Merge pull request #149 from zkamvar/znk-update-export-docs

Update conversion documentation

R/vcfR_conversion.R

@@ -27,6 +27,10 @@
 #' 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).
 #' 
+#' @note \subsection{For users of \pkg{poppr}}{
+#' If you wish to use \code{vcfR2genind()}, it is \strong{strongly recommended} to use it with the option \code{return.alleles = TRUE}.
+#' The reason for this is because the \pkg{poppr} package accomodates mixed-ploidy data by interpreting "0" alleles \emph{in genind objects} to be NULL alleles in both \code{poppr::poppr.amova()} and \code{poppr::locus_table()}.
+#' }
 #' 
 #' 
 #' @seealso
@@ -109,8 +113,20 @@ vcfR2loci <- function(x, return.alleles = FALSE)
 #' @param n.cores integer specifying the number of cores to use.
 #' 
 #' @examples 
-#' data(vcfR_test)
-#' gl <- vcfR2genlight(vcfR_test)
+#' adegenet_installed <- require("adegenet")
+#' if (adegenet_installed) {
+#'   data(vcfR_test)
+#'   # convert to genlight (preferred method with bi-allelic SNPs)
+#'   gl <- vcfR2genlight(vcfR_test)
+#'   
+#'   # convert to genind, keeping information about allelic state
+#'   # (slightly slower, but preferred method for use with the "poppr" package)
+#'   gid <- vcfR2genind(vcfR_test, return.alleles = TRUE) 
+#'
+#'   # convert to genind, returning allelic states as 0, 1, 2, etc.
+#'   # (not preferred, but slightly faster)
+#'   gid2 <- vcfR2genind(vcfR_test, return.alleles = FALSE)
+#' }
 #' 
 #' @export
 vcfR2genlight <- function(x, n.cores=1){