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Using R_xlen_t instead of int so that larger matrices can be computed… #32

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Using R_xlen_t instead of int so that larger matrices can be computed… #32

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59 changes: 30 additions & 29 deletions src/dists_vec.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,14 @@ using namespace arma;

using std::string;

static int proper_size(int nrw,int ncl){
static R_xlen_t proper_size(R_xlen_t nrw,R_xlen_t ncl){
return ncl*(ncl-1)*0.5;
}

//[[Rcpp::export]]
IntegerVector index_dist_vec(const int nrw,const int ncl){
IntegerVector index_dist_vec(const R_xlen_t nrw,const R_xlen_t ncl){
IntegerVector f(proper_size(nrw,ncl));
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
for(j=i+1;j<ncl;++j,++k){
f[k]=j+1;
Expand All @@ -31,12 +31,13 @@ IntegerVector index_dist_vec(const int nrw,const int ncl){

//[[Rcpp::export]]
List euclidean_dist_vec_ina(NumericMatrix x,const bool sqr){
const int ncl=x.ncol(),nrw=x.nrow(),n=proper_size(nrw,ncl);
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t n=proper_size(nrw,ncl);
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(n);
IntegerVector ind_i(n),ind_j(n);
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
if(sqr){
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
Expand All @@ -63,11 +64,11 @@ List euclidean_dist_vec_ina(NumericMatrix x,const bool sqr){


NumericVector euclidean_dist_vec(NumericMatrix x,const bool sqr){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
if(sqr)
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
Expand All @@ -86,11 +87,11 @@ NumericVector euclidean_dist_vec(NumericMatrix x,const bool sqr){
}

NumericVector manhattan_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -101,12 +102,12 @@ NumericVector manhattan_dist_vec(NumericMatrix x){
}

NumericVector hellinger_dist_vec(NumericMatrix x,const bool sqr){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
const double p=1.0/std::sqrt(2.0);
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
if(sqr)
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
Expand All @@ -125,11 +126,11 @@ NumericVector hellinger_dist_vec(NumericMatrix x,const bool sqr){
}

NumericVector max_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw),tmp(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -141,11 +142,11 @@ NumericVector max_dist_vec(NumericMatrix x){
}

NumericVector min_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -157,12 +158,12 @@ NumericVector min_dist_vec(NumericMatrix x){
}

NumericVector minkowski_dist_vec(NumericMatrix x,const double p){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
const double p_1=1.0/p;
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -173,11 +174,11 @@ NumericVector minkowski_dist_vec(NumericMatrix x,const double p){
}

NumericVector canberra1_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw),yv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -189,11 +190,11 @@ NumericVector canberra1_dist_vec(NumericMatrix x){
}

NumericVector canberra2_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw),yv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -207,11 +208,11 @@ NumericVector canberra2_dist_vec(NumericMatrix x){


NumericVector total_variation_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -223,12 +224,12 @@ NumericVector total_variation_dist_vec(NumericMatrix x){

//[[Rcpp::export]]
NumericVector kullback_leibler_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
NumericMatrix log_x(nrw,ncl);
NumericVector f(proper_size(nrw,ncl));
mat xx(x.begin(),nrw,ncl,false),log_xx(log_x.begin(),nrw,ncl,false);
colvec xv(nrw),log_xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
fill_with<std::log,double*,double*>(x.begin(),x.end(),log_xx.begin());
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
Expand All @@ -242,11 +243,11 @@ NumericVector kullback_leibler_dist_vec(NumericMatrix x){

//[[Rcpp::export]]
NumericVector bhattacharyya_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
mat xx(x.begin(),nrw,ncl,false);
NumericVector f(proper_size(nrw,ncl));
colvec xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
for(j=i+1;j<ncl;++j,++k){
Expand All @@ -258,12 +259,12 @@ NumericVector bhattacharyya_dist_vec(NumericMatrix x){

//[[Rcpp::export]]
NumericVector itakura_saito_dist_vec(NumericMatrix x){
const int ncl=x.ncol(),nrw=x.nrow();
const R_xlen_t ncl=x.ncol(),nrw=x.nrow();
NumericVector f(proper_size(nrw,ncl));
NumericMatrix log_x(nrw,ncl);
mat xx(x.begin(),nrw,ncl,false),log_xx(log_x.begin(),nrw,ncl,false);
colvec xv(nrw),log_xv(nrw);
int i,j,k=0;
R_xlen_t i,j,k=0;
fill_with<std::log,double*,double*>(x.begin(),x.end(),log_xx.begin());
for(i=0;i<ncl-1;++i){
xv=xx.col(i);
Expand Down