Fixed docs

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