Fix C++11 specification and style C++ code

DESCRIPTION

@@ -32,8 +32,6 @@ LinkingTo:
     Rcpp,
     RcppArmadillo
 RcppModules: miceFast, corrData
-SystemRequirements: 
-    C++11
 NeedsCompilation: yes
 LazyData: true
 RoxygenNote: 7.2.2

NEWS.md

@@ -1,5 +1,8 @@
 # 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.

README.md

@@ -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'.

src/Makevars

@@ -1,4 +1,2 @@
-## 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)

src/Makevars.win

@@ -1,5 +1,4 @@
 
 ## optional
-CXX_STD = CXX11
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/R_funs.cpp

@@ -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);
@@ -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);
@@ -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);
@@ -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;
 
@@ -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());
-// }