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Diff for /imach/src/imach.c between versions 1.223 and 1.231

-version 1.223, 2016/02/19 09:23:35
+version 1.231, 2016/08/22 07:17:15
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
- Line 630
+ Line 651
    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 669
+ Line 693
    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
+  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
-     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
+    double agemaxpar, double ftolpl, int *ncvyearp, double
-    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+    dateprev1,double dateprev2, int firstpass, int lastpass, int
-  - hBijx Back Probability to be in state i at age x-h being in j at x
+    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);
+    - 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
+      nhstepm*hstepm matrices.
-      p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
-,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+      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.
    This software have been partly granted by Euro-REVES, a concerted action
- Line 745  Back prevalence and projections:
+ Line 800  Back prevalence and projections:
  /* #define DEBUGLINMIN */
  /* #define DEBUGHESS */
  #define DEBUGHESSIJ
- /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
  #define POWELL /* Instead of NLOPT */
- #define POWELLF1F3 /* Skip test */
+ #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 *\/ */
- Line 755  Back prevalence and projections:
+ Line 810  Back prevalence and projections:
  #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
+ #include <ctype.h>
  #ifdef _WIN32
  #include <io.h>
- Line 841  typedef struct {
+ Line 897  typedef struct {
  /* $State$ */
  #include "version.h"
  char version[]=__IMACH_VERSION__;
- char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+ 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];
- Line 850  int nagesqr=0, nforce=0; /* nagesqr=1 if
+ Line 906  int nagesqr=0, nforce=0; /* nagesqr=1 if
  /* 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 V2+V1 =2 */
+ 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 ncoveff=0; /* Total number of effective 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;
- Line 875  int **dh; /* dh[mi][i] is number of step
+ Line 936  int **dh; /* dh[mi][i] is number of step
  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 */
- Line 999  double *agedc;
+ Line 1062  double *agedc;
  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]*age; */
- double ***cotvar; /* Time varying covariate */
+ double **coqvar; /* Fixed quantitative covariate iqv */
- double ***cotqvar; /* Time varying quantitative covariate */
+ double ***cotvar; /* Time varying covariate itv */
- double **coqvar; /* Fixed quantitative covariate */
+ double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ 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, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
+ 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;
+ #define FD 1; /* Fixed dummy covariate */
+ #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 */
- Line 1549  double brent(double ax, double bx, doubl
+ Line 1664  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 1568  double brent(double ax, double bx, doubl
+ Line 1683  double brent(double ax, double bx, doubl
      } else {
        if (u < x) a=u; else b=u;
        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) {
-         v=u;
+                                 v=u;
-         fv=fu;
+                                 fv=fu;
        }
      }
    }
- Line 1615  values at the three points, fa, fb , and
+ Line 1730  values at the three points, fa, fb , and
    *cx=(*bx)+GOLD*(*bx-*ax);
    *fc=(*func)(*cx);
  #ifdef DEBUG
-   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
-   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*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 */
+   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)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
- Line 1631  values at the three points, fa, fb , and
+ Line 1746  values at the three points, fa, fb , and
        double A, fparabu;
        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
        fparabu= *fa - A*(*ax-u)*(*ax-u);
-       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       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, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       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) */
- Line 1665  values at the three points, fa, fb , and
+ Line 1780  values at the three points, fa, fb , and
  /*      fu = *fc; */
  /*      *fc =dum; */
  /*       } */
- #ifdef DEBUG
+ #ifdef DEBUGMNBRAK
-       printf("mnbrak34  fu < or >= fc \n");
+                  double A, fparabu;
-       fprintf(ficlog, "mnbrak34 fu < fc\n");
+      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;
- Line 1678  values at the three points, fa, fb , and
+ Line 1796  values at the three points, fa, fb , and
  #endif
      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
  #ifdef DEBUG
-       printf("mnbrak2  u after c but before ulim\n");
+       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
-       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
+       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
  #endif
        fu=(*func)(u);
        if (fu < *fc) {
  #ifdef DEBUG
-       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
+                                 printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
+                           fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
+ #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
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         SHFT(*fb,*fc,fu,(*func)(u))
        }
      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
  #ifdef DEBUG
-       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
+       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
-       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
+       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 { /* u could be left to b (if r > q parabola has a maximum) */
  #ifdef DEBUG
-       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+       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, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+       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)
  #ifdef DEBUG
-       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
+       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
-       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
+       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) */
  }
- Line 1724  int ncom;
+ Line 1849  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 1768  void linmin(double p[], double xi[], int
+ Line 1897  void linmin(double p[], double xi[], int
  #ifdef LINMINORIGINAL
  #else
      if (fx != fx){
-         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+                         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
-         printf("|");
+                         printf("|");
-         fprintf(ficlog,"|");
+                         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);
+                         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);
+   }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 ");
- Line 1839  such that failure to decrease by more th
+ Line 1981  such that failure to decrease by more th
  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 1883  void powell(double p[], double **xi, int
+ Line 2041  void powell(double p[], double **xi, int
        rforecast_time=rcurr_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 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,rcurr_time-rlast_time);
        for(niterf=10;niterf<=30;niterf+=10){
-         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
+                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-         forecast_time = *localtime(&rforecast_time);
+                                 forecast_time = *localtime(&rforecast_time);
-         strcpy(strfor,asctime(&forecast_time));
+                                 strcpy(strfor,asctime(&forecast_time));
-         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(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(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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
        }
      }
      for (i=1;i<=n;i++) { /* For each direction i */
- Line 1906  void powell(double p[], double **xi, int
+ Line 2064  void powell(double p[], double **xi, int
  #endif
        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
        fprintf(ficlog,"%d",i);fflush(ficlog);
+ #ifdef LINMINORIGINAL
        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
+ #else
+       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 */
+                                 /* 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. */
+                                 /* 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 */
+                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-         /* with the new direction. */
+                                 /* with the new direction. */
-         del=fabs(fptt-(*fret));
+                                 del=fabs(fptt-(*fret));
-         ibig=i;
+                                 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(%d)=%.12e",j,p[j]);
+                                 printf(" p(%d)=%.12e",j,p[j]);
-         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
+                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);
        }
        printf("\n");
        fprintf(ficlog,"\n");
- Line 1935  void powell(double p[], double **xi, int
+ Line 2098  void powell(double p[], double **xi, int
      /* 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 */
- Line 1943  void powell(double p[], double **xi, int
+ Line 2114  void powell(double p[], double **xi, int
        /* 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 */
- Line 1971  void powell(double p[], double **xi, int
+ Line 2142  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);
- Line 1985  void powell(double p[], double **xi, int
+ Line 2159  void powell(double p[], double **xi, int
        pt[j]=p[j];
      }
      fptt=(*func)(ptt); /* f_3 */
- #ifdef POWELLF1F3
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+                 if (*iter <=4) {
+ #else
+ #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
- Line 1994  void powell(double p[], double **xi, int
+ Line 2172  void powell(double p[], double **xi, int
        /* 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 */
+       /* 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
- Line 2017  void powell(double p[], double **xi, int
+ Line 2203  void powell(double p[], double **xi, int
        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("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 <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,"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);
+                                 printf("Before linmin in direction P%d-P0\n",n);
-         for (j=1;j<=n;j++) {
+                                 for (j=1;j<=n;j++) {
-           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[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]);
+                                         fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-           if(j % ncovmodel == 0){
+                                         if(j % ncovmodel == 0){
-             printf("\n");
+                                                 printf("\n");
-             fprintf(ficlog,"\n");
+                                                 fprintf(ficlog,"\n");
-           }
+                                         }
-         }
+                                 }
  #endif
-         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+ #ifdef LINMINORIGINAL
- #ifdef DEBUGLINMIN
+                                 linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-         for (j=1;j<=n;j++) {
+ #else
-           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+                                 linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+                                 flatdir[i]=flat; /* Function is vanishing in that direction i */
-           if(j % ncovmodel == 0){
-             printf("\n");
-             fprintf(ficlog,"\n");
-           }
-         }
  #endif
-         for (j=1;j<=n;j++) {
-           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-         }
-         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 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]; /* Replace direction with biggest decrease by last direction n */
+                                         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);
+                                 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);
+                                 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++){
+                                 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");
+                                 printf("\n");
-         fprintf(ficlog,"\n");
+                                 fprintf(ficlog,"\n");
  #endif
        } /* end of t or directest negative */
- #ifdef POWELLF1F3
+ #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 */
  }
- Line 2619  double ***hpxij(double ***po, int nhstep
+ Line 2834  double ***hpxij(double ***po, int nhstep
        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
        cov[2]=agexact;
        if(nagesqr==1)
-                                 cov[3]= agexact*agexact;
+         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,k)];
-                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[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+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,k)]*cov[2];
-                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[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,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])]; */
+       /* 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]);*/
                          /* right multiplication of oldm by the current matrix */
- Line 2779  double ***hbxij(double ***po, int nhstep
+ Line 2994  double ***hbxij(double ***po, int nhstep
  double func( double *x)
  {
    int i, ii, j, k, mi, d, kk;
-         int ioffset;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
-   double sw; /* Sum of weights */
    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 */
+   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;
- Line 2801  double func( double *x)
+ Line 3015  double func( double *x)
    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 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.
-        */
+       */
-       ioffset=2+nagesqr;
+       ioffset=2+nagesqr+cptcovage;
-       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+       /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
-          cov[++ioffset]=covar[Tvar[k]][i];
+       for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
+         cov[++ioffset]=covar[Tvar[k]][i];
        }
-       for(iqv=1; iqv <= nqv; iqv++){ /* Varying quantitatives covariates */
+       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
-         /* cov[2+nagesqr+cptcovn+iqv]=varq[mw[mi+1][i]][iqv][i]; */
+         cov[++ioffset]=coqvar[Tvar[iqv]][i];
        }
        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
- Line 2824  double func( double *x)
+ Line 3039  double func( double *x)
        /* 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];
+          s2=s[mw[mi+1][i]][i];
-         And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][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:
+          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]
+          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
        */
        for(mi=1; mi<= wav[i]-1; mi++){
-         for(itv=1; itv <= ntv; itv++){ /* Varying dummy covariates */
+                                 for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
-           cov[++ioffset]=cotvar[mw[mi+1][i]][itv][i];
+                                         /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
-         }
+                                         cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
-         for(iqtv=1; iqtv <= nqtv; iqtv++){ /* Varying quantitatives covariates */
+                                 }
-           /* cov[2+nagesqr+cptcovn+nqv+ntv+iqtv]=varq[mw[mi+1][i]][iqtv][i]; */
+                                 for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
-         }
+                                         if(cotqvar[mw[mi][i]][iqtv][i] == -1){
-         ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv;
+                                                 printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+                                         }
-           for (j=1;j<=nlstate+ndeath;j++){
+                                         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+                                         /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+                                 }
-           }
+                                 /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
-         for(d=0; d<dh[mi][i]; d++){
+                                 for (ii=1;ii<=nlstate+ndeath;ii++)
-           newm=savm;
+                                         for (j=1;j<=nlstate+ndeath;j++){
-           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           cov[2]=agexact;
+                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           if(nagesqr==1)
+                                         }
-             cov[3]= agexact*agexact;  /* Should be changed here */
+                                 for(d=0; d<dh[mi][i]; d++){
-           for (kk=1; kk<=cptcovage;kk++) {
+                                         newm=savm;
-             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           }
+                                         cov[2]=agexact;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+                                         if(nagesqr==1)
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+                                                 cov[3]= agexact*agexact;  /* Should be changed here */
-           savm=oldm;
+                                         for (kk=1; kk<=cptcovage;kk++) {
-           oldm=newm;
+                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-         } /* end mult */
+                                         }
+                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+                                         savm=oldm;
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+                                         oldm=newm;
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+                                 } /* end mult */
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+                                 /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+                                 /* But now since version 0.9 we anticipate for bias at large stepm.
-          * probability in order to take into account the bias as a fraction of the way
+                                  * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+                                  * (in months) between two waves is not a multiple of stepm, we rounded to
-          * -stepm/2 to stepm/2 .
+                                  * the nearest (and in case of equal distance, to the lowest) interval but now
-          * For stepm=1 the results are the same as for previous versions of Imach.
+                                  * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * For stepm > 1 the results are less biased than in previous versions.
+                                  * (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
-         s1=s[mw[mi][i]][i];
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-         s2=s[mw[mi+1][i]][i];
+                                  * -stepm/2 to stepm/2 .
-         bbh=(double)bh[mi][i]/(double)stepm;
+                                  * For stepm=1 the results are the same as for previous versions of Imach.
-         /* bias bh is positive if real duration
+                                  * For stepm > 1 the results are less biased than in previous versions.
-          * is higher than the multiple of stepm and negative otherwise.
+                                  */
-          */
+                                 s1=s[mw[mi][i]][i];
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+                                 s2=s[mw[mi+1][i]][i];
-         if( s2 > nlstate){
+                                 bbh=(double)bh[mi][i]/(double)stepm;
-           /* i.e. if s2 is a death state and if the date of death is known
+                                 /* bias bh is positive if real duration
-              then the contribution to the likelihood is the probability to
+                                  * is higher than the multiple of stepm and negative otherwise.
-              die between last step unit time and current  step unit time,
+                                  */
-              which is also equal to probability to die before dh
+                                 /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-              minus probability to die before dh-stepm .
+                                 if( s2 > nlstate){
-              In version up to 0.92 likelihood was computed
+                                         /* i.e. if s2 is a death state and if the date of death is known
-         as if date of death was unknown. Death was treated as any other
+                                                  then the contribution to the likelihood is the probability to
-         health state: the date of the interview describes the actual state
+                                                  die between last step unit time and current  step unit time,
-         and not the date of a change in health state. The former idea was
+                                                  which is also equal to probability to die before dh
-         to consider that at each interview the state was recorded
+                                                  minus probability to die before dh-stepm .
-         (healthy, disable or death) and IMaCh was corrected; but when we
+                                                  In version up to 0.92 likelihood was computed
-         introduced the exact date of death then we should have modified
+                                                  as if date of death was unknown. Death was treated as any other
-         the contribution of an exact death to the likelihood. This new
+                                                  health state: the date of the interview describes the actual state
-         contribution is smaller and very dependent of the step unit
+                                                  and not the date of a change in health state. The former idea was
-         stepm. It is no more the probability to die between last interview
+                                                  to consider that at each interview the state was recorded
-         and month of death but the probability to survive from last
+                                                  (healthy, disable or death) and IMaCh was corrected; but when we
-         interview up to one month before death multiplied by the
+                                                  introduced the exact date of death then we should have modified
-         probability to die within a month. Thanks to Chris
+                                                  the contribution of an exact death to the likelihood. This new
-         Jackson for correcting this bug.  Former versions increased
+                                                  contribution is smaller and very dependent of the step unit
-         mortality artificially. The bad side is that we add another loop
+                                                  stepm. It is no more the probability to die between last interview
-         which slows down the processing. The difference can be up to 10%
+                                                  and month of death but the probability to survive from last
-         lower mortality.
+                                                  interview up to one month before death multiplied by the
-           */
+                                                  probability to die within a month. Thanks to Chris
-         /* If, at the beginning of the maximization mostly, the
+                                                  Jackson for correcting this bug.  Former versions increased
-            cumulative probability or probability to be dead is
+                                                  mortality artificially. The bad side is that we add another loop
-            constant (ie = 1) over time d, the difference is equal to
+                                                  which slows down the processing. The difference can be up to 10%
-.  out[s1][3] = savm[s1][3]: probability, being at state
+                                                  lower mortality.
-            s1 at precedent wave, to be dead a month before current
+                                         */
-            wave is equal to probability, being at state s1 at
+                                         /* If, at the beginning of the maximization mostly, the
-            precedent wave, to be dead at mont of the current
+                                                  cumulative probability or probability to be dead is
-            wave. Then the observed probability (that this person died)
+                                                  constant (ie = 1) over time d, the difference is equal to
-            is null according to current estimated parameter. In fact,
+.  out[s1][3] = savm[s1][3]: probability, being at state
-            it should be very low but not zero otherwise the log go to
+                                                  s1 at precedent wave, to be dead a month before current
-            infinity.
+                                                  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 */
- Line 2929  double func( double *x)
+ Line 3149  double func( double *x)
            /*survp += out[s1][j]; */
            lli= log(survp);
          }
          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) {
            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 2946  double func( double *x)
+ Line 3166  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)){ */
- Line 3107  double func( double *x)
+ Line 3327  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;
- Line 3126  double funcone( double *x)
+ Line 3349  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+nagesqr+k]=covar[Tvar[k]][i];
+     ioffset=2+nagesqr+cptcovage;
-     for(mi=1; mi<= wav[i]-1; mi++){
+     /* 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 */
+       cov[++ioffset]=covar[TvarFD[k]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
+     }
+     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 */
+       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);
-         }
+                                 }
        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][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.*/
+                                         and mw[mi+1][i]. dh depends on stepm.*/
-         newm=savm;
+                                 newm=savm;
-         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+                                 agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         cov[2]=agexact;
+                                 cov[2]=agexact;
-         if(nagesqr==1)
+                                 if(nagesqr==1)
-           cov[3]= agexact*agexact;
+                                         cov[3]= agexact*agexact;
-         for (kk=1; kk<=cptcovage;kk++) {
+                                 for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+                                         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); */
+                                 /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+                                 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, */
+                                 /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+                                 /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-         savm=oldm;
+                                 savm=oldm;
-         oldm=newm;
+                                 oldm=newm;
        } /* end mult */
        s1=s[mw[mi][i]][i];
- Line 3192  double funcone( double *x)
+ Line 3438  double funcone( double *x)
        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 %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
+         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], 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]);
- Line 3707  void pstamp(FILE *fichier)
+ Line 3953  void pstamp(FILE *fichier)
  }
  /************ Frequencies ********************/
-  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
+ 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 *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
-                                                                          int firstpass,  int lastpass, int stepm, int weightopt, char model[])
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
-  {  /* Some frequencies */
+ {  /* Some frequencies */
-          int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, k, iv;
-          int iind=0, iage=0;
+   int iind=0, iage=0;
-          int mi; /* Effective wave */
+   int mi; /* Effective wave */
-          int first;
+   int first;
-          double ***freq; /* Frequencies */
+   double ***freq; /* Frequencies */
-          double *pp, **prop, *posprop, *pospropt;
+   double *meanq;
-          double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
+   double **meanqt;
-          char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
+   double *pp, **prop, *posprop, *pospropt;
-          double agebegin, ageend;
+   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
-          pp=vector(1,nlstate);
+   double agebegin, ageend;
-          prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-          posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
+   pp=vector(1,nlstate);
-          pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-          /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
+   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
-          strcpy(fileresp,"P_");
+   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
-          strcat(fileresp,fileresu);
+   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
-          /*strcat(fileresphtm,fileresu);*/
+   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
-          if((ficresp=fopen(fileresp,"w"))==NULL) {
+   meanqt=matrix(1,lastpass,1,nqtveff);
-                  printf("Problem with prevalence resultfile: %s\n", fileresp);
+   strcpy(fileresp,"P_");
-                  fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+   strcat(fileresp,fileresu);
-                  exit(0);
+   /*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);
+   }
-          strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
-          if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
-                  printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     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));
+     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
-                  fflush(ficlog);
+     fflush(ficlog);
-                  exit(70);
+     exit(70);
-          }
+   }
-          else{
+   else{
-                  fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     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);
+             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</h4>\n",fileresphtm, fileresphtm);
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
-          strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
-          if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
-                  printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     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));
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
-                  fflush(ficlog);
+     fflush(ficlog);
-                  exit(70);
+     exit(70);
-          }
+   }
-          else{
+   else{
-                  fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     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);
+             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);
+   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);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-          j1=0;
+   j1=0;
-          j=cptcoveff;
+   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
-          if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   j=cptcoveff;  /* Only dummy covariates of the model */
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-          first=1;
-          /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
+   first=1;
-                         reference=low_education V1=0,V2=0
-                         med_educ                V1=1 V2=0,
-                         high_educ               V1=0 V2=1
-                         Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
-          */
-          for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
+   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
-                  posproptt=0.;
+      reference=low_education V1=0,V2=0
-                  /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+      med_educ                V1=1 V2=0,
-                          scanf("%d", i);*/
+      high_educ               V1=0 V2=1
-                  for (i=-5; i<=nlstate+ndeath; i++)
+      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
-                          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;
-                          posprop[i]=0;
-                          pospropt[i]=0;
-                  }
-                  dateintsum=0;
-                  k2cpt=0;
-                  for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+   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 */
-                          bool=1;
+     posproptt=0.;
-                          if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-                                  for (z1=1; z1<=cptcoveff; z1++) {
+       scanf("%d", i);*/
-                                          if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
+     for (i=-5; i<=nlstate+ndeath; i++)
-                                                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
+       for (jk=-5; jk<=nlstate+ndeath; jk++)
-                                                  bool=0;
+                                 for(m=iagemin; m <= iagemax+3; m++)
-                                                  /* 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",
+                                         freq[i][jk][m]=0;
-                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+     for (i=1; i<=nlstate; i++)  {
-                                                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+       for(m=iagemin; m <= iagemax+3; m++)
-                                          }
+                                 prop[i][m]=0;
-                                  } /* end z1 */
+       posprop[i]=0;
-                          } /* cptcovn > 0 */
+       pospropt[i]=0;
+     }
-                          if (bool==1){
+     /* for (z1=1; z1<= nqfveff; z1++) {   */
-                                  /* for(m=firstpass; m<=lastpass; m++){ */
+     /*   meanq[z1]+=0.; */
-                                  for(mi=1; mi<wav[iind];mi++){
+     /*   for(m=1;m<=lastpass;m++){ */
-                                          m=mw[mi][iind];
+     /*  meanqt[m][z1]=0.; */
-                                          /* 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. */
+     /* } */
-                                          agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-                                          ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+     dateintsum=0;
-                                          if(m >=firstpass && m <=lastpass){
+     k2cpt=0;
-                                                  k2=anint[m][iind]+(mint[m][iind]/12.);
+     /* For that combination of covariate j1, we count and print the frequencies in one pass */
-                                                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-                                                  if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+       bool=1;
-                                                  if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-                                                  if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                                 if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-                                                          prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+           /* for (z1=1; z1<= nqfveff; z1++) {   */
-                                                  if (m<lastpass) {
+           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
-                                                          /* 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]); */
+                                         for (z1=1; z1<=cptcoveff; z1++) {
-                                                          if(s[m][iind]==-1)
+                                                 /* if(Tvaraff[z1] ==-20){ */
-                                                                  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.));
+                                                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-                                                          freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                                                 /* }else  if(Tvaraff[z1] ==-10){ */
-                                                          /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                                                 /*       /\* sumnew+=coqvar[z1][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 */
+                                                 /* }else  */
-                                                  }
+                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-                                          }
+                                                         /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
-                                          if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+                                                         bool=0;
-                                                  dateintsum=dateintsum+k2;
+                                                         /* 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",
-                                                  k2cpt++;
+                                                                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-                                                  /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
+                                                                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-                                          }
+                                                         /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-                                          /*}*/
+                                                 } /* Onlyf fixed */
-                                  } /* end m */
+                                         } /* end z1 */
-                          } /* end bool */
+                                 } /* cptcovn > 0 */
-                  } /* end iind = 1 to imx */
+       } /* end any */
-        /* prop[s][age] is feeded for any initial and valid live state as well as
+       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
-                                         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+                                 /* for(m=firstpass; m<=lastpass; m++){ */
+                                 for(mi=1; mi<wav[iind];mi++){ /* For that wave */
+                                         m=mw[mi][iind];
-                  /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+                                         if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-                  pstamp(ficresp);
+                                                 for (z1=1; z1<=cptcoveff; z1++) {
-                  if  (cptcovn>0) {
+                                                         if( Fixed[Tmodelind[z1]]==1){
-                          fprintf(ficresp, "\n#********** Variable ");
+                                                                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-                          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+                                                                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
-                          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+                                                                         bool=0;
-                          for (z1=1; z1<=cptcoveff; z1++){
+                                                         }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-                                  fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+                                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-                                  fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+                                                                         bool=0;
-                                  fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+                                                                 }
-                          }
+                                                         }
-                          fprintf(ficresp, "**********\n#");
+                                                 }
-                          fprintf(ficresphtm, "**********</h3>\n");
+                                         }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
-                          fprintf(ficresphtmfr, "**********</h3>\n");
+                                         /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-                          fprintf(ficlog, "\n#********** Variable ");
+                                         if(bool==1){
-                          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+                                                 /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
-                          fprintf(ficlog, "**********\n");
+                                                          and mw[mi+1][iind]. dh depends on stepm. */
-                  }
+                                                 agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-                  fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
+                                                 ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
-                  for(i=1; i<=nlstate;i++) {
+                                                 if(m >=firstpass && m <=lastpass){
-                          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+                                                         k2=anint[m][iind]+(mint[m][iind]/12.);
-                          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
+                                                         /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-                  }
+                                                         if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
-                  fprintf(ficresp, "\n");
+                                                         if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
-                  fprintf(ficresphtm, "\n");
+                                                         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 */
-                  /* Header of frequency table by age */
+                                                         if (m<lastpass) {
-                  fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
+                                                                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-                  fprintf(ficresphtmfr,"<th>Age</th> ");
+                                                                 /*   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]); */
-                  for(jk=-1; jk <=nlstate+ndeath; jk++){
+                                                                 if(s[m][iind]==-1)
-                          for(m=-1; m <=nlstate+ndeath; m++){
+                                                                         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.));
-                                  if(jk!=0 && m!=0)
+                                                                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-                                          fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
+                                                                 /* 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 */
-                  }
+                                                         }
-                  fprintf(ficresphtmfr, "\n");
+                                                 } /* end if between passes */
+                                                 if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
-                  /* For each age */
+                                                         dateintsum=dateintsum+k2;
-                  for(iage=iagemin; iage <= iagemax+3; iage++){
+                                                         k2cpt++;
-                          fprintf(ficresphtm,"<tr>");
+                                                         /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-                          if(iage==iagemax+1){
+                                                 }
-                                  fprintf(ficlog,"1");
+                                         } /* end bool 2 */
-                                  fprintf(ficresphtmfr,"<tr><th>0</th> ");
+                                 } /* end m */
-                          }else if(iage==iagemax+2){
+       } /* end bool */
-                                  fprintf(ficlog,"0");
+     } /* end iind = 1 to imx */
-                                  fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+     /* prop[s][age] is feeded for any initial and valid live state as well as
-                          }else if(iage==iagemax+3){
+        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
-                                  fprintf(ficlog,"Total");
-                                  fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-                          }else{
+     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-                                  if(first==1){
+     pstamp(ficresp);
-                                          first=0;
+     /* if  (ncoveff>0) { */
-                                          printf("See log file for details...\n");
+     if  (cptcoveff>0) {
-                                  }
+       fprintf(ficresp, "\n#********** Variable ");
-                                  fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
-                                  fprintf(ficlog,"Age %d", iage);
+       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-                          }
+       for (z1=1; z1<=cptcoveff; z1++){
-                          for(jk=1; jk <=nlstate ; jk++){
+                                 fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                                  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+                                 fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                                          pp[jk] += freq[jk][m][iage];
+                                 fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                          }
+       }
-                          for(jk=1; jk <=nlstate ; jk++){
+       fprintf(ficresp, "**********\n#");
-                                  for(m=-1, pos=0; m <=0 ; m++)
+       fprintf(ficresphtm, "**********</h3>\n");
-                                          pos += freq[jk][m][iage];
+       fprintf(ficresphtmfr, "**********</h3>\n");
-                                  if(pp[jk]>=1.e-10){
+       fprintf(ficlog, "\n#********** Variable ");
-                                          if(first==1){
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                                                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+       fprintf(ficlog, "**********\n");
-                                          }
+     }
-                                          fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-                                  }else{
+     for(i=1; i<=nlstate;i++) {
-                                          if(first==1)
+       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-                                                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-                                          fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     }
-                                  }
+     fprintf(ficresp, "\n");
-                          }
+     fprintf(ficresphtm, "\n");
-                          for(jk=1; jk <=nlstate ; jk++){
+     /* Header of frequency table by age */
-                                  /* posprop[jk]=0; */
+     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-                                  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+     fprintf(ficresphtmfr,"<th>Age</th> ");
-                                          pp[jk] += freq[jk][m][iage];
+     for(jk=-1; jk <=nlstate+ndeath; jk++){
-                          }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
+       for(m=-1; m <=nlstate+ndeath; m++){
+                                 if(jk!=0 && m!=0)
-                          for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
+                                         fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
-                                  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] */
+     fprintf(ficresphtmfr, "\n");
-                                  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 each age */
-                          }
+     for(iage=iagemin; iage <= iagemax+3; iage++){
-                          for(jk=1; jk <=nlstate ; jk++){
+       fprintf(ficresphtm,"<tr>");
-                                  if(pos>=1.e-5){
+       if(iage==iagemax+1){
-                                          if(first==1)
+                                 fprintf(ficlog,"1");
-                                                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");
-                                          fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+       }else if(iage==iagemax+2){
-                                  }else{
+                                 fprintf(ficlog,"0");
-                                          if(first==1)
+                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-                                                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+       }else if(iage==iagemax+3){
-                                          fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                 fprintf(ficlog,"Total");
-                                  }
+                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-                                  if( iage <= iagemax){
+       }else{
-                                          if(pos>=1.e-5){
+                                 if(first==1){
-                                                  fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+                                         first=0;
-                                                  fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+                                         printf("See log file for details...\n");
-                                                  /*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]);*/
+                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
-                                          }
+                                 fprintf(ficlog,"Age %d", iage);
-                                          else{
+       }
-                                                  fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+       for(jk=1; jk <=nlstate ; jk++){
-                                                  fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
+                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-                                          }
+                                         pp[jk] += freq[jk][m][iage];
-                                  }
+       }
-                                  pospropt[jk] +=posprop[jk];
+       for(jk=1; jk <=nlstate ; jk++){
-                          } /* end loop jk */
+                                 for(m=-1, pos=0; m <=0 ; m++)
-                          /* pospropt=0.; */
+                                         pos += freq[jk][m][iage];
-                          for(jk=-1; jk <=nlstate+ndeath; jk++){
+                                 if(pp[jk]>=1.e-10){
-                                  for(m=-1; m <=nlstate+ndeath; m++){
+                                         if(first==1){
-                                          if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-                                                  if(first==1){
+                                         }
-                                                          printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-                                                  }
+                                 }else{
-                                                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                                         if(first==1)
-                                          }
+                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-                                          if(jk!=0 && m!=0)
+                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-                                                  fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
+                                 }
-                                  }
+       }
-                          } /* end loop jk */
-                          posproptt=0.;
+       for(jk=1; jk <=nlstate ; jk++){
-                          for(jk=1; jk <=nlstate; jk++){
+                                 /* posprop[jk]=0; */
-                                  posproptt += pospropt[jk];
+                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-                          }
+                                         pp[jk] += freq[jk][m][iage];
-                          fprintf(ficresphtmfr,"</tr>\n ");
+       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
-                          if(iage <= iagemax){
-                                  fprintf(ficresp,"\n");
+       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
-                                  fprintf(ficresphtm,"</tr>\n");
+                                 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
-                          if(first==1)
+                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-                                  printf("Others in log...\n");
+                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
-                          fprintf(ficlog,"\n");
+                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-                  } /* end loop age iage */
+       }
-                  fprintf(ficresphtm,"<tr><th>Tot</th>");
+       for(jk=1; jk <=nlstate ; jk++){
-                  for(jk=1; jk <=nlstate ; jk++){
+                                 if(pos>=1.e-5){
-                          if(posproptt < 1.e-5){
+                                         if(first==1)
-                                  fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                          }else{
+                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                                  fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+                                 }else{
-                          }
+                                         if(first==1)
-                  }
+                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-                  fprintf(ficresphtm,"</tr>\n");
+                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-                  fprintf(ficresphtm,"</table>\n");
+                                 }
-                  fprintf(ficresphtmfr,"</table>\n");
+                                 if( iage <= iagemax){
-                  if(posproptt < 1.e-5){
+                                         if(pos>=1.e-5){
-                          fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-                          fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-                          fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
-                          invalidvarcomb[j1]=1;
+                                                 /*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(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+                                         else{
-                          invalidvarcomb[j1]=0;
+                                                 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);
-                  fprintf(ficresphtmfr,"</table>\n");
+                                         }
-          } /* end selected combination of covariate j1 */
+                                 }
-          dateintmean=dateintsum/k2cpt;
+                                 pospropt[jk] +=posprop[jk];
+       } /* end loop jk */
-          fclose(ficresp);
+       /* pospropt=0.; */
-          fclose(ficresphtm);
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
-          fclose(ficresphtmfr);
+                                 for(m=-1; m <=nlstate+ndeath; m++){
-          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
-          free_vector(pospropt,1,nlstate);
+                                                 if(first==1){
-          free_vector(posprop,1,nlstate);
+                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
-          free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+                                                 }
-          free_vector(pp,1,nlstate);
+                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
-          /* End of Freq */
+                                         }
-  }
+                                         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);
+   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);
+   /* End of freqsummary */
+ }
  /************ Prevalence ********************/
-  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
-  {
+ {
-    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+   /* 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).
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-       We still use firstpass and lastpass as another selection.
+      We still use firstpass and lastpass as another selection.
-    */
+   */
-    int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, iv;
-    int mi; /* Effective wave */
+   int mi; /* Effective wave */
-    int iage;
+   int iage;
-    double agebegin, ageend;
+   double agebegin, ageend;
-    double **prop;
+   double **prop;
-    double posprop;
+   double posprop;
-    double  y2; /* in fractional years */
+   double  y2; /* in fractional years */
-    int iagemin, iagemax;
+   int iagemin, iagemax;
-    int first; /** to stop verbosity which is redirected to log file */
+   int first; /** to stop verbosity which is redirected to log file */
-    iagemin= (int) agemin;
+   iagemin= (int) agemin;
-    iagemax= (int) agemax;
+   iagemax= (int) agemax;
-    /*pp=vector(1,nlstate);*/
+   /*pp=vector(1,nlstate);*/
-    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-    j1=0;
+   j1=0;
-    /*j=cptcoveff;*/
+   /*j=cptcoveff;*/
-    if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-    first=1;
+   first=1;
-    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
-      for (i=1; i<=nlstate; i++)
+     for (i=1; i<=nlstate; i++)
-        for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
-          prop[i][iage]=0.0;
+         prop[i][iage]=0.0;
+     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
-      for (i=1; i<=imx; i++) { /* Each individual */
+     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
-        bool=1;
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
-        if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-          for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
+     for (i=1; i<=imx; i++) { /* Each individual */
-            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
+       bool=1;
-              bool=0;
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-        }
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
-        if (bool==1) { /* For this combination of covariates values, this individual fits */
+         m=mw[mi][i];
-          /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
-          for(mi=1; mi<wav[i];mi++){
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
-            m=mw[mi][i];
+         for (z1=1; z1<=cptcoveff; z1++){
-            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+           if( Fixed[Tmodelind[z1]]==1){
-            /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-            if(m >=firstpass && m <=lastpass){
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
-              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+               bool=0;
-              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-                if(agev[m][i]==0) agev[m][i]=iagemax+1;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-                if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               bool=0;
-                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
+             }
-                  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(bool==1){ /* Otherwise we skip that wave/person */
-                }
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
-                if (s[m][i]>0 && s[m][i]<=nlstate) {
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
-                  /*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]]);*/
+           if(m >=firstpass && m <=lastpass){
-                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-                  prop[s[m][i]][iagemax+3] += weight[i];
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-                } /* end valid statuses */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-              } /* end selection of dates */
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-            } /* end selection of waves */
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
-          } /* end effective waves */
+                 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);
-        } /* end bool */
+                 exit(1);
-      }
+               }
-      for(i=iagemin; i <= iagemax+3; i++){
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-        for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+                 /*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]]);*/
-          posprop += prop[jk][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 */
-        for(jk=1; jk <=nlstate ; jk++){
+             } /* end selection of dates */
-          if( i <=  iagemax){
+           } /* end selection of waves */
-            if(posprop>=1.e-5){
+         } /* end bool */
-              probs[i][jk][j1]= prop[jk][i]/posprop;
+       } /* end wave */
-            } else{
+     } /* end individual */
-              if(first==1){
+     for(i=iagemin; i <= iagemax+3; i++){
-                first=0;
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+         posprop += prop[jk][i];
-              }
+       }
-            }
-          }
+       for(jk=1; jk <=nlstate ; jk++){
-        }/* end jk */
+         if( i <=  iagemax){
-      }/* end i */
+           if(posprop>=1.e-5){
+             probs[i][jk][j1]= prop[jk][i]/posprop;
+           } else{
+             if(first==1){
+               first=0;
+               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 jk */
+     }/* end i */
       /*} *//* end i1 */
-    } /* end j1 */
+   } /* end j1 */
-    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-    /*free_vector(pp,1,nlstate);*/
+   /*free_vector(pp,1,nlstate);*/
-    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-  }  /* End of prevalence */
+ }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- Line 4129  void  concatwav(int wav[], int **dh, int
+ Line 4423  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, firstwo, firsthree, firstfour;
+   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
- Line 4144  void  concatwav(int wav[], int **dh, int
+ Line 4438  void  concatwav(int wav[], int **dh, int
    jmin=100000;
    jmax=-1;
    jmean=0.;
+ /* Treating live states */
    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
-     mi=0;
+     mi=0;  /* First valid wave */
+     mli=0; /* Last valid wave */
      m=firstpass;
      while(s[m][i] <= nlstate){  /* a live state */
-       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 */
+       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 */
-                                 mw[++mi][i]=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 */
-       if(m >=lastpass){
+         mw[++mi][i]=m;
-                                 if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+         mli=m;
-                                         if(firsthree == 0){
+       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
-                                                 printf("Information! Unknown health 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.\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);
+       if(m < lastpass){ /* m < lastpass, standard case */
-                                                 firsthree=1;
+         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
-                                         }
+       }
-                                         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.\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);
+       else{ /* m >= lastpass, eventual special issue with warning */
-                                         mw[++mi][i]=m;
+ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
-                                 }
+         break;
-                                 if(s[m][i]==-2){ /* Vital status is really unknown */
+ #else
-                                         nbwarn++;
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
-                                         if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+           if(firsthree == 0){
-                                                 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);
+             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);
-                                                 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.\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);
+             firsthree=1;
-                                         }
+           }
-                                         break;
+           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;
-                                 break;
+           mli=m;
-       }
+         }
-       else
+         if(s[m][i]==-2){ /* Vital status is really unknown */
-                                 m++;
+           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 */
+     /* 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;
-     }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
+     }
+ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
+     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; */
-       nberr++;
        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-                                 if(firstwo==0){
+         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 */
-                                         printf("Error! Death for individual %ld line=%d  occurred %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 );
+           nbwarn++;
-                                         firstwo=1;
+           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 );
-                                 fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %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 );
+             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 */
+         /* death is known but not confirmed by death status at any wave */
-                                 if(firstfour==0){
+         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 );
+           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;
+           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 );
+         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 */
-     wav[i]=mi;
+ #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){
-                                 printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-                                 first=1;
+         first=1;
        }
        if(first==1){
-                                 fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
        }
      } /* end mi==0 */
    } /* End individuals */
- Line 4219  void  concatwav(int wav[], int **dh, int
+ Line 4543  void  concatwav(int wav[], int **dh, int
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
-                                 dh[mi][i]=1;
+         dh[mi][i]=1;
        else{
-                                 if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-                                         if (agedc[i] < 2*AGESUP) {
+           if (agedc[i] < 2*AGESUP) {
-                                                 j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-                                                 if(j==0) j=1;  /* Survives at least one month after exam */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-                                                 else if(j<0){
+             else if(j<0){
-                                                         nberr++;
+               nberr++;
-                                                         printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                                         j=1; /* Temporary Dangerous patch */
+               j=1; /* Temporary Dangerous patch */
-                                                         printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-                                                         fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                                         fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-                                                 }
+             }
-                                                 k=k+1;
+             k=k+1;
-                                                 if (j >= jmax){
+             if (j >= jmax){
-                                                         jmax=j;
+               jmax=j;
-                                                         ijmax=i;
+               ijmax=i;
-                                                 }
+             }
-                                                 if (j <= jmin){
+             if (j <= jmin){
-                                                         jmin=j;
+               jmin=j;
-                                                         ijmin=i;
+               ijmin=i;
-                                                 }
+             }
-                                                 sum=sum+j;
+             sum=sum+j;
-                                                 /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-                                                 /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-                                         }
+           }
-                                 }
+         }
-                                 else{
+         else{
-                                         j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+           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;
+           k=k+1;
-                                         if (j >= jmax) {
+           if (j >= jmax) {
-                                                 jmax=j;
+             jmax=j;
-                                                 ijmax=i;
+             ijmax=i;
-                                         }
+           }
-                                         else if (j <= jmin){
+           else if (j <= jmin){
-                                                 jmin=j;
+             jmin=j;
-                                                 ijmin=i;
+             ijmin=i;
-                                         }
+           }
-                                         /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-                                         /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-                                         if(j<0){
+           if(j<0){
-                                                 nberr++;
+             nberr++;
-                                                 printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                                 fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                         }
+           }
-                                         sum=sum+j;
+           sum=sum+j;
-                                 }
+         }
-                                 jk= j/stepm;
+         jk= j/stepm;
-                                 jl= j -jk*stepm;
+         jl= j -jk*stepm;
-                                 ju= j -(jk+1)*stepm;
+         ju= j -(jk+1)*stepm;
-                                 if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-                                         if(jl==0){
+           if(jl==0){
-                                                 dh[mi][i]=jk;
+             dh[mi][i]=jk;
-                                                 bh[mi][i]=0;
+             bh[mi][i]=0;
-                                         }else{ /* We want a negative bias in order to only have interpolation ie
+           }else{ /* We want a negative bias in order to only have interpolation ie
-                                                                         * to avoid the price of an extra matrix product in likelihood */
+                   * to avoid the price of an extra matrix product in likelihood */
-                                                 dh[mi][i]=jk+1;
+             dh[mi][i]=jk+1;
-                                                 bh[mi][i]=ju;
+             bh[mi][i]=ju;
-                                         }
+           }
-                                 }else{
+         }else{
-                                         if(jl <= -ju){
+           if(jl <= -ju){
-                                                 dh[mi][i]=jk;
+             dh[mi][i]=jk;
-                                                 bh[mi][i]=jl;   /* bias is positive if real duration
+             bh[mi][i]=jl;       /* bias is positive if real duration
-                                                                                                          * is higher than the multiple of stepm and negative otherwise.
+                                  * is higher than the multiple of stepm and negative otherwise.
-                                                                                                          */
+                                  */
-                                         }
+           }
-                                         else{
+           else{
-                                                 dh[mi][i]=jk+1;
+             dh[mi][i]=jk+1;
-                                                 bh[mi][i]=ju;
+             bh[mi][i]=ju;
-                                         }
+           }
-                                         if(dh[mi][i]==0){
+           if(dh[mi][i]==0){
-                                                 dh[mi][i]=1; /* At least one step */
+             dh[mi][i]=1; /* At least one step */
-                                                 bh[mi][i]=ju; /* At least one step */
+             bh[mi][i]=ju; /* At least one step */
-                                                 /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-                                         }
+           }
-                                 } /* end if mle */
+         } /* end if mle */
        }
      } /* end wave */
    }
    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 *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
- Line 4312  void  concatwav(int wav[], int **dh, int
+ Line 4636  void  concatwav(int wav[], int **dh, int
    /**< 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
     * Boring subroutine which should only output nbcode[Tvar[j]][k]
-    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+    * 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[2][1]=0, nbcode[2][2]=1 (usually);
+    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
    */
    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
- Line 4323  void  concatwav(int wav[], int **dh, int
+ Line 4647  void  concatwav(int wav[], int **dh, int
    /* cptcoveff=0;  */
-         *cptcov=0;
+         /* *cptcov=0; */
    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   /* Loop on covariates without age and products */
+   /* Loop on covariates without age and products and no quantitative variable */
-   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
+   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
-     for (k=-1; k < maxncov; k++) Ndum[k]=0;
+   for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
+     for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-                                                                                                                                 modality of this covariate Vj*/
+     if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+       switch(Fixed[k]) {
-                                                                                                                                                 * If product of Vn*Vm, still boolean *:
+       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-                                                                                                                                                 * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                 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*/
-                                                                                                                                                 * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+                                         ij=(int)(covar[Tvar[k]][i]);
-       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-                                       modality of the nth covariate of individual i. */
+                                          * If product of Vn*Vm, still boolean *:
-       if (ij > modmaxcovj)
+                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-         modmaxcovj=ij;
+                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-       else if (ij < modmincovj)
+                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-                                 modmincovj=ij;
+                                                  modality of the nth covariate of individual i. */
-       if ((ij < -1) && (ij > NCOVMAX)){
+                                         if (ij > modmaxcovj)
-                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+                                                 modmaxcovj=ij;
-                                 exit(1);
+                                         else if (ij < modmincovj)
-       }else
+                                                 modmincovj=ij;
-       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+                                         if ((ij < -1) && (ij > NCOVMAX)){
-       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+                                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+                                                 exit(1);
-       /* getting the maximum value of the modality of the covariate
+                                         }else
-          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-          female is 1, then modmaxcovj=1.*/
+                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-     } /* end for loop on individuals i */
+                                         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+                                         /* getting the maximum value of the modality of the covariate
-     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-     cptcode=modmaxcovj;
+                                                  female ies 1, then modmaxcovj=1.
-     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+                                         */
-    /*for (i=0; i<=cptcode; i++) {*/
+                                 } /* end for loop on individuals i */
-     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
+                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+                                 cptcode=modmaxcovj;
-       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
+                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-                                 if( k != -1){
+                                 /*for (i=0; i<=cptcode; i++) {*/
-                                         ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
+                                 for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-                                                                                                                  covariate for which somebody answered excluding
+                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                                                                                                                  undefined. Usually 2: 0 and 1. */
+                                         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;
                                  }
-                                 ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
-                                                                                                                                 covariate for which somebody answered including
-                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
-       }
-       /* In fact  ncodemax[j]=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;
-                         }
+       default:
-         ij++;
+                                 break;
-         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
+       } /* end switch */
-         cptcode = ij; /* New max modality for covar j */
+     } /* end dummy test */
-     } /* end of loop on modality i=-1 to 1 or more */
      /*   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  */
- Line 4413  void  concatwav(int wav[], int **dh, int
+ Line 4753  void  concatwav(int wav[], int **dh, int
      /*   }  /\* 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=-1; 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-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]++; /* Might be supersed V1 + V1*age */
+     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=0;
-         for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+   ij=0;
-                 /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+   /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
-                 if((Ndum[i]!=0) && (i<=ncovcol)){
+   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]);*/
-                         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-                         Tvaraff[ij]=i; /*For printing (unclear) */
+     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-                 }else{
+       /* If product not in single variable we don't print results */
-                         /* Tvaraff[ij]=0; */
+       /*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*/
-         /* ij--; */
+       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-         /* cptcoveff=ij; /\*Number of total covariates*\/ */
+       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 */
-         *cptcov=ij; /*Number of total covariates*/
+       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 */
+   ;
  }
- Line 5286  To be simple, these graphs help to under
+ Line 5648  To be simple, these graphs help to under
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
-    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */
+    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
       if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- Line 5585  void printinghtml(char fileresu[], char
+ Line 5947  void printinghtml(char fileresu[], char
           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);
         }
+        /* 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);
- Line 5700  See page 'Matrix of variance-covariance
+ Line 6063  See page 'Matrix of variance-covariance
       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]][codtabm(jj1,cpt)]);
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
- Line 5780  void printinggnuplot(char fileresu[], ch
+ Line 6143  void printinggnuplot(char fileresu[], ch
    strcpy(optfileres,"vpl");
    /* 1eme*/
    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-     for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
+     for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
- Line 5839  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 6202  plot [%.f:%.f] \"%s\" every :::%d::%d u
              /*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)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-+(cpt-1),  cpt );
++(cpt-1),  cpt );  /* 4 or 6 ?*/
              }else{
                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                kl++;
- Line 5993  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6356  plot [%.f:%.f]  ", ageminpar, agemaxpar)
        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 */
+         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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(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 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                                 vlv= nbcode[Tvaraff[k]][lv];
+         vlv= nbcode[Tvaraff[k]][lv];
-                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        }
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
-                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                                 continue;
+         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                                                                                                                                                                                     \
+ set ter svg size 640, 480\n                                             \
- unset log y\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)
+         if(j==1)
-                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-                                 else
+         else
-                                         fprintf(ficgp,", '' ");
+           fprintf(ficgp,", '' ");
-                                 l=(nlstate+ndeath)*(cpt-1) +j;
+         l=(nlstate+ndeath)*(cpt-1) +j;
-                                 fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-                                 /* for (i=2; i<= nlstate+ndeath ; i ++) */
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
-                                 /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-                                 fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
        } /* nlstate */
        fprintf(ficgp,", '' ");
        fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-                                 l=(nlstate+ndeath)*(cpt-1) +j;
+         l=(nlstate+ndeath)*(cpt-1) +j;
-                                 if(j < nlstate)
+         if(j < nlstate)
-                                         fprintf(ficgp,"$%d +",k+l);
+           fprintf(ficgp,"$%d +",k+l);
-                                 else
+         else
-                                         fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+           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 (1 to m=2**k), if any covariate is present */
      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 */
+         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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(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 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                                 vlv= nbcode[Tvaraff[k]][lv];
+         vlv= nbcode[Tvaraff[k]][lv];
-                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        }
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
-                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                                 continue;
+         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                                                                                                                                                                              \
+ set ter svg size 640, 480\n                                             \
- unset log y\n                                                                                                                                                                                                                                    \
+ unset log y\n                                                           \
  plot [%.f:%.f]  ", ageminpar, agemaxpar);
        k=3; /* Offset */
        for (i=1; i<= nlstate ; i ++){
-                                 if(i==1)
+         if(i==1)
-                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-                                 else
+         else
-                                         fprintf(ficgp,", '' ");
+           fprintf(ficgp,", '' ");
-                                 l=(nlstate+ndeath)*(i-1)+1;
+         l=(nlstate+ndeath)*(i-1)+1;
-                                 fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-                                 for (j=2; j<= nlstate ; j ++)
+         for (j=2; j<= nlstate ; j ++)
-                                         fprintf(ficgp,"+$%d",k+l+j-1);
+           fprintf(ficgp,"+$%d",k+l+j-1);
-                                 fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+         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 (1 to m=2**k), if any covariate is present */
        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);
+         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 */
+         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 */
+           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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(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];
+           vlv= nbcode[Tvaraff[k]][lv];
-                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-                                 }
+         }
-                                 fprintf(ficgp,"\n#\n");
+         fprintf(ficgp,"\n#\n");
-                                 if(invalidvarcomb[k1]){
+         if(invalidvarcomb[k1]){
-                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                                         continue;
+           continue;
-                                 }
+         }
-                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
-                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+ set ter svg size 640, 480\n                                             \
- unset log y\n                                                                                                                                                                                                                                           \
+ unset log y\n                                                           \
  plot [%.f:%.f]  ", ageminpar, agemaxpar);
-                                 k=3; /* Offset */
+         k=3; /* Offset */
-                                 for (i=1; i<= nlstate ; i ++){
+         for (i=1; i<= nlstate ; i ++){
-                                         if(i==1)
+           if(i==1)
-                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
-                                         else
+           else
-                                                 fprintf(ficgp,", '' ");
+             fprintf(ficgp,", '' ");
-                                         /* l=(nlstate+ndeath)*(i-1)+1; */
+           /* l=(nlstate+ndeath)*(i-1)+1; */
-                                         l=(nlstate+ndeath)*(cpt-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); /\* 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/($%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 */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
-                                         /* for (j=2; j<= nlstate ; j ++) */
+           /* for (j=2; j<= nlstate ; j ++) */
-                                         /*      fprintf(ficgp,"+$%d",k+l+j-1); */
+           /*    fprintf(ficgp,"+$%d",k+l+j-1); */
-                                         /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
+           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
-                                         fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
-                                 } /* nlstate */
+         } /* nlstate */
-                                 fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if backcast */
- Line 6130  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6493  plot [%.f:%.f]  ", ageminpar, agemaxpar)
      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
        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);
+         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  */
+         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 */
+           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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(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 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                                         vlv= nbcode[Tvaraff[k]][lv];
+           vlv= nbcode[Tvaraff[k]][lv];
-                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-                                 }
+         }
-                                 fprintf(ficgp,"\n#\n");
+         fprintf(ficgp,"\n#\n");
-                                 if(invalidvarcomb[k1]){
+         if(invalidvarcomb[k1]){
-                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                                         continue;
+           continue;
-                                 }
+         }
-                                 fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
+         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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
-                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+ set ter svg size 640, 480\n                                             \
- unset log y\n                                                                                                                                                                                                                                           \
+ unset log y\n                                                           \
  plot [%.f:%.f]  ", ageminpar, agemaxpar);
-                                 for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+         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*/
+           /*#  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 */
+           /*#   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*/
+           /*# 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 */
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-                                         if(i==1){
+           if(i==1){
-                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
-                                         }else{
+           }else{
-                                                 fprintf(ficgp,",\\\n '' ");
+             fprintf(ficgp,",\\\n '' ");
-                                         }
+           }
-                                         if(cptcoveff ==0){ /* No covariate */
+           if(cptcoveff ==0){ /* No covariate */
-                                                 ioffset=2; /* Age is in 2 */
+             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*/
+             /*# 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 */
+             /*#   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*/
+             /*# 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 */
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
-                                                 fprintf(ficgp," u %d:(", ioffset);
+             fprintf(ficgp," u %d:(", ioffset);
-                                                 if(i==nlstate+1)
+             if(i==nlstate+1)
-                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \
+               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 );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-                                                 else
+             else
-                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
+               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 );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-                                         }else{ /* more than 2 covariates */
+           }else{ /* more than 2 covariates */
-                                                 if(cptcoveff ==1){
+             if(cptcoveff ==1){
-                                                         ioffset=4; /* Age is in 4 */
+               ioffset=4; /* Age is in 4 */
-                                                 }else{
+             }else{
-                                                         ioffset=6; /* Age is in 6 */
+               ioffset=6; /* Age is in 6 */
-                                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+               /*#  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 */
+               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-                                                 }
+             }
-                                                 fprintf(ficgp," u %d:(",ioffset);
+             fprintf(ficgp," u %d:(",ioffset);
-                                                 kl=0;
+             kl=0;
-                                                 strcpy(gplotcondition,"(");
+             strcpy(gplotcondition,"(");
-                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+             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 */
+               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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(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 */
+               /* 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] */
+               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
-                                                         kl++;
+               kl++;
-                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
-                                                         kl++;
+               kl++;
-                                                         if(k <cptcoveff && cptcoveff>1)
+               if(k <cptcoveff && cptcoveff>1)
-                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
-                                                 }
+             }
-                                                 strcpy(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 *\/ */
+             /* 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+(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 */
+             /*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*/
+             /* ''  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){
+             if(i==nlstate+1){
-                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+               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 );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-                                                 }else{
+             }else{
-                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
+               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 );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-                                                 }
+             }
-                                         } /* end if covariate */
+           } /* end if covariate */
-                                 } /* nlstate */
+         } /* nlstate */
-                                 fprintf(ficgp,"\nset out\n");
+         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);
+         fprintf(ficgp,"#   current state %d\n",k);
-                                 for(j=1; j <=ncovmodel; j++){
+         for(j=1; j <=ncovmodel; j++){
-                                         fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
-                                         jk++;
+           jk++;
-                                 }
+         }
-                                 fprintf(ficgp,"\n");
+         fprintf(ficgp,"\n");
        }
      }
    }
    fprintf(ficgp,"##############\n#\n");
    /*goto avoid;*/
    fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
- Line 6304  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6667  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                  }
                }
                else
-                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
              }
            }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);
- Line 6331  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6694  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                    }
                  }
                  else
-                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                   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,")");
              }
- Line 6567  void prevforecast(char fileres[], double
+ Line 6930  void prevforecast(char fileres[], double
    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(k=1;k<=i1;k++){
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     if(invalidvarcomb[k]){
-       k=k+1;
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
-       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+       continue;
-       for(j=1;j<=cptcoveff;j++) {
+     }
-                                 fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
-       }
+     for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresf," yearproj age");
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       for(j=1; j<=nlstate+ndeath;j++){
+     }
-                                 for(i=1; i<=nlstate;i++)
+     fprintf(ficresf," yearproj age");
-           fprintf(ficresf," p%d%d",i,j);
+     for(j=1; j<=nlstate+ndeath;j++){
-                                 fprintf(ficresf," wp.%d",j);
+       for(i=1; i<=nlstate;i++)
-       }
+         fprintf(ficresf," p%d%d",i,j);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficresf," wp.%d",j);
-                                 fprintf(ficresf,"\n");
+     }
-                                 fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-                                 for (agec=fage; agec>=(ageminpar-1); agec--){
+       fprintf(ficresf,"\n");
-                                         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-                                         nhstepm = nhstepm/hstepm;
+       for (agec=fage; agec>=(ageminpar-1); agec--){
-                                         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-                                         oldm=oldms;savm=savms;
+         nhstepm = nhstepm/hstepm;
-                                         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
-                                         for (h=0; h<=nhstepm; h++){
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-                                                 if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n");
+         for (h=0; h<=nhstepm; h++){
-               for(j=1;j<=cptcoveff;j++)
+           if (h*hstepm/YEARM*stepm ==yearp) {
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+             fprintf(ficresf,"\n");
-                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+             for(j=1;j<=cptcoveff;j++)
-                                                 }
+               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                                                 for(j=1; j<=nlstate+ndeath;j++) {
+             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-                                                         ppij=0.;
+           }
-                                                         for(i=1; i<=nlstate;i++) {
+           for(j=1; j<=nlstate+ndeath;j++) {
-                                                                 if (mobilav==1)
+             ppij=0.;
-                                                                         ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+             for(i=1; i<=nlstate;i++) {
-                                                                 else {
+               if (mobilav==1)
-                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
-                                                                 }
+               else {
-                                                                 if (h*hstepm/YEARM*stepm== yearp) {
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
-                                                                         fprintf(ficresf," %.3f", p3mat[i][j][h]);
+               }
-                                                                 }
+               if (h*hstepm/YEARM*stepm== yearp) {
-                                                         } /* end i */
+                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                                                         if (h*hstepm/YEARM*stepm==yearp) {
+               }
-                                                                 fprintf(ficresf," %.3f", ppij);
+             } /* end i */
-                                                         }
+             if (h*hstepm/YEARM*stepm==yearp) {
-                                                 }/* end j */
+               fprintf(ficresf," %.3f", ppij);
-                                         } /* end h */
+             }
-                                         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           }/* end j */
-                                 } /* end agec */
+         } /* end h */
-       } /* end yearp */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     } /* end cptcod */
+       } /* end agec */
-   } /* end  cptcov */
+     } /* end yearp */
+   } /* end  k */
    fclose(ficresf);
    printf("End of Computing forecasting \n");
- Line 6765  void prevforecast(char fileres[], double
+ Line 7129  void prevforecast(char fileres[], double
  /* } */
  /************** Forecasting *****not tested NB*************/
- void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+ /* 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){ */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+ /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
-   int *popage;
+ /*   int *popage; */
-   double calagedatem, agelim, kk1, kk2;
+ /*   double calagedatem, agelim, kk1, kk2; */
-   double *popeffectif,*popcount;
+ /*   double *popeffectif,*popcount; */
-   double ***p3mat,***tabpop,***tabpopprev;
+ /*   double ***p3mat,***tabpop,***tabpopprev; */
-   /* double ***mobaverage; */
+ /*   /\* double ***mobaverage; *\/ */
-   char filerespop[FILENAMELENGTH];
+ /*   char filerespop[FILENAMELENGTH]; */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   agelim=AGESUP;
+ /*   agelim=AGESUP; */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+ /*   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);
+ /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
-   strcpy(filerespop,"POP_");
+ /*   strcpy(filerespop,"POP_");  */
-   strcat(filerespop,fileresu);
+ /*   strcat(filerespop,fileresu); */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+ /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
-     fprintf(ficlog,"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);
+ /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
-   fprintf(ficlog,"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;
+ /*   agelim=AGESUP; */
-   hstepm=1;
+ /*   hstepm=1; */
-   hstepm=hstepm/stepm;
+ /*   hstepm=hstepm/stepm;  */
-   if (popforecast==1) {
+ /*   if (popforecast==1) { */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+ /*       printf("Problem with population file : %s\n",popfile);exit(0); */
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
-     }
+ /*     }  */
-     popage=ivector(0,AGESUP);
+ /*     popage=ivector(0,AGESUP); */
-     popeffectif=vector(0,AGESUP);
+ /*     popeffectif=vector(0,AGESUP); */
-     popcount=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]][codtabm(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++){
+ /*        for (h=0; h<=nhstepm; h++){ */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-             }
+ /*          }  */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               kk1=0.;kk2=0;
+ /*            kk1=0.;kk2=0; */
-               for(i=1; i<=nlstate;i++) {
+ /*            for(i=1; i<=nlstate;i++) {               */
-                 if (mobilav==1)
+ /*              if (mobilav==1)  */
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
-                 else {
+ /*              else { */
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
-                 }
+ /*              } */
-               }
+ /*            } */
-               if (h==(int)(calagedatem+12*cpt)){
+ /*            if (h==(int)(calagedatem+12*cpt)){ */
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+ /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
-                 /*fprintf(ficrespop," %.3f", kk1);
+ /*              /\*fprintf(ficrespop," %.3f", kk1); */
-                   if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+ /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
-               }
+ /*            } */
-             }
+ /*          } */
-             for(i=1; i<=nlstate;i++){
+ /*          for(i=1; i<=nlstate;i++){ */
-               kk1=0.;
+ /*            kk1=0.; */
-               for(j=1; j<=nlstate;j++){
+ /*            for(j=1; j<=nlstate;j++){ */
-                 kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+ /*              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)];
+ /*            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))
+ /*          if (h==(int)(calagedatem+12*cpt)) */
-               for(j=1; j<=nlstate;j++)
+ /*            for(j=1; j<=nlstate;j++)  */
-                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+ /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
-           }
+ /*        } */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-         }
+ /*      } */
-       }
+ /*       } */
-       /******/
+ /*       /\******\/ */
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+ /*       for (cpt=1; cpt<=(anpyram1-anpyram);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++){
+ /*        for (h=0; h<=nhstepm; h++){ */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-             }
+ /*          }  */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               kk1=0.;kk2=0;
+ /*            kk1=0.;kk2=0; */
-               for(i=1; i<=nlstate;i++) {
+ /*            for(i=1; i<=nlstate;i++) {               */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
-               }
+ /*            } */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+ /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
-             }
+ /*          } */
-           }
+ /*        } */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-         }
+ /*      } */
-       }
+ /*       } */
-     }
+ /*     }  */
-   }
+ /*   } */
-   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-   if (popforecast==1) {
+ /*   if (popforecast==1) { */
-     free_ivector(popage,0,AGESUP);
+ /*     free_ivector(popage,0,AGESUP); */
-     free_vector(popeffectif,0,AGESUP);
+ /*     free_vector(popeffectif,0,AGESUP); */
-     free_vector(popcount,0,AGESUP);
+ /*     free_vector(popcount,0,AGESUP); */
-   }
+ /*   } */
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   fclose(ficrespop);
+ /*   fclose(ficrespop); */
- } /* End of popforecast */
+ /* } /\* End of popforecast *\/ */
  int fileappend(FILE *fichier, char *optionfich)
  {
- Line 7227  int readdata(char datafile[], int firsto
+ Line 7591  int readdata(char datafile[], int firsto
      /* 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, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                 }else{
+           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
-                                         errno=0;
+           if(isalpha(strb[1])) { /* .m or .d Really Missing value */
-                                         /* what_kind_of_number(strb); */
+             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);
-                                         dval=strtod(strb,&endptr);
+             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);
-                                         /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+             return 1;
-                                         /* if(strb != endptr && *endptr == '\0') */
+           }
-                                         /*    dval=dlval; */
+         }else{
-                                         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+           errno=0;
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           /* what_kind_of_number(strb); */
-                                                 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);
+           dval=strtod(strb,&endptr);
-                                                 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);
+           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
-                                                 return 1;
+           /* if(strb != endptr && *endptr == '\0') */
-                                         }
+           /*    dval=dlval; */
-                                         cotqvar[j][iv][i]=dval;
+           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
-                                 }
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                 strcpy(line,stra);
+             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;
+         }
+         strcpy(line,stra);
        }/* end loop ntqv */
        for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                 }else{
+         }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 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);
+             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);
+             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;
+             return 1;
-                                         }
+           }
-                                 }
+         }
-                                 if(lval <-1 || lval >1){
+         if(lval <-1 || lval >1){
-                                         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+           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 \
+           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                                \
   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
-                                 cotvar[j][iv][i]=(double)(lval);
+         cotvar[j][iv][i]=(double)(lval);
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntv */
        /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
        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){
        }
        else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
-                                 month=99;
+         month=99;
-                                 year=9999;
+         year=9999;
        }else{
-                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
-                                 return 1;
+         return 1;
        }
        anint[j][i]= (double) year;
        mint[j][i]= (double)month;
        strcpy(line,stra);
      } /* End loop on waves */
      /* Date of death */
      cutv(stra, strb,line,' ');
      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
- Line 7331  int readdata(char datafile[], int firsto
+ Line 7701  int readdata(char datafile[], int firsto
        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;
- Line 7348  int readdata(char datafile[], int firsto
+ Line 7718  int readdata(char datafile[], int firsto
      }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;
- Line 7372  int readdata(char datafile[], int firsto
+ Line 7742  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;
+         lval=-1;
        }else{
-                                 errno=0;
+         errno=0;
-                                 /* what_kind_of_number(strb); */
+         /* what_kind_of_number(strb); */
-                                 dval=strtod(strb,&endptr);
+         dval=strtod(strb,&endptr);
-                                 /* if(strb != endptr && *endptr == '\0') */
+         /* if(strb != endptr && *endptr == '\0') */
-                                 /*   dval=dlval; */
+         /*   dval=dlval; */
-                                 /* 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 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);
+           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);
+           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;
+           return 1;
-                                 }
+         }
-                                 coqvar[iv][i]=dval;
+         coqvar[iv][i]=dval;
+         covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
        }
        strcpy(line,stra);
      }/* end loop nqv */
- Line 7398  int readdata(char datafile[], int firsto
+ Line 7769  int readdata(char datafile[], int firsto
      for (j=ncovcol;j>=1;j--){
        cutv(stra, strb,line,' ');
        if(strb[0]=='.') { /* Missing covariate value */
-                                 lval=-1;
+         lval=-1;
        }else{
-                                 errno=0;
+         errno=0;
-                                 lval=strtol(strb,&endptr,10);
+         lval=strtol(strb,&endptr,10);
-                                 if( strb[0]=='\0' || (*endptr != '\0')){
+         if( strb[0]=='\0' || (*endptr != '\0')){
-                                         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
-                                         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
        }
        if(lval <-1 || lval >1){
-                                 printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+         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 \
+         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;
+         return 1;
        }
        covar[j][i]=(double)(lval);
        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 7445  int readdata(char datafile[], int firsto
+ Line 7816  int readdata(char datafile[], int firsto
      i=i+1;
    } /* End loop reading  data */
    *imax=i-1; /* Number of individuals */
    fclose(fic);
    return (0);
    /* endread: */
-         printf("Exiting readdata: ");
+   printf("Exiting readdata: ");
-         fclose(fic);
+   fclose(fic);
-         return (1);
+   return (1);
  }
- void removespace(char *str) {
+ void removespace(char **stri){/*, char stro[]) {*/
-   char *p1 = str, *p2 = str;
+   char *p1 = *stri, *p2 = *stri;
    do
      while (*p2 == ' ')
        p2++;
    while (*p1++ == *p2++);
+   *stri=p1;
  }
- int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+ int decoderesult ( char resultline[])
-    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
+ /**< This routine decode one result line and returns the combination # of dummy covariates only **/
-    * - 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
+   int j=0, k=0;
-    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+   char resultsav[MAXLINE];
-    * - cptcovage number of covariates with age*products =2
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-    * - 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
+   removespace(&resultline);
-    *     which is a new column after the 9 (ncovcol) variables.
+   printf("decoderesult=%s\n",resultline);
-    * - 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
+   if (strstr(resultline,"v") !=0){
-    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
-    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+     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'=' */
+   }
+   for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
+     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 */
+     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 */
+   }
+   return (0);
+ }
+ int selected( int kvar){ /* Selected combination of covariates */
+   if(Tvarsel[kvar])
+     return (0);
+   else
+     return(1);
+ }
+ 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, ks;
-   int  j1, k1, k2;
+   int  j1, k1, k2, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
    char *strpt;
- Line 7502  int decodemodel ( char model[], int last
+ Line 7916  int decodemodel ( char model[], int last
      if ((strpt=strstr(model,"age*age")) !=0){
        printf(" strpt=%s, model=%s\n",strpt, model);
        if(strpt != model){
-       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+                                 printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
   corresponding column of parameters.\n",model);
-       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+                                 fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
   corresponding column of parameters.\n",model); fflush(ficlog);
-       return 1;
+                                 return 1;
-     }
+       }
        nagesqr=1;
        if (strstr(model,"+age*age") !=0)
-         substrchaine(modelsav, model, "+age*age");
+                                 substrchaine(modelsav, model, "+age*age");
        else if (strstr(model,"age*age+") !=0)
-         substrchaine(modelsav, model, "age*age+");
+                                 substrchaine(modelsav, model, "age*age+");
        else
-         substrchaine(modelsav, model, "age*age");
+                                 substrchaine(modelsav, model, "age*age");
      }else
        nagesqr=0;
      if (strlen(modelsav) >1){
        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
        cptcovt= j+1; /* Number of total covariates in the model, not including
-                    * cst, age and age*age
+                      * cst, age and age*age
-                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
+                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
-                   /* including age products which are counted in cptcovage.
+       /* including age products which are counted in cptcovage.
-                   * but the covariates which are products must be treated
+        * but the covariates which are products must be treated
-                   * separately: ncovn=4- 2=2 (V1+V3). */
+        * separately: ncovn=4- 2=2 (V1+V3). */
        cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
        /*   Design
         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
         *  <          ncovcol=8                >
- Line 7541  int decodemodel ( char model[], int last
+ Line 7954  int decodemodel ( char model[], int last
         *   k=  1    2      3       4     5       6      7        8
         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
         *  covar[k,i], value of kth covariate if not including age for individual i:
-        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
-        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
         *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
         *  Tage[++cptcovage]=k
         *       if products, new covar are created after ncovcol with k1
- Line 7567  int decodemodel ( char model[], int last
+ Line 7980  int decodemodel ( char model[], int last
         *       {2,   1,     4,      8,    5,      6,     3,       7}
         * Struct []
         */
        /* 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  */
- Line 7582  int decodemodel ( char model[], int last
+ Line 7995  int decodemodel ( char model[], int last
        /* 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 */
+       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
-         Tvar[k]=0;
+         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 '+'
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-                                                                                                                                                                  modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-                                 if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-                                 /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-                                 /*scanf("%d",i);*/
+         /*scanf("%d",i);*/
-                                 if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         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 */
+           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 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-                                                 /* covar is not filled and then is empty */
+             /* covar is not filled and then is empty */
-                                                 cptcovprod--;
+             cptcovprod--;
-                                                 cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             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 */
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
-                                                 cptcovage++; /* Sums the number of covariates which include age as a product */
+             Typevar[k]=1;  /* 1 for age product */
-                                                 Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
-                                                 /*printf("stre=%s ", stre);*/
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
-                                         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+             /*printf("stre=%s ", stre);*/
-                                                 cptcovprod--;
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-                                                 cutl(stre,strb,strc,'V');
+             cptcovprod--;
-                                                 Tvar[k]=atoi(stre);
+             cutl(stre,strb,strc,'V');
-                                                 cptcovage++;
+             Tvar[k]=atoi(stre);
-                                                 Tage[cptcovage]=k;
+             Typevar[k]=1;  /* 1 for age product */
-                                         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+             cptcovage++;
-                                                 /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             Tage[cptcovage]=k;
-                                                 cptcovn++;
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-                                                 cptcovprodnoage++;k1++;
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-                                                 cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+             cptcovn++;
-                                                 Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+             cptcovprodnoage++;k1++;
-                                                                                                                                          because this model-covariate is a construction we invent a new column
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-                                                                                                                                          ncovcol + k1
+             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
-                                                                                                                                          If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                    because this model-covariate is a construction we invent a new column
-                                                                                                                                          Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+                                    which is after existing variables ncovcol+nqv+ntv+nqtv + k1
-                                                 cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-                                                 Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-                                                 Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Typevar[k]=2;  /* 2 for double fixed dummy covariates */
-                                                 Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-                                                 k2=k2+2;
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-                                                 Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
-                                                 Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-                                                 for (i=1; i<=lastobs;i++){
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-                                                         /* Computes the new covariate which is a product of
+             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
-                                                                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+             /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
-                                                         covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+             /* 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 */
-                                         } /* End age is not in the model */
+             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
-                                 } /* End if model includes a product */
+             for (i=1; i<=lastobs;i++){
-                                 else { /* no more sum */
+               /* Computes the new covariate which is a product of
-                                         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-                                         /*  scanf("%d",i);*/
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-                                         cutl(strd,strc,strb,'V');
+             }
-                                         ks++; /**< Number of simple covariates */
+           } /* End age is not in the model */
-                                         cptcovn++;
+         } /* End if model includes a product */
-                                         Tvar[k]=atoi(strd);
+         else { /* no more sum */
-                                 }
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-                                 strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+           /*  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);*/
+                                   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, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+     if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+                         modell[k].maintype= FTYPE;
+       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;
+       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){
+       Fixed[k]= 1;
+       Dummy[k]= 0;
+       ntveff++; /* Only simple time varying dummy variable */
+                         modell[k].maintype= VTYPE;
+                         modell[k].subtype= VD;
+       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;
+       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 */
+       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 */
+                                 }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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 */
+                                 }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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 */
+                                 }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 */
+                                 }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 */
+                                 }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 */
+                                 }
+       }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);
    return (0); /* with covar[new additional covariate if product] and Tage if age */
    /*endread:*/
-     printf("Exiting decodemodel: ");
+   printf("Exiting decodemodel: ");
-     return (1);
+   return (1);
  }
  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
- Line 7981  int prevalence_limit(double *p, double *
+ Line 8610  int prevalence_limit(double *p, double *
      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("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing 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 ");
- Line 7994  int prevalence_limit(double *p, double *
+ Line 8623  int prevalence_limit(double *p, double *
    agebase=ageminpar;
    agelim=agemaxpar;
-   i1=pow(2,cptcoveff);
+   /* i1=pow(2,ncoveff); */
+   i1=pow(2,cptcoveff); /* Number of dummy covariates */
    if (cptcovn < 1){i1=1;}
    for(k=1; k<=i1;k++){
- Line 8007  int prevalence_limit(double *p, double *
+ Line 8637  int prevalence_limit(double *p, double *
      fprintf(ficrespl,"#******");
      printf("#******");
      fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff;j++) {
+     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       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)]);
      }
      fprintf(ficrespl,"******\n");
      printf("******\n");
      fprintf(ficlog,"******\n");
-                 if(invalidvarcomb[k]){
+     if(invalidvarcomb[k]){
-                                                 printf("\nCombination (%d) ignored because no cases \n",k);
+       printf("\nCombination (%d) ignored because no case \n",k);
-                                                 fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
+       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
-                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
                                                  continue;
-                 }
+     }
      fprintf(ficrespl,"#Age ");
      for(j=1;j<=cptcoveff;j++) {
- Line 8028  int prevalence_limit(double *p, double *
+ Line 8658  int prevalence_limit(double *p, double *
      }
      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);
        fprintf(ficrespl,"%.0f ",age );
        for(j=1;j<=cptcoveff;j++)
-                                                         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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];
+         tot +=  prlim[i][i];
-                                                         fprintf(ficrespl," %.5f", prlim[i][i]);
+         fprintf(ficrespl," %.5f", prlim[i][i]);
        }
        fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
      } /* Age */
- Line 8083  int back_prevalence_limit(double *p, dou
+ Line 8713  int back_prevalence_limit(double *p, dou
    i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-         for(k=1; k<=i1;k++){
+   for(k=1; k<=i1;k++){
-   /* 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(ficresplb,"#******");
      printf("#******");
      fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff;j++) {
+     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)]);
- Line 8102  int back_prevalence_limit(double *p, dou
+ Line 8727  int back_prevalence_limit(double *p, dou
      fprintf(ficresplb,"******\n");
      printf("******\n");
      fprintf(ficlog,"******\n");
-                 if(invalidvarcomb[k]){
+     if(invalidvarcomb[k]){
-                                                 printf("\nCombination (%d) ignored because no cases \n",k);
+       printf("\nCombination (%d) ignored because no cases \n",k);
-                                                 fprintf(ficresplb,"#Combination (%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);
+       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
-                                                 continue;
+       continue;
-                 }
+     }
      fprintf(ficresplb,"#Age ");
      for(j=1;j<=cptcoveff;j++) {
- Line 8122  int back_prevalence_limit(double *p, dou
+ Line 8747  int back_prevalence_limit(double *p, dou
        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);
+         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);
+         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);
+         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);
+         exit(1);
        }else{
-                                 /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+         /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-                                 bprevalim(bprlim, probs, nlstate, p, age, 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)]);
+         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        tot=0.;
        for(i=1; i<=nlstate;i++){
-                                 tot +=  bprlim[i][i];
+         tot +=  bprlim[i][i];
-                                 fprintf(ficresplb," %.5f", bprlim[i][i]);
+         fprintf(ficresplb," %.5f", bprlim[i][i]);
        }
        fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
      } /* Age */
- Line 8343  int main(int argc, char *argv[])
+ Line 8968  int main(int argc, char *argv[])
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
    char model[MAXLINE], modeltemp[MAXLINE];
+   char resultline[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
    char *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
- Line 8653  int main(int argc, char *argv[])
+ Line 9280  int main(int argc, char *argv[])
    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-   coqvar=matrix(1,nqv,1,n);  /**< used in readdata */
+   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
-   cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< used in readdata */
+   cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */
-   cotqvar=ma3x(1,maxwav,1,ntqv,1,n);  /**< used in readdata */
+   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
- Line 8805  run imach with mle=-1 to get a correct t
+ Line 9432  run imach with mle=-1 to get a correct t
      /* Scans npar lines */
      for(i=1; i <=npar; i++){
-       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
+       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
        if(count != 3){
-                                 printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+         printf("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);
-                                 fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+         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);
+         exit(1);
        }else{
-                                 if(mle==1)
+         if(mle==1)
-                                         printf("%1d%1d%1d",i1,j1,jk);
+           printf("%1d%1d%d",i1,j1,jk);
-                         }
+       }
-       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+       fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
-       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
        for(j=1; j <=i; j++){
-                                 fscanf(ficpar," %le",&matcov[i][j]);
+         fscanf(ficpar," %le",&matcov[i][j]);
-                                 if(mle==1){
+         if(mle==1){
-                                         printf(" %.5le",matcov[i][j]);
+           printf(" %.5le",matcov[i][j]);
-                                 }
+         }
-                                 fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficlog," %.5le",matcov[i][j]);
-                                 fprintf(ficparo," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
        }
        fscanf(ficpar,"\n");
        numlinepar++;
- Line 8838  Please run with mle=-1 to get a correct
+ Line 9465  Please run with mle=-1 to get a correct
      /* 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];
+         matcov[i][j]=matcov[j][i];
      if(mle==1)
        printf("\n");
- Line 8897  Please run with mle=-1 to get a correct
+ Line 9524  Please run with mle=-1 to get a correct
          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. */
+         Tvar=ivector(1,NCOVMAX); /* Was 15 changed to 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); /*  */
+   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 8907  Please run with mle=-1 to get a correct
+ Line 9548  Please run with mle=-1 to get a correct
      ncovcol + k1
      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
      Tvar[3=V1*V4]=4+1 etc */
-   Tprod=ivector(1,NCOVMAX); /* 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,NCOVMAX); /* Unclear */
    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
- Line 8919  Please run with mle=-1 to get a correct
+ Line 9562  Please run with mle=-1 to get a correct
 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 */
- Line 8978  Please run with mle=-1 to get a correct
+ Line 9633  Please run with mle=-1 to get a correct
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
    Ndum =ivector(-1,NCOVMAX);
-         cptcoveff=0;
+   cptcoveff=0;
    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-         }
+   }
-         ncovcombmax=pow(2,cptcoveff);
+   ncovcombmax=pow(2,cptcoveff);
-         invalidvarcomb=ivector(1, ncovcombmax);
+   invalidvarcomb=ivector(1, ncovcombmax);
-         for(i=1;i<ncovcombmax;i++)
+   for(i=1;i<ncovcombmax;i++)
-                 invalidvarcomb[i]=0;
+     invalidvarcomb[i]=0;
    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
    /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
    /*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).*/
- Line 9150  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 9805  Title=%s <br>Datafile=%s Firstpass=%d La
    /* 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, invalidvarcomb, 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);
+               firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 9184  Interval (in months) between two waves:
+ Line 9839  Interval (in months) between two waves:
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
        for (m=firstpass; m<=lastpass; m++)
-                                 if (s[m][i]>nlstate) {
+         if (s[m][i]>nlstate) {
-                                         dcwave[i]=m;
+           dcwave[i]=m;
-                                         /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-                                         break;
+           break;
-                                 }
+         }
      }
      for (i=1; i<=imx; i++) {
        if (wav[i]>0){
-                                 ageexmed[i]=agev[mw[1][i]][i];
+         ageexmed[i]=agev[mw[1][i]][i];
-                                 j=wav[i];
+         j=wav[i];
-                                 agecens[i]=1.;
+         agecens[i]=1.;
-                                 if (ageexmed[i]> 1 && wav[i] > 0){
+         if (ageexmed[i]> 1 && wav[i] > 0){
-                                         agecens[i]=agev[mw[j][i]][i];
+           agecens[i]=agev[mw[j][i]][i];
-                                         cens[i]= 1;
+           cens[i]= 1;
-                                 }else if (ageexmed[i]< 1)
+         }else if (ageexmed[i]< 1)
-                                         cens[i]= -1;
+           cens[i]= -1;
-                                 if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-                                         cens[i]=0 ;
+           cens[i]=0 ;
        }
        else cens[i]=-1;
      }
      for (i=1;i<=NDIM;i++) {
        for (j=1;j<=NDIM;j++)
-                                 ximort[i][j]=(i == j ? 1.0 : 0.0);
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
      /*p[1]=0.0268; p[NDIM]=0.083;*/
- Line 9425  Please run with mle=-1 to get a correct
+ Line 10080  Please run with mle=-1 to get a correct
      printf("\n");
      /*--------- 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=1+age+%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 9433  Please run with mle=-1 to get a correct
+ Line 10088  Please run with mle=-1 to get a correct
      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
-                                 if (k != i) {
+         if (k != i) {
-                                         printf("%d%d ",i,k);
+           printf("%d%d ",i,k);
-                                         fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
-                                         fprintf(ficres,"%1d%1d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
-                                         for(j=1; j <=ncovmodel; j++){
+           for(j=1; j <=ncovmodel; j++){
-                                                 printf("%12.7f ",p[jk]);
+             printf("%12.7f ",p[jk]);
-                                                 fprintf(ficlog,"%12.7f ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
-                                                 fprintf(ficres,"%12.7f ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
-                                                 jk++;
+             jk++;
-                                         }
+           }
-                                         printf("\n");
+           printf("\n");
-                                         fprintf(ficlog,"\n");
+           fprintf(ficlog,"\n");
-                                         fprintf(ficres,"\n");
+           fprintf(ficres,"\n");
-                                 }
+         }
        }
      }
      if(mle != 0){
- Line 9456  Please run with mle=-1 to get a correct
+ Line 10111  Please run with mle=-1 to get a correct
        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++){
+         for(k=1; k <=(nlstate+ndeath); k++){
-                                         if (k != i) {
+           if (k != i) {
-                                                 printf("%d%d ",i,k);
+             printf("%d%d ",i,k);
-                                                 fprintf(ficlog,"%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
-                                                 for(j=1; j <=ncovmodel; j++){
+             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]));
+               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]));
+               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++;
+               jk++;
-                                                 }
+             }
-                                                 printf("\n");
+             printf("\n");
-                                                 fprintf(ficlog,"\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");
      for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
-                                 if (j!=i) {
+         if (j!=i) {
-                                         fprintf(ficres,"%1d%1d",i,j);
+           fprintf(ficres,"%1d%1d",i,j);
-                                         printf("%1d%1d",i,j);
+           printf("%1d%1d",i,j);
-                                         fprintf(ficlog,"%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
-                                         for(k=1; k<=ncovmodel;k++){
+           for(k=1; k<=ncovmodel;k++){
-                                                 printf(" %.5e",delti[jk]);
+             printf(" %.5e",delti[jk]);
-                                                 fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
-                                                 fprintf(ficres," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
-                                                 jk++;
+             jk++;
-                                         }
+           }
-                                         printf("\n");
+           printf("\n");
-                                         fprintf(ficlog,"\n");
+           fprintf(ficlog,"\n");
-                                         fprintf(ficres,"\n");
+           fprintf(ficres,"\n");
-                                 }
+         }
        }
      }
- Line 9515  Please run with mle=-1 to get a correct
+ Line 10170  Please run with mle=-1 to get a correct
      for(itimes=1;itimes<=2;itimes++){
        jj=0;
        for(i=1; i <=nlstate; i++){
-                                 for(j=1; j <=nlstate+ndeath; j++){
+         for(j=1; j <=nlstate+ndeath; j++){
-                                         if(j==i) continue;
+           if(j==i) continue;
-                                         for(k=1; k<=ncovmodel;k++){
+           for(k=1; k<=ncovmodel;k++){
-                                                 jj++;
+             jj++;
-                                                 ca[0]= k+'a'-1;ca[1]='\0';
+             ca[0]= k+'a'-1;ca[1]='\0';
-                                                 if(itimes==1){
+             if(itimes==1){
-                                                         if(mle>=1)
+               if(mle>=1)
-                                                                 printf("#%1d%1d%d",i,j,k);
+                 printf("#%1d%1d%d",i,j,k);
-                                                         fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-                                                         fprintf(ficres,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
-                                                 }else{
+             }else{
-                                                         if(mle>=1)
+               if(mle>=1)
-                                                                 printf("%1d%1d%d",i,j,k);
+                 printf("%1d%1d%d",i,j,k);
-                                                         fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
-                                                         fprintf(ficres,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
-                                                 }
+             }
-                                                 ll=0;
+             ll=0;
-                                                 for(li=1;li <=nlstate; li++){
+             for(li=1;li <=nlstate; li++){
-                                                         for(lj=1;lj <=nlstate+ndeath; lj++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
-                                                                 if(lj==li) continue;
+                 if(lj==li) continue;
-                                                                 for(lk=1;lk<=ncovmodel;lk++){
+                 for(lk=1;lk<=ncovmodel;lk++){
-                                                                         ll++;
+                   ll++;
-                                                                         if(ll<=jj){
+                   if(ll<=jj){
-                                                                                 cb[0]= lk +'a'-1;cb[1]='\0';
+                     cb[0]= lk +'a'-1;cb[1]='\0';
-                                                                                 if(ll<jj){
+                     if(ll<jj){
-                                                                                         if(itimes==1){
+                       if(itimes==1){
-                                                                                                 if(mle>=1)
+                         if(mle>=1)
-                                                                                                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                                                                                                 fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                                                                                                 fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                                                                                         }else{
+                       }else{
-                                                                                                 if(mle>=1)
+                         if(mle>=1)
-                                                                                                         printf(" %.5e",matcov[jj][ll]);
+                           printf(" %.5e",matcov[jj][ll]);
-                                                                                                 fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-                                                                                                 fprintf(ficres," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                                                                                         }
+                       }
-                                                                                 }else{
+                     }else{
-                                                                                         if(itimes==1){
+                       if(itimes==1){
-                                                                                                 if(mle>=1)
+                         if(mle>=1)
-                                                                                                         printf(" Var(%s%1d%1d)",ca,i,j);
+                           printf(" Var(%s%1d%1d)",ca,i,j);
-                                                                                                 fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-                                                                                                 fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
-                                                                                         }else{
+                       }else{
-                                                                                                 if(mle>=1)
+                         if(mle>=1)
-                                                                                                         printf(" %.7e",matcov[jj][ll]);
+                           printf(" %.7e",matcov[jj][ll]);
-                                                                                                 fprintf(ficlog," %.7e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
-                                                                                                 fprintf(ficres," %.7e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
-                                                                                         }
+                       }
-                                                                                 }
+                     }
-                                                                         }
+                   }
-                                                                 } /* end lk */
+                 } /* end lk */
-                                                         } /* end lj */
+               } /* end lj */
-                                                 } /* end li */
+             } /* end li */
-                                                 if(mle>=1)
+             if(mle>=1)
-                                                         printf("\n");
+               printf("\n");
-                                                 fprintf(ficlog,"\n");
+             fprintf(ficlog,"\n");
-                                                 fprintf(ficres,"\n");
+             fprintf(ficres,"\n");
-                                                 numlinepar++;
+             numlinepar++;
-                                         } /* end k*/
+           } /* end k*/
-                                 } /*end j */
+         } /*end j */
        } /* end i */
      } /* end itimes */
      fflush(ficlog);
      fflush(ficres);
-                 while(fgets(line, MAXLINE, ficpar)) {
+     while(fgets(line, MAXLINE, ficpar)) {
-                         /* If line starts with a # it is a comment */
+       /* If line starts with a # it is a comment */
-                         if (line[0] == '#') {
+       if (line[0] == '#') {
-                                 numlinepar++;
+         numlinepar++;
-                                 fputs(line,stdout);
+         fputs(line,stdout);
-                                 fputs(line,ficparo);
+         fputs(line,ficparo);
-                                 fputs(line,ficlog);
+         fputs(line,ficlog);
-                                 continue;
+         continue;
-                         }else
+       }else
-                                 break;
+         break;
-                 }
+     }
      /* while((c=getc(ficpar))=='#' && c!= EOF){ */
      /*   ungetc(c,ficpar); */
      /*   fgets(line, MAXLINE, ficpar); */
- Line 9602  Please run with mle=-1 to get a correct
+ Line 10257  Please run with mle=-1 to get a correct
      estepm=0;
      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) {
+       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);
+         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);
+         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;
+         goto end;
-                         }
+       }
-                         printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
+       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*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 */
+     /*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) {
- Line 9685  Please run with mle=-1 to get a correct
+ Line 10340  Please run with mle=-1 to get a correct
      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 */
+     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);
+       }
+       printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
+       decoderesult(resultline);
+       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); */
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
-                         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+       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\
+       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{
        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
      }
      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-                                                                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
-                                                                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
-                 /*------------ free_vector  -------------*/
+     /*------------ free_vector  -------------*/
-                 /*  chdir(path); */
+     /*  chdir(path); */
      /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
- Line 9732  Please run with mle=-1 to get a correct
+ Line 10425  Please run with mle=-1 to get a correct
      /*#include "hpijx.h"*/
      hPijx(p, bage, fage);
      fclose(ficrespij);
      /* 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<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
-                                 for(k=1;k<=ncovcombmax;k++)
+         for(k=1;k<=ncovcombmax;k++)
-                                         probs[i][j][k]=0.;
+           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(i=1;i<=AGESUP;i++)
-                                 for(j=1;j<=nlstate;j++)
+         for(j=1;j<=nlstate;j++)
-                                         for(k=1;k<=ncovcombmax;k++)
+           for(k=1;k<=ncovcombmax;k++)
-                                                 mobaverages[i][j][k]=0.;
+             mobaverages[i][j][k]=0.;
        mobaverage=mobaverages;
        if (mobilav!=0) {
-                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
+         if (movingaverage(probs, ageminpar, agemaxpar, 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);
-                                 }
+         }
        }
        /* /\* 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) {
-                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
-                                         fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
+           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
-                                         printf(" 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){
- Line 9816  Please run with mle=-1 to get a correct
+ Line 10509  Please run with mle=-1 to get a correct
      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
        fprintf(ficreseij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
-                                 fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
        fprintf(ficreseij,"******\n");
- Line 9833  Please run with mle=-1 to get a correct
+ Line 10526  Please run with mle=-1 to get a correct
      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_");
- Line 9849  Please run with mle=-1 to get a correct
+ Line 10542  Please run with mle=-1 to get a correct
      strcpy(fileresstde,"STDE_");
      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_");
      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_");
      strcat(fileresv,fileresu);
- Line 9870  Please run with mle=-1 to get a correct
+ Line 10563  Please run with mle=-1 to get a correct
        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' ... ", fileresv);fflush(stdout);
+     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
-     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
+     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
      for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       printf("\n#****** ");
        fprintf(ficrest,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
+       fprintf(ficlog,"\n#****** ");
-                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for(j=1;j<=cptcoveff;j++){
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         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(ficrest,"******\n");
+       fprintf(ficlog,"******\n");
+       printf("******\n");
        fprintf(ficresstdeij,"\n#****** ");
        fprintf(ficrescveij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
-                                 fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                                 fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
        fprintf(ficresstdeij,"******\n");
        fprintf(ficrescveij,"******\n");
        fprintf(ficresvij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
-                                 fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        fprintf(ficresvij,"******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       printf(" cvevsij %d, ",k);
+       printf(" cvevsij combination#=%d, ",k);
-       fprintf(ficlog, " cvevsij %d, ",k);
+       fprintf(ficlog, " cvevsij combination#=%d, ",k);
        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
        printf(" end cvevsij \n ");
        fprintf(ficlog, " end cvevsij \n ");
- Line 9913  Please run with mle=-1 to get a correct
+ Line 10613  Please run with mle=-1 to get a correct
        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-                                 oldm=oldms;savm=savms; /* ZZ Segmentation fault */
+         oldm=oldms;savm=savms; /* ZZ Segmentation fault */
-                                 cptcod= 0; /* To be deleted */
+         cptcod= 0; /* To be deleted */
-                                 printf("varevsij %d \n",vpopbased);
+         printf("varevsij vpopbased=%d \n",vpopbased);
-                                 fprintf(ficlog, "varevsij %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); /* cptcod not initialized Intel */
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* 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 ");
+         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)
+         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);
+           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
+         else
-                                         fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-                                 fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
-                                 for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-                                 fprintf(ficrest,"\n");
+         fprintf(ficrest,"\n");
-                                 /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\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);
+         epj=vector(1,nlstate+1);
-                                 printf("Computing age specific period (stable) prevalences in each health state \n");
+         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");
+         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
-                                 for(age=bage; age <=fage ;age++){
+         for(age=bage; age <=fage ;age++){
-                                         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
-                                         if (vpopbased==1) {
+           if (vpopbased==1) {
-                                                 if(mobilav ==0){
+             if(mobilav ==0){
-                                                         for(i=1; i<=nlstate;i++)
+               for(i=1; i<=nlstate;i++)
-                                                                 prlim[i][i]=probs[(int)age][i][k];
+                 prlim[i][i]=probs[(int)age][i][k];
-                                                 }else{ /* mobilav */
+             }else{ /* mobilav */
-                                                         for(i=1; i<=nlstate;i++)
+               for(i=1; i<=nlstate;i++)
-                                                                 prlim[i][i]=mobaverage[(int)age][i][k];
+                 prlim[i][i]=mobaverage[(int)age][i][k];
-                                                 }
+             }
-                                         }
+           }
-                                         fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
-                                         /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
-                                         /* printf(" age %4.0f ",age); */
+           /* printf(" age %4.0f ",age); */
-                                         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-                                                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
-                                                         epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
-                                                         /*ZZZ  printf("%lf %lf ", 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]); */
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
-                                                 }
+             }
-                                                 epj[nlstate+1] +=epj[j];
+             epj[nlstate+1] +=epj[j];
-                                         }
+           }
-                                         /* printf(" age %4.0f \n",age); */
+           /* printf(" age %4.0f \n",age); */
-                                         for(i=1, vepp=0.;i <=nlstate;i++)
+           for(i=1, vepp=0.;i <=nlstate;i++)
-                                                 for(j=1;j <=nlstate;j++)
+             for(j=1;j <=nlstate;j++)
-                                                         vepp += vareij[i][j][(int)age];
+               vepp += vareij[i][j][(int)age];
-                                         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-                                         for(j=1;j <=nlstate;j++){
+           for(j=1;j <=nlstate;j++){
-                                                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
-                                         }
+           }
-                                         fprintf(ficrest,"\n");
+           fprintf(ficrest,"\n");
-                                 }
+         }
        } /* End vpopbased */
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
- Line 9973  Please run with mle=-1 to get a correct
+ Line 10673  Please run with mle=-1 to get a correct
        /*}*/
      } /* End k */
-     free_vector(weight,1,n);
-     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);
-     free_ivector(cod,1,n);
-     free_ivector(tab,1,NCOVMAX);
-     fclose(ficresstdeij);
-     fclose(ficrescveij);
-     fclose(ficresvij);
-     fclose(ficrest);
-     printf("done Health expectancies\n");fflush(stdout);
-     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
-     fclose(ficpar);
-     /*------- Variance of period (stable) prevalence------*/
+     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) {
- Line 9998  Please run with mle=-1 to get a correct
+ Line 10687  Please run with mle=-1 to get a correct
      }
      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++){*/
      for (k=1; k <= (int) pow(2,cptcoveff); k++){
-         fprintf(ficresvpl,"\n#****** ");
+       fprintf(ficresvpl,"\n#****** ");
-                         for(j=1;j<=cptcoveff;j++)
+       printf("\n#****** ");
-                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficlog,"\n#****** ");
-                         fprintf(ficresvpl,"******\n");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                         oldm=oldms;savm=savms;
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
+       }
-                         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       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);
+       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,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);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
      /*---------- End : free ----------------*/
      if (mobilav!=0 ||mobilavproj !=0)
        free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
- Line 10026  Please run with mle=-1 to get a correct
+ Line 10736  Please run with mle=-1 to get a correct
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
    }  /* mle==-3 arrives here for freeing */
-  /* endfree:*/
+   /* endfree:*/
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_ma3x(cotqvar,1,maxwav,1,ntqv,1,n);
+   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
-     free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
+   free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
-     free_matrix(coqvar,1,maxwav,1,n);
+   free_matrix(coqvar,1,maxwav,1,n);
-     free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(covar,0,NCOVMAX,1,n);
-     free_matrix(matcov,1,npar,1,npar);
+   free_matrix(matcov,1,npar,1,npar);
-     free_matrix(hess,1,npar,1,npar);
+   free_matrix(hess,1,npar,1,npar);
-     /*free_vector(delti,1,npar);*/
+   /*free_vector(delti,1,npar);*/
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_matrix(agev,1,maxwav,1,imx);
+   free_matrix(agev,1,maxwav,1,imx);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(ncodemax,1,NCOVMAX);
+   free_ivector(ncodemax,1,NCOVMAX);
-     free_ivector(ncodemaxwundef,1,NCOVMAX);
+   free_ivector(ncodemaxwundef,1,NCOVMAX);
-     free_ivector(Tvar,1,NCOVMAX);
+   free_ivector(Dummy,-1,NCOVMAX);
-     free_ivector(Tprod,1,NCOVMAX);
+   free_ivector(Fixed,-1,NCOVMAX);
-     free_ivector(Tvaraff,1,NCOVMAX);
+   free_ivector(Typevar,-1,NCOVMAX);
-     free_ivector(invalidvarcomb,1,ncovcombmax);
+   free_ivector(Tvar,1,NCOVMAX);
-     free_ivector(Tage,1,NCOVMAX);
+   free_ivector(TvarFD,1,NCOVMAX);
+   free_ivector(TvarFDind,1,NCOVMAX);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   free_ivector(TvarFQ,1,NCOVMAX);
-     /* free_imatrix(codtab,1,100,1,10); */
+   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. Please look at the log file for details.\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);
- Line 10072  Please run with mle=-1 to get a correct
+ Line 10799  Please run with mle=-1 to get a correct
    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(rend_time -rstart_time,tmpout));
    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
- Line 10085  Please run with mle=-1 to get a correct
+ Line 10812  Please run with mle=-1 to get a correct
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
-    printf("Before Current directory %s!\n",pathcd);
+   printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
-    if (_chdir(pathcd) != 0)
+   if (_chdir(pathcd) != 0)
-            printf("Can't move to directory %s!\n",path);
+     printf("Can't move to directory %s!\n",path);
-    if(_getcwd(pathcd,MAXLINE) > 0)
+   if(_getcwd(pathcd,MAXLINE) > 0)
  #else
-    if(chdir(pathcd) != 0)
+     if(chdir(pathcd) != 0)
-            printf("Can't move to directory %s!\n", path);
+       printf("Can't move to directory %s!\n", path);
-    if (getcwd(pathcd, MAXLINE) > 0)
+   if (getcwd(pathcd, MAXLINE) > 0)
  #endif
      printf("Current directory %s!\n",pathcd);
    /*strcat(plotcmd,CHARSEPARATOR);*/
- Line 10121  Please run with mle=-1 to get a correct
+ Line 10848  Please run with mle=-1 to get a correct
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
      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");
- Line 10149  Please run with mle=-1 to get a correct
+ Line 10876  Please run with mle=-1 to get a correct
      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: "); fflush(stdout);
      scanf("%s",z);

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.223
changed lines
	Added in v.1.231