// [[Rcpp::depends(RcppEigen)]]
 #include <Rcpp.h>
 using namespace Rcpp ;
 
 //' Fast normalization for numeric matrix
 //' 
 //' @param R_counts An integer matrix
 //' @param R_alpha A double value to be added to the matrix as a pseudocount
 //' @return A numeric matrix where the columns have been normalized to proportions
 // [[Rcpp::export]]
 SEXP fastNormProp(NumericMatrix R_counts, double R_alpha) {
 
   // Get colSums and instantiate new matrix
   NumericVector cs = colSums(R_counts);
   NumericMatrix res = NumericMatrix(R_counts.nrow(), R_counts.ncol());
   
   // Normalize cell counts to proportions after adding pseudocount  
   double alpha_tot = R_counts.nrow() * R_alpha;
   for (int i = 0; i < R_counts.ncol(); ++i) {

     if (cs[i] + alpha_tot == 0) {
       stop("Division by 0. Make sure colSums of counts does not contain 0 after rounding counts to integers.");
     }

     res(_,i) = (R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot);
   }
   
   return Rcpp::wrap(res);
 }
 
 
 // [[Rcpp::depends(RcppEigen)]]
 #include <Rcpp.h>
 using namespace Rcpp ;
 
 //' Fast normalization for numeric matrix
 //' 
 //' @param R_counts An integer matrix
 //' @param R_alpha A double value to be added to the matrix as a pseudocount
 //' @return A numeric matrix where the columns have been normalized to proportions
 // [[Rcpp::export]]
 SEXP fastNormPropLog(NumericMatrix R_counts, double R_alpha) {
 
   // Get colSums and instantiate new matrix
   NumericVector cs = colSums(R_counts);
   NumericMatrix res = NumericMatrix(R_counts.nrow(), R_counts.ncol());
   
   // Normalize cell counts to proportions after adding pseudocount  
   double alpha_tot = R_counts.nrow() * R_alpha;
   for (int i = 0; i < R_counts.ncol(); ++i) {

     if (cs[i] + alpha_tot == 0) {
       stop("Division by 0. Make sure colSums of counts does not contain 0 after rounding counts to integers.");
     }

     res(_,i) = log((R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot));
   }
   
   return Rcpp::wrap(res);
 }
 
 
 // [[Rcpp::depends(RcppEigen)]]
 #include <Rcpp.h>
 using namespace Rcpp ;
 
 //' Fast normalization for numeric matrix
 //' 
 //' @param R_counts An integer matrix
 //' @param R_alpha A double value to be added to the matrix as a pseudocount
 //' @return A numeric matrix where the columns have been normalized to proportions
 // [[Rcpp::export]]
 SEXP fastNormPropSqrt(NumericMatrix R_counts, double R_alpha) {
 
   // Get colSums and instantiate new matrix
   NumericVector cs = colSums(R_counts);
   NumericMatrix res = NumericMatrix(R_counts.nrow(), R_counts.ncol());
   
   // Normalize cell counts to proportions after adding pseudocount  
   double alpha_tot = R_counts.nrow() * R_alpha;
   for (int i = 0; i < R_counts.ncol(); ++i) {

     if (cs[i] + alpha_tot == 0) {
       stop("Division by 0. Make sure colSums of counts does not contain 0 after rounding counts to integers.");
     }

     res(_,i) = sqrt((R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot));
   }
   
   return Rcpp::wrap(res);
 }