we skip that wave/person */
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
+           if(m >=firstpass && m <=lastpass){
              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               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);
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
+                 exit(1);
+               }
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
                  /*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]]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                  prop[s[m][i]][iagemax+3] += weight[i];
-               }
+               } /* end valid statuses */
-             }
+             } /* end selection of dates */
            } /* end selection of waves */
-         }
+         } /* end bool */
-       }
+       } /* end wave */
-       for(i=iagemin; i <= iagemax+3; i++){
+     } /* end individual */
+     for(i=iagemin; i <= iagemax+3; i++){
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-           posprop += prop[jk][i];
+         posprop += prop[jk][i];
-         }
+       }
-         for(jk=1; jk <=nlstate ; jk++){
+       for(jk=1; jk <=nlstate ; jk++){
-           if( i <=  iagemax){
+         if( i <=  iagemax){
-             if(posprop>=1.e-5){
+           if(posprop>=1.e-5){
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+             probs[i][jk][j1]= prop[jk][i]/posprop;
-             } else
+           } else{
-               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
+             if(first==1){
-           }
+               first=0;
-         }/* end jk */
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
-       }/* end i */
+             }
-     } /* end i1 */
+           }
-   } /* end k1 */
+         }
+       }/* end jk */
+     }/* end i */
+      /*} *//* end i1 */
+   } /* end j1 */
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
  }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- Line 2428  void  concatwav(int wav[], int **dh, int
+ Line 4528  void  concatwav(int wav[], int **dh, int
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       and mw[mi+1][i]. dh depends on stepm.
-      */
+   */
-   int i, mi, m;
+   int i=0, mi=0, m=0, mli=0;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       double sum=0., jmean=0.;*/
-   int first;
+   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
-   jmin=1e+5;
+   firstwo=0;
+   firsthree=0;
+   firstfour=0;
+   jmin=100000;
    jmax=-1;
    jmean=0.;
-   for(i=1; i<=imx; i++){
-     mi=0;
+ /* Treating live states */
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
+     mi=0;  /* First valid wave */
+     mli=0; /* Last valid wave */
      m=firstpass;
-     while(s[m][i] <= nlstate){
+     while(s[m][i] <= nlstate){  /* a live state */
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
+         mli=m-1;/* mw[++mi][i]=m-1; */
+       }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
          mw[++mi][i]=m;
-       if(m >=lastpass)
+         mli=m;
+       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
+       if(m < lastpass){ /* m < lastpass, standard case */
+         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
+       }
+       else{ /* m >= lastpass, eventual special issue with warning */
+ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
          break;
-       else
+ #else
-         m++;
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+           if(firsthree == 0){
+             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+             firsthree=1;
+           }
+           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+           mw[++mi][i]=m;
+           mli=m;
+         }
+         if(s[m][i]==-2){ /* Vital status is really unknown */
+           nbwarn++;
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+           }
+           break;
+         }
+         break;
+ #endif
+       }/* End m >= lastpass */
      }/* end while */
-     if (s[m][i] > nlstate){
+     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
+     /* After last pass */
+ /* Treating death states */
+     if (s[m][i] > nlstate){  /* In a death state */
+       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
+       /* } */
        mi++;     /* Death is another wave */
        /* if(mi==0)  never been interviewed correctly before death */
-          /* Only death is a correct wave */
+       /* Only death is a correct wave */
        mw[mi][i]=m;
      }
+ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-     wav[i]=mi;
+     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
+       /* m++; */
+       /* mi++; */
+       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
+       /* mw[mi][i]=m; */
+       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
+           nbwarn++;
+           if(firstfiv==0){
+             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             firstfiv=1;
+           }else{
+             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+           }
+         }else{ /* Death occured afer last wave potential bias */
+           nberr++;
+           if(firstwo==0){
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+             firstwo=1;
+           }
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         }
+       }else{ /* end date of interview is known */
+         /* death is known but not confirmed by death status at any wave */
+         if(firstfour==0){
+           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           firstfour=1;
+         }
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+       }
+     } /* end if date of death is known */
+ #endif
+     wav[i]=mi; /* mi should be the last effective wave (or mli) */
+     /* wav[i]=mw[mi][i]; */
      if(mi==0){
        nbwarn++;
        if(first==0){
- Line 2470  void  concatwav(int wav[], int **dh, int
+ Line 4642  void  concatwav(int wav[], int **dh, int
        }
      } /* end mi==0 */
    } /* End individuals */
+   /* wav and mw are no more changed */
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
- Line 2505  void  concatwav(int wav[], int **dh, int
+ Line 4679  void  concatwav(int wav[], int **dh, int
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
  /*        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]); */
            k=k+1;
            if (j >= jmax) {
              jmax=j;
- Line 2559  void  concatwav(int wav[], int **dh, int
+ Line 4733  void  concatwav(int wav[], int **dh, int
    jmean=sum/k;
    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);
    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);
-  }
+ }
  /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx)
+  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
  {
-   /* Uses cptcovn+2*cptcovprod as the number of covariates */
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
+    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
+   */
-   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
    int modmaxcovj=0; /* Modality max of covariates j */
-   cptcoveff=0;
+   int cptcode=0; /* Modality max of covariates j */
+   int modmincovj=0; /* Modality min of covariates j */
+   /* cptcoveff=0;  */
+         /* *cptcov=0; */
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
+   /* Loop on covariates without age and products and no quantitative variable */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
+   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
-                                modality of this covariate Vj*/
+   for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
+     for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-                                       modality of the nth covariate of individual i. */
+     if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       switch(Fixed[k]) {
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-       if (ij > modmaxcovj) modmaxcovj=ij;
+                                 for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
-       /* getting the maximum value of the modality of the covariate
+                                         ij=(int)(covar[Tvar[k]][i]);
-          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-          female is 1, then modmaxcovj=1.*/
+                                          * If product of Vn*Vm, still boolean *:
-     }
+                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
+                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-       if( Ndum[i] != 0 )
+                                                  modality of the nth covariate of individual i. */
-         ncodemax[j]++;
+                                         if (ij > modmaxcovj)
-       /* Number of modalities of the j th covariate. In fact
+                                                 modmaxcovj=ij;
-          ncodemax[j]=2 (dichotom. variables only) but it could be more for
+                                         else if (ij < modmincovj)
-          historical reasons */
+                                                 modmincovj=ij;
-     } /* Ndum[-1] number of undefined modalities */
+                                         if ((ij < -1) && (ij > NCOVMAX)){
+                                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+                                                 exit(1);
-     ij=1;
+                                         }else
-     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
+                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-       for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
+                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+                                         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                         /* getting the maximum value of the modality of the covariate
-                                      k is a modality. If we have model=V1+V1*sex
+                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+                                                  female ies 1, then modmaxcovj=1.
-           ij++;
+                                         */
-         }
+                                 } /* end for loop on individuals i */
-         if (ij > ncodemax[j]) break;
+                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-       }  /* end of loop on */
+                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-     } /* end of loop on modality */
+                                 cptcode=modmaxcovj;
+                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+                                 /*for (i=0; i<=cptcode; i++) {*/
+                                 for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
+                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
+                                         fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
+                                         if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
+                                                 if( j != -1){
+                                                         ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
+                                                                                                                                  covariate for which somebody answered excluding
+                                                                                                                                  undefined. Usually 2: 0 and 1. */
+                                                 }
+                                                 ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+                                                                                                                                                 covariate for which somebody answered including
+                                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
+                                         }       /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
+                                                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+                                 } /* Ndum[-1] number of undefined modalities */
+                                 /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+                                 /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
+                                 /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
+                                 /* modmincovj=3; modmaxcovj = 7; */
+                                 /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
+                                 /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
+                           /*             defining two dummy variables: variables V1_1 and V1_2.*/
+               /* nbcode[Tvar[j]][ij]=k; */
+               /* nbcode[Tvar[j]][1]=0; */
+               /* nbcode[Tvar[j]][2]=1; */
+               /* nbcode[Tvar[j]][3]=2; */
+               /* To be continued (not working yet). */
+               ij=0; /* ij is similar to i but can jump over null modalities */
+                                 for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+                   break;
+                 }
+                                         ij++;
+                                         nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
+                                         cptcode = ij; /* New max modality for covar j */
+                                 } /* end of loop on modality i=-1 to 1 or more */
+                                 break;
+       case 1: /* Testing on varying covariate, could be simple and
+                * should look at waves or product of fixed *
+                * varying. No time to test -1, assuming 0 and 1 only */
+                                 ij=0;
+                                 for(i=0; i<=1;i++){
+                                         nbcode[Tvar[k]][++ij]=i;
+                                 }
+                                 break;
+       default:
+                                 break;
+       } /* end switch */
+     } /* end dummy test */
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+     /*  /\*recode from 0 *\/ */
+     /*                               k is a modality. If we have model=V1+V1*sex  */
+     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+     /*  } */
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+     /*  if (ij > ncodemax[j]) { */
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+     /*    break; */
+     /*  } */
+     /*   }  /\* end of loop on modality k *\/ */
    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   for (k=0; k< maxncov; k++) Ndum[k]=0;
+   for (k=-1; k< maxncov; k++) Ndum[k]=0;
+   /* Look at fixed dummy (single or product) covariates to check empty modalities */
-   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
+     ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
-    Ndum[ij]++;
+     Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
-  }
+     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
+   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
-  ij=1;
-  for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+   ij=0;
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+   /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
-      Tvaraff[ij]=i; /*For printing */
+   for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-      ij++;
+     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-    }
+     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-  }
+     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-  ij--;
+       /* If product not in single variable we don't print results */
-  cptcoveff=ij; /*Number of simple covariates*/
+       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+       ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
+       Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
+       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
+       TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
+       if(Fixed[k]!=0)
+         anyvaryingduminmodel=1;
+                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+                         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+                         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+                         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+     }
+   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+   /* ij--; */
+   /* cptcoveff=ij; /\*Number of total covariates*\/ */
+   *cptcov=ij; /*Number of total real effective covariates: effective
+                                                          * because they can be excluded from the model and real
+                                                          * if in the model but excluded because missing values, but how to get k from ij?*/
+   for(j=ij+1; j<= cptcovt; j++){
+     Tvaraff[j]=0;
+     Tmodelind[j]=0;
+   }
+   for(j=ntveff+1; j<= cptcovt; j++){
+     TmodelInvind[j]=0;
+   }
+   /* To be sorted */
+   ;
  }
  /*********** Health Expectancies ****************/
- void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
  {
    /* Health expectancies, no variances */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+   int i, j, nhstepm, hstepm, h, nstepm;
    int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
    double ***p3mat;
- Line 2704  void evsij(double ***eij, double x[], in
+ Line 4981  void evsij(double ***eij, double x[], in
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- Line 2739  void evsij(double ***eij, double x[], in
+ Line 5016  void evsij(double ***eij, double x[], in
  }
- 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[] )
+  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[], int nres )
  {
    /* Covariances of health expectancies eij and of total life expectancies according
-    to initial status i, ei. .
+      to initial status i, ei. .
    */
    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    int nhstepma, nstepma; /* Decreasing with age */
- Line 2837  void cvevsij(double ***eij, double x[],
+ Line 5114  void cvevsij(double ***eij, double x[],
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      /* If stepm=6 months */
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      /* Computing  Variances of health expectancies */
      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         decrease memory allocation */
- Line 2852  void cvevsij(double ***eij, double x[],
+ Line 5129  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
            for(h=0; h<=nhstepm-1; h++){
- Line 2863  void cvevsij(double ***eij, double x[],
+ Line 5140  void cvevsij(double ***eij, double x[],
            }
          }
        }
        for(ij=1; ij<= nlstate*nlstate; ij++)
          for(h=0; h<=nhstepm-1; h++){
            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- Line 2876  void cvevsij(double ***eij, double x[],
+ Line 5153  void cvevsij(double ***eij, double x[],
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+     for(ij=1;ij<=nlstate*nlstate;ij++)
        for(ji=1;ji<=nlstate*nlstate;ji++)
          varhe[ij][ji][(int)age] =0.;
-      printf("%d|",(int)age);fflush(stdout);
+     printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      for(h=0;h<=nhstepm-1;h++){
+     for(h=0;h<=nhstepm-1;h++){
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- Line 2892  void cvevsij(double ***eij, double x[],
+ Line 5169  void cvevsij(double ***eij, double x[],
              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
      /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
            /* 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]);*/
          }
      fprintf(ficresstdeij,"%3.0f",age );
      for(i=1; i<=nlstate;i++){
        eip=0.;
- Line 2917  void cvevsij(double ***eij, double x[],
+ Line 5194  void cvevsij(double ***eij, double x[],
        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      }
      fprintf(ficresstdeij,"\n");
      fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
- Line 2930  void cvevsij(double ***eij, double x[],
+ Line 5207  void cvevsij(double ***eij, double x[],
            }
        }
      fprintf(ficrescveij,"\n");
    }
    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- Line 2940  void cvevsij(double ***eij, double x[],
+ Line 5217  void cvevsij(double ***eij, double x[],
    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
    free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
- /************ Variance ******************/
- 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[])
- {
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   /* double **newm;*/
-   double **dnewm,**doldm;
-   double **dnewmp,**doldmp;
-   int i, j, nhstepm, hstepm, h, nstepm ;
-   int k, cptcode;
-   double *xp;
-   double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg; /*for var eij */
-   double **gradgp, **trgradgp; /* for var p point j */
-   double *gpp, *gmp; /* for var p point j */
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   double ***p3mat;
-   double age,agelim, hf;
-   double ***mobaverage;
-   int theta;
-   char digit[4];
-   char digitp[25];
-   char fileresprobmorprev[FILENAMELENGTH];
-   if(popbased==1){
-     if(mobilav!=0)
-       strcpy(digitp,"-populbased-mobilav-");
-     else strcpy(digitp,"-populbased-nomobil-");
-   }
-   else
-     strcpy(digitp,"-stablbased-");
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
-   strcpy(fileresprobmorprev,"prmorprev");
-   sprintf(digit,"%-d",ij);
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   pstamp(ficresprobmorprev);
-   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);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   }
-   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficgp,"\n# Routine varevsij");
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   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");
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
- /*   } */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   if(popbased==1)
-     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);
-   else
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(ficresvij,"# Age");
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=nlstate;j++)
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   fprintf(ficresvij,"\n");
-   xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,nlstate,1,nlstate);
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   gpp=vector(nlstate+1,nlstate+ndeath);
-   gmp=vector(nlstate+1,nlstate+ndeath);
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   if(estepm < stepm){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
-   else  hstepm=estepm;
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
-      Look at function hpijx to understand why (it is linked to memory size questions) */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-      survival function given by stepm (the optimization length). Unfortunately it
-      means that if the survival funtion is printed every two years of age and if
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      results. So we changed our mind and took the option of the best precision.
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
-     gm=matrix(0,nhstepm,1,nlstate);
-     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       if (popbased==1) {
-         if(mobilav ==0){
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
-       }
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         }
-       }
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
-       /* end probability of death */
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       if (popbased==1) {
+ /************ Variance ******************/
-         if(mobilav ==0){
+  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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
-           for(i=1; i<=nlstate;i++)
+  {
-             prlim[i][i]=probs[(int)age][i][ij];
+    /* Variance of health expectancies */
-         }else{ /* mobilav */
+    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-           for(i=1; i<=nlstate;i++)
+    /* double **newm;*/
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-         }
-       }
+    /* int movingaverage(); */
+    double **dnewm,**doldm;
-       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
+    double **dnewmp,**doldmp;
-         for(h=0; h<=nhstepm; h++){
+    int i, j, nhstepm, hstepm, h, nstepm ;
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+    int k;
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+    double *xp;
-         }
+    double **gp, **gm;  /* for var eij */
-       }
+    double ***gradg, ***trgradg; /*for var eij */
-       /* This for computing probability of death (h=1 means
+    double **gradgp, **trgradgp; /* for var p point j */
-          computed over hstepm matrices product = hstepm*stepm months)
+    double *gpp, *gmp; /* for var p point j */
-          as a weighted average of prlim.
+    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-       */
+    double ***p3mat;
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+    double age,agelim, hf;
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+    /* double ***mobaverage; */
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+    int theta;
-       }
+    char digit[4];
-       /* end probability of death */
+    char digitp[25];
-       for(j=1; j<= nlstate; j++) /* vareij */
+    char fileresprobmorprev[FILENAMELENGTH];
-         for(h=0; h<=nhstepm; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+    if(popbased==1){
-         }
+      if(mobilav!=0)
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+    }
-       }
+    else
+      strcpy(digitp,"-STABLBASED_");
-     } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     for(h=0; h<=nhstepm; h++) /* veij */
-       for(j=1; j<=nlstate;j++)
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       for(theta=1; theta <=npar; theta++)
-         trgradgp[j][theta]=gradgp[theta][j];
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     for(i=1;i<=nlstate;i++)
-       for(j=1;j<=nlstate;j++)
-         vareij[i][j][(int)age] =0.;
-     for(h=0;h<=nhstepm;h++){
+    /* if (mobilav!=0) { */
-       for(k=0;k<=nhstepm;k++){
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-         for(i=1;i<=nlstate;i++)
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
-           for(j=1;j<=nlstate;j++)
+    /*   } */
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+    /* } */
-       }
-     }
+    strcpy(fileresprobmorprev,"PRMORPREV-");
+    sprintf(digit,"%-d",ij);
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+    strcat(fileresprobmorprev,fileresu);
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    }
+    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    pstamp(ficresprobmorprev);
+    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);
+    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+      fprintf(ficresprobmorprev," p.%-d SE",j);
+      for(i=1; i<=nlstate;i++)
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+    }
+    fprintf(ficresprobmorprev,"\n");
+    fprintf(ficgp,"\n# Routine varevsij");
+    fprintf(ficgp,"\nunset title \n");
+    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+    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");
+    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+    /*   } */
+    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    pstamp(ficresvij);
+    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+    if(popbased==1)
+      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);
+    else
+      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+    fprintf(ficresvij,"# Age");
+    for(i=1; i<=nlstate;i++)
+      for(j=1; j<=nlstate;j++)
+        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+    fprintf(ficresvij,"\n");
+    xp=vector(1,npar);
+    dnewm=matrix(1,nlstate,1,npar);
+    doldm=matrix(1,nlstate,1,nlstate);
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+    gpp=vector(nlstate+1,nlstate+ndeath);
+    gmp=vector(nlstate+1,nlstate+ndeath);
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     /* pptj */
+    if(estepm < stepm){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      printf ("Problem %d lower than %d\n",estepm, stepm);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+    }
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+    else  hstepm=estepm;
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+    /* For example we decided to compute the life expectancy with the smallest unit */
-         varppt[j][i]=doldmp[j][i];
+    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     /* end ppptj */
+       nhstepm is the number of hstepm from age to agelim
-     /*  x centered again */
+       nstepm is the number of stepm from age to agelim.
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+       Look at function hpijx to understand why because of memory size limitations,
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+       we decided (b) to get a life expectancy respecting the most precise curvature of the
+       survival function given by stepm (the optimization length). Unfortunately it
-     if (popbased==1) {
+       means that if the survival funtion is printed every two years of age and if
-       if(mobilav ==0){
+       you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         for(i=1; i<=nlstate;i++)
+       results. So we changed our mind and took the option of the best precision.
-           prlim[i][i]=probs[(int)age][i][ij];
+    */
-       }else{ /* mobilav */
+    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for(i=1; i<=nlstate;i++)
+    agelim = AGESUP;
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       }
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     }
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* This for computing probability of death (h=1 means
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+      gp=matrix(0,nhstepm,1,nlstate);
-        as a weighted average of prlim.
+      gm=matrix(0,nhstepm,1,nlstate);
+      for(theta=1; theta <=npar; theta++){
+        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+        }
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+        for(j=1; j<= nlstate; j++){
+          for(h=0; h<=nhstepm; h++){
+            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+          }
+        }
+        /* Next for computing probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
+          for(i=1,gpp[j]=0.; i<= nlstate; i++)
+            gpp[j] += prlim[i][i]*p3mat[i][j][1];
+        }
+        /* end probability of death */
+        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+          xp[i] = x[i] - (i==theta ?delti[theta]:0);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nresult);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
+        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
+          for(h=0; h<=nhstepm; h++){
+            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+          }
+        }
+        /* This for computing probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
+          for(i=1,gmp[j]=0.; i<= nlstate; i++)
+            gmp[j] += prlim[i][i]*p3mat[i][j][1];
+        }
+        /* end probability of death */
+        for(j=1; j<= nlstate; j++) /* vareij */
+          for(h=0; h<=nhstepm; h++){
+            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+          }
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+        }
+      } /* End theta */
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+      for(h=0; h<=nhstepm; h++) /* veij */
+        for(j=1; j<=nlstate;j++)
+          for(theta=1; theta <=npar; theta++)
+            trgradg[h][j][theta]=gradg[h][theta][j];
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+        for(theta=1; theta <=npar; theta++)
+          trgradgp[j][theta]=gradgp[theta][j];
+      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+      for(i=1;i<=nlstate;i++)
+        for(j=1;j<=nlstate;j++)
+          vareij[i][j][(int)age] =0.;
+      for(h=0;h<=nhstepm;h++){
+        for(k=0;k<=nhstepm;k++){
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+          for(i=1;i<=nlstate;i++)
+            for(j=1;j<=nlstate;j++)
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+        }
+      }
+      /* pptj */
+      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++)
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
+          varppt[j][i]=doldmp[j][i];
+      /* end ppptj */
+      /*  x centered again */
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
+      if (popbased==1) {
+        if(mobilav ==0){
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=probs[(int)age][i][ij];
+        }else{ /* mobilav */
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=mobaverage[(int)age][i][ij];
+        }
+      }
+      /* This for computing probability of death (h=1 means
+         computed over hstepm (estepm) matrices product = hstepm*stepm months)
+         as a weighted average of prlim.
+      */
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++){
+        for(i=1,gmp[j]=0.;i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+      }
+      /* end probability of death */
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+        for(i=1; i<=nlstate;i++){
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+        }
+      }
+      fprintf(ficresprobmorprev,"\n");
+      fprintf(ficresvij,"%.0f ",age );
+      for(i=1; i<=nlstate;i++)
+        for(j=1; j<=nlstate;j++){
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+        }
+      fprintf(ficresvij,"\n");
+      free_matrix(gp,0,nhstepm,1,nlstate);
+      free_matrix(gm,0,nhstepm,1,nlstate);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    } /* End age */
+    free_vector(gpp,nlstate+1,nlstate+ndeath);
+    free_vector(gmp,nlstate+1,nlstate+ndeath);
+    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
+    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
+    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
+    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
+    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
+    /*  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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
      */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     }
-     /* end probability of death */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-       }
-     }
-     fprintf(ficresprobmorprev,"\n");
-     fprintf(ficresvij,"%.0f ",age );
+    free_vector(xp,1,npar);
-     for(i=1; i<=nlstate;i++)
+    free_matrix(doldm,1,nlstate,1,nlstate);
-       for(j=1; j<=nlstate;j++){
+    free_matrix(dnewm,1,nlstate,1,npar);
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       }
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-     fprintf(ficresvij,"\n");
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     free_matrix(gp,0,nhstepm,1,nlstate);
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-     free_matrix(gm,0,nhstepm,1,nlstate);
+    fclose(ficresprobmorprev);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+    fflush(ficgp);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+    fflush(fichtm);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  }  /* end varevsij */
-   } /* End age */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   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);
-   /*  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);
- */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,npar);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficresprobmorprev);
-   fflush(ficgp);
-   fflush(fichtm);
- }  /* end varevsij */
  /************ Variance of prevlim ******************/
- 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[])
+  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 *ncvyearp, int ij, char strstart[], int nres)
  {
-   /* Variance of prevalence limit */
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
    double **dnewm,**doldm;
    int i, j, nhstepm, hstepm;
-   int k, cptcode;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
+   double **mgm, **mgp;
    double age,agelim;
    int theta;
- Line 3286  void varprevlim(char fileres[], double *
+ Line 5573  void varprevlim(char fileres[], double *
      if (stepm >= YEARM) hstepm=1;
      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      gradg=matrix(1,npar,1,nlstate);
+     mgp=matrix(1,npar,1,nlstate);
+     mgm=matrix(1,npar,1,nlstate);
      gp=vector(1,nlstate);
      gm=vector(1,nlstate);
- Line 3293  void varprevlim(char fileres[], double *
+ Line 5582  void varprevlim(char fileres[], double *
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-       for(i=1;i<=nlstate;i++)
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
+       else
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
          gp[i] = prlim[i][i];
+         mgp[theta][i] = prlim[i][i];
+       }
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-       for(i=1;i<=nlstate;i++)
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
+       else
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
          gm[i] = prlim[i][i];
+         mgm[theta][i] = prlim[i][i];
+       }
        for(i=1;i<=nlstate;i++)
          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
      } /* End theta */
      trgradg =matrix(1,nlstate,1,npar);
- Line 3312  void varprevlim(char fileres[], double *
+ Line 5610  void varprevlim(char fileres[], double *
      for(j=1; j<=nlstate;j++)
        for(theta=1; theta <=npar; theta++)
          trgradg[j][theta]=gradg[theta][j];
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\nmgm mgp %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf("%d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] =0.;
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     }else{
      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     }
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
- Line 3326  void varprevlim(char fileres[], double *
+ Line 5647  void varprevlim(char fileres[], double *
      fprintf(ficresvpl,"\n");
      free_vector(gp,1,nlstate);
      free_vector(gm,1,nlstate);
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
      free_matrix(gradg,1,npar,1,nlstate);
      free_matrix(trgradg,1,nlstate,1,npar);
    } /* End age */
- Line 3338  void varprevlim(char fileres[], double *
+ Line 5661  void varprevlim(char fileres[], double *
  /************ Variance of one-step probabilities  ******************/
  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[])
- {
+  {
-   int i, j=0,  i1, k1, l1, t, tj;
+    int i, j=0,  k1, l1, tj;
-   int k2, l2, j1,  z1;
+    int k2, l2, j1,  z1;
-   int k=0,l, cptcode;
+    int k=0, l;
-   int first=1, first1;
+    int first=1, first1, first2;
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+    double **dnewm,**doldm;
-   double *xp;
+    double *xp;
-   double *gp, *gm;
+    double *gp, *gm;
-   double **gradg, **trgradg;
+    double **gradg, **trgradg;
-   double **mu;
+    double **mu;
-   double age,agelim, cov[NCOVMAX];
+    double age, cov[NCOVMAX+1];
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+    int theta;
-   char fileresprob[FILENAMELENGTH];
+    char fileresprob[FILENAMELENGTH];
-   char fileresprobcov[FILENAMELENGTH];
+    char fileresprobcov[FILENAMELENGTH];
-   char fileresprobcor[FILENAMELENGTH];
+    char fileresprobcor[FILENAMELENGTH];
+    double ***varpij;
-   double ***varpij;
+    strcpy(fileresprob,"PROB_");
-   strcpy(fileresprob,"prob");
+    strcat(fileresprob,fileres);
-   strcat(fileresprob,fileres);
+    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprob);
-     printf("Problem with resultfile: %s\n", fileresprob);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+    }
-   }
+    strcpy(fileresprobcov,"PROBCOV_");
-   strcpy(fileresprobcov,"probcov");
+    strcat(fileresprobcov,fileresu);
-   strcat(fileresprobcov,fileres);
+    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobcov);
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+    }
-   }
+    strcpy(fileresprobcor,"PROBCOR_");
-   strcpy(fileresprobcor,"probcor");
+    strcat(fileresprobcor,fileresu);
-   strcat(fileresprobcor,fileres);
+    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobcor);
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+    }
-   }
+    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    pstamp(ficresprob);
-   pstamp(ficresprob);
+    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+    fprintf(ficresprob,"# Age");
-   fprintf(ficresprob,"# Age");
+    pstamp(ficresprobcov);
-   pstamp(ficresprobcov);
+    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+    fprintf(ficresprobcov,"# Age");
-   fprintf(ficresprobcov,"# Age");
+    pstamp(ficresprobcor);
-   pstamp(ficresprobcor);
+    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    fprintf(ficresprobcor,"# Age");
-   fprintf(ficresprobcor,"# Age");
+    for(i=1; i<=nlstate;i++)
-   for(i=1; i<=nlstate;i++)
+      for(j=1; j<=(nlstate+ndeath);j++){
-     for(j=1; j<=(nlstate+ndeath);j++){
+        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+        fprintf(ficresprobcov," p%1d-%1d ",i,j);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+        fprintf(ficresprobcor," p%1d-%1d ",i,j);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+      }
-     }
+    /* fprintf(ficresprob,"\n");
-  /* fprintf(ficresprob,"\n");
+       fprintf(ficresprobcov,"\n");
-   fprintf(ficresprobcov,"\n");
+       fprintf(ficresprobcor,"\n");
-   fprintf(ficresprobcor,"\n");
+    */
-  */
+    xp=vector(1,npar);
-   xp=vector(1,npar);
+    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+    first=1;
-   first=1;
+    fprintf(ficgp,"\n# Routine varprob");
-   fprintf(ficgp,"\n# Routine varprob");
+    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+    fprintf(fichtm,"\n");
-   fprintf(fichtm,"\n");
+    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-   file %s<br>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
  and drawn. It helps understanding how is the covariance between two incidences.\
   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   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. \
+    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. \
  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
  standard deviations wide on each axis. <br>\
- Line 3427  standard deviations wide on each axis. <
+ Line 5748  standard deviations wide on each axis. <
   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   cov[1]=1;
+    cov[1]=1;
-   tj=cptcoveff;
+    /* tj=cptcoveff; */
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+    tj = (int) pow(2,cptcoveff);
-   j1=0;
+    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   for(t=1; t<=tj;t++){
+    j1=0;
-     for(i1=1; i1<=ncodemax[t];i1++){
+    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
-       j1++;
+      if  (cptcovn>0) {
-       if  (cptcovn>0) {
+        fprintf(ficresprob, "\n#********** Variable ");
-         fprintf(ficresprob, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(ficresprob, "**********\n#\n");
-         fprintf(ficresprob, "**********\n#\n");
+        fprintf(ficresprobcov, "\n#********** Variable ");
-         fprintf(ficresprobcov, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(ficresprobcov, "**********\n#\n");
-         fprintf(ficresprobcov, "**********\n#\n");
+        fprintf(ficgp, "\n#********** Variable ");
-         fprintf(ficgp, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(ficgp, "**********\n#\n");
-         fprintf(ficgp, "**********\n#\n");
+        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+        fprintf(ficresprobcor, "\n#********** Variable ");
-         fprintf(ficresprobcor, "\n#********** Variable ");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(ficresprobcor, "**********\n#");
-         fprintf(ficresprobcor, "**********\n#");
+        if(invalidvarcomb[j1]){
-       }
+          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
+          fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
-       for (age=bage; age<=fage; age ++){
+          continue;
-         cov[2]=age;
+        }
-         for (k=1; k<=cptcovn;k++) {
+      }
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-         }
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
-         for (k=1; k<=cptcovprod;k++)
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+      for (age=bage; age<=fage; age ++){
+        cov[2]=age;
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+        if(nagesqr==1)
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+          cov[3]= age*age;
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+        for (k=1; k<=cptcovn;k++) {
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-         for(theta=1; theta <=npar; theta++){
+                                                                     * 1  1 1 1 1
-           for(i=1; i<=npar; i++)
+                                                                     * 2  2 1 1 1
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+                                                                     * 3  1 2 1 1
+                                                                     */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+        }
-           k=0;
+        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           for(i=1; i<= (nlstate); i++){
+        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-             for(j=1; j<=(nlstate+ndeath);j++){
+        for (k=1; k<=cptcovprod;k++)
-               k=k+1;
+          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-               gp[k]=pmmij[i][j];
-             }
-           }
+        for(theta=1; theta <=npar; theta++){
+          for(i=1; i<=npar; i++)
-           for(i=1; i<=npar; i++)
+            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           k=0;
+          k=0;
-           for(i=1; i<=(nlstate); i++){
+          for(i=1; i<= (nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+            for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+              k=k+1;
-               gm[k]=pmmij[i][j];
+              gp[k]=pmmij[i][j];
-             }
+            }
-           }
+          }
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+          for(i=1; i<=npar; i++)
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-         }
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+          k=0;
-           for(theta=1; theta <=npar; theta++)
+          for(i=1; i<=(nlstate); i++){
-             trgradg[j][theta]=gradg[theta][j];
+            for(j=1; j<=(nlstate+ndeath);j++){
+              k=k+1;
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+              gm[k]=pmmij[i][j];
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+            }
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+          }
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+        }
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
-         k=0;
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
-             k=k+1;
-             mu[k][(int) age]=pmmij[i][j];
-           }
-         }
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-             varpij[i][j][(int)age] = doldm[i][j];
-         /*printf("\n%d ",(int)age);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
-         fprintf(ficresprob,"\n%d ",(int)age);
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         }
-         i=0;
-         for (k=1; k<=(nlstate);k++){
-           for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-             for (j=1; j<=i;j++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             }
-           }
-         }/* end of loop for state */
-       } /* end of loop for age */
-       /* Confidence intervalle of pij  */
-       /*
-         fprintf(ficgp,"\nunset parametric;unset label");
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         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);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-       */
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;
-       for (k2=1; k2<=(nlstate);k2++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
-           j=(k2-1)*(nlstate+ndeath)+l2;
-           for (k1=1; k1<=(nlstate);k1++){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
-               if(i<=j) continue;
-               for (age=bage; age<=fage; age ++){
-                 if ((int)age %5==0){
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
-                   c12=cv12/sqrt(v1*v2);
-                   /* Computing eigen value of matrix of covariance */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   if ((lc2 <0) || (lc1 <0) ){
-                     printf("Error: 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. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
-                     fprintf(ficlog,"Error: 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", lc1, lc2, v1, v2, cv12);fflush(ficlog);
-                     lc1=fabs(lc1);
-                     lc2=fabs(lc2);
-                   }
-                   /* Eigen vectors */
+        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+          for(theta=1; theta <=npar; theta++)
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+            trgradg[j][theta]=gradg[theta][j];
-                   v21=(lc1-v1)/cv12*v11;
-                   v12=-v21;
+        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                   v22=v11;
+        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                   tnalp=v21/v11;
-                   if(first1==1){
+        pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     first1=0;
-                     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);
+        k=0;
-                   }
+        for(i=1; i<=(nlstate); i++){
-                   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);
+          for(j=1; j<=(nlstate+ndeath);j++){
-                   /*printf(fignu*/
+            k=k+1;
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+            mu[k][(int) age]=pmmij[i][j];
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+          }
-                   if(first==1){
+        }
-                     first=0;
+        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-                     fprintf(ficgp,"\nset parametric;unset label");
+          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-                     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);
+            varpij[i][j][(int)age] = doldm[i][j];
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+        /*printf("\n%d ",(int)age);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+          }*/
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+        fprintf(ficresprob,"\n%d ",(int)age);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+        fprintf(ficresprobcov,"\n%d ",(int)age);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        fprintf(ficresprobcor,"\n%d ",(int)age);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                     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",\
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-                   }else{
+          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-                     first=0;
+          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+        }
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+        i=0;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        for (k=1; k<=(nlstate);k++){
-                     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",\
+          for (l=1; l<=(nlstate+ndeath);l++){
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+            i++;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-                   }/* if first */
+            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-                 } /* age mod 5 */
+            for (j=1; j<=i;j++){
-               } /* end loop age */
+              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               first=1;
+              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             } /*l12 */
+            }
-           } /* k12 */
+          }
-         } /*l1 */
+        }/* end of loop for state */
-       }/* k1 */
+      } /* end of loop for age */
-     } /* loop covariates */
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-   }
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+      /* Confidence intervalle of pij  */
-   free_vector(xp,1,npar);
+      /*
-   fclose(ficresprob);
+        fprintf(ficgp,"\nunset parametric;unset label");
-   fclose(ficresprobcov);
+        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   fclose(ficresprobcor);
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-   fflush(ficgp);
+        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);
-   fflush(fichtmcov);
+        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
- }
+        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+      */
+      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+      first1=1;first2=2;
+      for (k2=1; k2<=(nlstate);k2++){
+        for (l2=1; l2<=(nlstate+ndeath);l2++){
+          if(l2==k2) continue;
+          j=(k2-1)*(nlstate+ndeath)+l2;
+          for (k1=1; k1<=(nlstate);k1++){
+            for (l1=1; l1<=(nlstate+ndeath);l1++){
+              if(l1==k1) continue;
+              i=(k1-1)*(nlstate+ndeath)+l1;
+              if(i<=j) continue;
+              for (age=bage; age<=fage; age ++){
+                if ((int)age %5==0){
+                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  mu1=mu[i][(int) age]/stepm*YEARM ;
+                  mu2=mu[j][(int) age]/stepm*YEARM;
+                  c12=cv12/sqrt(v1*v2);
+                  /* Computing eigen value of matrix of covariance */
+                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  if ((lc2 <0) || (lc1 <0) ){
+                    if(first2==1){
+                      first1=0;
+                      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);
+                    }
+                    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);
+                    /* lc1=fabs(lc1); */ /* If we want to have them positive */
+                    /* lc2=fabs(lc2); */
+                  }
+                  /* Eigen vectors */
+                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  /*v21=sqrt(1.-v11*v11); *//* error */
+                  v21=(lc1-v1)/cv12*v11;
+                  v12=-v21;
+                  v22=v11;
+                  tnalp=v21/v11;
+                  if(first1==1){
+                    first1=0;
+                    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);
+                  }
+                  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);
+                  /*printf(fignu*/
+                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                  if(first==1){
+                    first=0;
+                    fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
+                    fprintf(ficgp,"\nset parametric;unset label");
+                    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);
+                    fprintf(ficgp,"\nset ter svg size 640, 480");
+                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                    fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                    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",      \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                  }else{
+                    first=0;
+                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                    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", \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                  }/* if first */
+                } /* age mod 5 */
+              } /* end loop age */
+              fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+              first=1;
+            } /*l12 */
+          } /* k12 */
+        } /*l1 */
+      }/* k1 */
+    }  /* loop on combination of covariates j1 */
+    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+    free_vector(xp,1,npar);
+    fclose(ficresprob);
+    fclose(ficresprobcov);
+    fclose(ficresprobcor);
+    fflush(ficgp);
+    fflush(fichtmcov);
+  }
  /******************* Printing html file ***********/
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int estepm ,\
+                   int popforecast, int prevfcast, int backcast, int estepm , \
-                   double jprev1, double mprev1,double anprev1, \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, \
-                   double jprev2, double mprev2,double anprev2){
+                   double jprev2, double mprev2,double anprev2, double dateprev2){
-   int jj1, k1, i1, cpt;
+   int jj1, k1, i1, cpt, k4, nres;
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  </ul>");
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+    fprintf(fichtm,"<ul><li> model=1+age+%s\n \
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+ </ul>", model);
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
+    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
+    fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
+    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
     fprintf(fichtm,"\
   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
+    fprintf(fichtm,"\
+  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
     fprintf(fichtm,"\
   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
     fprintf(fichtm,"\
-  - (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): \
+  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-    <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fprintf(fichtm,"\
-  - Population projections by age and states: \
+  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . 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): \
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
+    if(prevfcast==1){
+      fprintf(fichtm,"\
+  - Prevalence projections by age and states:                            \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
+    }
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+    m=pow(2,cptcoveff);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    jj1=0;
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){
+      if(TKresult[nres]!= k1)
+        continue;
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+        for (cpt=1; cpt<=cptcoveff;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
+       }
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
+          printf("\nCombination (%d) ignored because no cases \n",k1);
+          continue;
+        }
       }
+      /* aij, bij */
+      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
+ <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
       /* Pij */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
+      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
       /* Quasi-incidences */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+      fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
-        /* Period (stable) prevalence in each health state */
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
-        for(cpt=1; cpt<nlstate;cpt++){
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+      /* Survival functions (period) in state j */
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+      }
+      /* State specific survival functions (period) */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
+  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
+  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+      }
+      /* Period (stable) prevalence in each health state */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+      }
+      if(backcast==1){
+        /* Period (stable) back prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
         }
+      }
+      if(prevfcast==1){
+        /* Projection of prevalence up to period (stable) prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
+        }
+      }
       for(cpt=1; cpt<=nlstate;cpt++) {
-         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> \
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
       }
-    } /* end i1 */
+      /* } /\* end i1 *\/ */
-  }/* End k1 */
+    }/* End k1 */
-  fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"\
-  fprintf(fichtm,"\
  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
+ But because parameters are usually highly correlated (a higher incidence of disability \
+ and a higher incidence of recovery can give very close observed transition) it might \
+ be very useful to look not only at linear confidence intervals estimated from the \
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
+ covariance matrix of the one-step probabilities. \
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+            subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+            subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+            subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - 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): \
     <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - (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): \
     <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - 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",
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+            estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - 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",
-          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Line 3761  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 6169  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    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); */
-  fflush(fichtm);
+    fflush(fichtm);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+    m=pow(2,cptcoveff);
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  m=cptcoveff;
+    jj1=0;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
-  for(k1=1; k1<=m;k1++){
+    for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+      if(TKresult[nres]!= k1)
+        continue;
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
+          continue;
+        }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+ <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
       }
       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
  true period expectancies (those weighted with period prevalences are also\
   drawn in addition to the population based expectancies computed using\
-  observed and cahotic prevalences: %s%d.png<br>\
+  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+ <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
-    } /* end i1 */
+      /* } /\* end i1 *\/ */
-  }/* End k1 */
+    }/* End k1 */
-  fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"</ul>");
-  fflush(fichtm);
+    fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   char gplotcondition[132];
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
+   int lv=0, vlv=0, kl=0;
    int ng=0;
+   int vpopbased;
+   int ioffset; /* variable offset for columns */
+   int nres=0; /* Index of resultline */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 3807  void printinggnuplot(char fileres[], cha
+ Line 6235  void printinggnuplot(char fileres[], cha
    /*#ifdef windows */
    fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+   /*#endif */
    m=pow(2,cptcoveff);
+   /* Contribution to likelihood */
+   /* Plot the probability implied in the likelihood */
+   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
+   /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+   fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+ /* nice for mle=4 plot by number of matrix products.
+    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
+   /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+   fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
+   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
+   fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
+   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
+   for (i=1; i<= nlstate ; i ++) {
+     fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
+     fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
+     fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
+     for (j=2; j<= nlstate+ndeath ; j ++) {
+       fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
+     }
+     fprintf(ficgp,";\nset out; unset ylabel;\n");
+   }
+   /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
+   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
+   /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
+   fprintf(ficgp,"\nset out;unset log\n");
+   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
-  /* 1eme*/
+   /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-    for (k1=1; k1<= m ; k1 ++) {
+     for (k1=1; k1<= m ; k1 ++) /* For each valid combination of covariate */
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+     /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+       if(TKresult[nres]!= k1)
- set ylabel \"Probability\" \n\
+         continue;
- set ter png small\n\
+       /* We are interested in selected combination by the resultline */
- set size 0.65,0.65\n\
+       printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-      for (i=1; i<= nlstate ; i ++) {
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-        else        fprintf(ficgp," \%%*lf (\%%*lf)");
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-      }
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 1,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-      for (i=1; i<= nlstate ; i ++) {
+         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         printf(" V%d=%d ",Tvaraff[k],vlv);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-      }
+       }
-      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-      for (i=1; i<= nlstate ; i ++) {
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-      }
+       printf("\n#\n");
-      fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+       fprintf(ficgp,"\n#\n");
-    }
+       if(invalidvarcomb[k1]){
-   }
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-   /*2 eme*/
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \n\
+ set ylabel \"Probability\" \n             \
+ set ter svg size 640, 480\n                                             \
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+       for (i=1; i<= nlstate ; i ++) {
+         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         else        fprintf(ficgp," %%*lf (%%*lf)");
+       }
+       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+       for (i=1; i<= nlstate ; i ++) {
+         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         else fprintf(ficgp," %%*lf (%%*lf)");
+       }
+       fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+       for (i=1; i<= nlstate ; i ++) {
+         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         else fprintf(ficgp," %%*lf (%%*lf)");
+       }
+       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
+         if(cptcoveff ==0){
+           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
+         }else{
+           kl=0;
+           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+             vlv= nbcode[Tvaraff[k]][lv];
+             kl++;
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(k==cptcoveff){
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++(cpt-1),  cpt );  /* 4 or 6 ?*/
+             }else{
+               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+               kl++;
+             }
+           } /* end covariate */
+         } /* end if no covariate */
+       } /* end if backcast */
+       fprintf(ficgp,"\nset out \n");
+     } /* k1 */
+   } /* cpt */
-   for (k1=1; k1<= m ; k1 ++) {
+   /*2 eme*/
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+   for (k1=1; k1<= m ; k1 ++)
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(TKresult[nres]!= k1)
-     for (i=1; i<= nlstate+1 ; i ++) {
+       continue;
-       k=2*i;
+     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-       for (j=1; j<= nlstate+1 ; j ++) {
+       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       }
+       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       vlv= nbcode[Tvaraff[k]][lv];
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     }
-       for (j=1; j<= nlstate+1 ; j ++) {
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       }
+     }
-       fprintf(ficgp,"\" t\"\" w l lt 1,");
+     fprintf(ficgp,"\n#\n");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     if(invalidvarcomb[k1]){
-       for (j=1; j<= nlstate+1 ; j ++) {
+       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       continue;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
-       else fprintf(ficgp,"\" t\"\" w l lt 1,");
      }
-   }
+     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
+     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+       if(vpopbased==0)
+         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
+       else
+         fprintf(ficgp,"\nreplot ");
+       for (i=1; i<= nlstate+1 ; i ++) {
+         k=2*i;
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
+         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         fprintf(ficgp,"\" t\"\" w l lt 0,");
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+       } /* state */
+     } /* vpopbased */
+     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
+   } /* k1 end 2 eme*/
    /*3eme*/
+   for (k1=1; k1<= m ; k1 ++)
-   for (k1=1; k1<= m ; k1 ++) {
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(TKresult[nres]!= k)
+       continue;
      for (cpt=1; cpt<= nlstate ; cpt ++) {
+       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate dummy combination and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[k]][lv];
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       /* for(k=1; k <= ncovds; k++){ */
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
        /*       k=2+nlstate*(2*cpt-2); */
        k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+       fprintf(ficgp,"set ter svg size 640, 480\n\
- set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
- 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);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        */
        for (i=1; i< nlstate ; i ++) {
-         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);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
          /*      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);*/
        }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
      }
    }
-   /* CV preval stable (period) */
+   /* 4eme */
-   for (k1=1; k1<= m ; k1 ++) {
+   /* Survival functions (period) from state i in state j by initial state i */
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
-       k=3;
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+     if(TKresult[nres]!= k1)
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+       continue;
- set ter png small\nset size 0.65,0.65\n\
- unset log y\n\
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-       for (i=1; i< nlstate ; i ++)
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         fprintf(ficgp,"+$%d",k+i+1);
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       l=3+(nlstate+ndeath)*cpt;
+         vlv= nbcode[Tvaraff[k]][lv];
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       for (i=1; i< nlstate ; i ++) {
+       }
-         l=3+(nlstate+ndeath)*cpt;
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         fprintf(ficgp,"+$%d",l+i+1);
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
        }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+       fprintf(ficgp,"\n#\n");
-     }
+       if(invalidvarcomb[k1]){
-   }
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\n                                                                                                                                                                                     \
+ unset log y\n                                                                                                                                                                                                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3;
+       for (i=1; i<= nlstate ; i ++){
+         if(i==1){
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         }else{
+           fprintf(ficgp,", '' ");
+         }
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate+ndeath ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+ /* 5eme */
+   /* Survival functions (period) from state i in state j by final state j */
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(TKresult[nres]!= k1)
+       continue;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[k]][lv];
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3;
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+         if(j==1)
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(cpt-1) +j;
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+       } /* nlstate */
+       fprintf(ficgp,", '' ");
+       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+         l=(nlstate+ndeath)*(cpt-1) +j;
+         if(j < nlstate)
+           fprintf(ficgp,"$%d +",k+l);
+         else
+           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+       }
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+ /* 6eme */
+   /* CV preval stable (period) for each covariate */
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(TKresult[nres]!= k1)
+       continue;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[k]][lv];
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3; /* Offset */
+       for (i=1; i<= nlstate ; i ++){
+         if(i==1)
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+ /* 7eme */
+   if(backcast == 1){
+     /* CV back preval stable (period) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3; /* Offset */
+         for (i=1; i<= nlstate ; i ++){
+           if(i==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+           else
+             fprintf(ficgp,", '' ");
+           /* l=(nlstate+ndeath)*(i-1)+1; */
+           l=(nlstate+ndeath)*(cpt-1)+1;
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+           /* for (j=2; j<= nlstate ; j ++) */
+           /*    fprintf(ficgp,"+$%d",k+l+j-1); */
+           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if backcast */
+   /* 8eme */
+   if(prevfcast==1){
+     /* Projection from cross-sectional to stable (period) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\n                                             \
+ unset log y\n                                                           \
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           if(i==1){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
+           }else{
+             fprintf(ficgp,",\\\n '' ");
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             ioffset=2; /* Age is in 2 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             fprintf(ficgp," u %d:(", ioffset);
+             if(i==nlstate+1)
+               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+             else
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+           }else{ /* more than 2 covariates */
+             if(cptcoveff ==1){
+               ioffset=4; /* Age is in 4 */
+             }else{
+               ioffset=6; /* Age is in 6 */
+               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             }
+             fprintf(ficgp," u %d:(",ioffset);
+             kl=0;
+             strcpy(gplotcondition,"(");
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
+               kl++;
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               kl++;
+               if(k <cptcoveff && cptcoveff>1)
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+             }
+             strcpy(gplotcondition+strlen(gplotcondition),")");
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(i==nlstate+1){
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+             }else{
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+             }
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevfcast */
    /* proba elementaires */
+   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
+     fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) {
+         fprintf(ficgp,"#   current state %d\n",k);
          for(j=1; j <=ncovmodel; j++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
            jk++;
-           fprintf(ficgp,"\n");
          }
+         fprintf(ficgp,"\n");
        }
      }
-    }
+   }
+   fprintf(ficgp,"##############\n#\n");
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-      for(jk=1; jk <=m; jk++) {
+   /*goto avoid;*/
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
-        if (ng==2)
+   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
-        else
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-        i=1;
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-        for(k2=1; k2<=nlstate; k2++) {
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-          k3=i;
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
-          for(k=1; k<=(nlstate+ndeath); k++) {
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
-            if (k != k2){
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
-              if(ng==2)
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
-              else
+   fprintf(ficgp,"#\n");
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-              ij=1;/* To be checked else nbcode[0][0] wrong */
+     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year \n");
-              for(j=3; j <=ncovmodel; j++) {
+     fprintf(ficgp,"#model=%s \n",model);
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
+     fprintf(ficgp,"# ng=%d\n",ng);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
-                  ij++;
+     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
-                }
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-                else
+       if(TKresult[nres]!= jk)
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         continue;
-              }
+       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
-              fprintf(ficgp,")/(1");
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-              for(k1=1; k1 <=nlstate; k1++){
+       }
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+       fprintf(ficgp,"\n#\n");
-                ij=1;
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
-                for(j=3; j <=ncovmodel; j++){
+       fprintf(ficgp,"\nset ter svg size 640, 480 ");
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       if (ng==1){
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
-                    ij++;
+         fprintf(ficgp,"\nunset log y");
-                  }
+       }else if (ng==2){
-                  else
+         fprintf(ficgp,"\nset ylabel \"Probability\"\n");
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         fprintf(ficgp,"\nset log y");
-                }
+       }else if (ng==3){
-                fprintf(ficgp,")");
+         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-              }
+         fprintf(ficgp,"\nset log y");
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       }else
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+         fprintf(ficgp,"\nunset title ");
-              i=i+ncovmodel;
+       fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-            }
+       i=1;
-          } /* end k */
+       for(k2=1; k2<=nlstate; k2++) {
-        } /* end k2 */
+         k3=i;
-      } /* end jk */
+         for(k=1; k<=(nlstate+ndeath); k++) {
-    } /* end ng */
+           if (k != k2){
-    fflush(ficgp);
+             switch( ng) {
+             case 1:
+               if(nagesqr==0)
+                 fprintf(ficgp," p%d+p%d*x",i,i+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+               break;
+             case 2: /* ng=2 */
+               if(nagesqr==0)
+                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+               break;
+             case 3:
+               if(nagesqr==0)
+                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
+               break;
+             }
+             ij=1;/* To be checked else nbcode[0][0] wrong */
+             ijp=1; /* product no age */
+             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
+             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
+               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
+               if(j==Tage[ij]) { /* Product by age */
+                 if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                   if(Dummy[j]==0){
+                     fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                   }else{ /* quantitative */
+                     fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                   }
+                   ij++;
+                 }
+               }else if(j==Tprod[ijp]) { /* */
+                 /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                 if(ijp <=cptcovprod) { /* Product */
+                   if(Dummy[Tvard[ijp][1]]==0){/* Vn is dummy */
+                     if(Dummy[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                       /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
+                       fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                     }else{ /* Vn is dummy and Vm is quanti */
+                       /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                     }
+                   }else{ /* Vn*Vm Vn is quanti */
+                     if(Dummy[Tvard[ijp][2]]==0){
+                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                     }else{ /* Both quanti */
+                       fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                     }
+                   }
+                 }
+               } else{  /* simple covariate */
+                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
+                 if(Dummy[j]==0){
+                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
+                 }else{ /* quantitative */
+                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                 }
+               } /* end simple */
+             } /* end j */
+           }else{
+             i=i-ncovmodel;
+             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
+               fprintf(ficgp," (1.");
+           }
+           if(ng != 1){
+             fprintf(ficgp,")/(1");
+             for(k1=1; k1 <=nlstate; k1++){
+               if(nagesqr==0)
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+               else /* nagesqr =1 */
+                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
+               ij=1;
+               for(j=3; j <=ncovmodel-nagesqr; j++){
+                 if((j-2)==Tage[ij]) { /* Bug valgrind */
+                   if(ij <=cptcovage) { /* Bug valgrind */
+                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                     ij++;
+                   }
+                 }
+                 else
+                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
+               }
+               fprintf(ficgp,")");
+             }
+             fprintf(ficgp,")");
+             if(ng ==2)
+               fprintf(ficgp," t \"p%d%d\" ", k2,k);
+             else /* ng= 3 */
+               fprintf(ficgp," t \"i%d%d\" ", k2,k);
+           }else{ /* end ng <> 1 */
+             if( k !=k2) /* logit p11 is hard to draw */
+               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+           }
+           if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
+             fprintf(ficgp,",");
+           if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
+             fprintf(ficgp,",");
+           i=i+ncovmodel;
+         } /* end k */
+       } /* end k2 */
+       fprintf(ficgp,"\n set out\n");
+     } /* end jk */
+   } /* end ng */
+   /* avoid: */
+   fflush(ficgp);
  }  /* end gnuplot */
  /*************** Moving average **************/
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+ /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
+  int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
-   int i, cpt, cptcod;
-   int modcovmax =1;
+    int i, cpt, cptcod;
-   int mobilavrange, mob;
+    int modcovmax =1;
-   double age;
+    int mobilavrange, mob;
+    int iage=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-                            a covariate has 2 modalities */
+    double sum=0.;
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+    double age;
+    double *sumnewp, *sumnewm;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
-     if(mobilav==1) mobilavrange=5; /* default */
-     else mobilavrange=mobilav;
-     for (age=bage; age<=fage; age++)
+    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
-       for (i=1; i<=nlstate;i++)
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+    sumnewp = vector(1,ncovcombmax);
-     /* We keep the original values on the extreme ages bage, fage and for
+    sumnewm = vector(1,ncovcombmax);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+    agemingood = vector(1,ncovcombmax);
-        we use a 5 terms etc. until the borders are no more concerned.
+    agemaxgood = vector(1,ncovcombmax);
-     */
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+      sumnewm[cptcod]=0.;
-         for (i=1; i<=nlstate;i++){
+      sumnewp[cptcod]=0.;
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+      agemingood[cptcod]=0;
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+      agemaxgood[cptcod]=0;
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+    }
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               }
+    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+      if(mobilav==1) mobilavrange=5; /* default */
-           }
+      else mobilavrange=mobilav;
-         }
+      for (age=bage; age<=fage; age++)
-       }/* end age */
+        for (i=1; i<=nlstate;i++)
-     }/* end mob */
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
-   }else return -1;
+            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   return 0;
+      /* We keep the original values on the extreme ages bage, fage and for
- }/* End movingaverage */
+         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         we use a 5 terms etc. until the borders are no more concerned.
+      */
+      for (mob=3;mob <=mobilavrange;mob=mob+2){
+        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+          for (i=1; i<=nlstate;i++){
+            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+              for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+              }
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+            }
+          }
+        }/* end age */
+      }/* end mob */
+    }else
+      return -1;
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
+      if(invalidvarcomb[cptcod]){
+        printf("\nCombination (%d) ignored because no cases \n",cptcod);
+        continue;
+      }
+      agemingood[cptcod]=fage-(mob-1)/2;
+      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemingood[cptcod]=age;
+        }else{ /* bad */
+          for (i=1; i<=nlstate;i++){
+            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+          } /* i */
+        } /* end bad */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      }
+      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+      /* From youngest, finding the oldest wrong */
+      agemaxgood[cptcod]=bage+(mob-1)/2;
+      for (age=bage+(mob-1)/2; age<=fage; age++){
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemaxgood[cptcod]=age;
+        }else{ /* bad */
+          for (i=1; i<=nlstate;i++){
+            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+          } /* i */
+        } /* end bad */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      }
+      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      for (age=bage; age<=fage; age++){
+        /* printf("%d %d ", cptcod, (int)age); */
+        sumnewp[cptcod]=0.;
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewp[cptcod]+=probs[(int)age][i][cptcod];
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
+        }
+        /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
+      }
+      /* printf("\n"); */
+      /* } */
+      /* brutal averaging */
+      for (i=1; i<=nlstate;i++){
+        for (age=1; age<=bage; age++){
+          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+        }
+        for (age=fage; age<=AGESUP; age++){
+          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+        }
+      } /* end i status */
+      for (i=nlstate+1; i<=nlstate+ndeath;i++){
+        for (age=1; age<=AGESUP; age++){
+          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+          mobaverage[(int)age][i][cptcod]=0.;
+        }
+      }
+    }/* end cptcod */
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
+    free_vector(agemaxgood,1, ncovcombmax);
+    free_vector(agemingood,1, ncovcombmax);
+    return 0;
+  }/* End movingaverage */
  /************** Forecasting ******************/
- 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){
+  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
    /* proj1, year, month, day of starting projection
       agemin, agemax range of age
       dateprev1 dateprev2 range of dates during which prevalence is computed
       anproj2 year of en of projection (same day and month as proj1).
    */
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
-   int *popage;
    double agec; /* generic age */
    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    double *popeffectif,*popcount;
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
    char fileresf[FILENAMELENGTH];
    agelim=AGESUP;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
-   strcpy(fileresf,"f");
+   strcpy(fileresf,"F_");
-   strcat(fileresf,fileres);
+   strcat(fileresf,fileresu);
    if((ficresf=fopen(fileresf,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", fileresf);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
    stepsize=(int) (stepm+YEARM-1)/YEARM;
    if (stepm<=12) stepsize=1;
- Line 4086  prevforecast(char fileres[], double anpr
+ Line 7154  prevforecast(char fileres[], double anpr
    if(jprojmean==0) jprojmean=1;
    if(mprojmean==0) jprojmean=1;
-   i1=cptcoveff;
+   i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
    fprintf(ficresf,"#****** Routine prevforecast **\n");
  /*            if (h==(int)(YEARM*yearp)){ */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   for(k=1; k<=i1;k++){
-       k=k+1;
+     if(TKresult[nres]!= k)
-       fprintf(ficresf,"\n#******");
+       continue;
-       for(j=1;j<=cptcoveff;j++) {
+     if(invalidvarcomb[k]){
-         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]]);
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
-       }
+       continue;
-       fprintf(ficresf,"******\n");
+     }
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
-       for(j=1; j<=nlstate+ndeath;j++){
+     for(j=1;j<=cptcoveff;j++) {
-         for(i=1; i<=nlstate;i++)
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-           fprintf(ficresf," p%d%d",i,j);
+     }
-         fprintf(ficresf," p.%d",j);
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       }
+       printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         fprintf(ficresf,"\n");
+     }
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+     fprintf(ficresf," yearproj age");
+     for(j=1; j<=nlstate+ndeath;j++){
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+       for(i=1; i<=nlstate;i++)
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         fprintf(ficresf," p%d%d",i,j);
-           nhstepm = nhstepm/hstepm;
+       fprintf(ficresf," wp.%d",j);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     }
-           oldm=oldms;savm=savms;
+     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+       fprintf(ficresf,"\n");
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       for (agec=fage; agec>=(ageminpar-1); agec--){
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         nhstepm = nhstepm/hstepm;
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
-           for (h=0; h<=nhstepm; h++){
+         for (h=0; h<=nhstepm; h++){
-             if (h*hstepm/YEARM*stepm ==yearp) {
+           if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n");
+             fprintf(ficresf,"\n");
-               for(j=1;j<=cptcoveff;j++)
+             for(j=1;j<=cptcoveff;j++)
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-             }
+           }
-             for(j=1; j<=nlstate+ndeath;j++) {
+           for(j=1; j<=nlstate+ndeath;j++) {
-               ppij=0.;
+             ppij=0.;
-               for(i=1; i<=nlstate;i++) {
+             for(i=1; i<=nlstate;i++) {
-                 if (mobilav==1)
+               if (mobilav==1)
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
-                 else {
+               else {
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
-                 }
-                 if (h*hstepm/YEARM*stepm== yearp) {
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                 }
-               } /* end i */
-               if (h*hstepm/YEARM*stepm==yearp) {
-                 fprintf(ficresf," %.3f", ppij);
                }
-             }/* end j */
+               if (h*hstepm/YEARM*stepm== yearp) {
-           } /* end h */
+                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               }
-         } /* end agec */
+             } /* end i */
-       } /* end yearp */
+             if (h*hstepm/YEARM*stepm==yearp) {
-     } /* end cptcod */
+               fprintf(ficresf," %.3f", ppij);
-   } /* end  cptcov */
+             }
+           }/* end j */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         } /* end h */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+     } /* end yearp */
+   } /* end  k */
    fclose(ficresf);
- }
+   printf("End of Computing forecasting \n");
+   fprintf(ficlog,"End of Computing forecasting\n");
- /************** Forecasting *****not tested NB*************/
+ }
- 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){
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   int *popage;
-   double calagedatem, agelim, kk1, kk2;
-   double *popeffectif,*popcount;
-   double ***p3mat,***tabpop,***tabpopprev;
-   double ***mobaverage;
-   char filerespop[FILENAMELENGTH];
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /* /\************** Back Forecasting ******************\/ */
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
-   agelim=AGESUP;
+ /*   /\* back1, year, month, day of starting backection  */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+ /*      agemin, agemax range of age */
+ /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
+ /*      anback2 year of en of backection (same day and month as back1). */
+ /*   *\/ */
+ /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
+ /*   double agec; /\* generic age *\/ */
+ /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
+ /*   double *popeffectif,*popcount; */
+ /*   double ***p3mat; */
+ /*   /\* double ***mobaverage; *\/ */
+ /*   char fileresfb[FILENAMELENGTH]; */
+ /*   agelim=AGESUP; */
+ /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
+ /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
+ /*      We still use firstpass and lastpass as another selection. */
+ /*   *\/ */
+ /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
+ /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
+ /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+ /*   strcpy(fileresfb,"FB_");  */
+ /*   strcat(fileresfb,fileresu); */
+ /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
+ /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
+ /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
+ /*   } */
+ /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
+ /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
+ /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
+ /*   /\* if (mobilav!=0) { *\/ */
+ /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+ /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
+ /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
+ /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
+ /*   /\*   } *\/ */
+ /*   /\* } *\/ */
+ /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
+ /*   if (stepm<=12) stepsize=1; */
+ /*   if(estepm < stepm){ */
+ /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
+ /*   } */
+ /*   else  hstepm=estepm;    */
+ /*   hstepm=hstepm/stepm;  */
+ /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
+ /*                                fractional in yp1 *\/ */
+ /*   anprojmean=yp; */
+ /*   yp2=modf((yp1*12),&yp); */
+ /*   mprojmean=yp; */
+ /*   yp1=modf((yp2*30.5),&yp); */
+ /*   jprojmean=yp; */
+ /*   if(jprojmean==0) jprojmean=1; */
+ /*   if(mprojmean==0) jprojmean=1; */
+ /*   i1=cptcoveff; */
+ /*   if (cptcovn < 1){i1=1;} */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
+ /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+ /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
+ /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
+ /*       k=k+1; */
+ /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
+ /*       for(j=1;j<=cptcoveff;j++) { */
+ /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+ /*       } */
+ /*       fprintf(ficresfb," yearbproj age"); */
+ /*       for(j=1; j<=nlstate+ndeath;j++){  */
+ /*                              for(i=1; i<=nlstate;i++)               */
+ /*           fprintf(ficresfb," p%d%d",i,j); */
+ /*                              fprintf(ficresfb," p.%d",j); */
+ /*       } */
+ /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
+ /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
+ /*                              fprintf(ficresfb,"\n"); */
+ /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
+ /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
+ /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
+ /*                                      nhstepm = nhstepm/hstepm;  */
+ /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*                                      oldm=oldms;savm=savms; */
+ /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
+ /*                                      for (h=0; h<=nhstepm; h++){ */
+ /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
+ /*               fprintf(ficresfb,"\n"); */
+ /*               for(j=1;j<=cptcoveff;j++)  */
+ /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+ /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
+ /*                                              }  */
+ /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
+ /*                                                      ppij=0.; */
+ /*                                                      for(i=1; i<=nlstate;i++) { */
+ /*                                                              if (mobilav==1)  */
+ /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
+ /*                                                              else { */
+ /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
+ /*                                                              } */
+ /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
+ /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
+ /*                                                              } */
+ /*                                                      } /\* end i *\/ */
+ /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
+ /*                                                              fprintf(ficresfb," %.3f", ppij); */
+ /*                                                      } */
+ /*                                              }/\* end j *\/ */
+ /*                                      } /\* end h *\/ */
+ /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*                              } /\* end agec *\/ */
+ /*       } /\* end yearp *\/ */
+ /*     } /\* end cptcod *\/ */
+ /*   } /\* end  cptcov *\/ */
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+ /*   fclose(ficresfb); */
+ /*   printf("End of Computing Back forecasting \n"); */
+ /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
+ /* } */
+ /************** Forecasting *****not tested NB*************/
+ /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
-   strcpy(filerespop,"pop");
+ /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
-   strcat(filerespop,fileres);
+ /*   int *popage; */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ /*   double calagedatem, agelim, kk1, kk2; */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+ /*   double *popeffectif,*popcount; */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ /*   double ***p3mat,***tabpop,***tabpopprev; */
-   }
+ /*   /\* double ***mobaverage; *\/ */
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+ /*   char filerespop[FILENAMELENGTH]; */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   agelim=AGESUP; */
+ /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
+ /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+ /*   strcpy(filerespop,"POP_");  */
+ /*   strcat(filerespop,fileresu); */
+ /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
+ /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
+ /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
+ /*   } */
+ /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
+ /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
-   if (mobilav!=0) {
+ /*   /\* if (mobilav!=0) { *\/ */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-     }
+ /*   /\*   } *\/ */
-   }
+ /*   /\* } *\/ */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
-   if (stepm<=12) stepsize=1;
+ /*   if (stepm<=12) stepsize=1; */
-   agelim=AGESUP;
-   hstepm=1;
+ /*   agelim=AGESUP; */
-   hstepm=hstepm/stepm;
-   if (popforecast==1) {
+ /*   hstepm=1; */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /*   hstepm=hstepm/stepm;  */
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ /*   if (popforecast==1) { */
-     }
+ /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
-     popage=ivector(0,AGESUP);
+ /*       printf("Problem with population file : %s\n",popfile);exit(0); */
-     popeffectif=vector(0,AGESUP);
+ /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
-     popcount=vector(0,AGESUP);
+ /*     }  */
+ /*     popage=ivector(0,AGESUP); */
+ /*     popeffectif=vector(0,AGESUP); */
+ /*     popcount=vector(0,AGESUP); */
-     i=1;
+ /*     i=1;    */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
-     imx=i;
+ /*     imx=i; */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
-   }
+ /*   } */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
-       k=k+1;
+ /*       k=k+1; */
-       fprintf(ficrespop,"\n#******");
+ /*       fprintf(ficrespop,"\n#******"); */
-       for(j=1;j<=cptcoveff;j++) {
+ /*       for(j=1;j<=cptcoveff;j++) { */
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
-       }
+ /*       } */
-       fprintf(ficrespop,"******\n");
+ /*       fprintf(ficrespop,"******\n"); */
-       fprintf(ficrespop,"# Age");
+ /*       fprintf(ficrespop,"# Age"); */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+ /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
-       for (cpt=0; cpt<=0;cpt++) {
+ /*       for (cpt=0; cpt<=0;cpt++) {  */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
-           nhstepm = nhstepm/hstepm;
+ /*        nhstepm = nhstepm/hstepm;  */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-           oldm=oldms;savm=savms;
+ /*        oldm=oldms;savm=savms; */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
-                 if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-                 else {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-                 }
-               }
-               if (h==(int)(calagedatem+12*cpt)){
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-                   /*fprintf(ficrespop," %.3f", kk1);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-               }
-             }
-             for(i=1; i<=nlstate;i++){
-               kk1=0.;
-                 for(j=1; j<=nlstate;j++){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-                 }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-             }
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
-       }
-   /******/
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-           nhstepm = nhstepm/hstepm;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        for (h=0; h<=nhstepm; h++){ */
-           oldm=oldms;savm=savms;
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-           for (h=0; h<=nhstepm; h++){
+ /*          }  */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            kk1=0.;kk2=0; */
-             }
+ /*            for(i=1; i<=nlstate;i++) {               */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*              if (mobilav==1)  */
-               kk1=0.;kk2=0;
+ /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
-               for(i=1; i<=nlstate;i++) {
+ /*              else { */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
-               }
+ /*              } */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+ /*            } */
-             }
+ /*            if (h==(int)(calagedatem+12*cpt)){ */
-           }
+ /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*              /\*fprintf(ficrespop," %.3f", kk1); */
-         }
+ /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
-       }
+ /*            } */
-    }
+ /*          } */
-   }
+ /*          for(i=1; i<=nlstate;i++){ */
+ /*            kk1=0.; */
+ /*            for(j=1; j<=nlstate;j++){ */
+ /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
+ /*            } */
+ /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
+ /*          } */
+ /*          if (h==(int)(calagedatem+12*cpt)) */
+ /*            for(j=1; j<=nlstate;j++)  */
+ /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
+ /*        } */
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*      } */
+ /*       } */
+ /*       /\******\/ */
+ /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
+ /*        nhstepm = nhstepm/hstepm;  */
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*        oldm=oldms;savm=savms; */
+ /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+ /*        for (h=0; h<=nhstepm; h++){ */
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
+ /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
+ /*          }  */
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
+ /*            kk1=0.;kk2=0; */
+ /*            for(i=1; i<=nlstate;i++) {               */
+ /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
+ /*            } */
+ /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
+ /*          } */
+ /*        } */
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*      } */
+ /*       } */
+ /*     }  */
+ /*   } */
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+ /*   if (popforecast==1) { */
+ /*     free_ivector(popage,0,AGESUP); */
+ /*     free_vector(popeffectif,0,AGESUP); */
+ /*     free_vector(popcount,0,AGESUP); */
+ /*   } */
+ /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   fclose(ficrespop); */
+ /* } /\* End of popforecast *\/ */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if (popforecast==1) {
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
-   }
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficrespop);
- } /* End of popforecast */
  int fileappend(FILE *fichier, char *optionfich)
  {
    if((fichier=fopen(optionfich,"a"))==NULL) {
- Line 4332  void prwizard(int ncovmodel, int nlstate
+ Line 7538  void prwizard(int ncovmodel, int nlstate
    /* Wizard to print covariance matrix template */
-   char ca[32], cb[32], cc[32];
+   char ca[32], cb[32];
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
    int numlinepar;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- Line 4454  double gompertz(double x[])
+ Line 7660  double gompertz(double x[])
    double A,B,L=0.0,sump=0.,num=0.;
    int i,n=0; /* n is the size of the sample */
-   for (i=0;i<=imx-1 ; i++) {
+   for (i=1;i<=imx ; i++) {
      sump=sump+weight[i];
      /*    sump=sump+1;*/
      num=num+1;
- Line 4527  double gompertz_f(const gsl_vector *v, v
+ Line 7733  double gompertz_f(const gsl_vector *v, v
  #endif
  /******************* Printing html file ***********/
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+ void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,  double p[],double **matcov,double agemortsup){
    int i,k;
- Line 4536  void printinghtmlmort(char fileres[], ch
+ Line 7742  void printinghtmlmort(char fileres[], ch
    fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
    for (i=1;i<=2;i++)
      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]));
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
    fprintf(fichtm,"</ul>");
  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
- Line 4551  fprintf(fichtm,"<ul><li><h4>Life table</
+ Line 7757  fprintf(fichtm,"<ul><li><h4>Life table</
  }
  /******************* Gnuplot file **************/
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
    int ng;
- Line 4565  void printinggnuplotmort(char fileres[],
+ Line 7771  void printinggnuplotmort(char fileres[],
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set out \"graphmort.svg\"\n ");
    fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   fprintf(ficgp, "set ter png small\n set log y\n");
+   fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
-   fprintf(ficgp, "set size 0.65,0.65\n");
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
  }
- Line 4579  int readdata(char datafile[], int firsto
+ Line 7785  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i, j, n;
+   int i=0, j=0, n=0, iv=0;
+   int lstra;
    int linei, month, year,iout;
    char line[MAXLINE], linetmp[MAXLINE];
-   char stra[80], strb[80];
+   char stra[MAXLINE], strb[MAXLINE];
    char *stratrunc;
-   int lstra;
    if((fic=fopen(datafile,"r"))==NULL)    {
-     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
    }
    i=1;
- Line 4610  int readdata(char datafile[], int firsto
+ Line 7817  int readdata(char datafile[], int firsto
        continue;
      }
      trimbb(linetmp,line); /* Trims multiple blanks in line */
-     for (j=0; line[j]!='\0';j++){
+     strcpy(line, linetmp);
-       line[j]=linetmp[j];
-     }
+     /* Loops on waves */
      for (j=maxwav;j>=1;j--){
+       for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
+                                 cutv(stra, strb, line, ' ');
+                                 if(strb[0]=='.') { /* Missing value */
+                                         lval=-1;
+                                         cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+                                         cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
+                                         if(isalpha(strb[1])) { /* .m or .d Really Missing value */
+                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
+                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
+                                                 return 1;
+                                         }
+                                 }else{
+                                         errno=0;
+                                         /* what_kind_of_number(strb); */
+                                         dval=strtod(strb,&endptr);
+                                         /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+                                         /* if(strb != endptr && *endptr == '\0') */
+                                         /*    dval=dlval; */
+                                         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+                                         if( strb[0]=='\0' || (*endptr != '\0')){
+                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
+                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
+                                                 return 1;
+                                         }
+                                         cotqvar[j][iv][i]=dval;
+                                         cotvar[j][ntv+iv][i]=dval;
+                                 }
+                                 strcpy(line,stra);
+       }/* end loop ntqv */
+       for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
+                                 cutv(stra, strb, line, ' ');
+                                 if(strb[0]=='.') { /* Missing value */
+                                         lval=-1;
+                                 }else{
+                                         errno=0;
+                                         lval=strtol(strb,&endptr,10);
+                                         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+                                         if( strb[0]=='\0' || (*endptr != '\0')){
+                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
+                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
+                                                 return 1;
+                                         }
+                                 }
+                                 if(lval <-1 || lval >1){
+                                         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n                                                                 \
+  build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
+         V1=1 V2=0 for (2) \n                                                                                                                                                                            \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n                                                                                                                                \
+  Exiting.\n",lval,linei, i,line,j);
+                                         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n                                                                 \
+  build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
+         V1=1 V2=0 for (2) \n                                                                                                                                                                            \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n                                                                                                                                \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+                                         return 1;
+                                 }
+                                 cotvar[j][iv][i]=(double)(lval);
+                                 strcpy(line,stra);
+       }/* end loop ntv */
+       /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
-       if(strb[0]=='.') { /* Missing status */
+       if(strb[0]=='.') { /* Missing value */
-         lval=-1;
+                                 lval=-1;
        }else{
-         errno=0;
+                                 errno=0;
-         lval=strtol(strb,&endptr,10);
+                                 lval=strtol(strb,&endptr,10);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+                                 /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-         if( strb[0]=='\0' || (*endptr != '\0')){
+                                 if( strb[0]=='\0' || (*endptr != '\0')){
-           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);
+                                         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);
-           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);
+                                         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);
-           return 1;
+                                         return 1;
-         }
+                                 }
        }
        s[j][i]=lval;
+       /* Date of Interview */
        strcpy(line,stra);
        cutv(stra, strb,line,' ');
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
        }
-       else  if(iout=sscanf(strb,"%s.") != 0){
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
          month=99;
          year=9999;
        }else{
- Line 4646  int readdata(char datafile[], int firsto
+ Line 7923  int readdata(char datafile[], int firsto
        anint[j][i]= (double) year;
        mint[j][i]= (double)month;
        strcpy(line,stra);
-     } /* ENd Waves */
+     } /* End loop on waves */
+     /* Date of death */
      cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
        month=99;
        year=9999;
      }else{
        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);
-         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);
+       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);
-         return 1;
+       return 1;
      }
      andc[i]=(double) year;
      moisdc[i]=(double) month;
      strcpy(line,stra);
+     /* Date of birth */
      cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     else  if(iout=sscanf(strb,"%s.") != 0){
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
        month=99;
        year=9999;
      }else{
        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);
        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);
-         return 1;
+       return 1;
      }
      if (year==9999) {
        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);
        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);
-         return 1;
+       return 1;
      }
      annais[i]=(double)(year);
      moisnais[i]=(double)(month);
      strcpy(line,stra);
+     /* Sample weight */
      cutv(stra, strb,line,' ');
      errno=0;
      dval=strtod(strb,&endptr);
- Line 4696  int readdata(char datafile[], int firsto
+ Line 7976  int readdata(char datafile[], int firsto
      weight[i]=dval;
      strcpy(line,stra);
+     for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing value */
+         lval=-1;
+       }else{
+         errno=0;
+         /* what_kind_of_number(strb); */
+         dval=strtod(strb,&endptr);
+         /* if(strb != endptr && *endptr == '\0') */
+         /*   dval=dlval; */
+         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
+           return 1;
+         }
+         coqvar[iv][i]=dval;
+         covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
+       }
+       strcpy(line,stra);
+     }/* end loop nqv */
+     /* Covariate values */
      for (j=ncovcol;j>=1;j--){
        cutv(stra, strb,line,' ');
-       if(strb[0]=='.') { /* Missing status */
+       if(strb[0]=='.') { /* Missing covariate value */
          lval=-1;
        }else{
          errno=0;
- Line 4713  int readdata(char datafile[], int firsto
+ Line 8016  int readdata(char datafile[], int firsto
          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \n \
+         V1=1 V2=0 for (2) \n                                            \
   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n \
+  output of IMaCh is often meaningless.\n                                \
   Exiting.\n",lval,linei, i,line,j);
          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \n \
+         V1=1 V2=0 for (2) \n                                            \
   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n \
+  output of IMaCh is often meaningless.\n                                \
   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
          return 1;
        }
- Line 4734  int readdata(char datafile[], int firsto
+ Line 8037  int readdata(char datafile[], int firsto
        strcpy(line,stra);
      }
      lstra=strlen(stra);
      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
        stratrunc = &(stra[lstra-9]);
        num[i]=atol(stratrunc);
- Line 4746  int readdata(char datafile[], int firsto
+ Line 8049  int readdata(char datafile[], int firsto
      i=i+1;
    } /* End loop reading  data */
    *imax=i-1; /* Number of individuals */
    fclose(fic);
    return (0);
-   endread:
+   /* endread: */
-     printf("Exiting readdata: ");
+   printf("Exiting readdata: ");
-     fclose(fic);
+   fclose(fic);
-     return (1);
+   return (1);
+ }
+ void removefirstspace(char **stri){/*, char stro[]) {*/
+   char *p1 = *stri, *p2 = *stri;
+   while (*p2 == ' ')
+     p2++;
+   /* while ((*p1++ = *p2++) !=0) */
+   /*   ; */
+   /* do */
+   /*   while (*p2 == ' ') */
+   /*     p2++; */
+   /* while (*p1++ == *p2++); */
+   *stri=p2;
+ }
+ int decoderesult ( char resultline[], int nres)
+ /**< This routine decode one result line and returns the combination # of dummy covariates only **/
+ {
+   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
+   char resultsav[MAXLINE];
+   int resultmodel[MAXLINE];
+   int modelresult[MAXLINE];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   removefirstspace(&resultline);
+   printf("decoderesult:%s\n",resultline);
+   if (strstr(resultline,"v") !=0){
+     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
+     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
+     return 1;
+   }
+   trimbb(resultsav, resultline);
+   if (strlen(resultsav) >1){
+     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
+   }
+   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
+     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+   }
+   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
+     if(nbocc(resultsav,'=') >1){
+        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
+                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
+        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
+     }else
+       cutl(strc,strd,resultsav,'=');
+     Tvalsel[k]=atof(strc); /* 1 */
+     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
+     Tvarsel[k]=atoi(strc);
+     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
+     /* cptcovsel++;     */
+     if (nbocc(stra,'=') >0)
+       strcpy(resultsav,stra); /* and analyzes it */
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     if(Typevar[k1]==0){ /* Single covariate in model */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           match=1;
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+       }
+     }
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+     match=0;
+     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       if(Typevar[k1]==0){ /* Single */
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
+           resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
+           ++match;
+         }
+       }
+     }
+     if(match == 0){
+       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+     }else if(match > 1){
+       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+     }
+   }
+   /* We need to deduce which combination number is chosen and save quantitative values */
+   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
+   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
+   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
+   /*    1 0 0 0 */
+   /*    2 1 0 0 */
+   /*    3 0 1 0 */
+   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
+   /*    5 0 0 1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
+   /*    7 0 1 1 */
+   /*    8 1 1 1 */
+   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
+   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
+   /* V5*age V5 known which value for nres?  */
+   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
+   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
+       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
+       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
+       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
+       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
+       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
+       k4++;;
+     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
+       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
+       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
+       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+       k4q++;;
+     }
+   }
+   TKresult[nres]=++k; /* Combination for the nresult and the model */
+   return (0);
  }
- int decodemodel ( char model[], int lastobs)
+ int decodemodel( char model[], int lastobs)
+  /**< This routine decodes the model and returns:
+         * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
+         * - nagesqr = 1 if age*age in the model, otherwise 0.
+         * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
+         * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+         * - cptcovage number of covariates with age*products =2
+         * - cptcovs number of simple covariates
+         * - 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
+         *     which is a new column after the 9 (ncovcol) variables.
+         * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+         * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+         *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+         */
  {
-   int i, j, k;
+   int i, j, k, ks;
-   int i1, j1, k1, k2;
+   int  j1, k1, k2, k3, k4;
    char modelsav[80];
-    char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char *strpt;
+   /*removespace(model);*/
    if (strlen(model) >1){ /* If there is at least 1 covariate */
-     j=0, j1=0, k1=1, k2=1;
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     j=nbocc(model,'+'); /* j=Number of '+' */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
-     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
-                   but the covariates which are product must be computed and stored. */
-     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
-     strcpy(modelsav,model);
      if (strstr(model,"AGE") !=0){
-       printf("Error. AGE must be in lower case 'age' model=%s ",model);
+       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
-       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
        return 1;
      }
      if (strstr(model,"v") !=0){
- Line 4786  int decodemodel ( char model[], int last
+ Line 8226  int decodemodel ( char model[], int last
        fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
        return 1;
      }
+     strcpy(modelsav,model);
-     /* This loop fills the array Tvar from the string 'model'.*/
+     if ((strpt=strstr(model,"age*age")) !=0){
-     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       printf(" strpt=%s, model=%s\n",strpt, model);
-     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+       if(strpt != model){
-     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+  corresponding column of parameters.\n",model);
-     /*  k=1 Tvar[1]=2 (from V2) */
+         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-     /*  k=5 Tvar[5] */
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-     /* for (k=1; k<=cptcovn;k++) { */
+  corresponding column of parameters.\n",model); fflush(ficlog);
-     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+         return 1;
-     /*  } */
+       }
-     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+       nagesqr=1;
-     for(k=cptcovn; k>=1;k--){
+       if (strstr(model,"+age*age") !=0)
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+         substrchaine(modelsav, model, "+age*age");
-                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
+       else if (strstr(model,"age*age+") !=0)
-                                     */
+         substrchaine(modelsav, model, "age*age+");
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       else
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         substrchaine(modelsav, model, "age*age");
-       /*scanf("%d",i);*/
+     }else
-       if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
+       nagesqr=0;
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+     if (strlen(modelsav) >1){
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
-           cptcovprod--;
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-           cutv(strb,stre,strd,'V'); /* stre="V3" */
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
-           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
+       cptcovt= j+1; /* Number of total covariates in the model, not including
-           cptcovage++; /* Sums the number of covariates which include age as a product */
+                      * cst, age and age*age
-           Tage[cptcovage]=k;  /* Tage[1] = 4 */
+                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
-           /*printf("stre=%s ", stre);*/
+       /* including age products which are counted in cptcovage.
-         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+        * but the covariates which are products must be treated
-           cptcovprod--;
+        * separately: ncovn=4- 2=2 (V1+V3). */
-           cutv(strb,stre,strc,'V');
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-           Tvar[k]=atoi(stre);
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-           cptcovage++;
-           Tage[cptcovage]=k;
-         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+       /*   Design
-           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+        *  <          ncovcol=8                >
-           Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-                                   because this model-covariate is a construction we invent a new column
+        *   k=  1    2      3       4     5       6      7        8
-                                   ncovcol + k1
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+        *  covar[k,i], value of kth covariate if not including age for individual i:
-                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
-           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-           Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
+        *  Tage[++cptcovage]=k
-           Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
+        *       if products, new covar are created after ncovcol with k1
-           Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-           for (i=1; i<=lastobs;i++){
+        *  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
-             /* Computes the new covariate which is a product of
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-                covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-           }
+        *  <          ncovcol=8                >
-           k1++;
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-           k2=k2+2;
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-         } /* End age is not in the model */
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-       } /* End if model includes a product */
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-       else { /* no more sum */
+        * p Tprod[1]@2={                         6, 5}
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
-        /*  scanf("%d",i);*/
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-         cutv(strd,strc,strb,'V');
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         Tvar[k]=atoi(strc);
+        *How to reorganize?
-       }
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
-         scanf("%d",i);*/
+        * Struct []
-     } /* end of loop + */
+        */
-   } /* end model */
+       /* This loop fills the array Tvar from the string 'model'.*/
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
+       /*        k=1 Tvar[1]=2 (from V2) */
+       /*        k=5 Tvar[5] */
+       /* for (k=1; k<=cptcovn;k++) { */
+       /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       /*        } */
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
+       /*
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
+         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
+       }
+       cptcovage=0;
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*scanf("%d",i);*/
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+             /* covar is not filled and then is empty */
+             cptcovprod--;
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             Typevar[k]=1;  /* 1 for age product */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+             /*printf("stre=%s ", stre);*/
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+             cptcovprod--;
+             cutl(stre,strb,strc,'V');
+             Tvar[k]=atoi(stre);
+             Typevar[k]=1;  /* 1 for age product */
+             cptcovage++;
+             Tage[cptcovage]=k;
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             cptcovn++;
+             cptcovprodnoage++;k1++;
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
+                                                 because this model-covariate is a construction we invent a new column
+                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1
+                                                 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+             Typevar[k]=2;  /* 2 for double fixed dummy covariates */
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
+             /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
+             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
+             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
+             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
+             for (i=1; i<=lastobs;i++){
+               /* Computes the new covariate which is a product of
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+             }
+           } /* End age is not in the model */
+         } /* End if model includes a product */
+         else { /* no more sum */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*  scanf("%d",i);*/
+           cutl(strd,strc,strb,'V');
+           ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
+           cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
+           Tvar[k]=atoi(strd);
+           Typevar[k]=0;  /* 0 for simple covariates */
+         }
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+                                 /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+                                   scanf("%d",i);*/
+       } /* end of loop + on total covariates */
+     } /* end if strlen(modelsave == 0) age*age might exist */
+   } /* end if strlen(model == 0) */
    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   printf("cptcovprod=%d ", cptcovprod);
+      printf("cptcovprod=%d ", cptcovprod);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      scanf("%d ",i);*/
-   scanf("%d ",i);*/
+ /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
+    of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
+ /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
+    model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
+    k =           1    2   3     4       5       6      7      8        9
+    Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
+    Typevar[k]=   0    0   0     2       1       0      2      1        1
+    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
+    Dummy[k]      1    0   0     0       3       1      1      2        3
+           Tmodelind[combination of covar]=k;
+ */
+ /* Dispatching between quantitative and time varying covariates */
+   /* If Tvar[k] >ncovcol it is a product */
+   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
+         /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
+   printf("Model=%s\n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
+ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   fprintf(ficlog,"Model=%s\n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
+ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       nsd++;
+       modell[k].maintype= FTYPE;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       modell[k].maintype= FTYPE;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */
+       Fixed[k]= 0;
+       Dummy[k]= 1;
+       nqfveff++;
+       modell[k].maintype= FTYPE;
+       modell[k].subtype= FQ;
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       ncovf++;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */
+       Fixed[k]= 1;
+       Dummy[k]= 0;
+       ntveff++; /* Only simple time varying dummy variable */
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VD;
+       nsd++;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       ncovv++; /* Only simple time varying variables */
+       TvarV[ncovv]=Tvar[k];
+       TvarVind[ncovv]=k;
+       TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
+       TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
+       printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
+       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
+     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
+       Fixed[k]= 1;
+       Dummy[k]= 1;
+       nqtveff++;
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VQ;
+       ncovv++; /* Only simple time varying variables */
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       TvarV[ncovv]=Tvar[k];
+       TvarVind[ncovv]=k;
+       TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
+       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
+       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
+       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
+     }else if (Typevar[k] == 1) {  /* product with age */
+       ncova++;
+       TvarA[ncova]=Tvar[k];
+       TvarAind[ncova]=k;
+       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
+         Fixed[k]= 2;
+         Dummy[k]= 2;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APFD;
+         /* ncoveff++; */
+       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
+         Fixed[k]= 2;
+         Dummy[k]= 3;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
+         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
+       }else if( Tvar[k] <=ncovcol+nqv+ntv ){
+         Fixed[k]= 3;
+         Dummy[k]= 2;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APVD;                /*      Product age * varying dummy */
+         /* ntveff++; /\* Only simple time varying dummy variable *\/ */
+       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
+         Fixed[k]= 3;
+         Dummy[k]= 3;
+         modell[k].maintype= ATYPE;
+         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
+         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
+       }
+     }else if (Typevar[k] == 2) {  /* product without age */
+       k1=Tposprod[k];
+       if(Tvard[k1][1] <=ncovcol){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
+           ncovf++; /* Fixed variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 1;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
+           ncovf++; /* Varying variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 1;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
+           ncovf++; /* Fixed variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else{
+         printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+         fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+       } /* end k1 */
+     }else{
+       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
+       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
+     }
+     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
+     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+   }
+   /* Searching for doublons in the model */
+   for(k1=1; k1<= cptcovt;k1++){
+     for(k2=1; k2 <k1;k2++){
+       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
+         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
+           if(Tvar[k1]==Tvar[k2]){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             return(1);
+           }
+         }else if (Typevar[k1] ==2){
+           k3=Tposprod[k1];
+           k4=Tposprod[k2];
+           if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             return(1);
+           }
+         }
+       }
+     }
+   }
+   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
+   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
    return (0); /* with covar[new additional covariate if product] and Tage if age */
-   endread:
+   /*endread:*/
-     printf("Exiting decodemodel: ");
+   printf("Exiting decodemodel: ");
-     return (1);
+   return (1);
  }
- calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
  {
    int i, m;
+   int firstone=0;
    for (i=1; i<=imx; i++) {
      for(m=2; (m<= maxwav); m++) {
        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;
-         s[m][i]=-1;
+         if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
+           s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         *nberr++;
+         *nberr = *nberr + 1;
-         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);
+         if(firstone == 0){
-         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);
+           firstone=1;
+         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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         }
+         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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         *nberr++;
+         (*nberr)++;
          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]);
          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]);
          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
- Line 4900  calandcheckages(int imx, int maxwav, dou
+ Line 8725  calandcheckages(int imx, int maxwav, dou
    for (i=1; i<=imx; i++)  {
      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
      for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+       if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
          if (s[m][i] >= nlstate+1) {
-           if(agedc[i]>0)
+           if(agedc[i]>0){
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                agev[m][i]=agedc[i];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+               /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
+             }else {
                if ((int)andc[i]!=9999){
                  nbwarn++;
                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- Line 4914  calandcheckages(int imx, int maxwav, dou
+ Line 8739  calandcheckages(int imx, int maxwav, dou
                  agev[m][i]=-1;
                }
              }
-         }
+           } /* agedc > 0 */
+         } /* end if */
          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                   years but with the precision of a month */
            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
- Line 4926  calandcheckages(int imx, int maxwav, dou
+ Line 8752  calandcheckages(int imx, int maxwav, dou
            }
            else if(agev[m][i] >*agemax){
              *agemax=agev[m][i];
-             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
            }
            /*agev[m][i]=anint[m][i]-annais[i];*/
            /*     agev[m][i] = age[i]+2*m;*/
-         }
+         } /* en if 9*/
          else { /* =9 */
+           /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
            agev[m][i]=1;
            s[m][i]=-1;
          }
        }
-       else /*= 0 Unknown */
+       else if(s[m][i]==0) /*= 0 Unknown */
          agev[m][i]=1;
-     }
+       else{
+         printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         agev[m][i]=0;
+       }
+     } /* End for lastpass */
    }
    for (i=1; i<=imx; i++)  {
      for(m=firstpass; (m<=lastpass); m++){
        if (s[m][i] > (nlstate+ndeath)) {
-         *nberr++;
+         (*nberr)++;
          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);
          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);
          return 1;
- Line 4964  calandcheckages(int imx, int maxwav, dou
+ Line 8796  calandcheckages(int imx, int maxwav, dou
    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
    return (0);
-   endread:
+  /* endread:*/
      printf("Exiting calandcheckages: ");
      return (1);
  }
+ #if defined(_MSC_VER)
+ /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+ /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+ //#include "stdafx.h"
+ //#include <stdio.h>
+ //#include <tchar.h>
+ //#include <windows.h>
+ //#include <iostream>
+ typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
+ LPFN_ISWOW64PROCESS fnIsWow64Process;
+ BOOL IsWow64()
+ {
+         BOOL bIsWow64 = FALSE;
+         //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
+         //  (HANDLE, PBOOL);
+         //LPFN_ISWOW64PROCESS fnIsWow64Process;
+         HMODULE module = GetModuleHandle(_T("kernel32"));
+         const char funcName[] = "IsWow64Process";
+         fnIsWow64Process = (LPFN_ISWOW64PROCESS)
+                 GetProcAddress(module, funcName);
+         if (NULL != fnIsWow64Process)
+         {
+                 if (!fnIsWow64Process(GetCurrentProcess(),
+                         &bIsWow64))
+                         //throw std::exception("Unknown error");
+                         printf("Unknown error\n");
+         }
+         return bIsWow64 != FALSE;
+ }
+ #endif
+ void syscompilerinfo(int logged)
+  {
+    /* #include "syscompilerinfo.h"*/
+    /* command line Intel compiler 32bit windows, XP compatible:*/
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
+    /* 64 bits */
+    /*
+      /GS /W3 /Gy
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
+    /* Optimization are useless and O3 is slower than O2 */
+    /*
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
+    */
+    /* Link is */ /* /OUT:"visual studio
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
+       /PDB:"visual studio
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
+       /NOLOGO /TLBID:1
+    */
+ #if defined __INTEL_COMPILER
+ #if defined(__GNUC__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
+ #endif
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+    struct utsname sysInfo;
+    int cross = CROSS;
+    if (cross){
+            printf("Cross-");
+            if(logged) fprintf(ficlog, "Cross-");
+    }
+ #endif
+ #include <stdint.h>
+    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
+ #if defined(__clang__)
+    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
+    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+ #endif
+ #if defined(__HP_cc) || defined(__HP_aCC)
+    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+ #endif
+ #if defined(__IBMC__) || defined(__IBMCPP__)
+    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+ #endif
+ #if defined(_MSC_VER)
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
+ #if defined(__PGI)
+    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+ #endif
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
+    printf(" for "); if (logged) fprintf(ficlog, " for ");
+ // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
+ #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
+     // Windows (x64 and x86)
+    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
+ #elif __unix__ // all unices, not all compilers
+     // Unix
+    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
+ #elif __linux__
+     // linux
+    printf("linux ");if(logged) fprintf(ficlog,"linux ");
+ #elif __APPLE__
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
+    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
+ #endif
+ /*  __MINGW32__   */
+ /*  __CYGWIN__   */
+ /* __MINGW64__  */
+ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
+ /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
+ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
+ /* _WIN64  // Defined for applications for Win64. */
+ /* _M_X64 // Defined for compilations that target x64 processors. */
+ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
+ #if UINTPTR_MAX == 0xffffffff
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
+ #elif UINTPTR_MAX == 0xffffffffffffffff
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
+ #endif
+ #if defined(__GNUC__)
+ # if defined(__GNUC_PATCHLEVEL__)
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
+ # else
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100)
+ # endif
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
+    if (uname(&sysInfo) != -1) {
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+    //#ifndef __INTEL_COMPILER
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
+ #endif
+    //   void main()
+    //   {
+ #if defined(_MSC_VER)
+    if (IsWow64()){
+            printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+            if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
+    else{
+            printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+            if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+    }
+    //      printf("\nPress Enter to continue...");
+    //      getchar();
+    //   }
+ #endif
+ }
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   int i, j, k, i1, k4=0, nres=0 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   strcpy(filerespl,"PL_");
+   strcat(filerespl,fileresu);
+   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+   }
+   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   pstamp(ficrespl);
+   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   fprintf(ficrespl,"\n");
+   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+   agebase=ageminpar;
+   agelim=agemaxpar;
+   /* i1=pow(2,ncoveff); */
+   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+   if (cptcovn < 1){i1=1;}
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(k=1; k<=i1;k++){
+     if(TKresult[nres]!= k)
+       continue;
+   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     /* k=k+1; */
+     /* to clean */
+     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+     fprintf(ficrespl,"#******");
+     printf("#******");
+     fprintf(ficlog,"#******");
+     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     }
+     fprintf(ficrespl,"******\n");
+     printf("******\n");
+     fprintf(ficlog,"******\n");
+     if(invalidvarcomb[k]){
+       printf("\nCombination (%d) ignored because no case \n",k);
+       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+                                                 continue;
+     }
+     fprintf(ficrespl,"#Age ");
+     for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     }
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+     fprintf(ficrespl,"Total Years_to_converge\n");
+     for (age=agebase; age<=agelim; age++){
+       /* for (age=agebase; age<=agebase; age++){ */
+       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
+       fprintf(ficrespl,"%.0f ",age );
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       tot=0.;
+       for(i=1; i<=nlstate;i++){
+         tot +=  prlim[i][i];
+         fprintf(ficrespl," %.5f", prlim[i][i]);
+       }
+       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+     } /* Age */
+     /* was end of cptcod */
+   } /* cptcov */
+   return 0;
+ }
+ int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
+         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+         /* Computes the back prevalence limit  for any combination      of covariate values
+    * at any age between ageminpar and agemaxpar
+          */
+   int i, j, k, i1, nres=0 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   /* double ***mobaverage; */
+   /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
+   strcpy(fileresplb,"PLB_");
+   strcat(fileresplb,fileresu);
+   if((ficresplb=fopen(fileresplb,"w"))==NULL) {
+     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+   }
+   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   pstamp(ficresplb);
+   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficresplb,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
+   fprintf(ficresplb,"\n");
+   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+   agebase=ageminpar;
+   agelim=agemaxpar;
+   i1=pow(2,cptcoveff);
+   if (cptcovn < 1){i1=1;}
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+     if(TKresult[nres]!= k)
+       continue;
+     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+     fprintf(ficresplb,"#******");
+     printf("#******");
+     fprintf(ficlog,"#******");
+     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     }
+     for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+       printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+     }
+     fprintf(ficresplb,"******\n");
+     printf("******\n");
+     fprintf(ficlog,"******\n");
+     if(invalidvarcomb[k]){
+       printf("\nCombination (%d) ignored because no cases \n",k);
+       fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+       continue;
+     }
+     fprintf(ficresplb,"#Age ");
+     for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     }
+     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+     fprintf(ficresplb,"Total Years_to_converge\n");
+     for (age=agebase; age<=agelim; age++){
+       /* for (age=agebase; age<=agebase; age++){ */
+       if(mobilavproj > 0){
+         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
+         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+         bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
+       }else if (mobilavproj == 0){
+         printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+         fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+         exit(1);
+       }else{
+         /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+         bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
+       }
+       fprintf(ficresplb,"%.0f ",age );
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       tot=0.;
+       for(i=1; i<=nlstate;i++){
+         tot +=  bprlim[i][i];
+         fprintf(ficresplb," %.5f", bprlim[i][i]);
+       }
+       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+     } /* Age */
+     /* was end of cptcod */
+   } /* cptcov */
+   /* hBijx(p, bage, fage); */
+   /* fclose(ficrespijb); */
+   return 0;
+ }
+ int hPijx(double *p, int bage, int fage){
+     /*------------- h Pij x at various ages ------------*/
+   int stepsize;
+   int agelim;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k, k4, nres=0;
+   double agedeb;
+   double ***p3mat;
+     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* hstepm=1;   aff par mois*/
+     pstamp(ficrespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     i1= pow(2,cptcoveff);
+                 /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+                 /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+                 /*      k=k+1;  */
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(TKresult[nres]!= k)
+         continue;
+       fprintf(ficrespij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficrespij,"******\n");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+           for(i=1; i<=nlstate;i++)
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespij,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespij,"\n");
+       }
+       /*}*/
+     }
+     return 0;
+ }
+  int hBijx(double *p, int bage, int fage, double ***prevacurrent){
+     /*------------- h Bij x at various ages ------------*/
+   int stepsize;
+   /* int agelim; */
+         int ageminl;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k;
+   double agedeb;
+   double ***p3mat;
+   strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
+   if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
+     printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+     fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+   }
+   printf("Computing pij back: result on file '%s' \n", filerespijb);
+   fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   /*if (stepm<=24) stepsize=2;*/
+   /* agelim=AGESUP; */
+   ageminl=30;
+   hstepm=stepsize*YEARM; /* Every year of age */
+   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+   /* hstepm=1;   aff par mois*/
+   pstamp(ficrespijb);
+   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
+   i1= pow(2,cptcoveff);
+   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+   /*    k=k+1;  */
+   for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     fprintf(ficrespijb,"\n#****** ");
+     for(j=1;j<=cptcoveff;j++)
+       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     fprintf(ficrespijb,"******\n");
+     if(invalidvarcomb[k]){
+       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+       continue;
+     }
+     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+       /*          nhstepm=nhstepm*YEARM; aff par mois*/
+       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* oldm=oldms;savm=savms; */
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
+       for(i=1; i<=nlstate;i++)
+         for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficrespijb," %1d-%1d",i,j);
+       fprintf(ficrespijb,"\n");
+       for (h=0; h<=nhstepm; h++){
+         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
+         fprintf(ficrespijb,"\n");
+       }
+       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficrespijb,"\n");
+     }
+     /*}*/
+   }
+   return 0;
+  } /*  hBijx */
  /***********************************************/
  /**************** Main Program *****************/
- Line 4984  int main(int argc, char *argv[])
+ Line 9365  int main(int argc, char *argv[])
    double ssval;
  #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-   int linei, month, year,iout;
+   int ncvyear=0; /* Number of years needed for the period prevalence to converge */
-   int jj, ll, li, lj, lk, imk;
+   int jj, ll, li, lj, lk;
    int numlinepar=0; /* Current linenumber of parameter file */
+   int num_filled;
    int itimes;
    int NDIM=2;
    int vpopbased=0;
+   int nres=0;
-   char ca[32], cb[32], cc[32];
+   char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
    struct stat info;
-   double agedeb, agefin,hf;
+   double agedeb=0.;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-   double fret;
+   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
-   double **xi,tmp,delta;
+   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
-   double dum; /* Dummy variable */
+   double fret;
+   double dum=0.; /* Dummy variable */
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
-   int *indx;
-   char line[MAXLINE], linepar[MAXLINE];
+   char line[MAXLINE];
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+   char  modeltemp[MAXLINE];
+   char resultline[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
-   char **bp, *tok, *val; /* pathtot */
+   char *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
+   int c,  h , cpt, c2;
-   int c,  h , cpt,l;
+   int jl=0;
-   int ju,jl, mi;
+   int i1, j1, jk, stepsize=0;
-   int i1,j1, jk,aa,bb, stepsize, ij;
+   int count=0;
-   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
+   int *tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   int backcast=0;
    int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
+   int hstepm=0, nhstepm=0;
    int agemortsup;
    float  sumlpop=0.;
    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-   double bage, fage, age, agelim, agebase;
+   double bage=0, fage=110., age, agelim=0., agebase=0.;
    double ftolpl=FTOL;
    double **prlim;
+   double **bprlim;
    double ***param; /* Matrix of parameters */
    double  *p;
    double **matcov; /* Matrix of covariance */
+   double **hess; /* Hessian matrix */
    double ***delti3; /* Scale */
    double *delti; /* Scale */
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   double kk1, kk2;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
    double **ximort;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
    int *dcwave;
-   char z[1]="c", occ;
+   char z[1]="c";
    /*char  *strt;*/
    char strtend[80];
-   long total_usecs;
  /*   setlocale (LC_ALL, ""); */
  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
  /*   textdomain (PACKAGE); */
- Line 5055  int main(int argc, char *argv[])
+ Line 9447  int main(int argc, char *argv[])
  /*   setlocale (LC_MESSAGES, ""); */
    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-   (void) gettimeofday(&start_time,&tzp);
+   rstart_time = time(NULL);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
    curr_time=start_time;
-   tm = *localtime(&start_time.tv_sec);
+   /*tml = *localtime(&start_time.tm_sec);*/
-   tmg = *gmtime(&start_time.tv_sec);
+   /* strcpy(strstart,asctime(&tml)); */
-   strcpy(strstart,asctime(&tm));
+   strcpy(strstart,asctime(&start_time));
  /*  printf("Localtime (at start)=%s",strstart); */
- /*  tp.tv_sec = tp.tv_sec +86400; */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
- /*  tm = *localtime(&start_time.tv_sec); */
+ /*  tm = *localtime(&start_time.tm_sec); */
  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
  /*   tmg.tm_hour=tmg.tm_hour + 1; */
- /*   tp.tv_sec = mktime(&tmg); */
+ /*   tp.tm_sec = mktime(&tmg); */
  /*   strt=asctime(&tmg); */
  /*   printf("Time(after) =%s",strstart);  */
  /*  (void) time (&time_value);
- Line 5079  int main(int argc, char *argv[])
+ Line 9473  int main(int argc, char *argv[])
    nberr=0; /* Number of errors and warnings */
    nbwarn=0;
+ #ifdef WIN32
+   _getcwd(pathcd, size);
+ #else
    getcwd(pathcd, size);
+ #endif
-   printf("\n%s\n%s",version,fullversion);
+   syscompilerinfo(0);
+   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+     if(!fgets(pathr,FILENAMELENGTH,stdin)){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
      i=strlen(pathr);
      if(pathr[i-1]=='\n')
        pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+     i=strlen(pathr);
+     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
+     }
+     i=strlen(pathr);
+     if( i==0 ){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     for (tok = pathr; tok != NULL; ){
        printf("Pathr |%s|\n",pathr);
        while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
        printf("val= |%s| pathr=%s\n",val,pathr);
- Line 5112  int main(int argc, char *argv[])
+ Line 9522  int main(int argc, char *argv[])
    /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
    printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ #ifdef WIN32
+   _chdir(path); /* Can be a relative path */
+   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ #else
    chdir(path); /* Can be a relative path */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
-     printf("Current directory %s!\n",pathcd);
+ #endif
+   printf("Current directory %s!\n",pathcd);
    strcpy(command,"mkdir ");
    strcat(command,optionfilefiname);
    if((outcmd=system(command)) != 0){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
      /* fclose(ficlog); */
  /*     exit(1); */
- Line 5129  int main(int argc, char *argv[])
+ Line 9544  int main(int argc, char *argv[])
    /*-------- arguments in the command line --------*/
-   /* Log file */
+   /* Main Log file */
    strcat(filelog, optionfilefiname);
    strcat(filelog,".log");    /* */
    if((ficlog=fopen(filelog,"w"))==NULL)    {
- Line 5137  int main(int argc, char *argv[])
+ Line 9552  int main(int argc, char *argv[])
      goto end;
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   fprintf(ficlog,"Version %s %s",version,fullversion);
    fprintf(ficlog,"\nEnter the parameter file name: \n");
    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
   path=%s \n\
   optionfile=%s\n\
   optionfilext=%s\n\
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   syscompilerinfo(1);
    printf("Local time (at start):%s",strstart);
    fprintf(ficlog,"Local time (at start): %s",strstart);
    fflush(ficlog);
  /*   (void) gettimeofday(&curr_time,&tzp); */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
    /* */
    strcpy(fileres,"r");
    strcat(fileres, optionfilefiname);
+   strcat(fileresu, optionfilefiname); /* Without r in front */
    strcat(fileres,".txt");    /* Other files have txt extension */
+   strcat(fileresu,".txt");    /* Other files have txt extension */
-   /*---------arguments file --------*/
+   /* Main ---------arguments file --------*/
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     printf("Problem with optionfile %s\n",optionfile);
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
      fflush(ficlog);
-     goto end;
+     /* goto end; */
+     exit(70);
    }
    strcpy(filereso,"o");
-   strcat(filereso,fileres);
+   strcat(filereso,fileresu);
    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
      printf("Problem with Output resultfile: %s\n", filereso);
      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
- Line 5178  int main(int argc, char *argv[])
+ Line 9598  int main(int argc, char *argv[])
    /* Reads comments: lines beginning with '#' */
    numlinepar=0;
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+     /* First parameter line */
-     fgets(line, MAXLINE, ficpar);
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+     if (num_filled != 5) {
+       printf("Should be 5 parameters\n");
+     }
      numlinepar++;
-     fputs(line,stdout);
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
    }
-   ungetc(c,ficpar);
+   /* Second parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
-   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);
+     /* If line starts with a # it is a comment */
-   numlinepar++;
+     if (line[0] == '#') {
-   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);
+       numlinepar++;
-   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);
+       fputs(line,stdout);
-   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);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+                         &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+     if (num_filled != 11) {
+       printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       printf("but line=%s\n",line);
+     }
+     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+   }
+   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+   /* Third parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+     if (num_filled == 0)
+             model[0]='\0';
+     else if (num_filled != 1){
+       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       model[0]='\0';
+       goto end;
+     }
+     else{
+       if (model[0]=='+'){
+         for(i=1; i<=strlen(model);i++)
+           modeltemp[i-1]=model[i];
+         strcpy(model,modeltemp);
+       }
+     }
+     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+     printf("model=1+age+%s\n",model);fflush(stdout);
+   }
+   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+   /* numlinepar=numlinepar+3; /\* In general *\/ */
+   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
    fflush(ficlog);
+   /* if(model[0]=='#'|| model[0]== '\0'){ */
+   if(model[0]=='#'){
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
+     if(mle != -1){
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+       exit(1);
+     }
+   }
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
+     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+       z[0]=line[1];
+     }
+     /* printf("****line [1] = %c \n",line[1]); */
      fputs(line, stdout);
      //puts(line);
      fputs(line,ficparo);
- Line 5206  int main(int argc, char *argv[])
+ Line 9704  int main(int argc, char *argv[])
    ungetc(c,ficpar);
-   covar=matrix(0,NCOVMAX,1,n);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
+   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
+   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
       v1+v2*age+v2*v3 makes cptcovn = 3
    */
    if (strlen(model)>1)
-     cptcovn=nbocc(model,'+')+1;
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
-   /* ncovprod */
+   else
-   ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+     ncovmodel=2; /* Constant and age */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
    npar= nforce*ncovmodel; /* Number of parameters like aij*/
    if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
- Line 5230  int main(int argc, char *argv[])
+ Line 9730  int main(int argc, char *argv[])
    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
      goto end;
      exit(0);
-   }
+   }  else if(mle==-5) { /* Main Wizard */
-   else if(mle==-3) {
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      matcov=matrix(1,npar,1,npar);
-   }
+     hess=matrix(1,npar,1,npar);
-   else{
+   }  else{ /* Begin of mle != -1 or -5 */
-     /* Read guess parameters */
+     /* Read guessed parameters */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
- Line 5265  int main(int argc, char *argv[])
+ Line 9764  int main(int argc, char *argv[])
          if(jj==i) continue;
          j++;
          fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1 != i) && (j1 != j)){
+         if ((i1 != i) || (j1 != jj)){
            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
  It might be a problem of design; if ncovcol and the model are correct\n \
  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
- Line 5273  run imach with mle=-1 to get a correct t
+ Line 9772  run imach with mle=-1 to get a correct t
          }
          fprintf(ficparo,"%1d%1d",i1,j1);
          if(mle==1)
-           printf("%1d%1d",i,j);
+           printf("%1d%1d",i,jj);
-         fprintf(ficlog,"%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,jj);
          for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar," %lf",&param[i][j][k]);
            if(mle==1){
- Line 5294  run imach with mle=-1 to get a correct t
+ Line 9793  run imach with mle=-1 to get a correct t
        }
      }
      fflush(ficlog);
+     /* Reads scales values */
      p=param[1][1];
      /* Reads comments: lines beginning with '#' */
- Line 5311  run imach with mle=-1 to get a correct t
+ Line 9811  run imach with mle=-1 to get a correct t
      for(i=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath-1; j++){
          fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1-i)*(j1-j)!=0){
+         if ( (i1-i) * (j1-j) != 0){
            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
            exit(1);
          }
- Line 5332  run imach with mle=-1 to get a correct t
+ Line 9832  run imach with mle=-1 to get a correct t
        }
      }
      fflush(ficlog);
+     /* Reads covariance matrix */
      delti=delti3[1][1];
      /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
- Line 5348  run imach with mle=-1 to get a correct t
+ Line 9849  run imach with mle=-1 to get a correct t
        fputs(line,ficlog);
      }
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
+     hess=matrix(1,npar,1,npar);
      for(i=1; i <=npar; i++)
        for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     /* Scans npar lines */
      for(i=1; i <=npar; i++){
-       fscanf(ficpar,"%s",&str);
+       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
-       if(mle==1)
+       if(count != 3){
-         printf("%s",str);
+         printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
-       fprintf(ficlog,"%s",str);
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
-       fprintf(ficparo,"%s",str);
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         exit(1);
+       }else{
+         if(mle==1)
+           printf("%1d%1d%d",i1,j1,jk);
+       }
+       fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
        for(j=1; j <=i; j++){
          fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
- Line 5370  run imach with mle=-1 to get a correct t
+ Line 9883  run imach with mle=-1 to get a correct t
        fscanf(ficpar,"\n");
        numlinepar++;
        if(mle==1)
-         printf("\n");
+                                 printf("\n");
        fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
+     /* End of read covariance matrix npar lines */
      for(i=1; i <=npar; i++)
        for(j=i+1;j<=npar;j++)
          matcov[i][j]=matcov[j][i];
- Line 5390  run imach with mle=-1 to get a correct t
+ Line 9904  run imach with mle=-1 to get a correct t
      strcat(rfileres,".");    /* */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */
      if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
      }
      fprintf(ficres,"#%s\n",version);
    }    /* End of mle != -3 */
+   /*  Main data
+    */
    n= lastobs;
    num=lvector(1,n);
    moisnais=vector(1,n);
    annais=vector(1,n);
    moisdc=vector(1,n);
    andc=vector(1,n);
+   weight=vector(1,n);
    agedc=vector(1,n);
    cod=ivector(1,n);
-   weight=vector(1,n);
+   for(i=1;i<=n;i++){
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+     num[i]=0;
+     moisnais[i]=0;
+     annais[i]=0;
+     moisdc[i]=0;
+     andc[i]=0;
+     agedc[i]=0;
+     cod[i]=0;
+     weight[i]=1.0; /* Equal weights, 1 by default */
+   }
    mint=matrix(1,maxwav,1,n);
    anint=matrix(1,maxwav,1,n);
    s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
    tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8); /* hard coded ? */
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
    /* Reads data from file datafile */
    if (readdata(datafile, firstobs, lastobs, &imx)==1)
      goto end;
    /* Calculation of the number of parameters from char model */
-     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+   /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
          k=3 V4 Tvar[k=3]= 4 (from V4)
          k=2 V1 Tvar[k=2]= 1 (from V1)
          k=1 Tvar[1]=2 (from V2)
-     */
+   */
    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   TvarsDind=ivector(1,NCOVMAX); /*  */
+   TvarsD=ivector(1,NCOVMAX); /*  */
+   TvarsQind=ivector(1,NCOVMAX); /*  */
+   TvarsQ=ivector(1,NCOVMAX); /*  */
+   TvarF=ivector(1,NCOVMAX); /*  */
+   TvarFind=ivector(1,NCOVMAX); /*  */
+   TvarV=ivector(1,NCOVMAX); /*  */
+   TvarVind=ivector(1,NCOVMAX); /*  */
+   TvarA=ivector(1,NCOVMAX); /*  */
+   TvarAind=ivector(1,NCOVMAX); /*  */
+   TvarFD=ivector(1,NCOVMAX); /*  */
+   TvarFDind=ivector(1,NCOVMAX); /*  */
+   TvarFQ=ivector(1,NCOVMAX); /*  */
+   TvarFQind=ivector(1,NCOVMAX); /*  */
+   TvarVD=ivector(1,NCOVMAX); /*  */
+   TvarVDind=ivector(1,NCOVMAX); /*  */
+   TvarVQ=ivector(1,NCOVMAX); /*  */
+   TvarVQind=ivector(1,NCOVMAX); /*  */
+   Tvalsel=vector(1,NCOVMAX); /*  */
+   Tvarsel=ivector(1,NCOVMAX); /*  */
+   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
+   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
+   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
    /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
        For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
- Line 5434  run imach with mle=-1 to get a correct t
+ Line 9984  run imach with mle=-1 to get a correct t
      ncovcol + k1
      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
      Tvar[3=V1*V4]=4+1 etc */
-   Tprod=ivector(1,15); /* Gives the position of a product */
+   Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
+   Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
    /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
       if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
    */
-   Tvaraff=ivector(1,15);
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-   Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+   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
                              * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
                              * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-   Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
 covariates (3 plus signs)
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                        */
+   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual dummy, fixed or varying:
+                                 * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
+                                 * V1 df, V2 qf, V3 & V4 dv, V5 qv
+                                 * Tmodelind[1]@9={9,0,3,2,}*/
+   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
+   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual quantitative, fixed or varying:
+                                 * Tmodelqind[1]=1,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ /* Main decodemodel */
-   if(decodemodel(model, lastobs) == 1)
+   if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
      goto end;
    if((double)(lastobs-imx)/(double)imx > 1.10){
- Line 5472  run imach with mle=-1 to get a correct t
+ Line 10039  run imach with mle=-1 to get a correct t
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
-   free_vector(moisdc,1,n);
+   /* free_vector(moisdc,1,n); */
-   free_vector(andc,1,n);
+   /* free_vector(andc,1,n); */
+   /* */
    wav=ivector(1,imx);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
+   bh=imatrix(1,lastpass-firstpass+2,1,imx);
+   mw=imatrix(1,lastpass-firstpass+2,1,imx);
    /* Concatenates waves */
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+      Death is a valid wave (if date is known).
+      mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+      and mw[mi+1][i]. dh depends on stepm.
+   */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   Ndum =ivector(-1,NCOVMAX);
+   cptcoveff=0;
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
-                                  the estimations*/
+     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-   h=0;
+   }
-   m=pow(2,cptcoveff);
+   ncovcombmax=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
+   invalidvarcomb=ivector(1, ncovcombmax);
-     for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
+   for(i=1;i<ncovcombmax;i++)
-       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
+     invalidvarcomb[i]=0;
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-           h++;
+   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
-           if (h>m)
+      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
-             h=1;
+   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
-           codtab[h][k]=j;
-           codtab[h][Tvar[k]]=j;
+   /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-           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]]);
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
-         }
+   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
-       }
+   /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
-     }
+    * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
-   }
+    * (currently 0 or 1) in the data.
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+    * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
-      codtab[1][2]=1;codtab[2][2]=2; */
+    * corresponding modality (h,j).
-   /* for(i=1; i <=m ;i++){
+    */
-      for(k=1; k <=cptcovn; k++){
-        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+   h=0;
-      }
+   /*if (cptcovn > 0) */
-      printf("\n");
+   m=pow(2,cptcoveff);
-      }
-      scanf("%d",i);*/
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            * For k=4 covariates, h goes from 1 to m=2**k
+            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
+            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+            *     h\k   1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     2
+            *    10     2     1     1     2
+            *    11 i=6 1     2     1     2
+            *    12     2     2     1     2
+            *    13 i=7 1 i=4 1     2     2
+            *    14     2     1     2     2
+            *    15 i=8 1     2     2     2
+            *    16     2     2     2     2
+            */
+   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
+      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
+      * and the value of each covariate?
+      * V1=1, V2=1, V3=2, V4=1 ?
+      * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
+      * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
+      * In order to get the real value in the data, we use nbcode
+      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
+      * We are keeping this crazy system in order to be able (in the future?)
+      * to have more than 2 values (0 or 1) for a covariate.
+      * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+      * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
+      *              bbbbbbbb
+      *              76543210
+      *   h-1        00000101 (6-1=5)
+      *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
+      *           &
+      *     1        00000001 (1)
+      *              00000000        = 1 & ((h-1) >> (k-1))
+      *          +1= 00000001 =1
+      *
+      * h=14, k=3 => h'=h-1=13, k'=k-1=2
+      *          h'      1101 =2^3+2^2+0x2^1+2^0
+      *    >>k'            11
+      *          &   00000001
+      *            = 00000001
+      *      +1    = 00000010=2    =  codtabm(14,3)
+      * Reverse h=6 and m=16?
+      * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
+      * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
+      * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
+      * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
+      * V3=decodtabm(14,3,2**4)=2
+      *          h'=13   1101 =2^3+2^2+0x2^1+2^0
+      *(h-1) >> (j-1)    0011 =13 >> 2
+      *          &1 000000001
+      *           = 000000001
+      *         +1= 000000010 =2
+      *                  2211
+      *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
+      *                  V3=2
+                  * codtabm and decodtabm are identical
+      */
+  free_ivector(Ndum,-1,NCOVMAX);
-   /*------------ gnuplot -------------*/
+   /* Initialisation of ----------- gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
    if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+     strcat(optionfilegnuplot,"-MORT_");
    strcat(optionfilegnuplot,".gp");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
    else{
-     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"\n# IMaCh-%s\n", version);
      fprintf(ficgp,"# %s\n", optionfilegnuplot);
      //fprintf(ficgp,"set missing 'NaNq'\n");
      fprintf(ficgp,"set datafile missing 'NaNq'\n");
    }
    /*  fclose(ficgp);*/
-   /*--------- index.htm --------*/
+   /* Initialisation of --------- index.htm --------*/
    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
    if(mle==-3)
-     strcat(optionfilehtm,"-mort");
+     strcat(optionfilehtm,"-MORT_");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
      printf("Problem with %s \n",optionfilehtm);
- Line 5554  run imach with mle=-1 to get a correct t
+ Line 10206  run imach with mle=-1 to get a correct t
    else{
    fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+ <font size=\"2\">IMaCh-%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
- Line 5577  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 10231  Title=%s <br>Datafile=%s Firstpass=%d La
    strcpy(pathr,path);
    strcat(pathr,optionfilefiname);
+ #ifdef WIN32
+   _chdir(optionfilefiname); /* Move to directory named optionfile */
+ #else
    chdir(optionfilefiname); /* Move to directory named optionfile */
+ #endif
    /* Calculates basic frequencies. Computes observed prevalence at single age
+                  and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+               firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 5589  Youngest age at first (selected) pass %.
+ Line 10250  Youngest age at first (selected) pass %.
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
            imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
    /* For Powell, parameters are in a vector p[] starting at p[1]
       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   /* For mortality only */
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
- /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
+                 for(i=1;i<=NDIM;i++)
+                         for(j=1;j<=NDIM;j++)
+                                 ximort[i][j]=0.;
+     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
      cens=ivector(1,n);
      ageexmed=vector(1,n);
      agecens=vector(1,n);
      dcwave=ivector(1,n);
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
        for (m=firstpass; m<=lastpass; m++)
- Line 5618  Interval (in months) between two waves:
+ Line 10281  Interval (in months) between two waves:
            break;
          }
      }
      for (i=1; i<=imx; i++) {
        if (wav[i]>0){
          ageexmed[i]=agev[mw[1][i]][i];
          j=wav[i];
          agecens[i]=1.;
          if (ageexmed[i]> 1 && wav[i] > 0){
            agecens[i]=agev[mw[j][i]][i];
            cens[i]= 1;
- Line 5641  Interval (in months) between two waves:
+ Line 10304  Interval (in months) between two waves:
          ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
-     p[1]=0.0268; p[NDIM]=0.083;
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
      /*printf("%lf %lf", p[1], p[2]);*/
  #ifdef GSL
      printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
- #elsedef
+ #else
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
  #endif
-     strcpy(filerespow,"pow-mort");
+     strcpy(filerespow,"POW-MORT_");
-     strcat(filerespow,fileres);
+     strcat(filerespow,fileresu);
      if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
  #ifdef GSL
      fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
- #elsedef
+ #else
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
  #endif
      /*  for (i=1;i<=nlstate;i++)
- Line 5693  Interval (in months) between two waves:
+ Line 10356  Interval (in months) between two waves:
      /* Initialize method and iterate */
      /*     p[1]=0.0268; p[NDIM]=0.083; */
- /*     gsl_vector_set(x, 0, 0.0268); */
+     /*     gsl_vector_set(x, 0, 0.0268); */
- /*     gsl_vector_set(x, 1, 0.083); */
+     /*     gsl_vector_set(x, 1, 0.083); */
      gsl_vector_set(x, 0, p[1]);
      gsl_vector_set(x, 1, p[2]);
- Line 5747  Interval (in months) between two waves:
+ Line 10410  Interval (in months) between two waves:
  #endif
      fclose(ficrespow);
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
-         matcov[i][j]=matcov[j][i];
+                                 matcov[i][j]=matcov[j][i];
      printf("\nCovariance matrix\n ");
+     fprintf(ficlog,"\nCovariance matrix\n ");
      for(i=1; i <=NDIM; i++) {
        for(j=1;j<=NDIM;j++){
-         printf("%f ",matcov[i][j]);
+                                 printf("%f ",matcov[i][j]);
+                                 fprintf(ficlog,"%f ",matcov[i][j]);
        }
-       printf("\n ");
+       printf("\n ");  fprintf(ficlog,"\n ");
      }
      printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-     for (i=1;i<=NDIM;i++)
+     for (i=1;i<=NDIM;i++) {
        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     }
      lsurv=vector(1,AGESUP);
      lpop=vector(1,AGESUP);
      tpop=vector(1,AGESUP);
- Line 5796  Interval (in months) between two waves:
+ Line 10462  Interval (in months) between two waves:
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 ageminpar=50;
+                 agemaxpar=100;
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
+         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else{
+                         printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+                         fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 }
+     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                       stepm, weightopt,\
                       model,imx,p,matcov,agemortsup);
      free_vector(lsurv,1,AGESUP);
      free_vector(lpop,1,AGESUP);
      free_vector(tpop,1,AGESUP);
- #ifdef GSL
+     free_matrix(ximort,1,NDIM,1,NDIM);
      free_ivector(cens,1,n);
      free_vector(agecens,1,n);
      free_ivector(dcwave,1,n);
-     free_matrix(ximort,1,NDIM,1,NDIM);
+ #ifdef GSL
  #endif
-   } /* Endof if mle==-3 */
+   } /* Endof if mle==-3 mortality only */
+   /* Standard  */
-   else{ /* For mle >=1 */
+   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
-     globpr=0;/* debug */
+     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
        printf(" %d %8.5f",k,p[k]);
      printf("\n");
-     globpr=1; /* to print the contributions */
+     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
+       /* mlikeli uses func not funcone */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
+       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     }
+     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
        printf(" %d %8.5f",k,p[k]);
      printf("\n");
-     if(mle>=1){ /* Could be 1 or 2 */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     }
      /*--------- results files --------------*/
-     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);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- Line 5844  Interval (in months) between two waves:
+ Line 10529  Interval (in months) between two waves:
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){
-             printf("%lf ",p[jk]);
+             printf("%12.7f ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
-             fprintf(ficres,"%lf ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
              jk++;
            }
            printf("\n");
- Line 5855  Interval (in months) between two waves:
+ Line 10540  Interval (in months) between two waves:
          }
        }
      }
-     if(mle!=0){
+     if(mle != 0){
-       /* Computing hessian and covariance matrix */
+       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
        ftolhess=ftol; /* Usually correct */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
-     }
+       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       for(i=1,jk=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(j=1; j <=ncovmodel; j++){
+               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+     } /* end of hesscov and Wald tests */
+     /*  */
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
      printf("# Scales (for hessian or gradient estimation)\n");
      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
- Line 5883  Interval (in months) between two waves:
+ Line 10587  Interval (in months) between two waves:
      }
      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");
-     if(mle>=1)
+     if(mle >= 1) /* To big for the screen */
        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");
      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");
      /* # 121 Var(a12)\n\ */
- Line 5946  Interval (in months) between two waves:
+ Line 10650  Interval (in months) between two waves:
                          fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                        }else{
                          if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+                           printf(" %.7e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
                        }
                      }
                    }
- Line 5967  Interval (in months) between two waves:
+ Line 10671  Interval (in months) between two waves:
      fflush(ficlog);
      fflush(ficres);
+     while(fgets(line, MAXLINE, ficpar)) {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       /* If line starts with a # it is a comment */
-       ungetc(c,ficpar);
+       if (line[0] == '#') {
-       fgets(line, MAXLINE, ficpar);
+         numlinepar++;
-       fputs(line,stdout);
+         fputs(line,stdout);
-       fputs(line,ficparo);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         continue;
+       }else
+         break;
      }
-     ungetc(c,ficpar);
+     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
+     /*   ungetc(c,ficpar); */
+     /*   fgets(line, MAXLINE, ficpar); */
+     /*   fputs(line,stdout); */
+     /*   fputs(line,ficparo); */
+     /* } */
+     /* ungetc(c,ficpar); */
      estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
+       if (num_filled != 6) {
+         printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
+         fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
+         goto end;
+       }
+       printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
+     }
+     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+     /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+     /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
      if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
        bage = ageminpar;
- Line 5985  Interval (in months) between two waves:
+ Line 10712  Interval (in months) between two waves:
      }
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
+     /* Other stuffs, more or less useful */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
- Line 6015  Interval (in months) between two waves:
+ Line 10743  Interval (in months) between two waves:
      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
      fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficlog,"pop_based=%d\n",popbased);
      fprintf(ficparo,"pop_based=%d\n",popbased);
      fprintf(ficres,"pop_based=%d\n",popbased);
- Line 6033  Interval (in months) between two waves:
+ Line 10762  Interval (in months) between two waves:
      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);
      /* day and month of proj2 are not used but only year anproj2.*/
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
+     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+     /* Results */
+     nresult=0;
+     while(fgets(line, MAXLINE, ficpar)) {
+       /* If line starts with a # it is a comment */
+       if (line[0] == '#') {
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         continue;
+       }else
+         break;
+     }
+     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+       if (num_filled == 0)
+         resultline[0]='\0';
+       else if (num_filled != 1){
+         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
+       }
+       nresult++; /* Sum of resultlines */
+       printf("Result %d: result=%s\n",nresult, resultline);
+       if(nresult > MAXRESULTLINES){
+         printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+         fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+         goto end;
+       }
+       decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+       while(fgets(line, MAXLINE, ficpar)) {
+         /* If line starts with a # it is a comment */
+         if (line[0] == '#') {
+           numlinepar++;
+           fputs(line,stdout);
+           fputs(line,ficparo);
+           fputs(line,ficlog);
+           continue;
+         }else
+           break;
+       }
+       if (feof(ficpar))
+         break;
+       else{ /* Processess output results for this combination of covariate values */
+       }
+     }
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
+       printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+       fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
-    /*------------ free_vector  -------------*/
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
-    /*  chdir(path); */
+     }else{
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
-     free_ivector(wav,1,imx);
+     }
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+     /*------------ free_vector  -------------*/
+     /*  chdir(path); */
+     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
+     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
+     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
+     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
      free_lvector(num,1,n);
      free_vector(agedc,1,n);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
      fclose(ficres);
+     /* Other results (useful)*/
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
-     strcpy(filerespl,"pl");
-     strcat(filerespl,fileres);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     pstamp(ficrespl);
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
-     fprintf(ficrespl,"#Age ");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-     fprintf(ficrespl,"\n");
      prlim=matrix(1,nlstate,1,nlstate);
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
-     agebase=ageminpar;
-     agelim=agemaxpar;
-     ftolpl=1.e-10;
-     i1=cptcoveff;
-     if (cptcovn < 1){i1=1;}
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         /* to clean */
-         printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
-         fprintf(ficlog,"\n#******");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
-         fprintf(ficrespl,"******\n");
-         printf("******\n");
-         fprintf(ficlog,"******\n");
-         for (age=agebase; age<=agelim; age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           fprintf(ficrespl,"%.0f ",age );
-           for(j=1;j<=cptcoveff;j++)
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
-           fprintf(ficrespl,"\n");
-         }
-       }
-     }
      fclose(ficrespl);
      /*------------- h Pij x at various ages ------------*/
+     /*#include "hpijx.h"*/
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     hPijx(p, bage, fage);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-     }
-     printf("Computing pij: result on file '%s' \n", filerespij);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
-     /*if (stepm<=24) stepsize=2;*/
-     agelim=AGESUP;
-     hstepm=stepsize*YEARM; /* Every year of age */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-     /* hstepm=1;   aff par mois*/
-     pstamp(ficrespij);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrespij,"******\n");
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-             for(i=1; i<=nlstate;i++)
-               for(j=1; j<=nlstate+ndeath;j++)
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficrespij,"\n");
-         }
-       }
-     }
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
      fclose(ficrespij);
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /* ncovcombmax=  pow(2,cptcoveff); */
+     /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     /* Prevalence for each covariates in probs[age][status][cov] */
+     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
      for(i=1;i<=AGESUP;i++)
-       for(j=1;j<=NCOVMAX;j++)
+       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
-         for(k=1;k<=NCOVMAX;k++)
+         for(k=1;k<=ncovcombmax;k++)
            probs[i][j][k]=0.;
+     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     if (mobilav!=0 ||mobilavproj !=0 ) {
+       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+       for(i=1;i<=AGESUP;i++)
+         for(j=1;j<=nlstate;j++)
+           for(k=1;k<=ncovcombmax;k++)
+             mobaverages[i][j][k]=0.;
+       mobaverage=mobaverages;
+       if (mobilav!=0) {
+         printf("Movingaveraging observed prevalence\n");
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
+           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         }
+       }
+       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+       else if (mobilavproj !=0) {
+         printf("Movingaveraging projected observed prevalence\n");
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
+           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
+           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
+         }
+       }
+     }/* end if moving average */
      /*---------- Forecasting ------------------*/
      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
      if(prevfcast==1){
        /*    if(stepm ==1){*/
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
-       /*      }  */
-       /*      else{ */
-       /*        erreur=108; */
-       /*        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); */
-       /*        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); */
-       /*      } */
      }
+     if(backcast==1){
+       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     /*  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",\
+       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-     */
+       bprlim=matrix(1,nlstate,1,nlstate);
+       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
-     if (mobilav!=0) {
+       fclose(ficresplb);
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       hBijx(p, bage, fage, mobaverage);
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       fclose(ficrespijb);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
-       }
+       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
+          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
      }
+     /* ------ Other prevalence ratios------------ */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
      /*---------- Health expectancies, no variances ------------*/
-     strcpy(filerese,"e");
+     strcpy(filerese,"E_");
-     strcat(filerese,fileres);
+     strcat(filerese,fileresu);
      if((ficreseij=fopen(filerese,"w"))==NULL) {
        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
      }
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-         k=k+1;
+     if (cptcovn < 1){i1=1;}
-         fprintf(ficreseij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-         }
+       if(TKresult[nres]!= k)
-         fprintf(ficreseij,"******\n");
+         continue;
+       fprintf(ficreseij,"\n#****** ");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       printf("\n#****** ");
-         oldm=oldms;savm=savms;
+       for(j=1;j<=cptcoveff;j++) {
-         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficreseij,"******\n");
+       printf("******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
      }
      fclose(ficreseij);
+     printf("done evsij\n");fflush(stdout);
+     fprintf(ficlog,"done evsij\n");fflush(ficlog);
-     /*---------- Health expectancies and variances ------------*/
+     /*---------- State-specific expectancies and variances ------------*/
-     strcpy(filerest,"t");
-     strcat(filerest,fileres);
+     strcpy(filerest,"T_");
+     strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
      }
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
-     strcpy(fileresstde,"stde");
+     strcpy(fileresstde,"STDE_");
-     strcat(fileresstde,fileres);
+     strcat(fileresstde,fileresu);
      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
      }
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     strcpy(filerescve,"cve");
+     strcpy(filerescve,"CVE_");
-     strcat(filerescve,fileres);
+     strcat(filerescve,fileresu);
      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
      }
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
-     strcpy(fileresv,"v");
+     strcpy(fileresv,"V_");
-     strcat(fileresv,fileres);
+     strcat(fileresv,fileresu);
      if((ficresvij=fopen(fileresv,"w"))==NULL) {
        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
      }
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-         k=k+1;
-         fprintf(ficrest,"\n#****** ");
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-         for(j=1;j<=cptcoveff;j++)
+     if (cptcovn < 1){i1=1;}
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrest,"******\n");
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-         fprintf(ficresstdeij,"\n#****** ");
+       if(TKresult[nres]!= k)
-         fprintf(ficrescveij,"\n#****** ");
+         continue;
-         for(j=1;j<=cptcoveff;j++) {
+       printf("\n#****** Selected:");
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficrest,"\n#****** Selected:");
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficlog,"\n#****** Selected:");
-         }
+       for(j=1;j<=cptcoveff;j++){
-         fprintf(ficresstdeij,"******\n");
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficrescveij,"******\n");
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficresvij,"\n#****** ");
+       }
-         for(j=1;j<=cptcoveff;j++)
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-         fprintf(ficresvij,"******\n");
+         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       }
-         oldm=oldms;savm=savms;
+       fprintf(ficrest,"******\n");
-         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       fprintf(ficlog,"******\n");
+       printf("******\n");
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         pstamp(ficrest);
+       fprintf(ficresstdeij,"\n#****** ");
-         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+       fprintf(ficrescveij,"\n#****** ");
-           oldm=oldms;savm=savms;
+       for(j=1;j<=cptcoveff;j++) {
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   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 ");
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-           if(vpopbased==1)
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-             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);
+       }
-           else
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-           fprintf(ficrest,"# Age e.. (std) ");
+         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+       }
-           fprintf(ficrest,"\n");
+       fprintf(ficresstdeij,"******\n");
+       fprintf(ficrescveij,"******\n");
-           epj=vector(1,nlstate+1);
-           for(age=bage; age <=fage ;age++){
+       fprintf(ficresvij,"\n#****** ");
-             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       for(j=1;j<=cptcoveff;j++)
-             if (vpopbased==1) {
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-               if(mobilav ==0){
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-                 for(i=1; i<=nlstate;i++)
+         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-                   prlim[i][i]=probs[(int)age][i][k];
+       }
-               }else{ /* mobilav */
+       fprintf(ficresvij,"******\n");
-                 for(i=1; i<=nlstate;i++)
-                   prlim[i][i]=mobaverage[(int)age][i][k];
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-               }
+       oldm=oldms;savm=savms;
-             }
+       printf(" cvevsij ");
+       fprintf(ficlog, " cvevsij ");
-             fprintf(ficrest," %4.0f",age);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
-             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+       printf(" end cvevsij \n ");
-               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+       fprintf(ficlog, " end cvevsij \n ");
-                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
-                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+       /*
-               }
+        */
-               epj[nlstate+1] +=epj[j];
+       /* goto endfree; */
+       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       pstamp(ficrest);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+         oldm=oldms;savm=savms; /* ZZ Segmentation fault */
+         cptcod= 0; /* To be deleted */
+         printf("varevsij vpopbased=%d \n",vpopbased);
+         fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
+         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 ");
+         if(vpopbased==1)
+           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);
+         else
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         fprintf(ficrest,"\n");
+         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+         epj=vector(1,nlstate+1);
+         printf("Computing age specific period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
+           if (vpopbased==1) {
+             if(mobilav ==0){
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=probs[(int)age][i][k];
+             }else{ /* mobilav */
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=mobaverage[(int)age][i][k];
              }
+           }
-             for(i=1, vepp=0.;i <=nlstate;i++)
-               for(j=1;j <=nlstate;j++)
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
-                 vepp += vareij[i][j][(int)age];
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           /* printf(" age %4.0f ",age); */
-             for(j=1;j <=nlstate;j++){
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
              }
-             fprintf(ficrest,"\n");
+             epj[nlstate+1] +=epj[j];
+           }
+           /* printf(" age %4.0f \n",age); */
+           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(j=1;j <=nlstate;j++)
+               vepp += vareij[i][j][(int)age];
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           for(j=1;j <=nlstate;j++){
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
            }
+           fprintf(ficrest,"\n");
          }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       } /* End vpopbased */
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_vector(epj,1,nlstate+1);
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       }
+       free_vector(epj,1,nlstate+1);
+       printf("done selection\n");fflush(stdout);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
+       /*}*/
+     } /* End k selection */
+     printf("done State-specific expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"VPL_");
+     strcat(fileresvpl,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(TKresult[nres]!= k)
+         continue;
+       fprintf(ficresvpl,"\n#****** ");
+       printf("\n#****** ");
+       fprintf(ficlog,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficresvpl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
      }
+     fclose(ficresvpl);
+     printf("done variance-covariance of period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
      free_vector(weight,1,n);
-     free_imatrix(Tvard,1,15,1,2);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
      free_imatrix(s,1,maxwav+1,1,n);
      free_matrix(anint,1,maxwav,1,n);
      free_matrix(mint,1,maxwav,1,n);
- Line 6367  Interval (in months) between two waves:
+ Line 11214  Interval (in months) between two waves:
      fclose(ficresvij);
      fclose(ficrest);
      fclose(ficpar);
-     /*------- Variance of period (stable) prevalence------*/
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       exit(0);
-     }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         fprintf(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"******\n");
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       }
-     }
-     fclose(ficresvpl);
      /*---------- End : free ----------------*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (mobilav!=0 ||mobilavproj !=0)
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
-   }  /* mle==-3 arrives here for freeing */
+     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-  endfree:
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   }  /* mle==-3 arrives here for freeing */
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   /* endfree:*/
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(matcov,1,npar,1,npar);
+   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     /*free_vector(delti,1,npar);*/
+   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
-     free_matrix(agev,1,maxwav,1,imx);
+   free_matrix(coqvar,1,maxwav,1,n);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(matcov,1,npar,1,npar);
-     free_ivector(ncodemax,1,8);
+   free_matrix(hess,1,npar,1,npar);
-     free_ivector(Tvar,1,15);
+   /*free_vector(delti,1,npar);*/
-     free_ivector(Tprod,1,15);
+   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(Tvaraff,1,15);
+   free_matrix(agev,1,maxwav,1,imx);
-     free_ivector(Tage,1,15);
+   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   free_ivector(ncodemax,1,NCOVMAX);
-     free_imatrix(codtab,1,100,1,10);
+   free_ivector(ncodemaxwundef,1,NCOVMAX);
+   free_ivector(Dummy,-1,NCOVMAX);
+   free_ivector(Fixed,-1,NCOVMAX);
+   free_ivector(Typevar,-1,NCOVMAX);
+   free_ivector(Tvar,1,NCOVMAX);
+   free_ivector(TvarsQ,1,NCOVMAX);
+   free_ivector(TvarsQind,1,NCOVMAX);
+   free_ivector(TvarsD,1,NCOVMAX);
+   free_ivector(TvarsDind,1,NCOVMAX);
+   free_ivector(TvarFD,1,NCOVMAX);
+   free_ivector(TvarFDind,1,NCOVMAX);
+   free_ivector(TvarF,1,NCOVMAX);
+   free_ivector(TvarFind,1,NCOVMAX);
+   free_ivector(TvarV,1,NCOVMAX);
+   free_ivector(TvarVind,1,NCOVMAX);
+   free_ivector(TvarA,1,NCOVMAX);
+   free_ivector(TvarAind,1,NCOVMAX);
+   free_ivector(TvarFQ,1,NCOVMAX);
+   free_ivector(TvarFQind,1,NCOVMAX);
+   free_ivector(TvarVD,1,NCOVMAX);
+   free_ivector(TvarVDind,1,NCOVMAX);
+   free_ivector(TvarVQ,1,NCOVMAX);
+   free_ivector(TvarVQind,1,NCOVMAX);
+   free_ivector(Tvarsel,1,NCOVMAX);
+   free_vector(Tvalsel,1,NCOVMAX);
+   free_ivector(Tposprod,1,NCOVMAX);
+   free_ivector(Tprod,1,NCOVMAX);
+   free_ivector(Tvaraff,1,NCOVMAX);
+   free_ivector(invalidvarcomb,1,ncovcombmax);
+   free_ivector(Tage,1,NCOVMAX);
+   free_ivector(Tmodelind,1,NCOVMAX);
+   free_ivector(TmodelInvind,1,NCOVMAX);
+   free_ivector(TmodelInvQind,1,NCOVMAX);
+   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
    fflush(ficgp);
    if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
    }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
    }
    printf("See log file on %s\n",filelog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
-   (void) gettimeofday(&end_time,&tzp);
+   /*(void) gettimeofday(&end_time,&tzp);*/
-   tm = *localtime(&end_time.tv_sec);
+   rend_time = time(NULL);
-   tmg = *gmtime(&end_time.tv_sec);
+   end_time = *localtime(&rend_time);
-   strcpy(strtend,asctime(&tm));
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
    printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
    fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
-   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
-   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
    /*  printf("Total time was %d uSec.\n", total_usecs);*/
  /*   if(fileappend(fichtm,optionfilehtm)){ */
    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
- Line 6453  Interval (in months) between two waves:
+ Line 11309  Interval (in months) between two waves:
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
-    printf("Before Current directory %s!\n",pathcd);
+   printf("Before Current directory %s!\n",pathcd);
-    if(chdir(pathcd) != 0)
+ #ifdef WIN32
+   if (_chdir(pathcd) != 0)
      printf("Can't move to directory %s!\n",path);
-   if(getcwd(pathcd,MAXLINE) > 0)
+   if(_getcwd(pathcd,MAXLINE) > 0)
+ #else
+     if(chdir(pathcd) != 0)
+       printf("Can't move to directory %s!\n", path);
+   if (getcwd(pathcd, MAXLINE) > 0)
+ #endif
      printf("Current directory %s!\n",pathcd);
    /*strcat(plotcmd,CHARSEPARATOR);*/
    sprintf(plotcmd,"gnuplot");
- #ifndef UNIX
+ #ifdef _WIN32
    sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
  #endif
    if(!stat(plotcmd,&info)){
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
      if(!stat(getenv("GNUPLOTBIN"),&info)){
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
      }else
        strcpy(pplotcmd,plotcmd);
- #ifdef UNIX
+ #ifdef __unix
      strcpy(plotcmd,GNUPLOTPROGRAM);
      if(!stat(plotcmd,&info)){
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
      }else
        strcpy(pplotcmd,plotcmd);
  #endif
- Line 6482  Interval (in months) between two waves:
+ Line 11344  Interval (in months) between two waves:
      strcpy(pplotcmd,plotcmd);
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
-     printf("\n Problem with gnuplot\n");
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
    }
-   printf(" Wait...");
+   printf(" Successful, please wait...");
    while (z[0] != 'q') {
      /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
      scanf("%s",z);
  /*     if (z[0] == 'c') system("./imach"); */
      if (z[0] == 'e') {
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+ #ifdef __APPLE__
-       system(optionfilehtm);
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
      }
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   end:
+ end:
    while (z[0] != 'q') {
-     printf("\nType  q for exiting: ");
+     printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
  }

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