/* $Id: imach.c,v 1.217 2015/12/23 17:18:31 brouard Exp $ $State: Exp $ $Log: imach.c,v $ Revision 1.217 2015/12/23 17:18:31 brouard Summary: Experimental backcast Revision 1.216 2015/12/18 17:32:11 brouard Summary: 0.98r4 Warning and status=-2 Version 0.98r4 is now: - displaying an error when status is -1, date of interview unknown and date of death known; - permitting a status -2 when the vital status is unknown at a known date of right truncation. Older changes concerning s=-2, dating from 2005 have been supersed. Revision 1.215 2015/12/16 08:52:24 brouard Summary: 0.98r4 working Revision 1.214 2015/12/16 06:57:54 brouard Summary: temporary not working Revision 1.213 2015/12/11 18:22:17 brouard Summary: 0.98r4 Revision 1.212 2015/11/21 12:47:24 brouard Summary: minor typo Revision 1.211 2015/11/21 12:41:11 brouard Summary: 0.98r3 with some graph of projected cross-sectional Author: Nicolas Brouard Revision 1.210 2015/11/18 17:41:20 brouard Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard Summary: Adding ftolpl parameter Author: N Brouard We had difficulties to get smoothed confidence intervals. It was due to the period prevalence which wasn't computed accurately. The inner parameter ftolpl is now an outer parameter of the .imach parameter file after estepm. If ftolpl is small 1.e-4 and estepm too, computation are long. Revision 1.208 2015/11/17 14:31:57 brouard Summary: temporary Revision 1.207 2015/10/27 17:36:57 brouard *** empty log message *** Revision 1.206 2015/10/24 07:14:11 brouard *** empty log message *** Revision 1.205 2015/10/23 15:50:53 brouard Summary: 0.98r3 some clarification for graphs on likelihood contributions Revision 1.204 2015/10/01 16:20:26 brouard Summary: Some new graphs of contribution to likelihood Revision 1.203 2015/09/30 17:45:14 brouard Summary: looking at better estimation of the hessian Also a better criteria for convergence to the period prevalence And therefore adding the number of years needed to converge. (The prevalence in any alive state shold sum to one Revision 1.202 2015/09/22 19:45:16 brouard Summary: Adding some overall graph on contribution to likelihood. Might change Revision 1.201 2015/09/15 17:34:58 brouard Summary: 0.98r0 - Some new graphs like suvival functions - Some bugs fixed like model=1+age+V2. Revision 1.200 2015/09/09 16:53:55 brouard Summary: Big bug thanks to Flavia Even model=1+age+V2. did not work anymore Revision 1.199 2015/09/07 14:09:23 brouard Summary: 0.98q6 changing default small png format for graph to vectorized svg. Revision 1.198 2015/09/03 07:14:39 brouard Summary: 0.98q5 Flavia Revision 1.197 2015/09/01 18:24:39 brouard *** empty log message *** Revision 1.196 2015/08/18 23:17:52 brouard Summary: 0.98q5 Revision 1.195 2015/08/18 16:28:39 brouard Summary: Adding a hack for testing purpose After reading the title, ftol and model lines, if the comment line has a q, starting with #q, the answer at the end of the run is quit. It permits to run test files in batch with ctest. The former workaround was $ echo q | imach foo.imach Revision 1.194 2015/08/18 13:32:00 brouard Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line. Revision 1.193 2015/08/04 07:17:42 brouard Summary: 0.98q4 Revision 1.192 2015/07/16 16:49:02 brouard Summary: Fixing some outputs Revision 1.191 2015/07/14 10:00:33 brouard Summary: Some fixes Revision 1.190 2015/05/05 08:51:13 brouard Summary: Adding digits in output parameters (7 digits instead of 6) Fix 1+age+. Revision 1.189 2015/04/30 14:45:16 brouard Summary: 0.98q2 Revision 1.188 2015/04/30 08:27:53 brouard *** empty log message *** Revision 1.187 2015/04/29 09:11:15 brouard *** empty log message *** Revision 1.186 2015/04/23 12:01:52 brouard Summary: V1*age is working now, version 0.98q1 Some codes had been disabled in order to simplify and Vn*age was working in the optimization phase, ie, giving correct MLE parameters, but, as usual, outputs were not correct and program core dumped. Revision 1.185 2015/03/11 13:26:42 brouard Summary: Inclusion of compile and links command line for Intel Compiler Revision 1.184 2015/03/11 11:52:39 brouard Summary: Back from Windows 8. Intel Compiler Revision 1.183 2015/03/10 20:34:32 brouard Summary: 0.98q0, trying with directest, mnbrak fixed We use directest instead of original Powell test; probably no incidence on the results, but better justifications; We fixed Numerical Recipes mnbrak routine which was wrong and gave wrong results. Revision 1.182 2015/02/12 08:19:57 brouard Summary: Trying to keep directest which seems simpler and more general Author: Nicolas Brouard Revision 1.181 2015/02/11 23:22:24 brouard Summary: Comments on Powell added Author: Revision 1.180 2015/02/11 17:33:45 brouard Summary: Finishing move from main to function (hpijx and prevalence_limit) Revision 1.179 2015/01/04 09:57:06 brouard Summary: back to OS/X Revision 1.178 2015/01/04 09:35:48 brouard *** empty log message *** Revision 1.177 2015/01/03 18:40:56 brouard Summary: Still testing ilc32 on OSX Revision 1.176 2015/01/03 16:45:04 brouard *** empty log message *** Revision 1.175 2015/01/03 16:33:42 brouard *** empty log message *** Revision 1.174 2015/01/03 16:15:49 brouard Summary: Still in cross-compilation Revision 1.173 2015/01/03 12:06:26 brouard Summary: trying to detect cross-compilation Revision 1.172 2014/12/27 12:07:47 brouard Summary: Back from Visual Studio and Intel, options for compiling for Windows XP Revision 1.171 2014/12/23 13:26:59 brouard Summary: Back from Visual C Still problem with utsname.h on Windows Revision 1.170 2014/12/23 11:17:12 brouard Summary: Cleaning some \%% back to %% The escape was mandatory for a specific compiler (which one?), but too many warnings. Revision 1.169 2014/12/22 23:08:31 brouard Summary: 0.98p Outputs some informations on compiler used, OS etc. Testing on different platforms. Revision 1.168 2014/12/22 15:17:42 brouard Summary: update Revision 1.167 2014/12/22 13:50:56 brouard Summary: Testing uname and compiler version and if compiled 32 or 64 Testing on Linux 64 Revision 1.166 2014/12/22 11:40:47 brouard *** empty log message *** Revision 1.165 2014/12/16 11:20:36 brouard Summary: After compiling on Visual C * imach.c (Module): Merging 1.61 to 1.162 Revision 1.164 2014/12/16 10:52:11 brouard Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn * imach.c (Module): Merging 1.61 to 1.162 Revision 1.163 2014/12/16 10:30:11 brouard * imach.c (Module): Merging 1.61 to 1.162 Revision 1.162 2014/09/25 11:43:39 brouard Summary: temporary backup 0.99! Revision 1.1 2014/09/16 11:06:58 brouard Summary: With some code (wrong) for nlopt Author: Revision 1.161 2014/09/15 20:41:41 brouard Summary: Problem with macro SQR on Intel compiler Revision 1.160 2014/09/02 09:24:05 brouard *** empty log message *** Revision 1.159 2014/09/01 10:34:10 brouard Summary: WIN32 Author: Brouard Revision 1.158 2014/08/27 17:11:51 brouard *** empty log message *** Revision 1.157 2014/08/27 16:26:55 brouard Summary: Preparing windows Visual studio version Author: Brouard In order to compile on Visual studio, time.h is now correct and time_t and tm struct should be used. difftime should be used but sometimes I just make the differences in raw time format (time(&now). Trying to suppress #ifdef LINUX Add xdg-open for __linux in order to open default browser. Revision 1.156 2014/08/25 20:10:10 brouard *** empty log message *** Revision 1.155 2014/08/25 18:32:34 brouard Summary: New compile, minor changes Author: Brouard Revision 1.154 2014/06/20 17:32:08 brouard Summary: Outputs now all graphs of convergence to period prevalence Revision 1.153 2014/06/20 16:45:46 brouard Summary: If 3 live state, convergence to period prevalence on same graph Author: Brouard Revision 1.152 2014/06/18 17:54:09 brouard Summary: open browser, use gnuplot on same dir than imach if not found in the path Revision 1.151 2014/06/18 16:43:30 brouard *** empty log message *** Revision 1.150 2014/06/18 16:42:35 brouard Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) Author: brouard Revision 1.149 2014/06/18 15:51:14 brouard Summary: Some fixes in parameter files errors Author: Nicolas Brouard Revision 1.148 2014/06/17 17:38:48 brouard Summary: Nothing new Author: Brouard Just a new packaging for OS/X version 0.98nS Revision 1.147 2014/06/16 10:33:11 brouard *** empty log message *** Revision 1.146 2014/06/16 10:20:28 brouard Summary: Merge Author: Brouard Merge, before building revised version. Revision 1.145 2014/06/10 21:23:15 brouard Summary: Debugging with valgrind Author: Nicolas Brouard Lot of changes in order to output the results with some covariates After the Edimburgh REVES conference 2014, it seems mandatory to improve the code. No more memory valgrind error but a lot has to be done in order to continue the work of splitting the code into subroutines. Also, decodemodel has been improved. Tricode is still not optimal. nbcode should be improved. Documentation has been added in the source code. Revision 1.143 2014/01/26 09:45:38 brouard Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... (Module): Version 0.98nR Running ok, but output format still only works for three covariates. Revision 1.142 2014/01/26 03:57:36 brouard Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... Revision 1.141 2014/01/26 02:42:01 brouard * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... Revision 1.140 2011/09/02 10:37:54 brouard Summary: times.h is ok with mingw32 now. Revision 1.139 2010/06/14 07:50:17 brouard After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. I remember having already fixed agemin agemax which are pointers now but not cvs saved. Revision 1.138 2010/04/30 18:19:40 brouard *** empty log message *** Revision 1.137 2010/04/29 18:11:38 brouard (Module): Checking covariates for more complex models than V1+V2. A lot of change to be done. Unstable. Revision 1.136 2010/04/26 20:30:53 brouard (Module): merging some libgsl code. Fixing computation of likelione (using inter/intrapolation if mle = 0) in order to get same likelihood as if mle=1. Some cleaning of code and comments added. Revision 1.135 2009/10/29 15:33:14 brouard (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. Revision 1.134 2009/10/29 13:18:53 brouard (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. Revision 1.133 2009/07/06 10:21:25 brouard just nforces Revision 1.132 2009/07/06 08:22:05 brouard Many tings Revision 1.131 2009/06/20 16:22:47 brouard Some dimensions resccaled Revision 1.130 2009/05/26 06:44:34 brouard (Module): Max Covariate is now set to 20 instead of 8. A lot of cleaning with variables initialized to 0. Trying to make V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. Revision 1.129 2007/08/31 13:49:27 lievre Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting Revision 1.128 2006/06/30 13:02:05 brouard (Module): Clarifications on computing e.j Revision 1.127 2006/04/28 18:11:50 brouard (Module): Yes the sum of survivors was wrong since imach-114 because nhstepm was no more computed in the age loop. Now we define nhstepma in the age loop. (Module): In order to speed up (in case of numerous covariates) we compute health expectancies (without variances) in a first step and then all the health expectancies with variances or standard deviation (needs data from the Hessian matrices) which slows the computation. In the future we should be able to stop the program is only health expectancies and graph are needed without standard deviations. Revision 1.126 2006/04/28 17:23:28 brouard (Module): Yes the sum of survivors was wrong since imach-114 because nhstepm was no more computed in the age loop. Now we define nhstepma in the age loop. Version 0.98h Revision 1.125 2006/04/04 15:20:31 lievre Errors in calculation of health expectancies. Age was not initialized. Forecasting file added. Revision 1.124 2006/03/22 17:13:53 lievre Parameters are printed with %lf instead of %f (more numbers after the comma). The log-likelihood is printed in the log file Revision 1.123 2006/03/20 10:52:43 brouard * imach.c (Module):
=(p+1))(v[j-p-1] = t[j]); */
/* } */
/* } */
#ifdef _WIN32
char * strsep(char **pp, const char *delim)
{
char *p, *q;
if ((p = *pp) == NULL)
return 0;
if ((q = strpbrk (p, delim)) != NULL)
{
*pp = q + 1;
*q = '\0';
}
else
*pp = 0;
return p;
}
#endif
/********************** nrerror ********************/
void nrerror(char error_text[])
{
fprintf(stderr,"ERREUR ...\n");
fprintf(stderr,"%s\n",error_text);
exit(EXIT_FAILURE);
}
/*********************** vector *******************/
double *vector(int nl, int nh)
{
double *v;
v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
if (!v) nrerror("allocation failure in vector");
return v-nl+NR_END;
}
/************************ free vector ******************/
void free_vector(double*v, int nl, int nh)
{
free((FREE_ARG)(v+nl-NR_END));
}
/************************ivector *******************************/
int *ivector(long nl,long nh)
{
int *v;
v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
if (!v) nrerror("allocation failure in ivector");
return v-nl+NR_END;
}
/******************free ivector **************************/
void free_ivector(int *v, long nl, long nh)
{
free((FREE_ARG)(v+nl-NR_END));
}
/************************lvector *******************************/
long *lvector(long nl,long nh)
{
long *v;
v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
if (!v) nrerror("allocation failure in ivector");
return v-nl+NR_END;
}
/******************free lvector **************************/
void free_lvector(long *v, long nl, long nh)
{
free((FREE_ARG)(v+nl-NR_END));
}
/******************* imatrix *******************************/
int **imatrix(long nrl, long nrh, long ncl, long nch)
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
{
long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
int **m;
/* allocate pointers to rows */
m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
/* allocate rows and set pointers to them */
m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
/* return pointer to array of pointers to rows */
return m;
}
/****************** free_imatrix *************************/
void free_imatrix(m,nrl,nrh,ncl,nch)
int **m;
long nch,ncl,nrh,nrl;
/* free an int matrix allocated by imatrix() */
{
free((FREE_ARG) (m[nrl]+ncl-NR_END));
free((FREE_ARG) (m+nrl-NR_END));
}
/******************* matrix *******************************/
double **matrix(long nrl, long nrh, long ncl, long nch)
{
long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
double **m;
m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;
/* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
*/
}
/*************************free matrix ************************/
void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
{
free((FREE_ARG)(m[nrl]+ncl-NR_END));
free((FREE_ARG)(m+nrl-NR_END));
}
/******************* ma3x *******************************/
double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
{
long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
double ***m;
m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
if (!m) nrerror("allocation failure 1 in matrix()");
m += NR_END;
m -= nrl;
m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
m[nrl] += NR_END;
m[nrl] -= ncl;
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
m[nrl][ncl] += NR_END;
m[nrl][ncl] -= nll;
for (j=ncl+1; j<=nch; j++)
m[nrl][j]=m[nrl][j-1]+nlay;
for (i=nrl+1; i<=nrh; i++) {
m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
for (j=ncl+1; j<=nch; j++)
m[i][j]=m[i][j-1]+nlay;
}
return m;
/* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
&(m[i][j][k]) <=> *((*(m+i) + j)+k)
*/
}
/*************************free ma3x ************************/
void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
{
free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
free((FREE_ARG)(m[nrl]+ncl-NR_END));
free((FREE_ARG)(m+nrl-NR_END));
}
/*************** function subdirf ***********/
char *subdirf(char fileres[])
{
/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/"); /* Add to the right */
strcat(tmpout,fileres);
return tmpout;
}
/*************** function subdirf2 ***********/
char *subdirf2(char fileres[], char *preop)
{
/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/");
strcat(tmpout,preop);
strcat(tmpout,fileres);
return tmpout;
}
/*************** function subdirf3 ***********/
char *subdirf3(char fileres[], char *preop, char *preop2)
{
/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/");
strcat(tmpout,preop);
strcat(tmpout,preop2);
strcat(tmpout,fileres);
return tmpout;
}
/*************** function subdirfext ***********/
char *subdirfext(char fileres[], char *preop, char *postop)
{
strcpy(tmpout,preop);
strcat(tmpout,fileres);
strcat(tmpout,postop);
return tmpout;
}
/*************** function subdirfext3 ***********/
char *subdirfext3(char fileres[], char *preop, char *postop)
{
/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/");
strcat(tmpout,preop);
strcat(tmpout,fileres);
strcat(tmpout,postop);
return tmpout;
}
char *asc_diff_time(long time_sec, char ascdiff[])
{
long sec_left, days, hours, minutes;
days = (time_sec) / (60*60*24);
sec_left = (time_sec) % (60*60*24);
hours = (sec_left) / (60*60) ;
sec_left = (sec_left) %(60*60);
minutes = (sec_left) /60;
sec_left = (sec_left) % (60);
sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
return ascdiff;
}
/***************** f1dim *************************/
extern int ncom;
extern double *pcom,*xicom;
extern double (*nrfunc)(double []);
double f1dim(double x)
{
int j;
double f;
double *xt;
xt=vector(1,ncom);
for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
f=(*nrfunc)(xt);
free_vector(xt,1,ncom);
return f;
}
/*****************brent *************************/
double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
{
/* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
* between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
* the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
* the minimum is returned as xmin, and the minimum function value is returned as brent , the
* returned function value.
*/
int iter;
double a,b,d,etemp;
double fu=0,fv,fw,fx;
double ftemp=0.;
double p,q,r,tol1,tol2,u,v,w,x,xm;
double e=0.0;
a=(ax < cx ? ax : cx);
b=(ax > cx ? ax : cx);
x=w=v=bx;
fw=fv=fx=(*f)(x);
for (iter=1;iter<=ITMAX;iter++) {
xm=0.5*(a+b);
tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
/* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
printf(".");fflush(stdout);
fprintf(ficlog,".");fflush(ficlog);
#ifdef DEBUGBRENT
printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
/* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
#endif
if (fabs(x-xm) <= (tol2-0.5*(b-a))){
*xmin=x;
return fx;
}
ftemp=fu;
if (fabs(e) > tol1) {
r=(x-w)*(fx-fv);
q=(x-v)*(fx-fw);
p=(x-v)*q-(x-w)*r;
q=2.0*(q-r);
if (q > 0.0) p = -p;
q=fabs(q);
etemp=e;
e=d;
if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
d=CGOLD*(e=(x >= xm ? a-x : b-x));
else {
d=p/q;
u=x+d;
if (u-a < tol2 || b-u < tol2)
d=SIGN(tol1,xm-x);
}
} else {
d=CGOLD*(e=(x >= xm ? a-x : b-x));
}
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
fu=(*f)(u);
if (fu <= fx) {
if (u >= x) a=x; else b=x;
SHFT(v,w,x,u)
SHFT(fv,fw,fx,fu)
} else {
if (u < x) a=u; else b=u;
if (fu <= fw || w == x) {
v=w;
w=u;
fv=fw;
fw=fu;
} else if (fu <= fv || v == x || v == w) {
v=u;
fv=fu;
}
}
}
nrerror("Too many iterations in brent");
*xmin=x;
return fx;
}
/****************** mnbrak ***********************/
void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
double (*func)(double))
{ /* Given a function func , and given distinct initial points ax and bx , this routine searches in
the downhill direction (defined by the function as evaluated at the initial points) and returns
new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
*/
double ulim,u,r,q, dum;
double fu;
double scale=10.;
int iterscale=0;
*fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
*fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
/* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
/* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
/* *bx = *ax - (*ax - *bx)/scale; */
/* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
/* } */
if (*fb > *fa) {
SHFT(dum,*ax,*bx,dum)
SHFT(dum,*fb,*fa,dum)
}
*cx=(*bx)+GOLD*(*bx-*ax);
*fc=(*func)(*cx);
#ifdef DEBUG
printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
#endif
while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
r=(*bx-*ax)*(*fb-*fc);
q=(*bx-*cx)*(*fb-*fa);
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
fu=(*func)(u);
#ifdef DEBUG
/* f(x)=A(x-u)**2+f(u) */
double A, fparabu;
A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
fparabu= *fa - A*(*ax-u)*(*ax-u);
printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
/* And thus,it can be that fu > *fc even if fparabu < *fc */
/* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
(*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
/* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
#endif
#ifdef MNBRAKORIGINAL
#else
/* if (fu > *fc) { */
/* #ifdef DEBUG */
/* printf("mnbrak4 fu > fc \n"); */
/* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
/* #endif */
/* /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/ *\/ */
/* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
/* dum=u; /\* Shifting c and u *\/ */
/* u = *cx; */
/* *cx = dum; */
/* dum = fu; */
/* fu = *fc; */
/* *fc =dum; */
/* } else { /\* end *\/ */
/* #ifdef DEBUG */
/* printf("mnbrak3 fu < fc \n"); */
/* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
/* #endif */
/* dum=u; /\* Shifting c and u *\/ */
/* u = *cx; */
/* *cx = dum; */
/* dum = fu; */
/* fu = *fc; */
/* *fc =dum; */
/* } */
#ifdef DEBUG
printf("mnbrak34 fu < or >= fc \n");
fprintf(ficlog, "mnbrak34 fu < fc\n");
#endif
dum=u; /* Shifting c and u */
u = *cx;
*cx = dum;
dum = fu;
fu = *fc;
*fc =dum;
#endif
} else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
#ifdef DEBUG
printf("mnbrak2 u after c but before ulim\n");
fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
#endif
fu=(*func)(u);
if (fu < *fc) {
#ifdef DEBUG
printf("mnbrak2 u after c but before ulim AND fu < fc\n");
fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu ");
m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
jj1=0;
for(k1=1; k1<=m;k1++){
/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;
if (cptcovn > 0) {
fprintf(fichtm," ");
m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
jj1=0;
for(k1=1; k1<=m;k1++){
/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;
if (cptcovn > 0) {
fprintf(fichtm,"
File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
else if(mle >=1)
fprintf(fichtm,"\n
File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: %s
\n",subdirf(fileresilk),subdirf(fileresilk));
for (k=1; k<= nlstate ; k++) {
fprintf(fichtm,"
- Probability p%dj by origin %d and destination j. Dot's sizes are related to corresponding weight: %s-p%dj.png
\
",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
}
fprintf(fichtm,"
- The function drawn is -2Log(L) in Log scale: by state of origin %s-ori.png
\
",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
fprintf(fichtm,"
- and by state of destination %s-dest.png
\
",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
fflush(fichtm);
}
return;
}
/*********** Maximum Likelihood Estimation ***************/
void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
{
int i,j, iter=0;
double **xi;
double fret;
double fretone; /* Only one call to likelihood */
/* char filerespow[FILENAMELENGTH];*/
#ifdef NLOPT
int creturn;
nlopt_opt opt;
/* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
double *lb;
double minf; /* the minimum objective value, upon return */
double * p1; /* Shifted parameters from 0 instead of 1 */
myfunc_data dinst, *d = &dinst;
#endif
xi=matrix(1,npar,1,npar);
for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n"); fprintf(ficlog,"Powell\n");
strcpy(filerespow,"POW_");
strcat(filerespow,fileres);
if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
}
fprintf(ficrespow,"# Powell\n# iter -2*LL");
for (i=1;i<=nlstate;i++)
for(j=1;j<=nlstate+ndeath;j++)
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
fprintf(ficrespow,"\n");
#ifdef POWELL
powell(p,xi,npar,ftol,&iter,&fret,func);
#endif
#ifdef NLOPT
#ifdef NEWUOA
opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
#else
opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
#endif
lb=vector(0,npar-1);
for (i=0;i
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
fprintf(ficresphtm,"Current page is file %s
\n\nFrequencies and prevalence by age at begin of transition
\n",fileresphtm, fileresphtm);
strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
fflush(ficlog);
exit(70);
}
else{
fprintf(ficresphtmfr,"\n
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\
fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
fprintf(ficresphtmfr,"Current page is file %s
\n\nFrequencies of all effective transitions by age at begin of transition
Unknown status is -1
\n",fileresphtmfr, fileresphtmfr);
freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
j1=0;
j=cptcoveff;
if (cptcovn<1) {j=1;ncodemax[1]=1;}
first=1;
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)
for (jk=-5; jk<=nlstate+ndeath; jk++)
for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;
for (i=1; i<=nlstate; i++)
for(m=iagemin; m <= iagemax+3; m++)
prop[i][m]=0;
dateintsum=0;
k2cpt=0;
for (i=1; i<=imx; i++) { /* For each individual i */
bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
/* Tests if the value of each of the covariates of i is equal to filter j1 */
bool=0;
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
}
} /* cptcovn > 0 */
if (bool==1){
/* for(m=firstpass; m<=lastpass; m++){ */
for(mi=1; mi********** Variable ");
fprintf(ficresphtmfr, "\n
\n");
fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n");
}
fprintf(ficresphtm,"********** Variable ");
for (z1=1; z1<=cptcoveff; z1++){
fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}
fprintf(ficresp, "**********\n#");
fprintf(ficresphtm, "**********
\n");
fprintf(ficresphtmfr, "**********");
for(i=1; i<=nlstate;i++) {
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
fprintf(ficresphtm, "
\n");
/*}*/
} /* end j1 */
dateintmean=dateintsum/k2cpt;
fclose(ficresp);
fclose(ficresphtm);
fclose(ficresphtmfr);
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);
free_matrix(prop,1,nlstate,iagemin, iagemax+3);
/* End of Freq */
}
/************ Prevalence ********************/
void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
{
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
in each health status at the date of interview (if between dateprev1 and dateprev2).
We still use firstpass and lastpass as another selection.
*/
int i, m, jk, j1, bool, z1,j;
int mi; /* Effective wave */
int iage;
double agebegin, ageend;
double **prop;
double posprop;
double y2; /* in fractional years */
int iagemin, iagemax;
int first; /** to stop verbosity which is redirected to log file */
iagemin= (int) agemin;
iagemax= (int) agemax;
/*pp=vector(1,nlstate);*/
prop=matrix(1,nlstate,iagemin,iagemax+3);
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;
/*j=cptcoveff;*/
if (cptcovn<1) {j=1;ncodemax[1]=1;}
first=1;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
for (i=1; i<=nlstate; i++)
for(iage=iagemin; iage <= iagemax+3; iage++)
prop[i][iage]=0.0;
for (i=1; i<=imx; i++) { /* Each individual */
bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
bool=0;
}
if (bool==1) {
/* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
for(mi=1; miAge Prev(%d) N(%d) N ",i,i);
}
fprintf(ficresp, "\n");
fprintf(ficresphtm, "\n");
/* Header of frequency table by age */
fprintf(ficresphtmfr,"");
fprintf(ficresphtmfr,"
\n");
fprintf(ficresphtmfr,"Age ");
for(jk=-1; jk <=nlstate+ndeath; jk++){
for(m=-1; m <=nlstate+ndeath; m++){
if(jk!=0 && m!=0)
fprintf(ficresphtmfr,"%d%d ",jk,m);
}
}
fprintf(ficresphtmfr, "\n");
/* For each age */
for(i=iagemin; i <= iagemax+3; i++){
fprintf(ficresphtm,"");
if(i==iagemax+1){
fprintf(ficlog,"1");
fprintf(ficresphtmfr," 0 ");
}else if(i==iagemax+2){
fprintf(ficlog,"0");
fprintf(ficresphtmfr,"Unknown ");
}else if(i==iagemax+3){
fprintf(ficlog,"Total");
fprintf(ficresphtmfr,"Total ");
}else{
if(first==1){
first=0;
printf("See log file for details...\n");
}
fprintf(ficresphtmfr," \n ");
if(i <= iagemax){
fprintf(ficresp,"\n");
fprintf(ficresphtm,"\n");
}
if(first==1)
printf("Others in log...\n");
fprintf(ficlog,"\n");
} /* end loop i */
fprintf(ficresphtm,"%d ",i);
fprintf(ficlog,"Age %d", i);
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];
if(pp[jk]>=1.e-10){
if(first==1){
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}else{
if(first==1)
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
}
}
for(jk=1; jk <=nlstate ; jk++){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
pos += pp[jk];
posprop += prop[jk][i];
}
for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){
if(first==1)
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
}else{
if(first==1)
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
}
if( i <= iagemax){
if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
fprintf(ficresphtm,"%d %.5f %.0f %.0f ",i,prop[jk][i]/posprop, prop[jk][i],posprop);
/*probs[i][jk][j1]= pp[jk]/pos;*/
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
}
else{
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
fprintf(ficresphtm,"%d NaNq %.0f %.0f ",i, prop[jk][i],posprop);
}
}
}
for(jk=-1; jk <=nlstate+ndeath; jk++){
for(m=-1; m <=nlstate+ndeath; m++){
if(freq[jk][m][i] !=0 ) { /* minimizing output */
if(first==1){
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
}
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
}
if(jk!=0 && m!=0)
fprintf(ficresphtmfr,"%.0f ",freq[jk][m][i]);
}
}
fprintf(ficresphtmfr," Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)
%s
\n",digitp);
/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
if(popbased==1)
fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
else
fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
fprintf(ficresvij,"\n");
xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);
dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
gpp=vector(nlstate+1,nlstate+ndeath);
gmp=vector(nlstate+1,nlstate+ndeath);
trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
else hstepm=estepm;
/* For example we decided to compute the life expectancy with the smallest unit */
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelim.
Look at function hpijx to understand why because of memory size limitations,
we decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed every two years of age and if
you sum them up and add 1 year (area under the trapezoids) you won't get the same
results. So we changed our mind and took the option of the best precision.
*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
agelim = AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
gp=matrix(0,nhstepm,1,nlstate);
gm=matrix(0,nhstepm,1,nlstate);
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][ij];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}
}
/* Next for computing probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.
*/
for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];
}
/* end probability of death */
for(i=1; i<=npar; i++) /* Computes gradient x - delta */
xp[i] = x[i] - (i==theta ?delti[theta]:0);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][ij];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)
gm[h][j] += prlim[i][i]*p3mat[i][j][h];
}
}
/* This for computing probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.
*/
for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gmp[j]=0.; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];
}
/* end probability of death */
for(j=1; j<= nlstate; j++) /* vareij */
for(h=0; h<=nhstepm; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}
} /* End theta */
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
for(h=0; h<=nhstepm; h++) /* veij */
for(j=1; j<=nlstate;j++)
for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;
for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
}
}
/* pptj */
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
for(j=nlstate+1;j<=nlstate+ndeath;j++)
for(i=nlstate+1;i<=nlstate+ndeath;i++)
varppt[j][i]=doldmp[j][i];
/* end ppptj */
/* x centered again */
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][ij];
}else{ /* mobilav */
for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
/* This for computing probability of death (h=1 means
computed over hstepm (estepm) matrices product = hstepm*stepm months)
as a weighted average of prlim.
*/
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gmp[j]=0.;i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];
}
/* end probability of death */
fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
for(i=1; i<=nlstate;i++){
fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
}
}
fprintf(ficresprobmorprev,"\n");
fprintf(ficresvij,"%.0f ",age );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
}
fprintf(ficresvij,"\n");
free_matrix(gp,0,nhstepm,1,nlstate);
free_matrix(gm,0,nhstepm,1,nlstate);
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* End age */
free_vector(gpp,nlstate+1,nlstate+ndeath);
free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
/* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(fichtm,"\n
File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
fprintf(fichtm,"\n
Probability is computed over estepm=%d months.
\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
/* fprintf(fichtm,"\n
Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year
\n", stepm,YEARM,digitp,digit);
*/
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);
free_matrix(dnewm,1,nlstate,1,npar);
free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficresprobmorprev);
fflush(ficgp);
fflush(fichtm);
} /* end varevsij */
/************ Variance of prevlim ******************/
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
{
/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
double **dnewm,**doldm;
int i, j, nhstepm, hstepm;
double *xp;
double *gp, *gm;
double **gradg, **trgradg;
double **mgm, **mgp;
double age,agelim;
int theta;
pstamp(ficresvpl);
fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);
fprintf(ficresvpl,"\n");
xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);
hstepm=1*YEARM; /* Every year of age */
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
agelim = AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
if (stepm >= YEARM) hstepm=1;
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
gradg=matrix(1,npar,1,nlstate);
mgp=matrix(1,npar,1,nlstate);
mgm=matrix(1,npar,1,nlstate);
gp=vector(1,nlstate);
gm=vector(1,nlstate);
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){ /* Computes gradient */
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
else
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
for(i=1;i<=nlstate;i++){
gp[i] = prlim[i][i];
mgp[theta][i] = prlim[i][i];
}
for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);
if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
else
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
for(i=1;i<=nlstate;i++){
gm[i] = prlim[i][i];
mgm[theta][i] = prlim[i][i];
}
for(i=1;i<=nlstate;i++)
gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
/* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
} /* End theta */
trgradg =matrix(1,nlstate,1,npar);
for(j=1; j<=nlstate;j++)
for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];
/* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
/* printf("\nmgm mgp %d ",(int)age); */
/* for(j=1; j<=nlstate;j++){ */
/* printf(" %d ",j); */
/* for(theta=1; theta <=npar; theta++) */
/* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
/* printf("\n "); */
/* } */
/* } */
/* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
/* printf("\n gradg %d ",(int)age); */
/* for(j=1; j<=nlstate;j++){ */
/* printf("%d ",j); */
/* for(theta=1; theta <=npar; theta++) */
/* printf("%d %lf ",theta,gradg[theta][j]); */
/* printf("\n "); */
/* } */
/* } */
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;
if((int)age==79 ||(int)age== 80 ||(int)age== 81){
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
}else{
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
}
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
fprintf(ficresvpl,"%.0f ",age );
for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
fprintf(ficresvpl,"\n");
free_vector(gp,1,nlstate);
free_vector(gm,1,nlstate);
free_matrix(mgm,1,npar,1,nlstate);
free_matrix(mgp,1,npar,1,nlstate);
free_matrix(gradg,1,npar,1,nlstate);
free_matrix(trgradg,1,nlstate,1,npar);
} /* End age */
free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);
free_matrix(dnewm,1,nlstate,1,nlstate);
}
/************ Variance of one-step probabilities ******************/
void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
{
int i, j=0, k1, l1, tj;
int k2, l2, j1, z1;
int k=0, l;
int first=1, first1, first2;
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double **dnewm,**doldm;
double *xp;
double *gp, *gm;
double **gradg, **trgradg;
double **mu;
double age, cov[NCOVMAX+1];
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
int theta;
char fileresprob[FILENAMELENGTH];
char fileresprobcov[FILENAMELENGTH];
char fileresprobcor[FILENAMELENGTH];
double ***varpij;
strcpy(fileresprob,"PROB_");
strcat(fileresprob,fileres);
if((ficresprob=fopen(fileresprob,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprob);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
}
strcpy(fileresprobcov,"PROBCOV_");
strcat(fileresprobcov,fileresu);
if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobcov);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
}
strcpy(fileresprobcor,"PROBCOR_");
strcat(fileresprobcor,fileresu);
if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprobcor);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
}
printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
pstamp(ficresprob);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");
pstamp(ficresprobcov);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");
pstamp(ficresprobcor);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
fprintf(ficresprobcor,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=(nlstate+ndeath);j++){
fprintf(ficresprob," p%1d-%1d (SE)",i,j);
fprintf(ficresprobcov," p%1d-%1d ",i,j);
fprintf(ficresprobcor," p%1d-%1d ",i,j);
}
/* fprintf(ficresprob,"\n");
fprintf(ficresprobcov,"\n");
fprintf(ficresprobcor,"\n");
*/
xp=vector(1,npar);
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
first=1;
fprintf(ficgp,"\n# Routine varprob");
fprintf(fichtm,"\n Computing and drawing one step probabilities with their confidence intervals
Matrix of variance-covariance of one-step probabilities (drawings)
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.
\n\nMatrix of variance-covariance of pairs of step probabilities
\n",optionfilehtmcov, optionfilehtmcov);
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p
\n");
fprintf(fichtmcov,"\n
Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \
It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
standard deviations wide on each axis.
\
Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
and made the appropriate rotation to look at the uncorrelated principal directions.
\
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
\n");
cov[1]=1;
/* tj=cptcoveff; */
tj = (int) pow(2,cptcoveff);
if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;
for(j1=1; j1<=tj;j1++){
/*for(i1=1; i1<=ncodemax[t];i1++){ */
/*j1++;*/
if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcov, "**********\n#\n");
fprintf(ficgp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficgp, "**********\n#\n");
fprintf(fichtmcov, "\n
********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(fichtmcov, "**********\n
");
fprintf(ficresprobcor, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcor, "**********\n#");
}
gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
gp=vector(1,(nlstate)*(nlstate+ndeath));
gm=vector(1,(nlstate)*(nlstate+ndeath));
for (age=bage; age<=fage; age ++){
cov[2]=age;
if(nagesqr==1)
cov[3]= age*age;
for (k=1; k<=cptcovn;k++) {
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
/*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
* 1 1 1 1 1
* 2 2 1 1 1
* 3 1 2 1 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]; */
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
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)];
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)
xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;
for(i=1; i<= (nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
gp[k]=pmmij[i][j];
}
}
for(i=1; i<=npar; i++)
xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;
for(i=1; i<=(nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
gm[k]=pmmij[i][j];
}
}
for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
}
for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];
matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
pmij(pmmij,cov,ncovmodel,x,nlstate);
k=0;
for(i=1; i<=(nlstate); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
mu[k][(int) age]=pmmij[i][j];
}
}
for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
varpij[i][j][(int)age] = doldm[i][j];
/*printf("\n%d ",(int)age);
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
}*/
fprintf(ficresprob,"\n%d ",(int)age);
fprintf(ficresprobcov,"\n%d ",(int)age);
fprintf(ficresprobcor,"\n%d ",(int)age);
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
}
i=0;
for (k=1; k<=(nlstate);k++){
for (l=1; l<=(nlstate+ndeath);l++){
i++;
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
for (j=1; j<=i;j++){
/* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
}
}
}/* end of loop for state */
} /* end of loop for age */
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
/* Confidence intervalle of pij */
/*
fprintf(ficgp,"\nunset parametric;unset label");
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n
Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname);
fprintf(fichtm,"\n
",optionfilefiname);
fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
*/
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
first1=1;first2=2;
for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;
j=(k2-1)*(nlstate+ndeath)+l2;
for (k1=1; k1<=(nlstate);k1++){
for (l1=1; l1<=(nlstate+ndeath);l1++){
if(l1==k1) continue;
i=(k1-1)*(nlstate+ndeath)+l1;
if(i<=j) continue;
for (age=bage; age<=fage; age ++){
if ((int)age %5==0){
v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
mu1=mu[i][(int) age]/stepm*YEARM ;
mu2=mu[j][(int) age]/stepm*YEARM;
c12=cv12/sqrt(v1*v2);
/* Computing eigen value of matrix of covariance */
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
if ((lc2 <0) || (lc1 <0) ){
if(first2==1){
first1=0;
printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
}
fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
/* lc1=fabs(lc1); */ /* If we want to have them positive */
/* lc2=fabs(lc2); */
}
/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
v21=(lc1-v1)/cv12*v11;
v12=-v21;
v22=v11;
tnalp=v21/v11;
if(first1==1){
first1=0;
printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
}
fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
/*printf(fignu*/
/* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
if(first==1){
first=0;
fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
:\
%s_%d%1d%1d-%1d%1d.svg, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\n
",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\n
Correlation at age %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}else{
first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}/* if first */
} /* age mod 5 */
} /* end loop age */
fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
first=1;
} /*l12 */
} /* k12 */
} /*l1 */
}/* k1 */
/* } */ /* loop covariates */
}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
free_vector(xp,1,npar);
fclose(ficresprob);
fclose(ficresprobcov);
fclose(ficresprobcor);
fflush(ficgp);
fflush(fichtmcov);
}
/******************* Printing html file ***********/
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int prevfcast, int backcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, \
double jprev2, double mprev2,double anprev2, double dateprev2){
int jj1, k1, i1, cpt;
fprintf(fichtm,"");
fprintf(fichtm,"Result files (first order: no variance)
\n");
fprintf(fichtm,"
\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
fprintf(fichtm,"
\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: %s
\n ",
stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
fprintf(fichtm,"\
- Estimated back transition probabilities over %d (stepm) months: %s
\n ",
stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
fprintf(fichtm,"\
- Period (stable) prevalence in each health state: %s
\n",
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
fprintf(fichtm,"\
- Period (stable) back prevalence in each health state: %s
\n",
subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
fprintf(fichtm,"\
- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
%s
\n",
estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
if(prevfcast==1){
fprintf(fichtm,"\
- Prevalence projections by age and states: \
%s
\n
");
fprintf(fichtm,"\
\n
************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
}
fprintf(fichtm," ************\n
");
}
/* aij, bij */
fprintf(fichtm,"
- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: %s_%d-1.svg
\
",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Pij */
fprintf(fichtm,"
\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s_%d-2.svg
\
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Quasi-incidences */
fprintf(fichtm,"
\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
divided by h: hPij/h : %s_%d-3.svg
\
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
}
/* State specific survival functions (period) */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Survival functions from state %d in each live state and total.\
Or probability to survive in various states (1 to %d) being in state %d at different ages.\
%s%d_%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
}
/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d.svg
\
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
}
if(backcast==1){
/* Period (stable) back prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d.svg
\
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
}
}
if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
}
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n
- 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): %s_%d%d.svg
\
",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
}
/* } /\* end i1 *\/ */
}/* End k1 */
fprintf(fichtm," Result files (second order: variances)
\n\
- Parameter file with estimated parameters and covariance matrix: %s
\
- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).
\
But because parameters are usually highly correlated (a higher incidence of disability \
and a higher incidence of recovery can give very close observed transition) it might \
be very useful to look not only at linear confidence intervals estimated from the \
variances but at the covariance matrix. And instead of looking at the estimated coefficients \
(parameters) of the logistic regression, it might be more meaningful to visualize the \
covariance matrix of the one-step probabilities. \
See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
fprintf(fichtm," - Standard deviation of one-step probabilities: %s
\n",
subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
fprintf(fichtm,"\
- Variance-covariance of one-step probabilities: %s
\n",
subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
fprintf(fichtm,"\
- Correlation matrix of one-step probabilities: %s
\n",
subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
fprintf(fichtm,"\
- Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \
%s
\n
\n",
estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
fprintf(fichtm,"\
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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): %s
\n",
estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
fprintf(fichtm,"\
- Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): %s
\n",
estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: %s
\n",\
subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
/* if(popforecast==1) fprintf(fichtm,"\n */
/* - Prevalences forecasting: f%s
\n */
/* - Population forecasting (if popforecast=1): pop%s
\n */
/*
",fileres,fileres,fileres,fileres); */
/* else */
/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)
\n",popforecast, stepm, model); */
fflush(fichtm);
fprintf(fichtm,"
");
fflush(fichtm);
}
/******************* Gnuplot file **************/
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
char dirfileres[132],optfileres[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
int lv=0, vlv=0, kl=0;
int ng=0;
int vpopbased;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
/* } */
/*#ifdef windows */
fprintf(ficgp,"cd \"%s\" \n",pathc);
/*#endif */
m=pow(2,cptcoveff);
/* Contribution to likelihood */
/* Plot the probability implied in the likelihood */
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
/* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
fprintf(ficgp,"\nset ter pngcairo size 640, 480");
/* nice for mle=4 plot by number of matrix products.
replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
for (j=2; j<= nlstate+ndeath ; j ++) {
fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
}
fprintf(ficgp,";\nset out; unset ylabel;\n");
}
/* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
/* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
/* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
fprintf(ficgp,"\nset out;unset log\n");
/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");
/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n\
set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%*lf (%%*lf)");
}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%*lf (%%*lf)");
}
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%*lf (%%*lf)");
}
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
fprintf(ficgp,"\nset out \n");
} /* k1 */
} /* cpt */
/*2 eme*/
for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(vpopbased==0)
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else
fprintf(ficgp,"\nreplot ");
for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%*lf (%%*lf)");
}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%*lf (%%*lf)");
}
fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%*lf (%%*lf)");
}
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
} /* state */
} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
} /* k1 */
/*3eme*/
for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
/* k=2+nlstate*(2*cpt-2); */
k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
*/
for (i=1; i< nlstate ; i ++) {
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
}
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
}
}
/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\n\
unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;
for (i=1; i<= nlstate ; i ++){
if(i==1){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
}else{
fprintf(ficgp,", '' ");
}
l=(nlstate+ndeath)*(i-1)+1;
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (j=2; j<= nlstate+ndeath ; j ++)
fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
} /* nlstate */
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
/* Survival functions (period) from state i in state j by final state j */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\n\
unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
if(j==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
else
fprintf(ficgp,", '' ");
l=(nlstate+ndeath)*(cpt-1) +j;
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
/* for (i=2; i<= nlstate+ndeath ; i ++) */
/* fprintf(ficgp,"+$%d",k+l+i-1); */
fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
} /* nlstate */
fprintf(ficgp,", '' ");
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
l=(nlstate+ndeath)*(cpt-1) +j;
if(j < nlstate)
fprintf(ficgp,"$%d +",k+l);
else
fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
}
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\n\
unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){
if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
else
fprintf(ficgp,", '' ");
l=(nlstate+ndeath)*(i-1)+1;
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (j=2; j<= nlstate ; j ++)
fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
} /* nlstate */
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
/* CV back preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\n\
unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){
if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
else
fprintf(ficgp,", '' ");
l=(nlstate+ndeath)*(i-1)+1;
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /* a vérifier */
for (j=2; j<= nlstate ; j ++)
fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
} /* nlstate */
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
if(prevfcast==1){
/* Projection from cross-sectional to stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
fprintf(ficgp," V%d=%d ",k,vlv);
}
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\n\
unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
/*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
/*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
if(i==1){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
}else{
fprintf(ficgp,",\\\n '' ");
}
if(cptcoveff ==0){ /* No covariate */
fprintf(ficgp," u 2:("); /* Age is in 2 */
/*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
if(i==nlstate+1)
fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt );
else
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
}else{
fprintf(ficgp,"u 6:(("); /* Age is in 6 */
/*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each covariate */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[lv]][lv];
kl++;
/* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
/*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
/*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
if(k==cptcoveff)
if(i==nlstate+1)
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt );
else
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
else{
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
kl++;
}
} /* end covariate */
} /* end if covariate */
} /* nlstate */
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
} /* End if prevfcast */
/* proba elementaires */
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){
fprintf(ficgp,"# initial state %d\n",i);
for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {
fprintf(ficgp,"# current state %d\n",k);
for(j=1; j <=ncovmodel; j++){
fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
jk++;
}
fprintf(ficgp,"\n");
}
}
}
fprintf(ficgp,"##############\n#\n");
/*goto avoid;*/
fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
fprintf(ficgp,"#\n");
for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
fprintf(ficgp,"# ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"# jk=%d\n",jk);
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
fprintf(ficgp,"\nunset log y");
}else if (ng==2){
fprintf(ficgp,"\nset ylabel \"Probability\"\n");
fprintf(ficgp,"\nset log y");
}else if (ng==3){
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
fprintf(ficgp,"\nset log y");
}else
fprintf(ficgp,"\nunset title ");
fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;
for(k2=1; k2<=nlstate; k2++) {
k3=i;
for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){
switch( ng) {
case 1:
if(nagesqr==0)
fprintf(ficgp," p%d+p%d*x",i,i+1);
else /* nagesqr =1 */
fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
break;
case 2: /* ng=2 */
if(nagesqr==0)
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
else /* nagesqr =1 */
fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
break;
case 3:
if(nagesqr==0)
fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
else /* nagesqr =1 */
fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
break;
}
ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel-nagesqr; j++) {
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(ij <=cptcovage) { /* Bug valgrind */
if((j-2)==Tage[ij]) { /* Bug valgrind */
fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
ij++;
}
}
else
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
}
}else{
i=i-ncovmodel;
if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
fprintf(ficgp," (1.");
}
if(ng != 1){
fprintf(ficgp,")/(1");
for(k1=1; k1 <=nlstate; k1++){
if(nagesqr==0)
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
else /* nagesqr =1 */
fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){
if(ij <=cptcovage) { /* Bug valgrind */
if((j-2)==Tage[ij]) { /* Bug valgrind */
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
ij++;
}
}
else
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
}
fprintf(ficgp,")");
}
fprintf(ficgp,")");
if(ng ==2)
fprintf(ficgp," t \"p%d%d\" ", k2,k);
else /* ng= 3 */
fprintf(ficgp," t \"i%d%d\" ", k2,k);
}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */
fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
}
if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
fprintf(ficgp,",");
if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
fprintf(ficgp,",");
i=i+ncovmodel;
} /* end k */
} /* end k2 */
fprintf(ficgp,"\n set out\n");
} /* end jk */
} /* end ng */
/* avoid: */
fflush(ficgp);
} /* end gnuplot */
/*************** Moving average **************/
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
int i, cpt, cptcod;
int modcovmax =1;
int mobilavrange, mob;
double age;
modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
a covariate has 2 modalities */
if (cptcovn<1) modcovmax=1; /* At least 1 pass */
if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
if(mobilav==1) mobilavrange=5; /* default */
else mobilavrange=mobilav;
for (age=bage; age<=fage; age++)
for (i=1; i<=nlstate;i++)
for (cptcod=1;cptcod<=modcovmax;cptcod++)
mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
/* We keep the original values on the extreme ages bage, fage and for
fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
we use a 5 terms etc. until the borders are no more concerned.
*/
for (mob=3;mob <=mobilavrange;mob=mob+2){
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
for (i=1; i<=nlstate;i++){
for (cptcod=1;cptcod<=modcovmax;cptcod++){
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
for (cpt=1;cpt<=(mob-1)/2;cpt++){
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
}
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
}
}
}/* end age */
}/* end mob */
}else return -1;
return 0;
}/* End movingaverage */
/************** Forecasting ******************/
void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
/* proj1, year, month, day of starting projection
agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed
anproj2 year of en of projection (same day and month as proj1).
*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
double agec; /* generic age */
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double *popeffectif,*popcount;
double ***p3mat;
double ***mobaverage;
char fileresf[FILENAMELENGTH];
agelim=AGESUP;
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
in each health status at the date of interview (if between dateprev1 and dateprev2).
We still use firstpass and lastpass as another selection.
*/
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
/* firstpass, lastpass, stepm, weightopt, model); */
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
strcpy(fileresf,"F_");
strcat(fileresf,fileresu);
if((ficresf=fopen(fileresf,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", fileresf);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
}
printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
if (cptcoveff==0) ncodemax[cptcoveff]=1;
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
else hstepm=estepm;
hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
fractional in yp1 */
anprojmean=yp;
yp2=modf((yp1*12),&yp);
mprojmean=yp;
yp1=modf((yp2*30.5),&yp);
jprojmean=yp;
if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;
i1=cptcoveff;
if (cptcovn < 1){i1=1;}
fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
fprintf(ficresf,"#****** Routine prevforecast **\n");
/* if (h==(int)(YEARM*yearp)){ */
for(cptcov=1, k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;
fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}
fprintf(ficresf," yearproj age");
for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)
fprintf(ficresf," p%d%d",i,j);
fprintf(ficresf," p.%d",j);
}
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
for (agec=fage; agec>=(ageminpar-1); agec--){
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){
if (h*hstepm/YEARM*stepm ==yearp) {
fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
}
for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;
for(i=1; i<=nlstate;i++) {
if (mobilav==1)
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
else {
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
}
if (h*hstepm/YEARM*stepm== yearp) {
fprintf(ficresf," %.3f", p3mat[i][j][h]);
}
} /* end i */
if (h*hstepm/YEARM*stepm==yearp) {
fprintf(ficresf," %.3f", ppij);
}
}/* end j */
} /* end h */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */
} /* end yearp */
} /* end cptcod */
} /* end cptcov */
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficresf);
printf("End of Computing forecasting \n");
fprintf(ficlog,"End of Computing forecasting\n");
}
/************** Back Forecasting ******************/
void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
/* back1, year, month, day of starting backection
agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed
anback2 year of en of backection (same day and month as back1).
*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
double agec; /* generic age */
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double *popeffectif,*popcount;
double ***p3mat;
double ***mobaverage;
char fileresfb[FILENAMELENGTH];
agelim=AGESUP;
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
in each health status at the date of interview (if between dateprev1 and dateprev2).
We still use firstpass and lastpass as another selection.
*/
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
/* firstpass, lastpass, stepm, weightopt, model); */
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
strcpy(fileresfb,"FB_");
strcat(fileresfb,fileresu);
if((ficresfb=fopen(fileresfb,"w"))==NULL) {
printf("Problem with back forecast resultfile: %s\n", fileresfb);
fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
}
printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb);
fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb);
if (cptcoveff==0) ncodemax[cptcoveff]=1;
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
else hstepm=estepm;
hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
fractional in yp1 */
anprojmean=yp;
yp2=modf((yp1*12),&yp);
mprojmean=yp;
yp1=modf((yp2*30.5),&yp);
jprojmean=yp;
if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;
i1=cptcoveff;
if (cptcovn < 1){i1=1;}
fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
/* if (h==(int)(YEARM*yearp)){ */
for(cptcov=1, k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;
fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}
fprintf(ficresfb," yearbproj age");
for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)
fprintf(ficresfb," p%d%d",i,j);
fprintf(ficresfb," p.%d",j);
}
for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
fprintf(ficresfb,"\n");
fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
for (agec=fage; agec>=(ageminpar-1); agec--){
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
hbxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){
if (h*hstepm/YEARM*stepm ==yearp) {
fprintf(ficresfb,"\n");
for(j=1;j<=cptcoveff;j++)
fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm);
}
for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;
for(i=1; i<=nlstate;i++) {
if (mobilav==1)
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
else {
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
}
if (h*hstepm/YEARM*stepm== yearp) {
fprintf(ficresfb," %.3f", p3mat[i][j][h]);
}
} /* end i */
if (h*hstepm/YEARM*stepm==yearp) {
fprintf(ficresfb," %.3f", ppij);
}
}/* end j */
} /* end h */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */
} /* end yearp */
} /* end cptcod */
} /* end cptcov */
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficresfb);
printf("End of Computing Back forecasting \n");
fprintf(ficlog,"End of Computing Back forecasting\n");
}
/************** Forecasting *****not tested NB*************/
void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;
double calagedatem, agelim, kk1, kk2;
double *popeffectif,*popcount;
double ***p3mat,***tabpop,***tabpopprev;
double ***mobaverage;
char filerespop[FILENAMELENGTH];
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
agelim=AGESUP;
calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
strcpy(filerespop,"POP_");
strcat(filerespop,fileresu);
if((ficrespop=fopen(filerespop,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", filerespop);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
}
printf("Computing forecasting: result on file '%s' \n", filerespop);
fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
if (cptcoveff==0) ncodemax[cptcoveff]=1;
if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
}
stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;
agelim=AGESUP;
hstepm=1;
hstepm=hstepm/stepm;
if (popforecast==1) {
if((ficpop=fopen(popfile,"r"))==NULL) {
printf("Problem with population file : %s\n",popfile);exit(0);
fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
}
popage=ivector(0,AGESUP);
popeffectif=vector(0,AGESUP);
popcount=vector(0,AGESUP);
i=1;
while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
imx=i;
for (i=1; i
************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
fprintf(fichtm," ************\n
");
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"
- Observed (cross-sectional) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d.svg
\
",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
}
fprintf(fichtm,"\n
- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: %s_%d.svg
\
",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
/* } /\* end i1 *\/ */
}/* End k1 */
fprintf(fichtm,"
");
fprintf(fichtm,"Result files
\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):
");
fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year
",p[1],p[2],agegomp);
for (i=1;i<=2;i++)
fprintf(fichtm," p[%d] = %lf [%f ; %f]
\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
fprintf(fichtm,"
");
fprintf(fichtm,"Life table
\n
");
fprintf(fichtm,"\nAge l
");
for (k=agegomp;k<(agemortsup-2);k++)
fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf
\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
fflush(fichtm);
}
/******************* Gnuplot file **************/
void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
char dirfileres[132],optfileres[132];
int ng;
/*#ifdef windows */
fprintf(ficgp,"cd \"%s\" \n",pathc);
/*#endif */
strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");
fprintf(ficgp,"set out \"graphmort.svg\"\n ");
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
/* fprintf(ficgp, "set size 0.65,0.65\n"); */
fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
}
int readdata(char datafile[], int firstobs, int lastobs, int *imax)
{
/*-------- data file ----------*/
FILE *fic;
char dummy[]=" ";
int i=0, j=0, n=0;
int linei, month, year,iout;
char line[MAXLINE], linetmp[MAXLINE];
char stra[MAXLINE], strb[MAXLINE];
char *stratrunc;
int lstra;
if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
}
i=1;
linei=0;
while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
linei=linei+1;
for(j=strlen(line); j>=0;j--){ /* Untabifies line */
if(line[j] == '\t')
line[j] = ' ';
}
for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
;
};
line[j+1]=0; /* Trims blanks at end of line */
if(line[0]=='#'){
fprintf(ficlog,"Comment line\n%s\n",line);
printf("Comment line\n%s\n",line);
continue;
}
trimbb(linetmp,line); /* Trims multiple blanks in line */
strcpy(line, linetmp);
for (j=maxwav;j>=1;j--){
cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing status */
lval=-1;
}else{
errno=0;
lval=strtol(strb,&endptr,10);
/* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
if( strb[0]=='\0' || (*endptr != '\0')){
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
return 1;
}
}
s[j][i]=lval;
strcpy(line,stra);
cutv(stra, strb,line,' ');
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}
else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
month=99;
year=9999;
}else{
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
return 1;
}
anint[j][i]= (double) year;
mint[j][i]= (double)month;
strcpy(line,stra);
} /* ENd Waves */
cutv(stra, strb,line,' ');
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}
else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
month=99;
year=9999;
}else{
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;
}
andc[i]=(double) year;
moisdc[i]=(double) month;
strcpy(line,stra);
cutv(stra, strb,line,' ');
if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}
else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
month=99;
year=9999;
}else{
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;
}
if (year==9999) {
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;
}
annais[i]=(double)(year);
moisnais[i]=(double)(month);
strcpy(line,stra);
cutv(stra, strb,line,' ');
errno=0;
dval=strtod(strb,&endptr);
if( strb[0]=='\0' || (*endptr != '\0')){
printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
fflush(ficlog);
return 1;
}
weight[i]=dval;
strcpy(line,stra);
for (j=ncovcol;j>=1;j--){
cutv(stra, strb,line,' ');
if(strb[0]=='.') { /* Missing status */
lval=-1;
}else{
errno=0;
lval=strtol(strb,&endptr,10);
if( strb[0]=='\0' || (*endptr != '\0')){
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
return 1;
}
}
if(lval <-1 || lval >1){
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
return 1;
}
covar[j][i]=(double)(lval);
strcpy(line,stra);
}
lstra=strlen(stra);
if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
stratrunc = &(stra[lstra-9]);
num[i]=atol(stratrunc);
}
else
num[i]=atol(stra);
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
i=i+1;
} /* End loop reading data */
*imax=i-1; /* Number of individuals */
fclose(fic);
return (0);
/* endread: */
printf("Exiting readdata: ");
fclose(fic);
return (1);
}
void removespace(char *str) {
char *p1 = str, *p2 = str;
do
while (*p2 == ' ')
p2++;
while (*p1++ == *p2++);
}
int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
* Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
* - nagesqr = 1 if age*age in the model, otherwise 0.
* - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
* - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
* - cptcovage number of covariates with age*products =2
* - cptcovs number of simple covariates
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
* which is a new column after the 9 (ncovcol) variables.
* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
* Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
*/
{
int i, j, k, ks;
int j1, k1, k2;
char modelsav[80];
char stra[80], strb[80], strc[80], strd[80],stre[80];
char *strpt;
/*removespace(model);*/
if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
if (strstr(model,"AGE") !=0){
printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
return 1;
}
if (strstr(model,"v") !=0){
printf("Error. 'v' must be in upper case 'V' model=%s ",model);
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
return 1;
}
strcpy(modelsav,model);
if ((strpt=strstr(model,"age*age")) !=0){
printf(" strpt=%s, model=%s\n",strpt, model);
if(strpt != model){
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model);
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model); fflush(ficlog);
return 1;
}
nagesqr=1;
if (strstr(model,"+age*age") !=0)
substrchaine(modelsav, model, "+age*age");
else if (strstr(model,"age*age+") !=0)
substrchaine(modelsav, model, "age*age+");
else
substrchaine(modelsav, model, "age*age");
}else
nagesqr=0;
if (strlen(modelsav) >1){
j=nbocc(modelsav,'+'); /**< j=Number of '+' */
j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
cptcovt= j+1; /* Number of total covariates in the model, not including
* cst, age and age*age
* V1+V1*age+ V3 + V3*V4+age*age=> 4*/
/* including age products which are counted in cptcovage.
* but the covariates which are products must be treated
* separately: ncovn=4- 2=2 (V1+V3). */
cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
/* Design
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
* < ncovcol=8 >
* Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
* k= 1 2 3 4 5 6 7 8
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
* covar[k,i], value of kth covariate if not including age for individual i:
* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
* if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
* Tage[++cptcovage]=k
* if products, new covar are created after ncovcol with k1
* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
* < ncovcol=8 >
* 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
* 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 Tprod[1]@2={ 6, 5}
*p Tvard[1][1]@4= {7, 8, 5, 6}
* covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
*How to reorganize?
* 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}
* {2, 1, 4, 8, 5, 6, 3, 7}
* Struct []
*/
/* This loop fills the array Tvar from the string 'model'.*/
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
/* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
/* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
/* k=3 V4 Tvar[k=3]= 4 (from V4) */
/* k=2 V1 Tvar[k=2]= 1 (from V1) */
/* k=1 Tvar[1]=2 (from V2) */
/* k=5 Tvar[5] */
/* for (k=1; k<=cptcovn;k++) { */
/* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
/* } */
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
/*
* Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
for(k=cptcovt; k>=1;k--) /**< Number of covariates */
Tvar[k]=0;
cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/*scanf("%d",i);*/
if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
/* covar is not filled and then is empty */
cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
cptcovage++; /* Sums the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
/*printf("stre=%s ", stre);*/
} else if (strcmp(strd,"age")==0) { /* or age*Vn */
cptcovprod--;
cutl(stre,strb,strc,'V');
Tvar[k]=atoi(stre);
cptcovage++;
Tage[cptcovage]=k;
} else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
/* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
cptcovn++;
cptcovprodnoage++;k1++;
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column
ncovcol + k1
If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
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 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2;
Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
}
} /* End age is not in the model */
} /* End if model includes a product */
else { /* no more sum */
/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');
ks++; /**< Number of simple covariates */
cptcovn++;
Tvar[k]=atoi(strd);
}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/
} /* end of loop + on total covariates */
} /* end if strlen(modelsave == 0) age*age might exist */
} /* end if strlen(model == 0) */
/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
scanf("%d ",i);*/
return (0); /* with covar[new additional covariate if product] and Tage if age */
/*endread:*/
printf("Exiting decodemodel: ");
return (1);
}
int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
{
int i, m;
for (i=1; i<=imx; i++) {
for(m=2; (m<= maxwav); m++) {
if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
anint[m][i]=9999;
if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
s[m][i]=-1;
}
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
*nberr = *nberr + 1;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
s[m][i]=-1;
}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
(*nberr)++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
}
}
}
for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
if (s[m][i] >= nlstate+1) {
if(agedc[i]>0){
if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
agev[m][i]=agedc[i];
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
}else {
if ((int)andc[i]!=9999){
nbwarn++;
printf("Warning negative age at death: %ld line:%d\n",num[i],i);
fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
agev[m][i]=-1;
}
}
} /* agedc > 0 */
} /* end if */
else if(s[m][i] !=9){ /* Standard case, age in fractional
years but with the precision of a month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
agev[m][i]=1;
else if(agev[m][i] < *agemin){
*agemin=agev[m][i];
printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
}
else if(agev[m][i] >*agemax){
*agemax=agev[m][i];
/* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
}
/*agev[m][i]=anint[m][i]-annais[i];*/
/* agev[m][i] = age[i]+2*m;*/
} /* en if 9*/
else { /* =9 */
/* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
agev[m][i]=1;
s[m][i]=-1;
}
}
else if(s[m][i]==0) /*= 0 Unknown */
agev[m][i]=1;
else{
printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
agev[m][i]=0;
}
} /* End for lastpass */
}
for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {
(*nberr)++;
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
return 1;
}
}
}
/*for (i=1; i<=imx; i++){
for (m=firstpass; (m
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
fprintf(fichtm,"\n\n\n
\nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
\
\n\
IMaCh-%s
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n\
\n\
\
\n",\
optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
fflush(fichtm);
strcpy(pathr,path);
strcat(pathr,optionfilefiname);
#ifdef WIN32
_chdir(optionfilefiname); /* Move to directory named optionfile */
#else
chdir(optionfilefiname); /* Move to directory named optionfile */
#endif
/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
firstpass, lastpass, stepm, weightopt, model);
fprintf(fichtm,"\n");
fprintf(fichtm,"Parameter files
\n\
- Parameter file: %s.%s
\n\
- Copy of the parameter file: o%s
\n\
- Log file of the run: %s
\n\
- Gnuplot file name: %s
\n\
- Date and time at start: %s
Total number of observations=%d
\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f
\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
\n",\
imx,agemin,agemax,jmin,jmax,jmean);
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
/* For Powell, parameters are in a vector p[] starting at p[1]
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
p=param[1][1]; /* *(*(*(param +1)+1)+0) */
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
/* For mortality only */
if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);
ageexmed=vector(1,n);
agecens=vector(1,n);
dcwave=ivector(1,n);
for (i=1; i<=imx; i++){
dcwave[i]=-1;
for (m=firstpass; m<=lastpass; m++)
if (s[m][i]>nlstate) {
dcwave[i]=m;
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
break;
}
}
for (i=1; i<=imx; i++) {
if (wav[i]>0){
ageexmed[i]=agev[mw[1][i]][i];
j=wav[i];
agecens[i]=1.;
if (ageexmed[i]> 1 && wav[i] > 0){
agecens[i]=agev[mw[j][i]][i];
cens[i]= 1;
}else if (ageexmed[i]< 1)
cens[i]= -1;
if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
cens[i]=0 ;
}
else cens[i]=-1;
}
for (i=1;i<=NDIM;i++) {
for (j=1;j<=NDIM;j++)
ximort[i][j]=(i == j ? 1.0 : 0.0);
}
/*p[1]=0.0268; p[NDIM]=0.083;*/
/*printf("%lf %lf", p[1], p[2]);*/
#ifdef GSL
printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
#else
printf("Powell\n"); fprintf(ficlog,"Powell\n");
#endif
strcpy(filerespow,"POW-MORT_");
strcat(filerespow,fileresu);
if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
}
#ifdef GSL
fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
#else
fprintf(ficrespow,"# Powell\n# iter -2*LL");
#endif
/* for (i=1;i<=nlstate;i++)
for(j=1;j<=nlstate+ndeath;j++)
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
*/
fprintf(ficrespow,"\n");
#ifdef GSL
/* gsl starts here */
T = gsl_multimin_fminimizer_nmsimplex;
gsl_multimin_fminimizer *sfm = NULL;
gsl_vector *ss, *x;
gsl_multimin_function minex_func;
/* Initial vertex size vector */
ss = gsl_vector_alloc (NDIM);
if (ss == NULL){
GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
}
/* Set all step sizes to 1 */
gsl_vector_set_all (ss, 0.001);
/* Starting point */
x = gsl_vector_alloc (NDIM);
if (x == NULL){
gsl_vector_free(ss);
GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
}
/* Initialize method and iterate */
/* p[1]=0.0268; p[NDIM]=0.083; */
/* gsl_vector_set(x, 0, 0.0268); */
/* gsl_vector_set(x, 1, 0.083); */
gsl_vector_set(x, 0, p[1]);
gsl_vector_set(x, 1, p[2]);
minex_func.f = &gompertz_f;
minex_func.n = NDIM;
minex_func.params = (void *)&p; /* ??? */
sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
printf("Iterations beginning .....\n\n");
printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
iteri=0;
while (rval == GSL_CONTINUE){
iteri++;
status = gsl_multimin_fminimizer_iterate(sfm);
if (status) printf("error: %s\n", gsl_strerror (status));
fflush(0);
if (status)
break;
rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
ssval = gsl_multimin_fminimizer_size (sfm);
if (rval == GSL_SUCCESS)
printf ("converged to a local maximum at\n");
printf("%5d ", iteri);
for (it = 0; it < NDIM; it++){
printf ("%10.5f ", gsl_vector_get (sfm->x, it));
}
printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
}
printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
gsl_vector_free(x); /* initial values */
gsl_vector_free(ss); /* inital step size */
for (it=0; it
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtm);
fprintf(fichtmcov,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtmcov);
fclose(ficgp);
fclose(ficlog);
/*------ End -----------*/
printf("Before Current directory %s!\n",pathcd);
#ifdef WIN32
if (_chdir(pathcd) != 0)
printf("Can't move to directory %s!\n",path);
if(_getcwd(pathcd,MAXLINE) > 0)
#else
if(chdir(pathcd) != 0)
printf("Can't move to directory %s!\n", path);
if (getcwd(pathcd, MAXLINE) > 0)
#endif
printf("Current directory %s!\n",pathcd);
/*strcat(plotcmd,CHARSEPARATOR);*/
sprintf(plotcmd,"gnuplot");
#ifdef _WIN32
sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
#endif
if(!stat(plotcmd,&info)){
printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
if(!stat(getenv("GNUPLOTBIN"),&info)){
printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
}else
strcpy(pplotcmd,plotcmd);
#ifdef __unix
strcpy(plotcmd,GNUPLOTPROGRAM);
if(!stat(plotcmd,&info)){
printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
}else
strcpy(pplotcmd,plotcmd);
#endif
}else
strcpy(pplotcmd,plotcmd);
sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
if((outcmd=system(plotcmd)) != 0){
printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
if((outcmd=system(plotcmd)) != 0)
printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
}
printf(" Successful, please wait...");
while (z[0] != 'q') {
/* chdir(path); */
printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
scanf("%s",z);
/* if (z[0] == 'c') system("./imach"); */
if (z[0] == 'e') {
#ifdef __APPLE__
sprintf(pplotcmd, "open %s", optionfilehtm);
#elif __linux
sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
#else
sprintf(pplotcmd, "%s", optionfilehtm);
#endif
printf("Starting browser with: %s",pplotcmd);fflush(stdout);
system(pplotcmd);
}
else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);
}
end:
while (z[0] != 'q') {
printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);
}
}