added conversion functs

NAMESPACE

@@ -4,6 +4,7 @@ export("%>%")
 export(.CM_to_NM)
 export(.extract_GT_to_CM)
 export(.extract_haps)
+export(.grepa)
 export(.gt_to_popsum)
 export(.read_body_gz)
 export(.read_meta_gz)
@@ -64,6 +65,10 @@ export(seq2rects)
 export(var.win)
 export(variant.table)
 export(vcfR2chromR)
+export(vcfR2genind)
+export(vcfR2genlight)
+export(vcfR2loci)
+export(vcfR2migrate)
 export(vcfR2tidy)
 export(vcf_field_names)
 export(win.table)

NEWS.md

@@ -10,6 +10,7 @@ This may have been addressed at 64a308ba50b9119108e8946737460de5997b805b by addi
 
 # vcfR 1.5.0.9000
 Released on CRAN 201X-XX-XX.
+* removed `.Call()` statements to standardize style.
 * Created `vcfR2migrate()` to output MigrateN format data.
 * Addressed clang-UBSAN memory leak in `freq_peak()`.
 * Created `pairwise_genetic_diff()` to calculate pairwise differentiation.

R/RcppExports.R

@@ -63,6 +63,11 @@ AD_frequency <- function(ad, delim = ",", allele = 1L, sum_type = 0L, decreasing
     .Call(`_vcfR_extract_haps`, ref, alt, gt, unphased_as_NA, verbose)
 }
 
+#' @export
+.grepa <- function() {
+    invisible(.Call(`_vcfR_grepa`))
+}
+
 #' 
 #' @rdname freq_peak
 #' 

tools/R/vcfR2migrate.R → R/vcfR2migrate.R

@@ -123,7 +123,7 @@ vcfR2migrate <- function(vcf, pop, in_pop, out_file = "MigrateN_infile.txt", met
       var_info <- as.data.frame(vcf_list[[i]]@fix[,1:2, drop = FALSE])
       var_info$mask <- TRUE
       gt <- extract.gt(vcf_list[[i]])
-      popSum <- .Call("vcfR_gt_to_popsum", PACKAGE = "vcfR", var_info = var_info, gt = gt)
+      popSum <- .gt_to_popsum(var_info = var_info, gt = gt)
 #      popSum <- matrix(unlist(strsplit(as.character(popSum$Allele_counts), split = ",", fixed = TRUE)), ncol = 2, byrow = TRUE)
 
       # Populate matrix

tools/R/vcfR_conversion.R → R/vcfR_conversion.R

@@ -22,22 +22,22 @@
 #' 
 #' 
 #' The function vcfR2genlight calls the 'new' method for the genlight object.
-#' This method implements multi-threading through calls to the function \code{\link[parallel]{mclapply}}.
+#' This method implements multi-threading through calls to the function \code{parallel::mclapply}.
 #' Because 'forks' do not exist in the windows environment, this will only work for windows users when n.cores=1.
 #' In the Unix environment, users may increase this number to allow the use of multiple threads (i.e., cores).
 #' 
 #' 
 #' 
 #' @seealso
-#' \code{\link{extract.gt}},
-#' \code{\link{alleles2consensus}},
-#' \code{\link[adegenet]{df2genind}},
-#' \code{\link[adegenet]{genind}},
+#' \code{extract.gt},
+#' \code{alleles2consensus},
+#' \code{adegenet::df2genind},
+#' \code{adegenet::genind},
 #' \href{https://cran.r-project.org/package=pegas}{pegas},
 #' \href{https://cran.r-project.org/package=adegenet}{adegenet},
 #' and 
 #' \href{https://cran.r-project.org/package=poppr}{poppr}.
-#' To convert to objects of class \strong{DNAbin} see \code{\link{vcfR2DNAbin}}.
+#' To convert to objects of class \strong{DNAbin} see \code{vcfR2DNAbin}.
 #'
 
 

src/RcppExports.cpp

@@ -62,6 +62,15 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// grepa
+void grepa();
+RcppExport SEXP _vcfR_grepa() {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    grepa();
+    return R_NilValue;
+END_RCPP
+}
 // freq_peak
 Rcpp::List freq_peak(Rcpp::NumericMatrix myMat, Rcpp::NumericVector pos, int winsize, float bin_width, Rcpp::LogicalVector lhs);
 RcppExport SEXP _vcfR_freq_peak(SEXP myMatSEXP, SEXP posSEXP, SEXP winsizeSEXP, SEXP bin_widthSEXP, SEXP lhsSEXP) {
@@ -293,6 +302,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_vcfR_extract_GT_to_CM", (DL_FUNC) &_vcfR_extract_GT_to_CM, 6},
     {"_vcfR_CM_to_NM", (DL_FUNC) &_vcfR_CM_to_NM, 1},
     {"_vcfR_extract_haps", (DL_FUNC) &_vcfR_extract_haps, 5},
+    {"_vcfR_grepa", (DL_FUNC) &_vcfR_grepa, 0},
     {"_vcfR_freq_peak", (DL_FUNC) &_vcfR_freq_peak, 5},
     {"_vcfR_gt_to_popsum", (DL_FUNC) &_vcfR_gt_to_popsum, 2},
     {"_vcfR_is_het", (DL_FUNC) &_vcfR_is_het, 2},

src/extract_gt.cpp

@@ -456,4 +456,13 @@ Rcpp::StringMatrix extract_haps(Rcpp::StringVector ref,
 }
 
 
+//' @export
+// [[Rcpp::export(name=".grepa")]]
+void grepa(){
+  Rcpp::Rcout << "Hola Javier!\n";
+  Rcpp::Rcout << "Eres un verdadero amigo!\n";
+  return;
+}
+
+
 // EOF.

tools/src/extractGT2NM.cpp

@@ -89,10 +89,4 @@ Rcpp::CharacterMatrix extract_GT_to_CM(Rcpp::DataFrame x, std::string element="D
 
 
 
-// [[Rcpp::export]]
-void grepa(){
-  Rcout << "Hola Javier!\n";
-  Rcout << "Eres un verdadero amigo!\n";
-  return;
-}