#include <RcppArmadillo.h>
#include <algorithm>
#include <iostream>
#include <vector>
#include <complex.h>
#include "twostage.h"

using namespace arma;
using namespace Rcpp;

double claytonoakesP(double theta,int status1,int status2,double cif1,double cif2,vec &dp,vec &ps,vec &dp00) 
{ // {{{
double valr=1,x,y,z;
double p00,p10,p01,p11; 

//double cifs=cif1+cif2; //double S=1+(cifs*(theta-1)); 
x=theta; y=cif1; z=cif2; 

valr=  pow((1/pow(y,1/x) + 1/pow(z,1/x)) - 1,-x);
dp(0)= (-((x*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x))) - log(-1 + pow(y,-1/x) + pow(z,-1/x)))/pow(-1 + pow(y,-1/x) + pow(z,-1/x),x);

p11=valr; 
p10=cif1-p11; 
p01=cif2-p11; 
p00=1-cif1-cif2+p11; 

ps(0)=p00; ps(1)=p10; ps(2)=p01; ps(3)=p11; 
dp00(0)=dp(0); 
//printf(" %lf %lf %lf %lf %lf %lf %lf \n",theta,y,z,p11,p10,p01,p00); 

if (status1==1 && status2==1) { valr=p11; dp(0)= dp(0); }
if (status1==1 && status2==0) { valr=p10; dp(0)=-dp(0); }
if (status1==0 && status2==1) { valr=p01; dp(0)=-dp(0); }
if (status1==0 && status2==0) { valr=p00; dp(0)= dp(0); } 

//printf(" %lf \n",valr); 

//if (status1==0 && status2==0) { // {{{
//valr=  pow((1/pow(y,1/x) + 1/pow(z,1/x)) - 1,-x);
//dp(0)= (-((x*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x))) - log(-1 + pow(y,-1/x) + pow(z,-1/x)))/pow(-1 + pow(y,-1/x) + pow(z,-1/x),x);
//} // }}}
//
//if (status1==1 && status2==0) { // {{{
//valr=pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x);
//dp(0)=(pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*log(y))/pow(x,2) + pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*(((-1 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x)));
//} // }}}
//
//if (status1==0 && status2==1) { // {{{
//valr=pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x);
//dp(0)=(pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*log(z))/pow(x,2) + pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*(((-1 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x)));
//} // }}}
//
//if (status1==1 && status2==1) { // {{{
//valr= -(((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/x);
//dp(0)=((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/pow(x,2) + (pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/x - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*log(y))/pow(x,3) - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*log(z))/pow(x,3) - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*(((-2 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x))))/x;
//} // }}}

return(valr); 
} // }}}

double placklikeP(double theta,int status1,int status2,double cif1,double cif2,vec &dp,vec &ps,vec &dp00) 
{ // {{{
//double S,S2,a;
//S=1+cifs*(theta-1); S2=4*cif1*cif2*theta*(theta-1);
double x,y,z,valr=1,p11,p10,p01,p00; 
//double cifs=cif1+cif2; 
//a=(1+(theta-1)*(cifs)); 
x=theta; y=cif1; z=cif2; 

dp(0)=0; 

if (theta!=1) {
p11=(1+(y+z)*(x-1)-sqrt(pow(1+(y+z)*(x-1),2)-4*x*(x-1)*y*z))/(2*(x-1));
dp(0)= (y + z - (-4*(-1 + x)*y*z - 4*x*y*z + 2*(y + z)*(1 + (-1 + x)*(y + z)))/(2.*sqrt(-4*(-1 + x)*x*y*z + pow(1 + (  -1 + x)*(y + z),2))))/(2.*(-1 + x)) - (1 + (-1 + x)*(y + z) - sqrt(-4*(-1 + x)*x*y*z + pow(1 + (-1 + x)*(y + z  ),2)))/(2.*pow(-1 + x,2));
} else p11=cif1*cif2;

p10=y-p11; 
p01=z-p11; 
p00=1-y-z+p11; 
ps(0)=p00; ps(1)=p10; ps(2)=p01; ps(3)=p11; 
dp00(0)=dp(0); 

if (status1==1 && status2==1) { valr=p11; dp(0)= dp(0); }
if (status1==1 && status2==0) { valr=p10; dp(0)=-dp(0); }
if (status1==0 && status2==1) { valr=p01; dp(0)=-dp(0); }
if (status1==0 && status2==0) { valr=p00; dp(0)= dp(0); } 

return(valr); 
} // }}}

//RcppExport SEXP claytonoakesPR(SEXP itheta,SEXP istatus1,SEXP istatus2,SEXP icif1,SEXP icif2) 
//{ // {{{
// colvec theta = Rcpp::as<colvec>(itheta);
// colvec cif1 = Rcpp::as<colvec>(icif1);
// colvec cif2 = Rcpp::as<colvec>(icif2);
// colvec status1 = Rcpp::as<colvec>(iistatus1);
// colvec status2 = Rcpp::as<colvec>(iistatus2);
//
// colvec L=theta; 
// colvec dL=theta; 
// int n=cif1.size(); 
//
//double valr=1,x,y,z;
//double p00,p10,p01,p11; 
//
////double cifs=cif1+cif2; //double S=1+(cifs*(theta-1)); 
//x=theta; y=cif1; z=cif2; 
//
//valr=  pow((1/pow(y,1/x) + 1/pow(z,1/x)) - 1,-x);
//dp(0)= (-((x*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x))) - log(-1 + pow(y,-1/x) + pow(z,-1/x)))/pow(-1 + pow(y,-1/x) + pow(z,-1/x),x);
//
//p11=valr; 
//p10=x-p11; 
//p01=y-p11; 
//p00=1-x-y+p11; 
//
//if (status1==1 && status2==1) { valr=p11; dp(0)= dp(0); }
//if (status1==1 && status2==0) { valr=p10; dp(0)=-dp(0); }
//if (status1==0 && status2==1) { valr=p01; dp(0)=-dp(0); }
//if (status1==0 && status2==0) { valr=p00; dp(0)= dp(0); } 
//
//if (status1==0 && status2==0) { // {{{
//valr=  pow((1/pow(y,1/x) + 1/pow(z,1/x)) - 1,-x);
//dp(0)= (-((x*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x))) - log(-1 + pow(y,-1/x) + pow(z,-1/x)))/pow(-1 + pow(y,-1/x) + pow(z,-1/x),x);
//} // }}}
//
//if (status1==1 && status2==0) { // {{{
//valr=pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x);
//dp(0)=(pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*log(y))/pow(x,2) + pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*(((-1 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x)));
//} // }}}
//
//if (status1==0 && status2==1) { // {{{
//valr=pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x);
//dp(0)=(pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*log(z))/pow(x,2) + pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*(((-1 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x)));
//} // }}}
//
//if (status1==1 && status2==1) { // {{{
//valr= -(((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/x);
//dp(0)=((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/pow(x,2) + (pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/x - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*log(y))/pow(x,3) - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*log(z))/pow(x,3) - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*(((-2 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x))))/x;
//} // }}}
//
//return(valr); 
//} // }}}
//
//RcppExport SEXP placklikePR(SEXP itheta,SEXP istatus1,SEXP istatus2,SEXP icif1,SEXP icif2)
//{ // {{{
////double S,S2,a;
////S=1+cifs*(theta-1); S2=4*cif1*cif2*theta*(theta-1);
//double x,y,z,valr=1,p11,p10,p01,p00; 
////double cifs=cif1+cif2; 
////a=(1+(theta-1)*(cifs)); 
//x=theta; y=cif1; z=cif2; 
//
//dp(0)=0; 
//
//if (theta!=1) {
//p11=(1+(y+z)*(x-1)-sqrt(pow(1+(y+z)*(x-1),2)-4*x*(x-1)*y*z))/(2*(x-1));
//dp(0)= (y + z - (-4*(-1 + x)*y*z - 4*x*y*z + 2*(y + z)*(1 + (-1 + x)*(y + z)))/(2.*sqrt(-4*(-1 + x)*x*y*z + pow(1 + (  -1 + x)*(y + z),2))))/(2.*(-1 + x)) - (1 + (-1 + x)*(y + z) - sqrt(-4*(-1 + x)*x*y*z + pow(1 + (-1 + x)*(y + z  ),2)))/(2.*pow(-1 + x,2));
//} else p11=cif1*cif2;
//
//p11=p11;
//p10=y-p11; 
//p01=z-p11; 
//p00=1-y-z+p11; 
//
//if (status1==1 && status2==1) { valr=p11; dp(0)= dp(0); }
//if (status1==1 && status2==0) { valr=p10; dp(0)=-dp(0); }
//if (status1==0 && status2==1) { valr=p01; dp(0)=-dp(0); }
//if (status1==0 && status2==0) { valr=p00; dp(0)= dp(0); } 
//
//return(valr); 
//} // }}}


// double CclaytonoakesP(double theta,int status1,int status2,double cif1,double cif2,vec &dp) 
//{ // {{{
//double valr=1,x,y,z;
//double p00,p10,p01,p11; 
//
////double cifs=cif1+cif2; //double S=1+(cifs*(theta-1)); 
//x=theta; y=cif1; z=cif2; 
//
//valr=  pow((1/pow(y,1/x) + 1/pow(z,1/x)) - 1,-x);
//dp(0)= (-((x*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x))) - log(-1 + pow(y,-1/x) + pow(z,-1/x)))/pow(-1 + pow(y,-1/x) + pow(z,-1/x),x);
//
//p11=valr; 
//p10=x-p11; 
//p01=y-p11; 
//p00=1-x-y+p11; 
//
//double epsilon=1E-20; 
//cx_double Ctheta,Cvalr,Cy,Cz; 
//Ctheta=cx_double(theta,epsilon); 
//Cy=cx_double(y,0); 
//Cz=cx_double(z,0); 
//
//printf(" mig \n"); 
////Cvalr=  pow((1/pow(Cy,1/Ctheta) + 1/pow(Cz,1/Ctheta)) - 1,-Ctheta);
//double dd=imag(Cvalr)/epsilon; 
//
//printf("complex  %lf ",dd); 
//
//if (status1==1 && status2==1) { valr=p11; dp(0)= dp(0); }
//if (status1==1 && status2==0) { valr=p10; dp(0)=-dp(0); }
//if (status1==0 && status2==1) { valr=p01; dp(0)=-dp(0); }
//if (status1==0 && status2==0) { valr=p00; dp(0)= dp(0); } 
//
//if (status1==0 && status2==0) { // {{{
//valr=  pow((1/pow(y,1/x) + 1/pow(z,1/x)) - 1,-x);
//dp(0)= (-((x*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x))) - log(-1 + pow(y,-1/x) + pow(z,-1/x)))/pow(-1 + pow(y,-1/x) + pow(z,-1/x),x);
//} // }}}
//
//if (status1==1 && status2==0) { // {{{
//valr=pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x);
//dp(0)=(pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*log(y))/pow(x,2) + pow(y,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*(((-1 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x)));
//} // }}}
//
//if (status1==0 && status2==1) { // {{{
//valr=pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x);
//dp(0)=(pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*log(z))/pow(x,2) + pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-1 - x)*(((-1 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x)));
//} // }}}
//
//if (status1==1 && status2==1) { // {{{
//valr= -(((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/x);
//dp(0)=((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/pow(x,2) + (pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x))/x - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*log(y))/pow(x,3) - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*log(z))/pow(x,3) - ((-1 - x)*pow(y,-1 - 1/x)*pow(z,-1 - 1/x)*pow(-1 + pow(y,-1/x) + pow(z,-1/x),-2 - x)*(((-2 - x)*(log(y)/(pow(x,2)*pow(y,1/x)) + log(z)/(pow(x,2)*pow(z,1/x))))/(-1 + pow(y,-1/x) + pow(z,-1/x)) - log(-1 + pow(y,-1/x) + pow(z,-1/x))))/x;
//} // }}}
//
//printf(" %lf \n",dp(0)); 
//return(valr); 
//} // }}}

cx_double Cpij(cx_double x, cx_double y, cx_double z,int status1, int status2)
{ // {{{ 
cx_double p11,one,two,four; 
one=cx_double(1,0); two=cx_double(2,0); four=cx_double(4,0); 
//p11=(1+(y+z)*(x-1)-sqrt(exp(ln(1+(y+z)*(x-1))*2)-4*x*(x-1)*y*z))/(2*(x-1));
p11=(one+(y+z)*(x-one)-sqrt(pow((one+(y+z)*(x-one)),two)-four*x*(x-one)*y*z));
//p11=one+(y+z)*(x-one); 
p11=p11/(two*(x-one));

// calculates probs depending on status 
if (status1==1 && status2==0) p11=y-p11;
if (status1==0 && status2==1) p11=z-p11; 
if (status1==0 && status2==0) p11=one-y-z+p11; 

return(p11); 
} // }}}

double CplacklikeP(double theta,int status1,int status2,double cif1,double cif2,vec &dp) 
{ // {{{
//double S,S2,a;
//S=1+cifs*(theta-1); S2=4*cif1*cif2*theta*(theta-1);
double x,y,z,valr=1,p11,p10,p01,p00; 
//double cifs=cif1+cif2; 
//a=(1+(theta-1)*(cifs)); 
x=theta; y=cif1; z=cif2; 

dp(0)=0; 

if (theta!=1) {
p11=(1+(y+z)*(x-1)-sqrt(pow(1+(y+z)*(x-1),2)-4*x*(x-1)*y*z))/(2*(x-1));
dp(0)= (y + z - (-4*(-1 + x)*y*z - 4*x*y*z + 2*(y + z)*(1 + (-1 + x)*(y + z)))/(2.*sqrt(-4*(-1 + x)*x*y*z + pow(1 + (  -1 + x)*(y + z),2))))/(2.*(-1 + x)) - (1 + (-1 + x)*(y + z) - sqrt(-4*(-1 + x)*x*y*z + pow(1 + (-1 + x)*(y + z  ),2)))/(2.*pow(-1 + x,2));
} else p11=cif1*cif2;

////det komplekse trick, derivative wrt y og zi, dvs D_1 P(y,z,theta) og D_2 P
//cx_double CCp11,Ctheta,Cy,Cz; 
//Ctheta=cx_double(theta,0); 
//Cy=cx_double(y,1E-20); 
//Cz=(cx_double) z; 
//CCp11=Cpij(Ctheta,Cy,Cz,status1,status2); 
//dp(1)=imag(CCp11)/1E-20; 
//Cz=cx_double(z,1E-20); 
//Cy=(cx_double) y; 
//CCp11=Cpij(Ctheta,Cy,Cz,status1,status2); 
//dp(2)=imag(CCp11)/1E-20; 
//printf(" %lf  ",imag(CCp11)/1E-20); 

p10=y-p11; 
p01=z-p11; 
p00=1-y-z+p11; 

if (status1==1 && status2==1) { valr=p11; dp(0)= dp(0); }
if (status1==1 && status2==0) { valr=p10; dp(0)=-dp(0); }
if (status1==0 && status2==1) { valr=p01; dp(0)=-dp(0); }
if (status1==0 && status2==0) { valr=p00; dp(0)= dp(0); } 
//printf(" %lf \n",dp(0)); 

return(valr); 
} // }}}
               
//double min(double a, double b) { if (a<b) return(a); else return(b); }
//double max(double a, double b) { if (a>b) return(a); else return(b); }


RcppExport SEXP twostageloglikebin( 
       SEXP icause, SEXP ipmargsurv, SEXP itheta, SEXP ithetades,
       SEXP icluster,SEXP iclustsize,SEXP iclusterindex, SEXP ivarlink, 
       SEXP iiid, SEXP  iweights, SEXP isilent, SEXP idepmodel, // SEXP ientryage,
       SEXP itrunkp , SEXP istrata, SEXP isecluster, SEXP  iantiid , 
       SEXP irvdes, SEXP iags, SEXP ibetaiid, SEXP ipairascertained, 
       SEXP itwostage
) // {{{
{
	try {
// {{{ setting matrices and vectors, and exporting to armadillo matrices
 mat thetades = Rcpp::as<mat>(ithetades); 
 mat clusterindex = Rcpp::as<mat>(iclusterindex);
 colvec theta = Rcpp::as<colvec>(itheta);
 mat ags= Rcpp::as<mat>(iags);
 int pt=theta.n_rows; 
 colvec clustsize = Rcpp::as<colvec>(iclustsize);
 int antclust = clusterindex.n_rows; 
 colvec cause = Rcpp::as<colvec>(icause);
 colvec pmargsurv = Rcpp::as<colvec>(ipmargsurv);
 colvec cluster = Rcpp::as<colvec>(icluster);
 colvec weights = Rcpp::as<colvec>(iweights);
// colvec entryage = Rcpp::as<colvec>(ientryage);
 colvec trunkp = Rcpp::as<colvec>(itrunkp);
 colvec secluster = Rcpp::as<colvec>(isecluster);
 mat rvdes= Rcpp::as<mat>(irvdes); 
 int depmodel= Rcpp::as<int>(idepmodel); 
 int twostage= Rcpp::as<int>(itwostage); 
 int pairascertained = Rcpp::as<int>(ipairascertained); 

 IntegerVector strata(istrata);
 int varlink= Rcpp::as<int>(ivarlink);
 int silent = Rcpp::as<int>(isilent);
 int iid= Rcpp::as<int>(iiid); 
 int antiid = Rcpp::as<int>(iantiid);
 double loglikecont=0; 

  int ci,ck,i,j,c,k,v,c1; 
  double ll=1,llt=1,Li,Lk,diff=0;
  double deppar=1,ssf=0,thetak=0; 
  vec dplack(pt); dplack.fill(pt);
  vec dp00(pt); 
  vec ps(8); 
  vec ckij(4),dckij(4),ckijvv(4),dckijvv(4),ckijtv(4),dckijtv(4),ckijvt(4),dckijvt(4);
  i=silent+1; 

  mat betaiid= Rcpp::as<mat>(ibetaiid);
  int dimbeta=betaiid.n_cols; 
  mat DbetaDtheta(pt,dimbeta); 
  vec vDbetaDtheta(2*pt); 
  DbetaDtheta.fill(0); 
  vec Du1(pt),Du2(pt); 

  colvec p11tvec(antclust); 
  int scoredim; 
  if (twostage==1) scoredim=pt; else scoredim=pt+dimbeta; 

  colvec Utheta(scoredim); 
  colvec vthetascore(scoredim); 
  colvec pthetavec(scoredim); 
  vec vtheta2(scoredim); 
  mat DUtheta(scoredim,scoredim); 
  DUtheta.fill(0); Utheta.fill(0); 

  mat thetiid(antiid,scoredim); 
  colvec loglikeiid(antiid); 
  if (iid==1) { thetiid.fill(0); loglikeiid.fill(0); }

  int nr=rvdes.n_cols; 
  vec rv2(nr),rv1(nr);

  vec etheta=theta; 
  colvec likepairs(antclust); 
  // }}}
  
  colvec Xtheta; 
if (depmodel!=3) Xtheta= thetades * theta; 

for (j=0;j<antclust;j++) if (clustsize(j)>=2) { 

   if (i % 1000 == 0) Rcpp::checkUserInterrupt();
//    R_CheckUserInterrupt(); 
    diff=0; //sdj=0; 

  for (c=0;c<clustsize(j)-1;c++) for (v=c+1;v<clustsize(j);v++) // {{{ //  if ((c<v)) 
  { 
     i=clusterindex(j,c); k=clusterindex(j,v); 
     if (strata(i)==strata(k)) { // {{{

     ci=cause(i); ck=cause(k); Li=pmargsurv(i); Lk=pmargsurv(k); 
         
     if (depmodel!=3) {
        thetak=Xtheta(i);  
        pthetavec= trans(thetades.row(i)); 
        vthetascore=1*pthetavec; 
      }

  if (depmodel==1){ if (varlink==1) deppar=1/exp(thetak); else deppar=1/thetak;}
  if (depmodel==2){ if (varlink==1) deppar=exp(thetak); else deppar=thetak; }

	if (depmodel==1) { // clayton-oakes  // {{{
	   ll=claytonoakesP(deppar,ci,ck,Li,Lk,dplack,ps,dp00);
	   loglikecont=log(ll); 
	   ssf+=weights(i)*log(ll); 
	   diff=dplack(0)/ll; 
	if (j<-10) {
	Rprintf(" %d %d %d %d %d %d %d %lf %lf %lf %lf %lf %lf \n",j,c,v,i,k,ci,ck,thetak,Li,Lk,weights(i),ll,log(ll)); 
	dplack.print("dtheta"); 
	}

	if (varlink==1) diff=-pow(deppar,1)*diff;  
	if (varlink==0) diff=-1*pow(deppar,2)*diff; 

          if (pairascertained==1) {
                ssf-=weights(i)*log(1-ps(0)); 
	        loglikecont=log(ll)-log(1-ps(0));
		diff+=dp00(0)/(1-ps(0));
	   if (varlink==1) diff+=-pow(deppar,1)*dp00(0)/(1-ps(0));  
	   if (varlink==0) diff+=-1*pow(deppar,2)*dp00(0)/(1-ps(0)); 
	   }

	   } // }}}
	   else if (depmodel==3) { // clayton-oakes addtive gamma  // {{{

	   rv1=trans(rvdes.row(i)); 
	   rv2=trans(rvdes.row(k)); 
	   ll=claytonoakesbinRVC(etheta,thetades,ags,ci,ck,Li,Lk,rv1,rv2,dplack,vDbetaDtheta,ps,dp00);

	   if (j<-10) {
		   rv1.print("rv1"); rv2.print("rv1"); ps.print("ps"); 
		   thetades.print("theta.des"); etheta.print("theta"); 
	           Rprintf("%d  %d %d %lf %lf %lf \n",j,ci,ck,Li,Lk,ll); 
	   }

           ssf+=weights(i)*log(ll); 
	   loglikecont=log(ll);
	   vthetascore.subvec(0,pt-1)=dplack/ll; 
	   if (twostage==0) 
	      vthetascore.subvec(pt,pt+dimbeta-1)=(ps(4)*trans(betaiid.row(i))+ps(5)*trans(betaiid.row(k)))/ll; 
	   
	if (pairascertained==1) {
           ssf-=weights(i)*log(1-ps(0)); 
	   loglikecont=log(ll)-log(1-ps(0));
           vthetascore.subvec(0,pt-1)+=dp00/(1-ps(0)); 
	   if (twostage==0) {
	      llt=(1-ps(0)); 
              vthetascore.subvec(pt,pt+dimbeta-1)+=(ps(6)*trans(betaiid.row(i))+ps(7)*trans(betaiid.row(k)))/llt; 
	   }
	}
	   // }}}
	} else if (depmodel==2) { // plackett model  // {{{
           ll=placklikeP(deppar,ci,ck,Li,Lk,dplack,ps,dp00);
	   loglikecont=log(ll); 
	   ssf+=weights(i)*log(ll); 
	   // sdj=pow(dplack(0)/ll,2); 
	   if (varlink==1) diff=deppar*dplack(0)/ll; 
	   if (varlink==0) diff=dplack(0)/ll;

	   if (pairascertained==1) {
                ssf-=weights(i)*log(1-ps(0)); 
	        loglikecont-=log(1-ps(0));
	   if (varlink==1) diff+=deppar*dp00(0)/(1-ps(0)); 
	   if (varlink==0) diff+=dp00(0)/(1-ps(0));
	   }
	} // }}}

     if (depmodel!=3) {
	DUtheta+=weights(i)*pow(diff,2)*vthetascore*trans(vthetascore);
        vthetascore=weights(i)*diff*vthetascore; 
        Utheta=Utheta+vthetascore; 
     } else  { // additive gamma structure 
	     DUtheta+=weights(i)*vthetascore*trans(vthetascore);
	     vthetascore=weights(i)*vthetascore; 
	     Utheta=Utheta+vthetascore; 
	     if (twostage==1) {
		     Du1=vDbetaDtheta.subvec(0,pt-1); 
		     Du2=vDbetaDtheta.subvec(pt,2*pt-1); 
	            DbetaDtheta+= Du1*betaiid.row(i)+ Du2*betaiid.row(k); 
	     }
	}

     if (iid==1) { 
	 for (c1=0;c1<pt;c1++) thetiid((int) secluster(i),c1)+=vthetascore(c1); 
	 loglikeiid(secluster(i))+=loglikecont; 

     }
     } // }}} strata(i)==strata(k) indenfor strata

  } /* for (c=0....... */   // }}}

if (iid==1)  likepairs(j)=loglikecont; 
} /* j in antclust */ 

//printf("Sum of squares %lf \n",ssf);theta.print("theta");Utheta.print("Utheta");DUtheta.print("DUtheta"); 
List res; 
res["loglike"]=ssf; 
res["score"]=Utheta; 
res["Dscore"]=DUtheta; 
res["DbetaDtheta"]=DbetaDtheta; 
if (iid==1) { 
             res["theta.iid"]=thetiid; 
             res["DbetaDtheta.iid"]=thetiid; 
	     res["loglikeiid"]=loglikeiid; 
             res["likepairs"]=likepairs; 
            }

return(res); 
} catch( std::exception &ex ) {
    forward_exception_to_r( ex );
  } catch(...) {  
    (Rf_error)( "c++ exception (unknown reason)" ); 
  }
  return R_NilValue; // -Wall



} // }}}

RcppExport SEXP twostageloglikebinpairs( 
	SEXP icause, SEXP ipmargsurv, SEXP itheta, SEXP ithetades,
	SEXP icluster,SEXP iclustsize,SEXP iclusterindex, SEXP ivarlink, 
        SEXP iiid, SEXP  iweights, SEXP isilent, SEXP idepmodel, // SEXP ientryage,
	SEXP itrunkp , SEXP istrata, SEXP isecluster, SEXP  iantiid , 
        SEXP irvdes, SEXP iags, SEXP ibetaiid, SEXP ipairascertained, 
	SEXP itwostage,SEXP icasecontrol 
) // {{{
{
  try {
// {{{ setting matrices and vectors, and exporting to armadillo matrices
 mat clusterindex = Rcpp::as<mat>(iclusterindex);
 colvec theta = Rcpp::as<colvec>(itheta);
 mat ags= Rcpp::as<colvec>(iags);
 int pt=theta.n_rows; 
 colvec clustsize = Rcpp::as<colvec>(iclustsize);
 // this is number of pairs (rather than clusters)
 int antclust = clusterindex.n_rows; 
 colvec cause = Rcpp::as<colvec>(icause);
 colvec pmargsurv = Rcpp::as<colvec>(ipmargsurv);
 colvec cluster = Rcpp::as<colvec>(icluster);
 colvec weights = Rcpp::as<colvec>(iweights);
 colvec trunkp = Rcpp::as<colvec>(itrunkp);
 colvec secluster = Rcpp::as<colvec>(isecluster);
 int depmodel= Rcpp::as<int>(idepmodel); 
 IntegerVector strata(istrata);

 uvec pairascertained = Rcpp::as<uvec>(ipairascertained); 
 uvec casecontrol     = Rcpp::as<uvec>(icasecontrol); 

 mat thetades= Rcpp::as<mat>(ithetades);
 mat rvdes= Rcpp::as<mat>(irvdes); 

 int varlink= Rcpp::as<int>(ivarlink);
 int silent = Rcpp::as<int>(isilent);
 int iid= Rcpp::as<int>(iiid); 
 int antiid = Rcpp::as<int>(iantiid);
 double loglikecont=0; 
 int twostage= Rcpp::as<int>(itwostage); 

  int sss=1,ci,ck,i,j,k,c1; 
  double llt=1,ll=1,Li,Lk,diff=0;
  double deppar=1,ssf=0,thetak=0; 
  vec dplack(pt); dplack.fill(0);
  vec dp00(pt); dp00.fill(0);
  vec ps(8); ps.fill(0);
  vec ckij(4),dckij(4),ckijvv(4),dckijvv(4),ckijtv(4),dckijtv(4),ckijvt(4),dckijvt(4);
  i=silent+1; 

  colvec p11tvec(antclust); 
  int scoredim; 
  mat betaiid= Rcpp::as<mat>(ibetaiid);
  int dimbeta=betaiid.n_cols; 
  if (twostage==1) scoredim=pt; else scoredim=pt+dimbeta; 
  colvec Utheta(scoredim); 
  colvec vthetascore(scoredim); 
  colvec pthetavec(scoredim); 
  vec vtheta2(scoredim); 
  mat DUtheta(scoredim,scoredim); 
  DUtheta.fill(0); Utheta.fill(0); 

  mat thetiid(antiid,scoredim); 
  colvec loglikeiid(antiid); 
  if (iid==1) { thetiid.fill(0); loglikeiid.fill(0); }

  mat DbetaDtheta(pt,dimbeta); 
  vec vDbetaDtheta(2*pt); 
  DbetaDtheta.fill(0); 
  vec Du1(pt),Du2(pt); 

  vec etheta=theta; 
  colvec likepairs(antclust); 
  colvec Xtheta; 
  if (depmodel!=3) { Xtheta= thetades * theta; }
  // }}}

for (j=0;j<antclust;j++) { 

   if (j % 1000 == 0) Rcpp::checkUserInterrupt();
//   R_CheckUserInterrupt(); 
   diff=0; //sdj=0; 
   i=clusterindex(j,0); 
   k=clusterindex(j,1); 

  if (strata(i)==strata(k)) { // {{{

     ci=cause(i); ck=cause(k); Li=pmargsurv(i); Lk=pmargsurv(k); 
     if (depmodel!=3) {
          int itrow=clusterindex(j,2); 
	  thetak=Xtheta(itrow);  
	  pthetavec= trans(thetades.row(itrow)); 
	  vthetascore=1*pthetavec; 
     }

  if (depmodel==1){ if (varlink==1) deppar=1/exp(thetak); else deppar=1/thetak;}
  if (depmodel==2){ if (varlink==1) deppar=exp(thetak); else deppar=thetak; }

	if (depmodel==1) { // clayton-oakes  // {{{
	   ll=claytonoakesP(deppar,ci,ck,Li,Lk,dplack,ps,dp00);
	   loglikecont=log(ll); 
	   ssf+=weights(i)*log(ll); 
	   diff=dplack(0)/ll; 
	   if (varlink==1) diff=-pow(deppar,1)*diff;  
	   if (varlink==0) diff=-1*pow(deppar,2)*diff; 
	   
	   if (pairascertained[j]==1) {
                ssf-=weights(i)*log(1-ps(0)); 
	        loglikecont=log(ll)-log(1-ps(0));
		diff+=dp00(0)/(1-ps(0));
	   if (varlink==1) diff=-pow(deppar,1)*diff;  
	   if (varlink==0) diff=-1*pow(deppar,2)*diff; 
	   }

	   } // }}}
	   else if (depmodel==3) { // clayton-oakes addtive gamma  // {{{

	// number of random effects for this cluster 	
	// and rows of random.design matrix, and theta.des to be organized
        int irv1=clusterindex(j,2); 
        int irv2=clusterindex(j,3); 
        int itrow=clusterindex(j,4); 
        int lnrv=clusterindex(j,5); 

        vec rv1= trans(rvdes(irv1,span(0,lnrv-1)));
        vec rv2= trans(rvdes(irv2,span(0,lnrv-1)));

	// takes parameter relations for each pair
	// 2-dimensional array pairs*(random effects* pars )
	mat thetadesv= reshape(thetades(itrow,span(0,lnrv*pt-1)),lnrv,pt); 

	if (j< -10)  {/*{{{*/
	   Rprintf(" %d %d \n",lnrv,pt); 
           rv1.print("rv1");    rv2.print("rv2"); 
	   thetadesv.print("thetades "); 
	   etheta.print("e-theta"); 
	}/*}}}*/

	ll=claytonoakesbinRVC(etheta,thetadesv,ags,ci,ck,Li,Lk,rv1,rv2,dplack,vDbetaDtheta,ps,dp00);
        if (j<-10) { 
	Rprintf("==============================\n"); 
	rv1.print("rv1"); rv2.print("rv1"); 
	thetadesv.print("theta.des"); 
	etheta.print("theta"); 
	Rprintf("%d  %d %d %lf %lf %lf \n",j,ci,ck,Li,Lk,ll); ps.print("ps"); 
	}

        ssf+=weights(i)*log(ll); 
	loglikecont=log(ll);
	vthetascore.subvec(0,pt-1)=dplack/ll; 
	if (twostage==0) 
	   vthetascore.subvec(pt,pt+dimbeta-1)=(ps(4)*trans(betaiid.row(i))+ps(5)*trans(betaiid.row(k)))/ll; 

	if (pairascertained(j)==1) {
           ssf-=weights(i)*log(1-ps(0)); 
	   loglikecont=log(ll)-log(1-ps(0));
	   vthetascore.subvec(0,pt-1)+=dp00/(1-ps(0)); 
	   if (twostage==0) {
	      llt=(1-ps(0)); 
              vthetascore.subvec(pt,pt+dimbeta-1)+=(ps(6)*trans(betaiid.row(i))+ps(7)*trans(betaiid.row(k)))/llt; 
	   }
	}

	if (casecontrol(j)==1) { //         marginal of second person Lk
	   llt=(ck==1)*(Lk)+(ck==0)*(1-Lk); 
           ssf-=weights(i)*log(llt); 
	   loglikecont=log(ll)-log(llt);
	   if (twostage==0) {
	      sss=-1; 
	      if (ck==0) sss=1; 
              vthetascore.subvec(pt,pt+dimbeta-1)=vthetascore.subvec(pt,pt+dimbeta-1)+sss*trans(betaiid.row(k))/llt; 
	   }
	}
	   // }}}
	} else if (depmodel==2) { // plackett model  // {{{
           ll=placklikeP(deppar,ci,ck,Li,Lk,dplack,ps,dp00);
	   loglikecont=log(ll); 
	   ssf+=weights(i)*log(ll); 
	   
	   if (varlink==1) diff=deppar*dplack(0)/ll; 
	   if (varlink==0) diff=dplack(0)/ll;

	   if (pairascertained(j)==1) {
                ssf-=weights(i)*log(1-ps(0)); 
	        loglikecont-=log(1-ps(0));
	   if (varlink==1) diff+=deppar*dp00(0)/(1-ps(0)); 
	   if (varlink==0) diff+=dp00(0)/(1-ps(0));
	   }
	   
	} // }}}


     if (depmodel!=3) {
	     DUtheta+=weights(i)*pow(diff,2)*vthetascore*trans(vthetascore);
	     vthetascore=weights(i)*diff*vthetascore; 
	     Utheta=Utheta+vthetascore; 
     } else  { // additive gamma structure 
	     DUtheta+=weights(i)*vthetascore*trans(vthetascore);
	     vthetascore=weights(i)*vthetascore; 
	     Utheta=Utheta+vthetascore; 

	     if (twostage==1) {
		     Du1=vDbetaDtheta.subvec(0,pt-1); 
		     Du2=vDbetaDtheta.subvec(pt,2*pt-1); 
		     DbetaDtheta+= Du1*betaiid.row(i)+ Du2*betaiid.row(k); 
	     }
	}

     if (iid==1) { 
	 for (c1=0;c1<pt;c1++) thetiid((int) secluster(i),c1)+=vthetascore(c1); 
	 loglikeiid((int) secluster(i))+=loglikecont; 
     }
     } // }}} strata(i)==strata(k) indenfor strata

if (iid==1)  likepairs(j)=ll; 
} /* j in antclust */ 

//printf("Sum of squares %lf \n",ssf);theta.print("theta");Utheta.print("Utheta");DUtheta.print("DUtheta"); 
List res; 
res["loglike"]=ssf; 
res["score"]=Utheta; 
res["Dscore"]=DUtheta; 
res["DbetaDtheta"]=DbetaDtheta; 
if (iid==1) { res["theta.iid"]=thetiid; 
	      res["loglikeiid"]=loglikeiid; 
              res["likepairs"]=likepairs; 
            }

return(res); 
} catch( std::exception &ex ) {
    forward_exception_to_r( ex );
  } catch(...) {  
    (Rf_error)( "c++ exception (unknown reason)" ); 
  }
  return R_NilValue; // -Wall

} // }}}

