Diff for /imach/src/imach.c between versions 1.284 and 1.320

version 1.284, 2018/04/20 05:22:13 version 1.320, 2022/06/02 05:10:11
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.320  2022/06/02 05:10:11  brouard
     *** empty log message ***
   
     Revision 1.319  2022/06/02 04:45:11  brouard
     * imach.c (Module): Adding the Wald tests from the log to the main
     htm for better display of the maximum likelihood estimators.
   
     Revision 1.318  2022/05/24 08:10:59  brouard
     * imach.c (Module): Some attempts to find a bug of wrong estimates
     of confidencce intervals with product in the equation modelC
   
     Revision 1.317  2022/05/15 15:06:23  brouard
     * imach.c (Module):  Some minor improvements
   
     Revision 1.316  2022/05/11 15:11:31  brouard
     Summary: r27
   
     Revision 1.315  2022/05/11 15:06:32  brouard
     *** empty log message ***
   
     Revision 1.314  2022/04/13 17:43:09  brouard
     * imach.c (Module): Adding link to text data files
   
     Revision 1.313  2022/04/11 15:57:42  brouard
     * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
   
     Revision 1.312  2022/04/05 21:24:39  brouard
     *** empty log message ***
   
     Revision 1.311  2022/04/05 21:03:51  brouard
     Summary: Fixed quantitative covariates
   
             Fixed covariates (dummy or quantitative)
           with missing values have never been allowed but are ERRORS and
           program quits. Standard deviations of fixed covariates were
           wrongly computed. Mean and standard deviations of time varying
           covariates are still not computed.
   
     Revision 1.310  2022/03/17 08:45:53  brouard
     Summary: 99r25
   
     Improving detection of errors: result lines should be compatible with
     the model.
   
     Revision 1.309  2021/05/20 12:39:14  brouard
     Summary: Version 0.99r24
   
     Revision 1.308  2021/03/31 13:11:57  brouard
     Summary: Version 0.99r23
   
   
     * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
   
     Revision 1.307  2021/03/08 18:11:32  brouard
     Summary: 0.99r22 fixed bug on result:
   
     Revision 1.306  2021/02/20 15:44:02  brouard
     Summary: Version 0.99r21
   
     * imach.c (Module): Fix bug on quitting after result lines!
     (Module): Version 0.99r21
   
     Revision 1.305  2021/02/20 15:28:30  brouard
     * imach.c (Module): Fix bug on quitting after result lines!
   
     Revision 1.304  2021/02/12 11:34:20  brouard
     * imach.c (Module): The use of a Windows BOM (huge) file is now an error
   
     Revision 1.303  2021/02/11 19:50:15  brouard
     *  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
   
     Revision 1.302  2020/02/22 21:00:05  brouard
     *  (Module): imach.c Update mle=-3 (for computing Life expectancy
     and life table from the data without any state)
   
     Revision 1.301  2019/06/04 13:51:20  brouard
     Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
   
     Revision 1.300  2019/05/22 19:09:45  brouard
     Summary: version 0.99r19 of May 2019
   
     Revision 1.299  2019/05/22 18:37:08  brouard
     Summary: Cleaned 0.99r19
   
     Revision 1.298  2019/05/22 18:19:56  brouard
     *** empty log message ***
   
     Revision 1.297  2019/05/22 17:56:10  brouard
     Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
   
     Revision 1.296  2019/05/20 13:03:18  brouard
     Summary: Projection syntax simplified
   
   
     We can now start projections, forward or backward, from the mean date
     of inteviews up to or down to a number of years of projection:
     prevforecast=1 yearsfproj=15.3 mobil_average=0
     or
     prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
     or
     prevbackcast=1 yearsbproj=12.3 mobil_average=1
     or
     prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
   
     Revision 1.295  2019/05/18 09:52:50  brouard
     Summary: doxygen tex bug
   
     Revision 1.294  2019/05/16 14:54:33  brouard
     Summary: There was some wrong lines added
   
     Revision 1.293  2019/05/09 15:17:34  brouard
     *** empty log message ***
   
     Revision 1.292  2019/05/09 14:17:20  brouard
     Summary: Some updates
   
     Revision 1.291  2019/05/09 13:44:18  brouard
     Summary: Before ncovmax
   
     Revision 1.290  2019/05/09 13:39:37  brouard
     Summary: 0.99r18 unlimited number of individuals
   
     The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
   
     Revision 1.289  2018/12/13 09:16:26  brouard
     Summary: Bug for young ages (<-30) will be in r17
   
     Revision 1.288  2018/05/02 20:58:27  brouard
     Summary: Some bugs fixed
   
     Revision 1.287  2018/05/01 17:57:25  brouard
     Summary: Bug fixed by providing frequencies only for non missing covariates
   
     Revision 1.286  2018/04/27 14:27:04  brouard
     Summary: some minor bugs
   
     Revision 1.285  2018/04/21 21:02:16  brouard
     Summary: Some bugs fixed, valgrind tested
   
   Revision 1.284  2018/04/20 05:22:13  brouard    Revision 1.284  2018/04/20 05:22:13  brouard
   Summary: Computing mean and stdeviation of fixed quantitative variables    Summary: Computing mean and stdeviation of fixed quantitative variables
   
Line 968  Important routines Line 1107  Important routines
 #define POWELLNOF3INFF1TEST /* Skip test */  #define POWELLNOF3INFF1TEST /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 1034  typedef struct { Line 1174  typedef struct {
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 30  /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
 #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
 #define MAXN 20000  /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 /* #define AGESUP 130 */  /* #define AGESUP 130 */
 #define AGESUP 150  /* #define AGESUP 150 */
   #define AGESUP 200
 #define AGEINF 0  #define AGEINF 0
 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
 #define AGEBASE 40  #define AGEBASE 40
Line 1061  typedef struct { Line 1202  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";  char copyright[]="May 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 1085  int nqfveff=0; /**< nqfveff Number of Qu Line 1226  int nqfveff=0; /**< nqfveff Number of Qu
 int ntveff=0; /**< ntveff number of effective time varying variables */  int ntveff=0; /**< ntveff number of effective time varying variables */
 int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int nobs=10;  /* Number of observations in the data lastobs-firstobs */
 int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
Line 1225  double **pmmij, ***probs; /* Global poin Line 1367  double **pmmij, ***probs; /* Global poin
 double ***mobaverage, ***mobaverages; /* New global variable */  double ***mobaverage, ***mobaverages; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
     double anprojd, mprojd, jprojd; /* For eventual projections */
     double anprojf, mprojf, jprojf;
   
     double anbackd, mbackd, jbackd; /* For eventual backprojections */
     double anbackf, mbackf, jbackf;
     double jintmean,mintmean,aintmean;  
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
 double *agedc;  double *agedc;
Line 1237  double ***cotvar; /* Time varying covari Line 1384  double ***cotvar; /* Time varying covari
 double ***cotqvar; /* Time varying quantitative covariate itqv */  double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  /* Some documentation */
 /*k          1  2   3   4     5    6    7     8    9 */        /*   Design original data
 /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */         *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12 
 /* Tndvar[k]    1   2   3               4          5 */         *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
 /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */         *                                                             ntv=3     nqtv=1
 /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */         *  cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11
 /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */         * For time varying covariate, quanti or dummies
 /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */         *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
 /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */         *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
 /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */         *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
 /* Tprod[i]=k           4               7            */         *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
 /* Tage[i]=k                  5               8      */         *       covar[k,i], value of kth fixed covariate dummy or quanti :
 /* */         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
          *   k=  1    2      3       4     5       6      7        8   9     10       11 
          */
   /* According to the model, more columns can be added to covar by the product of covariates */
   /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
     # States 1=Coresidence, 2 Living alone, 3 Institution
     # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
   */
   /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /*    k        1  2   3   4     5    6    7     8    9 */
   /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/
                                                            /* fixed or varying), 1 for age product, 2 for*/
                                                            /* product */
   /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
                                                            /*(single or product without age), 2 dummy*/
                                                            /* with age product, 3 quant with age product*/
   /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
   /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
   /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
   /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
   /*    nsq      1                     2                 */ /* Counting single quantit tv */
   /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
   /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
   /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */
   /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */
   /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */
   /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */
   /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
   /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
 /* Type                    */  /* Type                    */
 /* V         1  2  3  4  5 */  /* V         1  2  3  4  5 */
 /*           F  F  V  V  V */  /*           F  F  V  V  V */
Line 1260  int *TvarsDind; Line 1436  int *TvarsDind;
 int *TvarsQ;  int *TvarsQ;
 int *TvarsQind;  int *TvarsQind;
   
 #define MAXRESULTLINES 10  #define MAXRESULTLINESPONE 10+1
 int nresult=0;  int nresult=0;
 int parameterline=0; /* # of the parameter (type) line */  int parameterline=0; /* # of the parameter (type) line */
 int TKresult[MAXRESULTLINES];  int TKresult[MAXRESULTLINESPONE];
 int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */  int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
 int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */  int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
 int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */  int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
 double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */  double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
 double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */  double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
 int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */  int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */
   
   /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
     # States 1=Coresidence, 2 Living alone, 3 Institution
     # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
   */
 /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */  /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
 int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
 int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
Line 1472  char *cutl(char *blocc, char *alocc, cha Line 1652  char *cutl(char *blocc, char *alocc, cha
 {  {
   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'     /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      gives blocc="abcdef" and alocc="ghi2j".       gives alocc="abcdef" and blocc="ghi2j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
   char *s, *t;    char *s, *t;
Line 1754  char *subdirf(char fileres[]) Line 1934  char *subdirf(char fileres[])
 /*************** function subdirf2 ***********/  /*************** function subdirf2 ***********/
 char *subdirf2(char fileres[], char *preop)  char *subdirf2(char fileres[], char *preop)
 {  {
       /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
    Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs */
   /* Caution optionfilefiname is hidden */    /* Caution optionfilefiname is hidden */
   strcpy(tmpout,optionfilefiname);    strcpy(tmpout,optionfilefiname);
   strcat(tmpout,"/");    strcat(tmpout,"/");
Line 2125  void linmin(double p[], double xi[], int Line 2307  void linmin(double p[], double xi[], int
 #endif  #endif
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
         if(fb == fx){ /* Flat function in the direction */    if(fb == fx){ /* Flat function in the direction */
                 xmin=xx;      xmin=xx;
     *flat=1;      *flat=1;
         }else{    }else{
     *flat=0;      *flat=0;
 #endif  #endif
                 /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */                  /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
Line 2186  void linmin(double p[], double xi[], int Line 2368  void linmin(double p[], double xi[], int
   
 /*************** powell ************************/  /*************** powell ************************/
 /*  /*
 Minimization of a function func of n variables. Input consists of an initial starting point  Minimization of a function func of n variables. Input consists in an initial starting point
 p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-  p[1..n] ; an initial matrix xi[1..n][1..n]  whose columns contain the initial set of di-
 rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value  rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
 such that failure to decrease by more than this amount on one iteration signals doneness. On  such that failure to decrease by more than this amount in one iteration signals doneness. On
 output, p is set to the best point found, xi is the then-current direction set, fret is the returned  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.  function value at p , and iter is the number of iterations taken. The routine linmin is used.
  */   */
Line 2214  void powell(double p[], double **xi, int Line 2396  void powell(double p[], double **xi, int
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
 #ifdef LINMINORIGINAL  
 #else  
   
   flatdir=ivector(1,n);   
   for (j=1;j<=n;j++) flatdir[j]=0;   
 #endif  
   
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
Line 2343  void powell(double p[], double **xi, int Line 2519  void powell(double p[], double **xi, int
     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */       /* 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  */      /* 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) */      /* New value of last point Pn is not computed, P(n-1) */
       for(j=1;j<=n;j++) {      for(j=1;j<=n;j++) {
                                 if(flatdir[j] >0){        if(flatdir[j] >0){
                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);          printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);          fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                 }        }
                                 /* printf("\n"); */        /* printf("\n"); */
                                 /* fprintf(ficlog,"\n"); */        /* fprintf(ficlog,"\n"); */
                         }      }
     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */      /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */      if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
Line 2388  void powell(double p[], double **xi, int Line 2564  void powell(double p[], double **xi, int
       }        }
 #endif  #endif
   
 #ifdef LINMINORIGINAL  
 #else  
       free_ivector(flatdir,1,n);   
 #endif  
       free_vector(xit,1,n);         free_vector(xit,1,n); 
       free_vector(xits,1,n);         free_vector(xits,1,n); 
       free_vector(ptt,1,n);         free_vector(ptt,1,n); 
Line 2505  void powell(double p[], double **xi, int Line 2677  void powell(double p[], double **xi, int
           }            }
           printf("\n");            printf("\n");
           fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
   #ifdef FLATSUP
             free_vector(xit,1,n); 
             free_vector(xits,1,n); 
             free_vector(ptt,1,n); 
             free_vector(pt,1,n); 
             return;
   #endif
         }          }
 #endif  #endif
         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
Line 2568  void powell(double p[], double **xi, int Line 2747  void powell(double p[], double **xi, int
   double **newm;    double **newm;
   double agefin, delaymax=200. ; /* 100 Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
     int first=0;
       
   min=vector(1,nlstate);    min=vector(1,nlstate);
   max=vector(1,nlstate);    max=vector(1,nlstate);
Line 2588  void powell(double p[], double **xi, int Line 2768  void powell(double p[], double **xi, int
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)       if(nagesqr==1){
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;
        }
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
         /* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */
       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */        /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
     }      }
     for (k=1; k<=nsq;k++) { /* For single varying covariates only */      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
         /* cov[++k1]=Tqresult[nres][k];  */
       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */        /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
     }      }
     for (k=1; k<=cptcovage;k++){  /* For product with age */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       if(Dummy[Tvar[Tage[k]]]){        if(Dummy[Tage[k]]==2){ /* dummy with age */
         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];
       } else{          /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];         } else if(Dummy[Tage[k]]==3){ /* quantitative with age */
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
           /* cov[++k1]=Tqresult[nres][k];  */
       }        }
       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */        /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
     }      }
Line 2613  void powell(double p[], double **xi, int Line 2798  void powell(double p[], double **xi, int
       if(Dummy[Tvard[k][1]==0]){        if(Dummy[Tvard[k][1]==0]){
         if(Dummy[Tvard[k][2]==0]){          if(Dummy[Tvard[k][2]==0]){
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
             /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
         }else{          }else{
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
             /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
         }          }
       }else{        }else{
         if(Dummy[Tvard[k][2]==0]){          if(Dummy[Tvard[k][2]==0]){
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
             /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
         }else{          }else{
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
             /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
         }          }
       }        }
     }      }
Line 2629  void powell(double p[], double **xi, int Line 2818  void powell(double p[], double **xi, int
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
                 /* age and covariate values of ij are in 'cov' */      /* age and covariate values of ij are in 'cov' */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           
     savm=oldm;      savm=oldm;
Line 2664  void powell(double p[], double **xi, int Line 2853  void powell(double p[], double **xi, int
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\    if(!first){
 Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);      first=1;
       printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
       fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
     }else if (first >=1 && first <10){
       fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
       first++;
     }else if (first ==10){
       fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
       printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
       fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
       first++;
     }
   
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   free_vector(min,1,nlstate);    free_vector(min,1,nlstate);
   free_vector(max,1,nlstate);    free_vector(max,1,nlstate);
Line 2733  Earliest age to start was %d-%d=%d, ncvl Line 2934  Earliest age to start was %d-%d=%d, ncvl
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */    /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */    /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
     ncvloop++;      ncvloop++;
     newm=savm; /* oldm should be kept from previous iteration or unity at start */      newm=savm; /* oldm should be kept from previous iteration or unity at start */
                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1){
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
       }
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
Line 2761  Earliest age to start was %d-%d=%d, ncvl Line 2964  Earliest age to start was %d-%d=%d, ncvl
     /*   /\* 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])]; *\/ */
     /*   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)]; */
     for (k=1; k<=cptcovage;k++){  /* For product with age */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       if(Dummy[Tvar[Tage[k]]]){        /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ ERROR ???*/
         if(Dummy[Tage[k]]== 2){ /* dummy with age */
         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];
       } else{        } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
       }        }
       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */        /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
     }      }
Line 2834  Earliest age to start was %d-%d=%d, ncvl Line 3038  Earliest age to start was %d-%d=%d, ncvl
                                   
     maxmax=0.;      maxmax=0.;
     for(i=1; i<=nlstate; i++){      for(i=1; i<=nlstate; i++){
       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */
       maxmax=FMAX(maxmax,meandiff[i]);        maxmax=FMAX(maxmax,meandiff[i]);
       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */        /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
     } /* i loop */      } /* i loop */
Line 2847  Earliest age to start was %d-%d=%d, ncvl Line 3051  Earliest age to start was %d-%d=%d, ncvl
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return bprlim;        return bprlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   if(first){    if(!first){
     first=1;      first=1;
     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\      printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
 Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
Line 2932  double **pmij(double **ps, double *cov, Line 3136  double **pmij(double **ps, double *cov,
       ps[ii][ii]=1;        ps[ii][ii]=1;
     }      }
   }    }
     
     
   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
Line 2953  double **pmij(double **ps, double *cov, Line 3157  double **pmij(double **ps, double *cov,
 /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
 {  {
   /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.    /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
    */     */
   int i, ii, j,k;    int i, ii, j,k;
Line 2961  double **pmij(double **ps, double *cov, Line 3165  double **pmij(double **ps, double *cov,
   double **out, **pmij();    double **out, **pmij();
   double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
   double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */    double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
   double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
   double **bbmij;    double **bbmij;
       
   doldm=ddoldms; /* global pointers */    doldm=ddoldms; /* global pointers */
   dnewm=ddnewms;    dnewm=ddnewms;
   dsavm=ddsavms;    dsavm=ddsavms;
     
     /* Debug */
     /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
   agefin=cov[2];    agefin=cov[2];
   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */    /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
   /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* bmij *//* age is cov[2], ij is included in cov, but we need for
Line 2980  double **pmij(double **ps, double *cov, Line 3186  double **pmij(double **ps, double *cov,
   /* outputs pmmij which is a stochastic matrix in row */    /* outputs pmmij which is a stochastic matrix in row */
   
   /* Diag(w_x) */    /* Diag(w_x) */
   /* Problem with prevacurrent which can be zero */    /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
   sumnew=0.;    sumnew=0.;
   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/    /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */    for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */      /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
     sumnew+=prevacurrent[(int)agefin][ii][ij];      sumnew+=prevacurrent[(int)agefin][ii][ij];
   }    }
   if(sumnew >0.01){  /* At least some value in the prevalence */    if(sumnew >0.01){  /* At least some value in the prevalence */
Line 3007  double **pmij(double **ps, double *cov, Line 3213  double **pmij(double **ps, double *cov,
   }    }
   /* End doldm, At the end doldm is diag[(w_i)] */    /* End doldm, At the end doldm is diag[(w_i)] */
       
   /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */    /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */    bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
   
   /* Diag(Sum_i w^i_x p^ij_x */    /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */    /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
   for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
     sumnew=0.;      sumnew=0.;
Line 3028  double **pmij(double **ps, double *cov, Line 3234  double **pmij(double **ps, double *cov,
     } /*End ii */      } /*End ii */
   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */    } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
   
   ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */    /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
   /* end bmij */    /* end bmij */
   return ps; /*pointer is unchanged */    return ps; /*pointer is unchanged */
Line 3100  double **bpmij(double **ps, double *cov, Line 3306  double **bpmij(double **ps, double *cov,
       ps[ii][ii]=1;        ps[ii][ii]=1;
     }      }
   }    }
   /* Added for backcast */ /* Transposed matrix too */    /* Added for prevbcast */ /* Transposed matrix too */
   for(jj=1; jj<= nlstate+ndeath; jj++){    for(jj=1; jj<= nlstate+ndeath; jj++){
     s1=0.;      s1=0.;
     for(ii=1; ii<= nlstate+ndeath; ii++){      for(ii=1; ii<= nlstate+ndeath; ii++){
Line 3188  double ***hpxij(double ***po, int nhstep Line 3394  double ***hpxij(double ***po, int nhstep
       cov[1]=1.;        cov[1]=1.;
       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1){
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
         }
       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */  /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
           /* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 */
   /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /*    k        1  2   3   4     5    6    7     8    9 */
   /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
   /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
   /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
   /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
         /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */          /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
       }        }
       for (k=1; k<=nsq;k++) { /* For single varying covariates only */        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];           cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       }        }
       for (k=1; k<=cptcovage;k++){        for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1*age +V4 +age*V3 */
         if(Dummy[Tvar[Tage[k]]]){          /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/
           /* */
           if(Dummy[Tage[k]]== 2){ /* dummy with age */
           /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ */
           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];
         } else{          } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
         }          }
         /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */          /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }        }
       for (k=1; k<=cptcovprod;k++){ /*  */        for (k=1; k<=cptcovprod;k++){ /*  For product without age */
         /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */          /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
           if(Dummy[Tvard[k][1]==0]){
             if(Dummy[Tvard[k][2]==0]){
               cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
             }else{
               cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
             }
           }else{
             if(Dummy[Tvard[k][2]==0]){
               cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
             }else{
               cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
             }
           }
       }        }
       /* for (k=1; k<=cptcovn;k++)  */        /* 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)]; */
Line 3222  double ***hpxij(double ***po, int nhstep Line 3452  double ***hpxij(double ***po, int nhstep
               
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                         /* right multiplication of oldm by the current matrix */        /* right multiplication of oldm by the current matrix */
       out=matprod2(newm,oldm,1,nlstate+ndeath,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));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       /* if((int)age == 70){ */        /* if((int)age == 70){ */
Line 3292  double ***hbxij(double ***po, int nhstep Line 3522  double ***hbxij(double ***po, int nhstep
       cov[1]=1.;        cov[1]=1.;
       agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */        agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
           /* Debug */
         /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
Line 3306  double ***hbxij(double ***po, int nhstep Line 3538  double ***hbxij(double ***po, int nhstep
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];           cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       }        }
       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */        for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */
         if(Dummy[Tvar[Tage[k]]]){          /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */
           if(Dummy[Tage[k]]== 2){ /* dummy with age */
           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];
         } else{          } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
         }          }
         /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */          /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
Line 3411  double func( double *x) Line 3644  double func( double *x)
       */        */
       ioffset=2+nagesqr ;        ioffset=2+nagesqr ;
    /* Fixed */     /* Fixed */
       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */        for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/          /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
           /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
           /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
           /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
           cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
           /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
       }        }
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]            is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6 
          has been calculated etc */           has been calculated etc */
       /* For an individual i, wav[i] gives the number of effective waves */        /* For an individual i, wav[i] gives the number of effective waves */
       /* We compute the contribution to Likelihood of each effective transition        /* We compute the contribution to Likelihood of each effective transition
Line 3427  double func( double *x) Line 3665  double func( double *x)
          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(mi=1; mi<= wav[i]-1; mi++){
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/          for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */            /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];            cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
         }          }
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
Line 3443  double func( double *x) Line 3681  double func( double *x)
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;  /* Should be changed here */              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
           if(!FixedV[Tvar[Tage[kk]]])              if(!FixedV[Tvar[Tage[kk]]])
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */                cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
           else              else
             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;                cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
           }            }
           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));
Line 3554  double func( double *x) Line 3792  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }  else if(mle==2){    }  else if(mle==2){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      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 ;
         for (k=1; k<=ncovf;k++)
           cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(k=1; k <= ncovv ; k++){
             cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
           }
         for (ii=1;ii<=nlstate+ndeath;ii++)          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);
Line 3733  double funcone( double *x) Line 3976  double funcone( double *x)
     /* Fixed */      /* Fixed */
     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */      for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
       cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/        cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
 /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */  /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
 /*    cov[2+6]=covar[Tvar[6]][i];  */  /*    cov[2+6]=covar[Tvar[6]][i];  */
Line 3860  return -l; Line 4103  return -l;
   
   
 /*************** function likelione ***********/  /*************** function likelione ***********/
 void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
 {  {
   /* This routine should help understanding what is done with     /* This routine should help understanding what is done with 
      the selection of individuals/waves and       the selection of individuals/waves and
Line 3884  void likelione(FILE *ficres,double p[], Line 4127  void likelione(FILE *ficres,double p[],
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   
   *fretone=(*funcone)(p);    *fretone=(*func)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     if (mle ==0)      if (mle ==0)
Line 3912  void likelione(FILE *ficres,double p[], Line 4155  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter=0;    int i,j,k, jk, jkk=0, iter=0;
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
Line 3946  void mlikeli(FILE *ficres,double p[], in Line 4189  void mlikeli(FILE *ficres,double p[], in
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");    fprintf(ficrespow,"\n");
 #ifdef POWELL  #ifdef POWELL
   #ifdef LINMINORIGINAL
   #else /* LINMINORIGINAL */
     
     flatdir=ivector(1,npar); 
     for (j=1;j<=npar;j++) flatdir[j]=0; 
   #endif /*LINMINORIGINAL */
   
   #ifdef FLATSUP
     powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
     /* reorganizing p by suppressing flat directions */
     for(i=1, jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
           if(flatdir[jk]==1){
             printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
           }
           for(j=1; j <=ncovmodel; j++){
             printf("%12.7f ",p[jk]);
             jk++; 
           }
           printf("\n");
         }
       }
     }
   /* skipping */
     /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
     for(i=1, jk=1, jkk=1;i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
           if(flatdir[jk]==1){
             printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
             for(j=1; j <=ncovmodel;  jk++,j++){
               printf(" p[%d]=%12.7f",jk, p[jk]);
               /*q[jjk]=p[jk];*/
             }
           }else{
             printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
             for(j=1; j <=ncovmodel;  jk++,jkk++,j++){
               printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
               /*q[jjk]=p[jk];*/
             }
           }
           printf("\n");
         }
         fflush(stdout);
       }
     }
     powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
   #else  /* FLATSUP */
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
 #endif  #endif  /* FLATSUP */
   
   #ifdef LINMINORIGINAL
   #else
         free_ivector(flatdir,1,npar); 
   #endif  /* LINMINORIGINAL*/
   #endif /* POWELL */
   
 #ifdef NLOPT  #ifdef NLOPT
 #ifdef NEWUOA  #ifdef NEWUOA
Line 3975  void mlikeli(FILE *ficres,double p[], in Line 4275  void mlikeli(FILE *ficres,double p[], in
   }    }
   nlopt_destroy(opt);    nlopt_destroy(opt);
 #endif  #endif
   #ifdef FLATSUP
     /* npared = npar -flatd/ncovmodel; */
     /* xired= matrix(1,npared,1,npared); */
     /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
     /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
     /* free_matrix(xire,1,npared,1,npared); */
   #else  /* FLATSUP */
   #endif /* FLATSUP */
   free_matrix(xi,1,npar,1,npar);    free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
Line 4359  void pstamp(FILE *fichier) Line 4667  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
   void date2dmy(double date,double *day, double *month, double *year){
     double yp=0., yp1=0., yp2=0.;
     
     yp1=modf(date,&yp);/* extracts integral of date in yp  and
                           fractional in yp1 */
     *year=yp;
     yp2=modf((yp1*12),&yp);
     *month=yp;
     yp1=modf((yp2*30.5),&yp);
     *day=yp;
     if(*day==0) *day=1;
     if(*month==0) *month=1;
   }
   
   
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
Line 4412  void  freqsummary(char fileres[], double Line 4734  void  freqsummary(char fileres[], double
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\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 and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);    fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
       
   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
Line 4422  Title=%s <br>Datafile=%s Firstpass=%d La Line 4744  Title=%s <br>Datafile=%s Firstpass=%d La
     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                                    \  ,<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",\  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 of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);
       
   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);    y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);    x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
Line 4574  Title=%s <br>Datafile=%s Firstpass=%d La Line 4896  Title=%s <br>Datafile=%s Firstpass=%d La
                   if(s[m][iind]==-1)                    if(s[m][iind]==-1)
                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));                      printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */                    for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
                     idq[z1]=idq[z1]+weight[iind];                      if(!isnan(covar[ncovcol+z1][iind])){
                     meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */                          idq[z1]=idq[z1]+weight[iind];
                     stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */                          meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                           /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
                           stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                       }
                   }                    }
                   /* if((int)agev[m][iind] == 55) */                    /* if((int)agev[m][iind] == 55) */
                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */                    /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
Line 4601  Title=%s <br>Datafile=%s Firstpass=%d La Line 4926  Title=%s <br>Datafile=%s Firstpass=%d La
           /* } */            /* } */
         } /* end bool */          } /* end bool */
       } /* end iind = 1 to imx */        } /* end iind = 1 to imx */
       /* prop[s][age] is feeded for any initial and valid live state as well as        /* prop[s][age] is fed for any initial and valid live state as well as
          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */           freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
               
               
Line 4640  Title=%s <br>Datafile=%s Firstpass=%d La Line 4965  Title=%s <br>Datafile=%s Firstpass=%d La
         Printing means of quantitative variables if any          Printing means of quantitative variables if any
       */        */
       for (z1=1; z1<= nqfveff; z1++) {        for (z1=1; z1<= nqfveff; z1++) {
         fprintf(ficlog,"Mean of quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);          fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
         fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);          fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
         if(weightopt==1){          if(weightopt==1){
           printf(" Weighted mean and standard deviation of");            printf(" Weighted mean and standard deviation of");
           fprintf(ficlog," Weighted mean and standard deviation of");            fprintf(ficlog," Weighted mean and standard deviation of");
           fprintf(ficresphtmfr," Weighted mean and standard deviation of");            fprintf(ficresphtmfr," Weighted mean and standard deviation of");
         }          }
         printf(" quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));          /* mu = \frac{w x}{\sum w}
         fprintf(ficlog," quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));             var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2 
         fprintf(ficresphtmfr," quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));          */
           printf(" fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
           fprintf(ficlog," fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
           fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
       }        }
       /* for (z1=1; z1<= nqtveff; z1++) { */        /* for (z1=1; z1<= nqtveff; z1++) { */
       /*        for(m=1;m<=lastpass;m++){ */        /*        for(m=1;m<=lastpass;m++){ */
Line 4933  Title=%s <br>Datafile=%s Firstpass=%d La Line 5261  Title=%s <br>Datafile=%s Firstpass=%d La
     }      }
   } /* end mle=-2 */    } /* end mle=-2 */
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
     date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
       
   fclose(ficresp);    fclose(ficresp);
   fclose(ficresphtm);    fclose(ficresphtm);
Line 5046  void prevalence(double ***probs, double Line 5375  void prevalence(double ***probs, double
   /*j=cptcoveff;*/    /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;    first=0;
   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+4+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
Line 5104  void prevalence(double ***probs, double Line 5433  void prevalence(double ***probs, double
           if(posprop>=1.e-5){             if(posprop>=1.e-5){ 
             probs[i][jk][j1]= prop[jk][i]/posprop;              probs[i][jk][j1]= prop[jk][i]/posprop;
           } else{            } else{
             if(first==1){              if(!first){
               first=0;                first=1;
               printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);                printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);  
             }else{              }else{
               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);                fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
             }              }
           }            }
         }           } 
Line 5127  void prevalence(double ***probs, double Line 5455  void prevalence(double ***probs, double
   
 void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 {  {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
      Death is a valid wave (if date is known).       Death is a valid wave (if date is known).
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       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]       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. s[m][i] exists for any wave from firstpass to lastpass
   */    */
   
   int i=0, mi=0, m=0, mli=0;    int i=0, mi=0, m=0, mli=0;
Line 5152  void  concatwav(int wav[], int **dh, int Line 5480  void  concatwav(int wav[], int **dh, int
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;  /* First valid wave */      mi=0;  /* First valid wave */
     mli=0; /* Last valid wave */      mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;  /* Loop on waves */
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state or unknown state  */
       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 */        if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
         mli=m-1;/* mw[++mi][i]=m-1; */          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 */        }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
         mw[++mi][i]=m;          mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
         mli=m;          mli=m;
       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
       if(m < lastpass){ /* m < lastpass, standard case */        if(m < lastpass){ /* m < lastpass, standard case */
         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */          m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }        }
       else{ /* m >= lastpass, eventual special issue with warning */        else{ /* m = lastpass, eventual special issue with warning */
 #ifdef UNKNOWNSTATUSNOTCONTRIBUTING  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
         break;          break;
 #else  #else
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\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, s[m][i], nlstate+ndeath);              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 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
             firsthree=1;              firsthree=1;
             }else if(firsthree >=1 && firsthree < 10){
               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 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
               firsthree++;
             }else if(firsthree == 10){
               printf("Information, too many Information flags: no more reported to log either\n");
               fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
               firsthree++;
             }else{
               firsthree++;
           }            }
           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 1-p%d%d .\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, s[m][i], nlstate+ndeath);            mw[++mi][i]=m; /* Valid transition with unknown status */
           mw[++mi][i]=m;  
           mli=m;            mli=m;
         }          }
         if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
           nbwarn++;            nbwarn++;
           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */            if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
             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("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);              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);
           }            }
Line 5203  void  concatwav(int wav[], int **dh, int Line 5539  void  concatwav(int wav[], int **dh, int
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     else if ((int) andc[i] != 9999) {  /* Date of death is known */      else if ((int) andc[i] != 9999) {  /* Date of death is known */
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
           nbwarn++;            nbwarn++;
           if(firstfiv==0){            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 );              printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
             firstfiv=1;              firstfiv=1;
           }else{            }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 );              fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %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 */              s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
           }else{ /* Month of Death occured afer last wave month, potential bias */
           nberr++;            nberr++;
           if(firstwo==0){            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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\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 at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\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 );
             firstwo=1;              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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\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 at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\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{ /* if date of interview is unknown */        }else{ /* if date of interview is unknown */
         /* 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 with status %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], s[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  with status %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], s[m][i], i,m );
       }        }
     } /* end if date of death is known */      } /* end if date of death is known */
 #endif  #endif
     wav[i]=mi; /* mi should be the last effective wave (or mli) */      wav[i]=mi; /* mi should be the last effective wave (or mli),  */
     /* wav[i]=mw[mi][i]; */      /* wav[i]=mw[mi][i];   */
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
Line 5244  void  concatwav(int wav[], int **dh, int Line 5581  void  concatwav(int wav[], int **dh, int
   } /* End individuals */    } /* End individuals */
   /* wav and mw are no more changed */    /* wav and mw are no more changed */
                   
       printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
     fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
   
   
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
Line 5355  void  concatwav(int wav[], int **dh, int Line 5695  void  concatwav(int wav[], int **dh, int
    /* *cptcov=0; */     /* *cptcov=0; */
     
    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
      for (k=1; k <= maxncov; k++)
        for(j=1; j<=2; j++)
          nbcode[k][j]=0; /* Valgrind */
   
    /* Loop on covariates without age and products and no quantitative variable */     /* 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 (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */     for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
      for (j=-1; (j < maxncov); j++) Ndum[j]=0;       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */        if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
        switch(Fixed[k]) {         switch(Fixed[k]) {
        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
            modmaxcovj=0;
            modmincovj=0;
          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*/           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*/
            ij=(int)(covar[Tvar[k]][i]);             ij=(int)(covar[Tvar[k]][i]);
            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
Line 5375  void  concatwav(int wav[], int **dh, int Line 5719  void  concatwav(int wav[], int **dh, int
              modmaxcovj=ij;                modmaxcovj=ij; 
            else if (ij < modmincovj)              else if (ij < modmincovj) 
              modmincovj=ij;                modmincovj=ij; 
            if ((ij < -1) && (ij > NCOVMAX)){             if (ij <0 || ij >1 ){
                printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
                fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
                fflush(ficlog);
                exit(1);
              }
              if ((ij < -1) || (ij > NCOVMAX)){
              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
              exit(1);               exit(1);
            }else             }else
Line 5421  void  concatwav(int wav[], int **dh, int Line 5771  void  concatwav(int wav[], int **dh, int
          /* nbcode[Tvar[j]][3]=2; */           /* nbcode[Tvar[j]][3]=2; */
          /* To be continued (not working yet). */           /* To be continued (not working yet). */
          ij=0; /* ij is similar to i but can jump over null modalities */           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*/  
            /* 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*/
            /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
            /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
             * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
            /*, could be restored in the future */
            for (i=0; i<=1; 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 */             if (Ndum[i] == 0) { /* If nobody responded to this modality k */
              break;               break;
            }             }
            ij++;             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*/             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 . Could be -1*/
            cptcode = ij; /* New max modality for covar j */             cptcode = ij; /* New max modality for covar j */
          } /* end of loop on modality i=-1 to 1 or more */           } /* end of loop on modality i=-1 to 1 or more */
          break;           break;
Line 5442  void  concatwav(int wav[], int **dh, int Line 5798  void  concatwav(int wav[], int **dh, int
          break;           break;
        } /* end switch */         } /* end switch */
      } /* end dummy test */       } /* end dummy test */
            if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */         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*/
      /*         /\*recode from 0 *\/ */           if(isnan(covar[Tvar[k]][i])){
      /*                                      k is a modality. If we have model=V1+V1*sex  */             printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */             fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */             fflush(ficlog);
      /*         } */             exit(1);
      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */           }
      /*         if (ij > ncodemax[j]) { */         }
      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */       }
      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */     } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
      /*           break; */  
      /*         } */  
      /*   }  /\* end of loop on modality k *\/ */  
    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/    
       
    for (k=-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 */     /* Look at fixed dummy (single or product) covariates to check empty modalities */
Line 5769  void  concatwav(int wav[], int **dh, int Line 6121  void  concatwav(int wav[], int **dh, int
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                       /* if((int)age ==50){ */
       /*   printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
       /* } */
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
Line 5840  void  concatwav(int wav[], int **dh, int Line 6194  void  concatwav(int wav[], int **dh, int
    double **dnewm,**doldm;     double **dnewm,**doldm;
    double **dnewmp,**doldmp;     double **dnewmp,**doldmp;
    int i, j, nhstepm, hstepm, h, nstepm ;     int i, j, nhstepm, hstepm, h, nstepm ;
      int first=0;
    int k;     int k;
    double *xp;     double *xp;
    double **gp, **gm;  /**< for var eij */     double **gp, **gm;  /**< for var eij */
Line 5964  void  concatwav(int wav[], int **dh, int Line 6319  void  concatwav(int wav[], int **dh, int
        }         }
        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and          /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
         * returns into prlim .          * returns into prlim .
         */                        */
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
   
        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */         /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
Line 5977  void  concatwav(int wav[], int **dh, int Line 6332  void  concatwav(int wav[], int **dh, int
              prlim[i][i]=mobaverage[(int)age][i][ij];               prlim[i][i]=mobaverage[(int)age][i][ij];
          }           }
        }         }
        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.         /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
         */                                */                      
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability         /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
         * at horizon h in state j including mortality.          * at horizon h in state j including mortality.
         */          */
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
Line 6002  void  concatwav(int wav[], int **dh, int Line 6357  void  concatwav(int wav[], int **dh, int
                                                   
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);           xp[i] = x[i] - (i==theta ?delti[theta]:0);
                           
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
Line 6188  void  concatwav(int wav[], int **dh, int Line 6543  void  concatwav(int wav[], int **dh, int
   int theta;    int theta;
       
   pstamp(ficresvpl);    pstamp(ficresvpl);
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");    fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
   fprintf(ficresvpl,"# Age ");    fprintf(ficresvpl,"# Age ");
   if(nresult >=1)    if(nresult >=1)
     fprintf(ficresvpl," Result# ");      fprintf(ficresvpl," Result# ");
Line 6217  void  concatwav(int wav[], int **dh, int Line 6572  void  concatwav(int wav[], int **dh, int
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
         mgp[theta][i] = prlim[i][i];          mgp[theta][i] = prlim[i][i];
       }        }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
         mgm[theta][i] = prlim[i][i];          mgm[theta][i] = prlim[i][i];
Line 6279  void  concatwav(int wav[], int **dh, int Line 6634  void  concatwav(int wav[], int **dh, int
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficresvpl,"%.0f ",age );
     if(nresult >=1)      if(nresult >=1)
       fprintf(ficresvpl,"%d ",nres );        fprintf(ficresvpl,"%d ",nres );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         /* for(j=1;j<=nlstate;j++) */
         /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
       }
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
Line 6497  void varprob(char optionfilefiname[], do Line 6855  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");     fprintf(fichtm,"\n");
   
    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov);     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
Line 6530  To be simple, these graphs help to under Line 6888  To be simple, these graphs help to under
                                                   
                                                   
        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                                                   
        fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "\n#********** Variable ");    
Line 6559  To be simple, these graphs help to under Line 6918  To be simple, these graphs help to under
                                                                     */                                                                      */
          /* nbcode[1][1]=0 nbcode[1][2]=1;*/           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
        }         }
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */         /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];         /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
          /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          for (k=1; k<=cptcovage;k++)
            cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
        for (k=1; k<=cptcovprod;k++)         for (k=1; k<=cptcovprod;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,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                                                   
Line 6767  To be simple, these graphs help to under Line 7129  To be simple, these graphs help to under
 void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \                    int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
   int jj1, k1, i1, cpt, k4, nres;    int jj1, k1, i1, cpt, k4, nres;
     /* In fact some results are already printed in fichtm which is open */
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 </ul>");  </ul>");
    fprintf(fichtm,"<ul><li> model=1+age+%s\n \  /*    fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
 </ul>", model);  /* </ul>", model); */
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 6790  void printinghtml(char fileresu[], char Line 7152  void printinghtml(char fileresu[], char
  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));             stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
Line 6809  void printinghtml(char fileresu[], char Line 7171  void printinghtml(char fileresu[], char
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
   
    jj1=0;     jj1=0;
   
Line 6844  void printinghtml(char fileresu[], char Line 7206  void printinghtml(char fileresu[], char
        fprintf(fichtm,"</a></li>");         fprintf(fichtm,"</a></li>");
      } /* cptcovn >0 */       } /* cptcovn >0 */
    }     }
      fprintf(fichtm," \n</ul>");     fprintf(fichtm," \n</ul>");
   
    jj1=0;     jj1=0;
   
Line 6899  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7261  divided by h: <sub>h</sub>P<sub>ij</sub>
 <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\         fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   And probability to be observed in various states (up to %d) being in state %d at different ages.       \
  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);   <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (forward stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(backcast==1){       if(prevbcast==1){
        /* Period (stable) back prevalence in each health state */         /* Backward prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
        }         }
      }       }
      if(prevfcast==1){       if(prevfcast==1){
        /* Projection of prevalence up to period (stable) prevalence in each health state */         /* Projection of prevalence up to period (forward stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
            fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
                    subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
        }         }
      }       }
      if(backcast==1){       if(prevbcast==1){
       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */        /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \           fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \   from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \   account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
 with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \  with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
            fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
        }         }
      }       }
                     
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);         fprintf(fichtm," (data from text file  <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
      }       }
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
Line 6976  See page 'Matrix of variance-covariance Line 7342  See page 'Matrix of variance-covariance
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
Line 6992  See page 'Matrix of variance-covariance Line 7358  See page 'Matrix of variance-covariance
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);     fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  
   
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
   
     jj1=0;
   
      fprintf(fichtm," \n<ul>");
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\">");
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          fprintf(fichtm,"************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          if(invalidvarcomb[k1]){
            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
            continue;
          }
          fprintf(fichtm,"</a></li>");
        } /* cptcovn >0 */
      }
      fprintf(fichtm," \n</ul>");
   
    jj1=0;     jj1=0;
   
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
Line 7006  See page 'Matrix of variance-covariance Line 7408  See page 'Matrix of variance-covariance
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
          fprintf(fichtm,"\n<p><a name=\"rescovsecond");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\"</a>");
          
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */         for (cpt=1; cpt<=cptcoveff;cpt++){  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
            printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */           /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          }
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }        }
Line 7023  See page 'Matrix of variance-covariance Line 7436  See page 'Matrix of variance-covariance
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
 <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);       fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
        fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
   }/* End nres */    }/* End nres */
Line 7040  true period expectancies (those weighted Line 7455  true period expectancies (those weighted
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   char gplotcondition[132], gplotlabel[132];    char gplotcondition[132], gplotlabel[132];
Line 7118  void printinggnuplot(char fileresu[], ch Line 7533  void printinggnuplot(char fileresu[], ch
           continue;            continue;
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
Line 7156  void printinggnuplot(char fileresu[], ch Line 7571  void printinggnuplot(char fileresu[], ch
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else        fprintf(ficgp," %%*lf (%%*lf)");            else        fprintf(ficgp," %%*lf (%%*lf)");
         }          }
         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         for (i=1; i<= nlstate ; i ++) {          for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
Line 7194  void printinggnuplot(char fileresu[], ch Line 7609  void printinggnuplot(char fileresu[], ch
           } /* end covariate */            } /* end covariate */
         } /* end if no covariate */          } /* end if no covariate */
   
         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */          if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */            fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
           if(cptcoveff ==0){            if(cptcoveff ==0){
Line 7221  void printinggnuplot(char fileresu[], ch Line 7636  void printinggnuplot(char fileresu[], ch
               }                }
             } /* end covariate */              } /* end covariate */
           } /* end if no covariate */            } /* end if no covariate */
           if(backcast == 1){            if(prevbcast == 1){
             fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);              fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
             /* k1-1 error should be nres-1*/              /* k1-1 error should be nres-1*/
             for (i=1; i<= nlstate ; i ++) {              for (i=1; i<= nlstate ; i ++) {
Line 7240  void printinggnuplot(char fileresu[], ch Line 7655  void printinggnuplot(char fileresu[], ch
             }               } 
             fprintf(ficgp,"\" t\"\" w l lt 4");              fprintf(ficgp,"\" t\"\" w l lt 4");
           } /* end if backprojcast */            } /* end if backprojcast */
         } /* end if backcast */          } /* end if prevbcast */
         /* fprintf(ficgp,"\nset out ;unset label;\n"); */          /* fprintf(ficgp,"\nset out ;unset label;\n"); */
         fprintf(ficgp,"\nset out ;unset title;\n");          fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */        } /* nres */
Line 7485  set ter svg size 640, 480\nunset log y\n Line 7900  set ter svg size 640, 480\nunset log y\n
       continue;        continue;
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
       strcpy(gplotlabel,"(");              strcpy(gplotlabel,"(");      
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): '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 */
Line 7528  set ter svg size 640, 480\nunset log y\n Line 7943  set ter svg size 640, 480\nunset log y\n
       
       
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(prevbcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV backward prevalence  for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' 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 */
Line 7580  set ter svg size 640, 480\nunset log y\n Line 7995  set ter svg size 640, 480\nunset log y\n
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if prevbcast */
       
   /* 8eme */    /* 8eme */
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
Line 7592  set ter svg size 640, 480\nunset log y\n Line 8007  set ter svg size 640, 480\nunset log y\n
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         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 forward stable prevalence (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 */
Line 7696  set ter svg size 640, 480\nunset log y\n Line 8111  set ter svg size 640, 480\nunset log y\n
     } /* end covariate */      } /* end covariate */
   } /* End if prevfcast */    } /* End if prevfcast */
       
   if(backcast==1){    if(prevbcast==1){
     /* Back projection from cross-sectional to stable (mixed) for each covariate */      /* Back projection from cross-sectional to stable (mixed) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
Line 7809  set ter svg size 640, 480\nunset log y\n Line 8224  set ter svg size 640, 480\nunset log y\n
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/        } /* end cpt state*/
     } /* end covariate */      } /* end covariate */
   } /* End if backcast */    } /* End if prevbcast */
       
       
   /* 9eme writing MLE parameters */    /* 9eme writing MLE parameters */
Line 8026  set ter svg size 640, 480\nunset log y\n Line 8441  set ter svg size 640, 480\nunset log y\n
    int modcovmax =1;     int modcovmax =1;
    int mobilavrange, mob;     int mobilavrange, mob;
    int iage=0;     int iage=0;
      int firstA1=0, firstA2=0;
   
    double sum=0., sumr=0.;     double sum=0., sumr=0.;
    double age;     double age;
Line 8123  set ter svg size 640, 480\nunset log y\n Line 8539  set ter svg size 640, 480\nunset log y\n
      } /* age */       } /* age */
      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */       /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
      /* but they will change */       /* but they will change */
        firstA1=0;firstA2=0;
      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */       for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
        sumnewmr[cptcod]=0.;         sumnewmr[cptcod]=0.;
Line 8155  set ter svg size 640, 480\nunset log y\n Line 8572  set ter svg size 640, 480\nunset log y\n
          sumr+=probs[(int)age][i][cptcod];           sumr+=probs[(int)age][i][cptcod];
        }         }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */         if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);           if(!firstA1){
              firstA1=1;
              printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        if(fabs(sumr - 1.) > 1.e-3) { /* bad */         if(fabs(sumr - 1.) > 1.e-3) { /* bad */
          printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);           if(!firstA2){
              firstA2=1;
              printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
      }/* age */       }/* age */
   
Line 8247  set ter svg size 640, 480\nunset log y\n Line 8672  set ter svg size 640, 480\nunset log y\n
  }/* End movingaverage */   }/* End movingaverage */
     
   
    
 /************** Forecasting ******************/  /************** Forecasting ******************/
  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
   /* proj1, year, month, day of starting projection   void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
     /* dateintemean, mean date of interviews
        dateprojd, year, month, day of starting projection 
        dateprojf date of end of projection;year of end of projection (same day and month as proj1).
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).  
   */    */
     /* double anprojd, mprojd, jprojd; */
     /* double anprojf, mprojf, jprojf; */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
Line 8293  set ter svg size 640, 480\nunset log y\n Line 8723  set ter svg size 640, 480\nunset log y\n
   if(estepm > stepm){ /* Yes every two year */    if(estepm > stepm){ /* Yes every two year */
     stepsize=2;      stepsize=2;
   }    }
     hstepm=hstepm/stepm;
   
     
     /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
     /*                              fractional in yp1 *\/ */
     /* aintmean=yp; */
     /* yp2=modf((yp1*12),&yp); */
     /* mintmean=yp; */
     /* yp1=modf((yp2*30.5),&yp); */
     /* jintmean=yp; */
     /* if(jintmean==0) jintmean=1; */
     /* if(mintmean==0) mintmean=1; */
   
   hstepm=hstepm/stepm;   
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and  
                                fractional in yp1 */  
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;  
   
     /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
     /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
     /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
   i1=pow(2,cptcoveff);    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    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,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
       
Line 8334  set ter svg size 640, 480\nunset log y\n Line 8769  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresf," p%d%d",i,j);          fprintf(ficresf," p%d%d",i,j);
       fprintf(ficresf," wp.%d",j);        fprintf(ficresf," wp.%d",j);
     }      }
     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {      for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
       fprintf(ficresf,"\n");        fprintf(ficresf,"\n");
       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);   
       /* for (agec=fage; agec>=(ageminpar-1); agec--){  */        /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
       for (agec=fage; agec>=(bage); agec--){         for (agec=fage; agec>=(bage); agec--){ 
         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
Line 8354  set ter svg size 640, 480\nunset log y\n Line 8789  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);          fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
                   
         for(j=1; j<=nlstate+ndeath;j++) {          for(j=1; j<=nlstate+ndeath;j++) {
           ppij=0.;            ppij=0.;
Line 8382  set ter svg size 640, 480\nunset log y\n Line 8817  set ter svg size 640, 480\nunset log y\n
 }  }
   
 /************** Back Forecasting ******************/  /************** Back Forecasting ******************/
  void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){   /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
   /* back1, year, month, day of starting backection   void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
     /* back1, year, month, day of starting backprojection
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anback2 year of end of backprojection (same day and month as back1).       anback2 year of end of backprojection (same day and month as back1).
Line 8391  set ter svg size 640, 480\nunset log y\n Line 8827  set ter svg size 640, 480\nunset log y\n
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
Line 8434  set ter svg size 640, 480\nunset log y\n Line 8870  set ter svg size 640, 480\nunset log y\n
   }    }
       
   hstepm=hstepm/stepm;    hstepm=hstepm/stepm;
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and    /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                                fractional in yp1 */    /*                              fractional in yp1 *\/ */
   anprojmean=yp;    /* aintmean=yp; */
   yp2=modf((yp1*12),&yp);    /* yp2=modf((yp1*12),&yp); */
   mprojmean=yp;    /* mintmean=yp; */
   yp1=modf((yp2*30.5),&yp);    /* yp1=modf((yp2*30.5),&yp); */
   jprojmean=yp;    /* jintmean=yp; */
   if(jprojmean==0) jprojmean=1;    /* if(jintmean==0) jintmean=1; */
   if(mprojmean==0) jprojmean=1;    /* if(mintmean==0) jintmean=1; */
       
   i1=pow(2,cptcoveff);    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);    fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
       
   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
       
Line 8473  set ter svg size 640, 480\nunset log y\n Line 8909  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresfb," b%d%d",i,j);          fprintf(ficresfb," b%d%d",i,j);
       fprintf(ficresfb," b.%d",j);        fprintf(ficresfb," b.%d",j);
     }      }
     for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {      for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
       fprintf(ficresfb,"\n");        fprintf(ficresfb,"\n");
       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);        fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */        /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
       /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */        /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
       for (agec=bage; agec<=fage; agec++){  /* testing */        for (agec=bage; agec<=fage; agec++){  /* testing */
Line 8499  set ter svg size 640, 480\nunset log y\n Line 8935  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresfb,"\n");          fprintf(ficresfb,"\n");
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;j++)
           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);          fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
         for(i=1; i<=nlstate+ndeath;i++) {          for(i=1; i<=nlstate+ndeath;i++) {
           ppij=0.;ppi=0.;            ppij=0.;ppi=0.;
           for(j=1; j<=nlstate;j++) {            for(j=1; j<=nlstate;j++) {
Line 8534  set ter svg size 640, 480\nunset log y\n Line 8970  set ter svg size 640, 480\nunset log y\n
   
 /* Variance of prevalence limit: varprlim */  /* Variance of prevalence limit: varprlim */
  void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){   void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of forward period (stable) prevalence------*/   
     
    char fileresvpl[FILENAMELENGTH];       char fileresvpl[FILENAMELENGTH];  
    FILE *ficresvpl;     FILE *ficresvpl;
Line 8545  set ter svg size 640, 480\nunset log y\n Line 8981  set ter svg size 640, 480\nunset log y\n
     strcpy(fileresvpl,"VPL_");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileresu);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);      printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);      fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
           
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
Line 8586  set ter svg size 640, 480\nunset log y\n Line 9022  set ter svg size 640, 480\nunset log y\n
     }      }
           
     fclose(ficresvpl);      fclose(ficresvpl);
     printf("done variance-covariance of period prevalence\n");fflush(stdout);      printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);      fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
   
  }   }
 /* Variance of back prevalence: varbprlim */  /* Variance of back prevalence: varbprlim */
Line 8947  void prwizard(int ncovmodel, int nlstate Line 9383  void prwizard(int ncovmodel, int nlstate
 /******************* Gompertz Likelihood ******************************/  /******************* Gompertz Likelihood ******************************/
 double gompertz(double x[])  double gompertz(double x[])
 {   { 
   double A,B,L=0.0,sump=0.,num=0.;    double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
   for (i=1;i<=imx ; i++) {    for (i=1;i<=imx ; i++) {
Line 8955  double gompertz(double x[]) Line 9391  double gompertz(double x[])
     /*    sump=sump+1;*/      /*    sump=sump+1;*/
     num=num+1;      num=num+1;
   }    }
      L=0.0;
      /* agegomp=AGEGOMP; */
   /* for (i=0; i<=imx; i++)     /* for (i=0; i<=imx; i++) 
      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/       if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
   for (i=1;i<=imx ; i++)    for (i=1;i<=imx ; i++) {
     {      /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
       if (cens[i] == 1 && wav[i]>1)         mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));       * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month) 
              *   and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
       if (cens[i] == 0 && wav[i]>1)       * +
        * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
        */
        if (wav[i] > 1 || agedc[i] < AGESUP) {
          if (cens[i] == 1){
            A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
          } else if (cens[i] == 0){
         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);              +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
               } else
            printf("Gompertz cens[%d] neither 1 nor 0\n",i);
       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
       if (wav[i] > 1 ) { /* ??? */         L=L+A*weight[i];
         L=L+A*weight[i];  
         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/          /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
       }       }
     }    }
   
  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     
   return -2*L*num/sump;    return -2*L*num/sump;
 }  }
Line 8985  double gompertz(double x[]) Line 9427  double gompertz(double x[])
 /******************* Gompertz_f Likelihood ******************************/  /******************* Gompertz_f Likelihood ******************************/
 double gompertz_f(const gsl_vector *v, void *params)  double gompertz_f(const gsl_vector *v, void *params)
 {   { 
   double A,B,LL=0.0,sump=0.,num=0.;    double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
   double *x= (double *) v->data;    double *x= (double *) v->data;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
Line 9078  int readdata(char datafile[], int firsto Line 9520  int readdata(char datafile[], int firsto
   int i=0, j=0, n=0, iv=0, v;    int i=0, j=0, n=0, iv=0, v;
   int lstra;    int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
     int noffset=0; /* This is the offset if BOM data file */
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
Line 9111  int readdata(char datafile[], int firsto Line 9554  int readdata(char datafile[], int firsto
     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
   }    }
   
   i=1;      /* Is it a BOM UTF-8 Windows file? */
     /* First data line */
   linei=0;    linei=0;
     while(fgets(line, MAXLINE, fic)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
         fprintf(ficlog,"# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
         fflush(ficlog); return 1;
       }
       /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
       else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
       {
         noffset=noffset+2;
         printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
         fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
         fflush(ficlog); return 1;
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
           fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
           fflush(ficlog); return 1;
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
           /* If line starts with a # it is a comment */
       if (line[noffset] == '#') {
         linei=linei+1;
         break;
       }else{
         break;
       }
     }
     fclose(fic);
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
     }
     /* Not a Bom file */
     
     i=1;
   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
     linei=linei+1;      linei=linei+1;
     for(j=strlen(line); j>=0;j--){  /* Untabifies line */      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
Line 9179  int readdata(char datafile[], int firsto Line 9667  int readdata(char datafile[], int firsto
         }          }
         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 \   Should be a value of %d(nth) covariate of wave %d (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 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 \   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);   Exiting.\n",lval,linei, i,line,iv,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 \   Should be a value of %d(nth) covariate of wave %d (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 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 \   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);   Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
           return 1;            return 1;
         }          }
         cotvar[j][iv][i]=(double)(lval);          cotvar[j][iv][i]=(double)(lval);
Line 9233  int readdata(char datafile[], int firsto Line 9721  int readdata(char datafile[], int firsto
         return 1;          return 1;
       }        }
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month;
         /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
         /*        printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
         /*        fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
         /* } */
       strcpy(line,stra);        strcpy(line,stra);
     } /* End loop on waves */      } /* End loop on waves */
           
Line 9272  int readdata(char datafile[], int firsto Line 9764  int readdata(char datafile[], int firsto
               
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month);
       for (j=1;j<=maxwav;j++){
         if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
           printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
           fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
         }
       }
   
     strcpy(line,stra);      strcpy(line,stra);
           
     /* Sample weight */      /* Sample weight */
Line 9292  int readdata(char datafile[], int firsto Line 9791  int readdata(char datafile[], int firsto
       cutv(stra, strb, line, ' ');         cutv(stra, strb, line, ' '); 
       if(strb[0]=='.') { /* Missing value */        if(strb[0]=='.') { /* Missing value */
         lval=-1;          lval=-1;
           coqvar[iv][i]=NAN; 
           covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */ 
       }else{        }else{
         errno=0;          errno=0;
         /* what_kind_of_number(strb); */          /* what_kind_of_number(strb); */
Line 9395  int decoderesult ( char resultline[], in Line 9896  int decoderesult ( char resultline[], in
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
   removefirstspace(&resultline);    removefirstspace(&resultline);
   printf("decoderesult:%s\n",resultline);  
   
   if (strstr(resultline,"v") !=0){    if (strstr(resultline,"v") !=0){
     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);      printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
Line 9410  int decoderesult ( char resultline[], in Line 9910  int decoderesult ( char resultline[], in
     TKresult[nres]=0; /* Combination for the nresult and the model */      TKresult[nres]=0; /* Combination for the nresult and the model */
     return (0);      return (0);
   }    }
       
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      printf("ERROR: the number of variables in this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
   }    }
   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */    for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
     if(nbocc(resultsav,'=') >1){      if(nbocc(resultsav,'=') >1){
        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '         cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
                                       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" */
        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */  
     }else      }else
       cutl(strc,strd,resultsav,'=');        cutl(strc,strd,resultsav,'=');
     Tvalsel[k]=atof(strc); /* 1 */      Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
           
     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;      cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
     Tvarsel[k]=atoi(strc);      Tvarsel[k]=atoi(strc);  /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */      /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
     /* cptcovsel++;     */      /* cptcovsel++;     */
     if (nbocc(stra,'=') >0)      if (nbocc(stra,'=') >0)
       strcpy(resultsav,stra); /* and analyzes it */        strcpy(resultsav,stra); /* and analyzes it */
   }    }
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */    for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     if(Typevar[k1]==0){ /* Single covariate in model */      if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
       match=0;        match=0;
       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */        for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */          if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */            modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
           match=1;            match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
           break;            break;
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);          printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
           fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
           return 1;
       }        }
     }      }
   }    }
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     match=0;      match=0;
     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */      for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single */        if(Typevar[k1]==0){ /* Single */
         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */          if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
           resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */            resultmodel[k1]=k2;  /* k2th variable of the model corresponds to k1 variable of the model. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
           ++match;            ++match;
         }          }
       }        }
     }      }
     if(match == 0){      if(match == 0){
       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);        printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         return 1;
     }else if(match > 1){      }else if(match > 1){
       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);        printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
         fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
         return 1;
     }      }
   }    }
               
Line 9483  int decoderesult ( char resultline[], in Line 9987  int decoderesult ( char resultline[], in
   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */    /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
   /* V5*age V5 known which value for nres?  */    /* V5*age V5 known which value for nres?  */
   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */    /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */    for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop on model line */
     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */        k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */        k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
Line 9494  int decoderesult ( char resultline[], in Line 9998  int decoderesult ( char resultline[], in
       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);        printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
       k4++;;        k4++;;
     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */      }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */        k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */        k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */        Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */        Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
Line 9518  int decodemodel( char model[], int lasto Line 10022  int decodemodel( char model[], int lasto
         * - cptcovs number of simple covariates          * - 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          * - 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.           *     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          * - 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[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.          *    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 .          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
         */          */
   /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
 {  {
   int i, j, k, ks, v;    int i, j, k, ks, v;
   int  j1, k1, k2, k3, k4;    int  j1, k1, k2, k3, k4;
Line 9600  int decodemodel( char model[], int lasto Line 10105  int decodemodel( char model[], int lasto
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2         *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12         *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8         *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}         * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}         * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}         *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8            * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];         *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?         *How to reorganize? Tvars(orted)
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age         * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}         * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}         *       {2,   1,     4,      8,    5,      6,     3,       7}
Line 9630  int decodemodel( char model[], int lasto Line 10135  int decodemodel( char model[], int lasto
         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
       }        }
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */                                            modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
         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+V5*age+ 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,'*'); /**< k=1 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+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
             Typevar[k]=1;  /* 1 for age product */              Typevar[k]=1;  /* 1 for age product */
             cptcovage++; /* Sums the number of covariates which include age as a product */              cptcovage++; /* Counts the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */              Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/              /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */            } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;              cptcovprod--;
Line 9662  int decodemodel( char model[], int lasto Line 10168  int decodemodel( char model[], int lasto
             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                                 because this model-covariate is a construction we invent a new column                                                  because this model-covariate is a construction we invent a new column
                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1                                                  which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                                 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                                  If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2
                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                  thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
                                                   Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */
             Typevar[k]=2;  /* 2 for double fixed dummy covariates */              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */              Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
Line 9682  int decodemodel( char model[], int lasto Line 10189  int decodemodel( char model[], int lasto
             }              }
           } /* End age is not in the model */            } /* End age is not in the model */
         } /* End if model includes a product */          } /* End if model includes a product */
         else { /* no more sum */          else { /* not a product */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
Line 9713  int decodemodel( char model[], int lasto Line 10220  int decodemodel( char model[], int lasto
    model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place     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     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     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     Typevar[k]=   0    0   0     2       1       0      2      1        0
    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3     Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
    Dummy[k]      1    0   0     0       3       1      1      2        3     Dummy[k]      1    0   0     0       3       1      1      2        3
           Tmodelind[combination of covar]=k;            Tmodelind[combination of covar]=k;
Line 9722  int decodemodel( char model[], int lasto Line 10229  int decodemodel( char model[], int lasto
   /* If Tvar[k] >ncovcol it is a product */    /* 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 */    /* 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 */          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
   printf("Model=%s\n\    printf("Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \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\  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);  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\    fprintf(ficlog,"Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \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\  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);  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;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}    for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */    for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
       Fixed[k]= 0;        Fixed[k]= 0;
Line 9793  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10300  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].subtype= VQ;        modell[k].subtype= VQ;
       ncovv++; /* Only simple time varying variables */        ncovv++; /* Only simple time varying variables */
       nsq++;        nsq++;
       TvarsQ[nsq]=Tvar[k];        TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
       TvarsQind[nsq]=k;        TvarsQind[nsq]=k;
       TvarV[ncovv]=Tvar[k];        TvarV[ncovv]=Tvar[k];
       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */        TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
Line 9980  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10487  Dummy[k] 0=dummy (0 1), 1 quantitative (
   /* Searching for doublons in the model */    /* Searching for doublons in the model */
   for(k1=1; k1<= cptcovt;k1++){    for(k1=1; k1<= cptcovt;k1++){
     for(k2=1; k2 <k1;k2++){      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]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
         if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */          if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
           if(Tvar[k1]==Tvar[k2]){            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]]);              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[k1],Dummy[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);              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[k1],Dummy[k1]); fflush(ficlog);
             return(1);              return(1);
           }            }
         }else if (Typevar[k1] ==2){          }else if (Typevar[k1] ==2){
Line 10156  BOOL IsWow64() Line 10664  BOOL IsWow64()
 #endif  #endif
   
 void syscompilerinfo(int logged)  void syscompilerinfo(int logged)
  {  {
    /* #include "syscompilerinfo.h"*/  #include <stdint.h>
   
     /* #include "syscompilerinfo.h"*/
    /* command line Intel compiler 32bit windows, XP compatible:*/     /* command line Intel compiler 32bit windows, XP compatible:*/
    /* /GS /W3 /Gy     /* /GS /W3 /Gy
       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
Line 10192  void syscompilerinfo(int logged) Line 10702  void syscompilerinfo(int logged)
       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
       /NOLOGO /TLBID:1        /NOLOGO /TLBID:1
    */     */
   
   
 #if defined __INTEL_COMPILER  #if defined __INTEL_COMPILER
 #if defined(__GNUC__)  #if defined(__GNUC__)
         struct utsname sysInfo;  /* For Intel on Linux and OS/X */          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
Line 10208  void syscompilerinfo(int logged) Line 10720  void syscompilerinfo(int logged)
    }     }
 #endif  #endif
   
 #include <stdint.h>  
   
    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)  #if defined(__clang__)
    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
Line 10295  void syscompilerinfo(int logged) Line 10805  void syscompilerinfo(int logged)
 #endif  #endif
 #endif  #endif
   
    //   void main()     //   void main ()
    //   {     //   {
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    if (IsWow64()){     if (IsWow64()){
Line 10316  void syscompilerinfo(int logged) Line 10826  void syscompilerinfo(int logged)
 }  }
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
   int i, j, k, i1, k4=0, nres=0 ;    int i, j, k, i1, k4=0, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
Line 10325  int prevalence_limit(double *p, double * Line 10835  int prevalence_limit(double *p, double *
   strcpy(filerespl,"PL_");    strcpy(filerespl,"PL_");
   strcat(filerespl,fileresu);    strcat(filerespl,fileresu);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
   }    }
   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   pstamp(ficrespl);    pstamp(ficrespl);
   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
   fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
Line 10406  int prevalence_limit(double *p, double * Line 10916  int prevalence_limit(double *p, double *
 }  }
   
 int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/          /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
                   
         /* Computes the back prevalence limit  for any combination      of covariate values           /* Computes the back prevalence limit  for any combination      of covariate values 
    * at any age between ageminpar and agemaxpar     * at any age between ageminpar and agemaxpar
Line 10421  int back_prevalence_limit(double *p, dou Line 10931  int back_prevalence_limit(double *p, dou
   strcpy(fileresplb,"PLB_");    strcpy(fileresplb,"PLB_");
   strcat(fileresplb,fileresu);    strcat(fileresplb,fileresu);
   if((ficresplb=fopen(fileresplb,"w"))==NULL) {    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
   }    }
   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
   pstamp(ficresplb);    pstamp(ficresplb);
   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficresplb,"#Age ");    fprintf(ficresplb,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
   fprintf(ficresplb,"\n");    fprintf(ficresplb,"\n");
Line 10616  int hPijx(double *p, int bage, int fage) Line 11126  int hPijx(double *p, int bage, int fage)
   /*if (stepm<=24) stepsize=2;*/    /*if (stepm<=24) stepsize=2;*/
       
   /* agelim=AGESUP; */    /* agelim=AGESUP; */
   ageminl=30;    ageminl=AGEINF; /* was 30 */
   hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
       
Line 10646  int hPijx(double *p, int bage, int fage) Line 11156  int hPijx(double *p, int bage, int fage)
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */          /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */          nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
                   
         /*        nhstepm=nhstepm*YEARM; aff par mois*/          /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   
Line 10695  int main(int argc, char *argv[]) Line 11205  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
     /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
   int ncvyear=0; /* Number of years needed for the period prevalence to converge */    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
Line 10721  int main(int argc, char *argv[]) Line 11232  int main(int argc, char *argv[])
   double dum=0.; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
     double wald;
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
Line 10730  int main(int argc, char *argv[]) Line 11242  int main(int argc, char *argv[])
       
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
   int c,  h , cpt, c2;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
Line 10738  int main(int argc, char *argv[]) Line 11250  int main(int argc, char *argv[])
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int backcast=0;    /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
     /* double anprojf, mprojf, jprojf; */
     /* double jintmean,mintmean,aintmean;   */
     int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
     int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
     double yrfproj= 10.0; /* Number of years of forward projections */
     double yrbproj= 10.0; /* Number of years of backward projections */
     int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
Line 10750  int main(int argc, char *argv[]) Line 11269  int main(int argc, char *argv[])
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
   double **bprlim;    double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel) 
                       state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
   double ***paramstart; /* Matrix of starting parameter values */    double ***paramstart; /* Matrix of starting parameter values */
   double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */    double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
Line 10763  int main(int argc, char *argv[]) Line 11283  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2;    double dateprev1, dateprev2;
   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;    double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;    double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
   
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
Line 10959  int main(int argc, char *argv[]) Line 11480  int main(int argc, char *argv[])
       noffset=noffset+3;        noffset=noffset+3;
       printf("# File is an UTF8 Bom.\n"); // 0xBF        printf("# File is an UTF8 Bom.\n"); // 0xBF
     }      }
     else if( line[0] == (char)0xFE && line[1] == (char)0xFF)  /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
       else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
     {      {
       noffset=noffset+2;        noffset=noffset+2;
       printf("# File is an UTF16BE BOM file\n");        printf("# File is an UTF16BE BOM file\n");
Line 11019  int main(int argc, char *argv[]) Line 11541  int main(int argc, char *argv[])
       fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");        fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
       fprintf(ficlog,"but line=%s\n",line);        fprintf(ficlog,"but line=%s\n",line);
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);      if( lastpass > maxwav){
         printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fflush(ficlog);
         goto end;
       }
         printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
     fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);      fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
     fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);      fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
     fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);      fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
   }    }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
Line 11041  int main(int argc, char *argv[]) Line 11569  int main(int argc, char *argv[])
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
     if (num_filled != 1){      if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);        printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       model[0]='\0';        model[0]='\0';
       goto end;        goto end;
     }      }
Line 11091  int main(int argc, char *argv[]) Line 11619  int main(int argc, char *argv[])
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
   if(nqv>=1)coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */    if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */    if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/    if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/    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+v3+v2*v4+v5*age makes cptcovn = 5
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
Line 11157  int main(int argc, char *argv[]) Line 11685  int main(int argc, char *argv[])
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;          if(jj==i) continue;
         j++;          j++;
           while((c=getc(ficpar))=='#' && c!= EOF){
             ungetc(c,ficpar);
             fgets(line, MAXLINE, ficpar);
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficlog);
           }
           ungetc(c,ficpar);
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) || (j1 != jj)){          if ((i1 != i) || (j1 != jj)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
Line 11297  Please run with mle=-1 to get a correct Line 11834  Please run with mle=-1 to get a correct
       
   /*  Main data    /*  Main data
    */     */
   n= lastobs;    nobs=lastobs-firstobs+1; /* was = lastobs;*/
   num=lvector(1,n);    /* num=lvector(1,n); */
   moisnais=vector(1,n);    /* moisnais=vector(1,n); */
   annais=vector(1,n);    /* annais=vector(1,n); */
   moisdc=vector(1,n);    /* moisdc=vector(1,n); */
   andc=vector(1,n);    /* andc=vector(1,n); */
   weight=vector(1,n);    /* weight=vector(1,n); */
   agedc=vector(1,n);    /* agedc=vector(1,n); */
   cod=ivector(1,n);    /* cod=ivector(1,n); */
   for(i=1;i<=n;i++){    /* for(i=1;i<=n;i++){ */
     num=lvector(firstobs,lastobs);
     moisnais=vector(firstobs,lastobs);
     annais=vector(firstobs,lastobs);
     moisdc=vector(firstobs,lastobs);
     andc=vector(firstobs,lastobs);
     weight=vector(firstobs,lastobs);
     agedc=vector(firstobs,lastobs);
     cod=ivector(firstobs,lastobs);
     for(i=firstobs;i<=lastobs;i++){
     num[i]=0;      num[i]=0;
     moisnais[i]=0;      moisnais[i]=0;
     annais[i]=0;      annais[i]=0;
Line 11316  Please run with mle=-1 to get a correct Line 11862  Please run with mle=-1 to get a correct
     cod[i]=0;      cod[i]=0;
     weight[i]=1.0; /* Equal weights, 1 by default */      weight[i]=1.0; /* Equal weights, 1 by default */
   }    }
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,firstobs,lastobs);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,firstobs,lastobs);
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */ 
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
Line 11420  Please run with mle=-1 to get a correct Line 11966  Please run with mle=-1 to get a correct
   
   
   agegomp=(int)agemin;    agegomp=(int)agemin;
   free_vector(moisnais,1,n);    free_vector(moisnais,firstobs,lastobs);
   free_vector(annais,1,n);    free_vector(annais,firstobs,lastobs);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   /* free_vector(moisdc,1,n); */    /* free_vector(moisdc,1,n); */
Line 11447  Please run with mle=-1 to get a correct Line 11993  Please run with mle=-1 to get a correct
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   /* Concatenates waves */    /* Concatenates waves */
     
   free_vector(moisdc,1,n);    free_vector(moisdc,firstobs,lastobs);
   free_vector(andc,1,n);    free_vector(andc,firstobs,lastobs);
   
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
Line 11630  Title=%s <br>Datafile=%s Firstpass=%d La Line 12176  Title=%s <br>Datafile=%s Firstpass=%d La
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\    fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
           ftol, stepm);            ftol, stepm);
   fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);    fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
   ncurrv=1;    ncurrv=1;
Line 11638  Title=%s <br>Datafile=%s Firstpass=%d La Line 12184  Title=%s <br>Datafile=%s Firstpass=%d La
   fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);     fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
   ncurrv=i;    ncurrv=i;
   for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);    for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
   fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);    fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
   ncurrv=i;    ncurrv=i;
   for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);    for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
   fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);    fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
   ncurrv=i;    ncurrv=i;
   for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);    for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
   fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \    fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
Line 11651  Title=%s <br>Datafile=%s Firstpass=%d La Line 12197  Title=%s <br>Datafile=%s Firstpass=%d La
 <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));  <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
   
       
   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
   imx,agemin,agemax,jmin,jmax,jmean);    imx,agemin,agemax,jmin,jmax,jmean);
Line 11673  Interval (in months) between two waves: Line 12219  Interval (in months) between two waves:
       for(j=1;j<=NDIM;j++)        for(j=1;j<=NDIM;j++)
         ximort[i][j]=0.;          ximort[i][j]=0.;
     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(firstobs,lastobs);
     ageexmed=vector(1,n);      ageexmed=vector(firstobs,lastobs);
     agecens=vector(1,n);      agecens=vector(firstobs,lastobs);
     dcwave=ivector(1,n);      dcwave=ivector(firstobs,lastobs);
                                   
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
Line 11710  Interval (in months) between two waves: Line 12256  Interval (in months) between two waves:
         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;*/      p[1]=0.0268; p[NDIM]=0.083;
     /*printf("%lf %lf", p[1], p[2]);*/      /* printf("%lf %lf", p[1], p[2]); */
           
           
 #ifdef GSL  #ifdef GSL
Line 11837  Interval (in months) between two waves: Line 12383  Interval (in months) between two waves:
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));        fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     }      }
     lsurv=vector(1,AGESUP);      lsurv=vector(agegomp,AGESUP);
     lpop=vector(1,AGESUP);      lpop=vector(agegomp,AGESUP);
     tpop=vector(1,AGESUP);      tpop=vector(agegomp,AGESUP);
     lsurv[agegomp]=100000;      lsurv[agegomp]=100000;
           
     for (k=agegomp;k<=AGESUP;k++) {      for (k=agegomp;k<=AGESUP;k++) {
Line 11886  Please run with mle=-1 to get a correct Line 12432  Please run with mle=-1 to get a correct
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
           
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,agegomp,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,agegomp,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,agegomp,AGESUP);
     free_matrix(ximort,1,NDIM,1,NDIM);      free_matrix(ximort,1,NDIM,1,NDIM);
     free_ivector(cens,1,n);      free_ivector(dcwave,firstobs,lastobs);
     free_vector(agecens,1,n);      free_vector(agecens,firstobs,lastobs);
     free_ivector(dcwave,1,n);      free_vector(ageexmed,firstobs,lastobs);
       free_ivector(cens,firstobs,lastobs);
 #ifdef GSL  #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
Line 11930  Please run with mle=-1 to get a correct Line 12477  Please run with mle=-1 to get a correct
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   
       printf("#model=  1      +     age ");
       fprintf(ficres,"#model=  1      +     age ");
       fprintf(ficlog,"#model=  1      +     age ");
       fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
   </ul>", model);
   
       fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
       fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
       if(nagesqr==1){
         printf("  + age*age  ");
         fprintf(ficres,"  + age*age  ");
         fprintf(ficlog,"  + age*age  ");
         fprintf(fichtm, "<th>+ age*age</th>");
       }
       for(j=1;j <=ncovmodel-2;j++){
         if(Typevar[j]==0) {
           printf("  +      V%d  ",Tvar[j]);
           fprintf(ficres,"  +      V%d  ",Tvar[j]);
           fprintf(ficlog,"  +      V%d  ",Tvar[j]);
           fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
         }else if(Typevar[j]==1) {
           printf("  +    V%d*age ",Tvar[j]);
           fprintf(ficres,"  +    V%d*age ",Tvar[j]);
           fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
         }else if(Typevar[j]==2) {
           printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }
       }
       printf("\n");
       fprintf(ficres,"\n");
       fprintf(ficlog,"\n");
       fprintf(fichtm, "</tr>");
       fprintf(fichtm, "\n");
       
       
     for(i=1,jk=1; i <=nlstate; i++){      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) {
             fprintf(fichtm, "<tr>");
           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);
             fprintf(fichtm, "<td>%1d%1d</td>",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]);
               fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
             jk++;               jk++; 
           }            }
           printf("\n");            printf("\n");
           fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
           fprintf(ficres,"\n");            fprintf(ficres,"\n");
             fprintf(fichtm, "</tr>\n");
         }          }
       }        }
     }      }
       /* fprintf(fichtm,"</tr>\n"); */
       fprintf(fichtm,"</table>\n");
       fprintf(fichtm, "\n");
   
     if(mle != 0){      if(mle != 0){
       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */        /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
       ftolhess=ftol; /* Usually correct */        ftolhess=ftol; /* Usually correct */
       hesscov(matcov, hess, p, npar, delti, ftolhess, func);        hesscov(matcov, hess, p, npar, delti, ftolhess, func);
       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        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");        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");
         fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
         fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
         if(nagesqr==1){
           printf("  + age*age  ");
           fprintf(ficres,"  + age*age  ");
           fprintf(ficlog,"  + age*age  ");
           fprintf(fichtm, "<th>+ age*age</th>");
         }
         for(j=1;j <=ncovmodel-2;j++){
           if(Typevar[j]==0) {
             printf("  +      V%d  ",Tvar[j]);
             fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
           }else if(Typevar[j]==1) {
             printf("  +    V%d*age ",Tvar[j]);
             fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
           }else if(Typevar[j]==2) {
             fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           }
         }
         fprintf(fichtm, "</tr>\n");
    
       for(i=1,jk=1; i <=nlstate; i++){        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) {
               fprintf(fichtm, "<tr valign=top>");
             printf("%d%d ",i,k);              printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);              fprintf(ficlog,"%d%d ",i,k);
               fprintf(fichtm, "<td>%1d%1d</td>",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]));                wald=p[jk]/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]));                printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][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(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                 if(fabs(wald) > 1.96){
                   fprintf(fichtm, "<td><b>%12.7f</b> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
                   fprintf(fichtm,"<b>W=%8.3f</b></br>",wald);
                 }else{
                   fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
                   fprintf(fichtm,"W=%8.3f</br>",wald);
                 }
                 fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", 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");
               fprintf(fichtm, "</tr>\n");
           }            }
         }          }
       }        }
     } /* end of hesscov and Wald tests */      } /* end of hesscov and Wald tests */
       fprintf(fichtm,"</table>\n");
           
     /*  */      /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
Line 12088  Please run with mle=-1 to get a correct Line 12717  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else        }else
         break;          break;
Line 12133  Please run with mle=-1 to get a correct Line 12763  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else        }else
         break;          break;
Line 12158  Please run with mle=-1 to get a correct Line 12789  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else        }else
         break;          break;
Line 12180  Please run with mle=-1 to get a correct Line 12812  Please run with mle=-1 to get a correct
     }      }
             
     /* Results */      /* Results */
       endishere=0;
     nresult=0;      nresult=0;
       parameterline=0;
     do{      do{
       if(!fgets(line, MAXLINE, ficpar)){        if(!fgets(line, MAXLINE, ficpar)){
         endishere=1;          endishere=1;
         parameterline=14;          parameterline=15;
       }else if (line[0] == '#') {        }else if (line[0] == '#') {
         /* If line starts with a # it is a comment */          /* If line starts with a # it is a comment */
         numlinepar++;          numlinepar++;
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))        }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
         parameterline=11;          parameterline=11;
       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))        else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
         parameterline=12;          parameterline=12;
       else if(sscanf(line,"result:%[^\n]\n",modeltemp))        else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
         parameterline=13;          parameterline=13;
         }
       else{        else{
         parameterline=14;          parameterline=14;
       }        }
       switch (parameterline){         switch (parameterline){ /* =0 only if only comments */
       case 11:        case 11:
         if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){          if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
           if (num_filled != 8) {                    fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
             goto end;  
           }  
           fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
           printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           /* day and month of proj2 are not used but only year anproj2.*/            /* day and month of proj2 are not used but only year anproj2.*/
           dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;            dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
           dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;            dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
             prvforecast = 1;
           } 
           else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
             printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             prvforecast = 2;
           }
           else {
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             goto end;
         }          }
         break;          break;
       case 12:        case 12:
         /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/          if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
         if((num_filled=sscanf(line,"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)) !=EOF){            fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
           if (num_filled != 8) {            printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);            fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);            fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             goto end;            /* day and month of back2 are not used but only year anback2.*/
           }  
           printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
           fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
           /* day and month of proj2 are not used but only year anproj2.*/  
           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;            dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;            dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
             prvbackcast = 1;
           } 
           else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
             printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             prvbackcast = 2;
           }
           else {
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             goto end;
         }          }
         break;          break;
       case 13:        case 13:
         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){          num_filled=sscanf(line,"result:%[^\n]\n",resultline);
           if (num_filled == 0){          nresult++; /* Sum of resultlines */
             resultline[0]='\0';          printf("Result %d: result:%s\n",nresult, resultline);
             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);          if(nresult > MAXRESULTLINESPONE-1){
             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);            printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
             break;            fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
           } else if (num_filled != 1){            goto end;
             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);          }
             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);          if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
           }  
           nresult++; /* Sum of resultlines */  
           printf("Result %d: result=%s\n",nresult, resultline);  
           if(nresult > MAXRESULTLINES){  
             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);  
             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);  
             goto end;  
           }  
           decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */  
           fprintf(ficparo,"result: %s\n",resultline);            fprintf(ficparo,"result: %s\n",resultline);
           fprintf(ficres,"result: %s\n",resultline);            fprintf(ficres,"result: %s\n",resultline);
           fprintf(ficlog,"result: %s\n",resultline);            fprintf(ficlog,"result: %s\n",resultline);
           break;          } else
         case 14:             goto end;
           if(ncovmodel >2 && nresult==0 ){          break;
             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);        case 14:
             goto end;          printf("Error: Unknown command '%s'\n",line);
           }          fprintf(ficlog,"Error: Unknown command '%s'\n",line);
           break;          if(line[0] == ' ' || line[0] == '\n'){
         default:            printf("It should not be an empty line '%s'\n",line);
           nresult=1;            fprintf(ficlog,"It should not be an empty line '%s'\n",line);
           decoderesult(".",nresult ); /* No covariate */          }         
           if(ncovmodel >=2 && nresult==0 ){
             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
             fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
         }          }
           /* goto end; */
           break;
         case 15:
           printf("End of resultlines.\n");
           fprintf(ficlog,"End of resultlines.\n");
           break;
         default: /* parameterline =0 */
           nresult=1;
           decoderesult(".",nresult ); /* No covariate */
       } /* End switch parameterline */        } /* End switch parameterline */
     }while(endishere==0); /* End do */      }while(endishere==0); /* End do */
           
Line 12285  This is probably because your parameter Line 12936  This is probably because your parameter
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else{      }else{
       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */        /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);        /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
         /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
         if(prvforecast==1){
           dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
           jprojd=jproj1;
           mprojd=mproj1;
           anprojd=anproj1;
           dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
           jprojf=jproj2;
           mprojf=mproj2;
           anprojf=anproj2;
         } else if(prvforecast == 2){
           dateprojd=dateintmean;
           date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
           dateprojf=dateintmean+yrfproj;
           date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
         }
         if(prvbackcast==1){
           datebackd=(jback1+12*mback1+365*anback1)/365;
           jbackd=jback1;
           mbackd=mback1;
           anbackd=anback1;
           datebackf=(jback2+12*mback2+365*anback2)/365;
           jbackf=jback2;
           mbackf=mback2;
           anbackf=anback2;
         } else if(prvbackcast == 2){
           datebackd=dateintmean;
           date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
           datebackf=dateintmean-yrbproj;
           date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
         }
         
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
     }      }
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
                  jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);                   jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
                                   
     /*------------ free_vector  -------------*/      /*------------ free_vector  -------------*/
     /*  chdir(path); */      /*  chdir(path); */
Line 12298  Please run with mle=-1 to get a correct Line 12982  Please run with mle=-1 to get a correct
     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */      /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,firstobs,lastobs);
     free_vector(agedc,1,n);      free_vector(agedc,firstobs,lastobs);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
Line 12362  Please run with mle=-1 to get a correct Line 13046  Please run with mle=-1 to get a correct
     }/* end if moving average */      }/* end if moving average */
           
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     if(prevfcast==1){      if(prevfcast==1){ 
       /*    if(stepm ==1){*/        /*   /\*    if(stepm ==1){*\/ */
       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
         /*This done previously after freqsummary.*/
         /*   dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
         /*   dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
         
         /* } else if (prvforecast==2){ */
         /*   /\*    if(stepm ==1){*\/ */
         /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
         /* } */
         /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
         prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
     }      }
   
     /* Backcasting */      /* Prevbcasting */
     if(backcast==1){      if(prevbcast==1){
       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
Line 12383  Please run with mle=-1 to get a correct Line 13077  Please run with mle=-1 to get a correct
       hBijx(p, bage, fage, mobaverage);        hBijx(p, bage, fage, mobaverage);
       fclose(ficrespijb);        fclose(ficrespijb);
   
       prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,        /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
                        mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);        /* /\*                   mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
         /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
         /*                       mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
         prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
                          mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
   
         
       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);        varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
               
Line 12392  Please run with mle=-1 to get a correct Line 13092  Please run with mle=-1 to get a correct
       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
     }    /* end  Backcasting */      }    /* end  Prevbcasting */
     
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
Line 12556  Please run with mle=-1 to get a correct Line 13256  Please run with mle=-1 to get a correct
         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 forward 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"); */
         printf("Computing age specific period (stable) prevalences in each health state \n");          printf("Computing age specific forward 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 forward 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, nres); /*ZZ Is it the correct prevalim */            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
           if (vpopbased==1) {            if (vpopbased==1) {
Line 12609  Please run with mle=-1 to get a correct Line 13309  Please run with mle=-1 to get a correct
     printf("done State-specific expectancies\n");fflush(stdout);      printf("done State-specific expectancies\n");fflush(stdout);
     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
     /* variance-covariance of period prevalence*/      /* variance-covariance of forward period prevalence*/
     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);      varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
           
     free_vector(weight,1,n);      free_vector(weight,firstobs,lastobs);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,firstobs,lastobs);
     free_matrix(anint,1,maxwav,1,n);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,firstobs,lastobs);
     free_ivector(cod,1,n);      free_ivector(cod,firstobs,lastobs);
     free_ivector(tab,1,NCOVMAX);      free_ivector(tab,1,NCOVMAX);
     fclose(ficresstdeij);      fclose(ficresstdeij);
     fclose(ficrescveij);      fclose(ficrescveij);
Line 12638  Please run with mle=-1 to get a correct Line 13338  Please run with mle=-1 to get a correct
   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);
   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);    if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
   if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);    if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
   free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
   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);*/
Line 12761  Please run with mle=-1 to get a correct Line 13461  Please run with mle=-1 to get a correct
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     strcpy(pplotcmd,plotcmd);
       
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);      printf("Error in 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");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
     if((outcmd=system(plotcmd)) != 0)      if((outcmd=system(plotcmd)) != 0){
       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
         strcpy(plotcmd,pplotcmd);
       }
   }    }
   printf(" Successful, please wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {

Removed from v.1.284  
changed lines
  Added in v.1.320


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