Fixed docs

NAMESPACE

@@ -3,7 +3,6 @@
 export(greedyMix)
 export(handleData)
 export(importFile)
-export(load_fasta)
 importFrom(R6,R6Class)
 importFrom(Rsamtools,scanBam)
 importFrom(adegenet,.readExt)

R/greedyMix.R

@@ -3,11 +3,7 @@
 #' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"
 #' @param partitionCompare a list of partitions to compare
 #' @param ninds number of individuals
-#' @param rowsFromInd a list of rows for each individual
-#' @param noalle number of alleles
-#' @param adjprior ajuster prior probabilities
 #' @param npops number of populations
-#' @param priorTerm prior terms
 #' @param counts counts
 #' @param sumcounts sumcounts
 #' @param max_iter maximum number of iterations

R/load_fasta.R

@@ -5,16 +5,17 @@
 #'
 #' @param msa Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered
 #' @param keep_singletons A logical indicating whether to consider singleton mutations in calculating the clusters
+#' @param output_numbers A logical indicating whether to output the data as
+#' numbers (TRUE) or letters (FALSE)
 #'
 #' @return A character matrix with filtered SNP data
 #'
 #' @examples
 #' msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
-#' snp.matrix <- load_fasta(msa)
+#' snp.matrix <- rBAPS:::load_fasta(msa)
 #' @author Gerry Tonkin-Hill, Waldir Leoncio
 #' @seealso rhierbaps::load_fasta
 #' @importFrom ape read.FASTA as.DNAbin
-#' @export
 load_fasta <- function(msa, keep_singletons = FALSE, output_numbers = TRUE) {
 
   # Check inputs

man/greedyMix.Rd

@@ -46,14 +46,6 @@ greedyMix(
 \item{fixedK}{if \code{TRUE}, the number of populations is fixed}
 
 \item{verbose}{if \code{TRUE}, prints extra output information}
-
-\item{rowsFromInd}{a list of rows for each individual}
-
-\item{noalle}{number of alleles}
-
-\item{adjprior}{ajuster prior probabilities}
-
-\item{priorTerm}{prior terms}
 }
 \description{
 Clustering of individuals

man/load_fasta.Rd

@@ -10,6 +10,9 @@ load_fasta(msa, keep_singletons = FALSE, output_numbers = TRUE)
 \item{msa}{Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered}
 
 \item{keep_singletons}{A logical indicating whether to consider singleton mutations in calculating the clusters}
+
+\item{output_numbers}{A logical indicating whether to output the data as
+numbers (TRUE) or letters (FALSE)}
 }
 \value{
 A character matrix with filtered SNP data
@@ -20,7 +23,7 @@ running the hierBAPS algorithm.
 }
 \examples{
 msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
-snp.matrix <- load_fasta(msa)
+snp.matrix <- rBAPS:::load_fasta(msa)
 }
 \seealso{
 rhierbaps::load_fasta