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Fix C++11 specification and style C++ code (#25)
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* Fix C++11 specification and style C++ code
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@Polkas
Polkas authored Jan 16, 2025
1 parent f5ab848 commit 91f5b46
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2 changes: 0 additions & 2 deletions DESCRIPTION
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Expand Up @@ -32,8 +32,6 @@ LinkingTo:
Rcpp,
RcppArmadillo
RcppModules: miceFast, corrData
SystemRequirements:
C++11
NeedsCompilation: yes
LazyData: true
RoxygenNote: 7.2.2
3 changes: 3 additions & 0 deletions NEWS.md
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# miceFast 0.8.2.9000

* fixed CRAN Notes.
* style the cpp code.

# miceFast 0.8.2

* simplified `naive_fill_NA`, It is a regular sampling imputation now.
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -6,7 +6,7 @@ Maciej Nasinski
[![R build status](https://github.com/polkas/miceFast/workflows/R-CMD-check/badge.svg)](https://github.com/polkas/miceFast/actions)
[![CRAN](http://www.r-pkg.org/badges/version/miceFast)](https://cran.r-project.org/package=miceFast)
[![codecov](https://codecov.io/gh/Polkas/miceFast/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Polkas/miceFast)
[![Dependencies](https://tinyverse.netlify.com/badge/miceFast)](https://cran.r-project.org/package=miceFast)
[![Dependencies](https://tinyverse.netlify.app/badge/miceFast)](https://cran.r-project.org/package=miceFast)

Fast imputations under the object-oriented programming paradigm.
Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
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6 changes: 2 additions & 4 deletions src/Makevars
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## optional
CXX_STD = CXX11
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
1 change: 0 additions & 1 deletion src/Makevars.win
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## optional
CXX_STD = CXX11
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
174 changes: 77 additions & 97 deletions src/R_funs.cpp
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Expand Up @@ -2,8 +2,7 @@
#include "miceFast.h"
#include <math.h>


arma::uvec get_index_full_R(arma::mat &x,int posit_y, arma::uvec posit_x){
arma::uvec get_index_full_R(arma::mat &x, int posit_y, arma::uvec posit_x) {
arma::colvec y_col = x.col(posit_y);
arma::mat x_cols = x.cols(posit_x);
arma::uvec full_y = complete_cases_vec(y_col);
Expand All @@ -12,73 +11,74 @@ arma::uvec get_index_full_R(arma::mat &x,int posit_y, arma::uvec posit_x){
return index_Full;
}

arma::uvec get_index_NA_R(arma::mat &x,int posit_y, arma::uvec posit_x){
arma::uvec get_index_NA_R(arma::mat &x, int posit_y, arma::uvec posit_x) {
arma::colvec y_col = x.col(posit_y);
arma::mat x_cols = x.cols(posit_x);
arma::uvec full_y = complete_cases_vec(y_col);
arma::uvec full_x = complete_cases_mat(x_cols);
arma::uvec index(x.n_rows,arma::fill::zeros);
for(unsigned int i=0;i<x.n_rows;i++){
if( (full_y(i)==0) && (full_x(i)==1) ){index(i) = 1;}
arma::uvec index(x.n_rows, arma::fill::zeros);
for (unsigned int i = 0; i < x.n_rows; i++) {
if ((full_y(i) == 0) && (full_x(i) == 1)) {
index(i) = 1;
}
}
arma::uvec index_NA = arma::find(index==1);
arma::uvec index_NA = arma::find(index == 1);
return index_NA;
}

arma::colvec impute_raw_R(arma::mat &x,std::string s, int posit_y,arma::uvec posit_x,int k, double ridge = 1e-6){
typedef arma::colvec (*pfunc)(arma::colvec&,arma::mat&,arma::mat&,int,double);
arma::colvec impute_raw_R(arma::mat &x, std::string s, int posit_y, arma::uvec posit_x, int k, double ridge = 1e-6) {
typedef arma::colvec (*pfunc)(arma::colvec &, arma::mat &, arma::mat &, int, double);
std::map<std::string, pfunc> funMap = {
{"lda",fastLda},
{"lm_pred",fastLm_pred},
{"lm_noise",fastLm_noise},
{"lm_bayes",fastLm_bayes},
{"pmm",pmm_neibo}};
{"lda", fastLda},
{"lm_pred", fastLm_pred},
{"lm_noise", fastLm_noise},
{"lm_bayes", fastLm_bayes},
{"pmm", pmm_neibo}};

arma::uvec posit_y_uvec(1);
posit_y_uvec(0) = posit_y;
arma::uvec index_full = get_index_full_R(x,posit_y, posit_x);
arma::uvec index_NA = get_index_NA_R(x,posit_y, posit_x);
arma::colvec pred = x(index_NA,posit_y_uvec);

if((!(index_NA.n_elem==0)) && ((index_full.n_elem>15 && s=="lda")|| (index_full.n_elem>posit_x.n_elem && s!="lda"))){
arma::mat X_full = x(index_full,posit_x);
arma::mat X_NA = x(index_NA,posit_x);
arma::colvec Y_full = x(index_full,posit_y_uvec);
arma::uvec index_full = get_index_full_R(x, posit_y, posit_x);
arma::uvec index_NA = get_index_NA_R(x, posit_y, posit_x);
arma::colvec pred = x(index_NA, posit_y_uvec);

if ((!(index_NA.n_elem == 0)) && ((index_full.n_elem > 15 && s == "lda") || (index_full.n_elem > posit_x.n_elem && s != "lda"))) {
arma::mat X_full = x(index_full, posit_x);
arma::mat X_NA = x(index_NA, posit_x);
arma::colvec Y_full = x(index_full, posit_y_uvec);
pfunc f = funMap[s];
pred = (*f)(Y_full,X_full,X_NA,k,ridge);
pred = (*f)(Y_full, X_full, X_NA, k, ridge);
}

arma::colvec Y = x.col(posit_y);
Y.rows(index_NA) = pred;
return Y;
}

arma::colvec imputeW_R(arma::mat &x, std::string s, int posit_y, arma::uvec posit_x, arma::colvec w, int k, double ridge = 1e-6) {

arma::colvec imputeW_R(arma::mat &x,std::string s,int posit_y,arma::uvec posit_x,arma::colvec w,int k, double ridge = 1e-6){

typedef arma::colvec (*pfuncw)(arma::colvec&,arma::mat&,arma::colvec&,arma::mat&,int, double);
std::map<std::string, pfuncw> funMapw = {{"lm_pred",fastLm_weighted},
{"lm_noise",fastLm_weighted_noise},
{"lm_bayes",fastLm_weighted_bayes},
{"pmm",pmm_weighted_neibo}};
typedef arma::colvec (*pfuncw)(arma::colvec &, arma::mat &, arma::colvec &, arma::mat &, int, double);
std::map<std::string, pfuncw> funMapw = {{"lm_pred", fastLm_weighted},
{"lm_noise", fastLm_weighted_noise},
{"lm_bayes", fastLm_weighted_bayes},
{"pmm", pmm_weighted_neibo}};

arma::uvec posit_y_uvec(1);
posit_y_uvec(0) = posit_y;

arma::uvec index_full = get_index_full_R(x,posit_y, posit_x);
arma::uvec index_NA = get_index_NA_R(x,posit_y, posit_x);
arma::uvec index_full = get_index_full_R(x, posit_y, posit_x);
arma::uvec index_NA = get_index_NA_R(x, posit_y, posit_x);

arma::colvec pred = x(index_NA,posit_y_uvec);
arma::colvec pred = x(index_NA, posit_y_uvec);

if((!(index_NA.n_elem==0)) && ((index_full.n_elem>15 && s=="lda")|| (index_full.n_elem>posit_x.n_elem && s!="lda"))){
if ((!(index_NA.n_elem == 0)) && ((index_full.n_elem > 15 && s == "lda") || (index_full.n_elem > posit_x.n_elem && s != "lda"))) {

//dividing data to NA and full
arma::mat X_full = x(index_full,posit_x);
arma::mat X_NA = x(index_NA,posit_x);
arma::colvec Y_full = x(index_full,posit_y_uvec);
// dividing data to NA and full
arma::mat X_full = x(index_full, posit_x);
arma::mat X_NA = x(index_NA, posit_x);
arma::colvec Y_full = x(index_full, posit_y_uvec);
arma::colvec w_full = w.elem(index_full);
pfuncw f = funMapw[s];
pred = (*f)(Y_full,X_full,w_full,X_NA,k,ridge);
pred = (*f)(Y_full, X_full, w_full, X_NA, k, ridge);
}

arma::colvec Y = x.col(posit_y);
Expand All @@ -87,16 +87,15 @@ arma::colvec imputeW_R(arma::mat &x,std::string s,int posit_y,arma::uvec posit_x
return Y;
}

//eval vifs
// eval vifs

arma::mat cov2cor(arma::mat & X){
arma::mat corr = arma::diagmat(1/arma::sqrt(X.diag())) * X * arma::diagmat(1/arma::sqrt(X.diag()));
arma::mat cov2cor(arma::mat &X) {
arma::mat corr = arma::diagmat(1 / arma::sqrt(X.diag())) * X * arma::diagmat(1 / arma::sqrt(X.diag()));
return corr;
}


// [[Rcpp::export]]
arma::vec VIF_(arma::mat &x, int posit_y, arma::uvec posit_x, arma::uvec posit_x_var, bool correct){
arma::vec VIF_(arma::mat &x, int posit_y, arma::uvec posit_x, arma::uvec posit_x_var, bool correct) {

arma::mat x_cols = x.cols(posit_x - 1);
arma::colvec y_cols = x.col(posit_y - 1);
Expand All @@ -105,19 +104,22 @@ arma::vec VIF_(arma::mat &x, int posit_y, arma::uvec posit_x, arma::uvec posit_x

arma::vec vifs(Nvar_o, arma::fill::none);

arma::uvec full_rows = get_index_full_R(x,posit_y - 1,posit_x - 1);
arma::uvec full_rows = get_index_full_R(x, posit_y - 1, posit_x - 1);
arma::mat full_x = x_cols.rows(full_rows);
arma::mat full_y = y_cols.rows(full_rows);

arma::uvec vols = arma::find(arma::var(full_x)>0);
arma::uvec vols = arma::find(arma::var(full_x) > 0);
int vols_n = vols.n_elem;
arma::mat x_vols = full_x.cols(vols);

if(vols_n<Nvar_o){Rcpp::warning("There is at least a one zero variance variable");return vifs;}
if (vols_n < Nvar_o) {
Rcpp::warning("There is at least a one zero variance variable");
return vifs;
}

arma::uvec posit_x_v = posit_x.elem(vols);
arma::uvec posit_x_var_v = posit_x_var.elem(vols);
arma::mat col_means = arma::mean(x_vols,0);
arma::mat col_means = arma::mean(x_vols, 0);

x_vols.each_row() -= col_means;

Expand All @@ -126,93 +128,71 @@ arma::vec VIF_(arma::mat &x, int posit_y, arma::uvec posit_x, arma::uvec posit_x
arma::uvec Nvar_x = arma::unique(posit_x_var_v);
int Nvar = Nvar_x.n_elem;

arma::mat xtx = x_vols.t()*x_vols;
arma::mat xtx = x_vols.t() * x_vols;
arma::mat XXinv = arma::inv(xtx);
if(Nvar<Ncol){ XXinv = cov2cor(XXinv) ;}
if (Nvar < Ncol) {
XXinv = cov2cor(XXinv);
}
double det_XXinv = arma::det(XXinv);

arma::vec dfs(Nvar);
arma::uvec pp = arma::linspace<arma::uvec>(0, Ncol-1, Ncol);
arma::uvec pp = arma::linspace<arma::uvec>(0, Ncol - 1, Ncol);

for(int i=0;i<(Nvar);i++){
for (int i = 0; i < (Nvar); i++) {
int a = Nvar_x(i);
arma::mat XXinv_small = XXinv;
arma::uvec ii = pp.elem(arma::find(posit_x_var_v==a));
arma::uvec ii = pp.elem(arma::find(posit_x_var_v == a));
int ii_len = ii.n_elem;
int ii_first = ii(0);
int ii_last = ii(ii_len-1);
int ii_last = ii(ii_len - 1);
dfs(i) = ii_len;
XXinv_small.shed_rows(ii_first,ii_last);
XXinv_small.shed_cols(ii_first,ii_last);
double vif = arma::as_scalar(arma::det(XXinv(ii,ii)) * arma::det(XXinv_small)/det_XXinv);
XXinv_small.shed_rows(ii_first, ii_last);
XXinv_small.shed_cols(ii_first, ii_last);
double vif = arma::as_scalar(arma::det(XXinv(ii, ii)) * arma::det(XXinv_small) / det_XXinv);
vifs(i) = vif;
}

if(correct){
for(unsigned int i=0;i<(vifs.n_elem);i++){
vifs(i) = pow(vifs(i),(1/(2*dfs(i))));
if (correct) {
for (unsigned int i = 0; i < (vifs.n_elem); i++) {
vifs(i) = pow(vifs(i), (1 / (2 * dfs(i))));
}
}

return vifs;
}



// [[Rcpp::export]]
arma::colvec fill_NA_N_(arma::mat &x, std::string model, int posit_y,arma::uvec posit_x,arma::colvec w,int k=10, double ridge = 1e-6){
arma::colvec fill_NA_N_(arma::mat &x, std::string model, int posit_y, arma::uvec posit_x, arma::colvec w, int k = 10, double ridge = 1e-6) {

posit_x = posit_x - 1;
posit_x = posit_x - 1;
posit_y = posit_y - 1;

arma::colvec pred_avg;

if(w.is_empty() || (model.compare("lda") == 0)){
pred_avg = impute_raw_R(x,model,posit_y,posit_x,k, ridge);
} else{
pred_avg = imputeW_R(x,model,posit_y,posit_x,w,k, ridge);
if (w.is_empty() || (model.compare("lda") == 0)) {
pred_avg = impute_raw_R(x, model, posit_y, posit_x, k, ridge);
} else {
pred_avg = imputeW_R(x, model, posit_y, posit_x, w, k, ridge);
}

//index
// index
return pred_avg;
}


// [[Rcpp::export]]
arma::colvec fill_NA_(arma::mat &x,std::string model, int posit_y,arma::uvec posit_x,arma::colvec w, double ridge = 1e-6){
arma::colvec fill_NA_(arma::mat &x, std::string model, int posit_y, arma::uvec posit_x, arma::colvec w, double ridge = 1e-6) {

posit_x = posit_x - 1;
posit_x = posit_x - 1;
posit_y = posit_y - 1;

arma::colvec pred_avg;

if(w.is_empty() || (model.compare("lda") == 0)){
pred_avg = impute_raw_R(x,model,posit_y,posit_x,1, ridge);
if (w.is_empty() || (model.compare("lda") == 0)) {
pred_avg = impute_raw_R(x, model, posit_y, posit_x, 1, ridge);
} else {
pred_avg = imputeW_R(x,model,posit_y,posit_x,w,1, ridge);
pred_avg = imputeW_R(x, model, posit_y, posit_x, w, 1, ridge);
}

//index
// index
return pred_avg;
}

//
// // [[Rcpp::export]]
// SEXP cpp_miceFast() {
// miceFast *v = new miceFast();
// Rcpp::XPtr<miceFast> ptr(v, true);
// return ptr;
// }
//
//
// // [[Rcpp::export]]
// void cpp_miceFast_set_data(SEXP ptr, arma::mat &doc) {
// Rcpp::XPtr<miceFast> v(ptr);
// v->set_data(doc);
// }
//
// // [[Rcpp::export]]
// arma::mat cpp_miceFast_get_data(SEXP ptr) {
// Rcpp::XPtr<miceFast> v(ptr);
// return(v->get_data());
// }
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