Added missing documentation for arguments (#25)

R/greedyMix.R

@@ -1,6 +1,20 @@
 #' @title Clustering of individuals
 #' @param data data file
 #' @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
+#' @param alleleCodes allele codes
+#' @param inp input file
+#' @param popnames population names
+#' @param fixedK if \code{TRUE}, the number of populations is fixed
 #' @param verbose if \code{TRUE}, prints extra output information
 #' @importFrom utils read.delim
 #' @importFrom vcfR read.vcfR
@@ -33,7 +47,7 @@ greedyMix <- function(
   # Comparing partitions =======================================================
   if (!is.null(partitionCompare)) {
     logmls <- comparePartitions(
-      data, nrows(data), partitionCompare[["partitions"]], ninds, rowsFromInd,
+      data, nrow(data), partitionCompare[["partitions"]], ninds, rowsFromInd,
       noalle, adjprior
     )
   }

man/greedyMix.Rd

@@ -7,17 +7,21 @@
 greedyMix(
   data,
   format,
-  partitionCompare,
+  partitionCompare = NULL,
-  ninds,
+  ninds = NULL,
-  rowsFromInd,
+  rowsFromInd = NULL,
-  noalle,
+  noalle = NULL,
-  adjprior,
+  adjprior = NULL,
-  priorTerm,
+  npops = 1L,
-  alleleCodesinp,
+  priorTerm = NULL,
-  popnames,
+  counts = NULL,
+  sumcounts = NULL,
+  max_iter = 100L,
+  alleleCodes = NULL,
+  inp = NULL,
+  popnames = NULL,
   fixedK = FALSE,
-  partition_compare = FALSE,
+  verbose = FALSE
-  verbose = TRUE
 )
 }
 \arguments{
@@ -25,6 +29,34 @@ greedyMix(
 
 \item{format}{Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"}
 
+\item{partitionCompare}{a list of partitions to compare}
+
+\item{ninds}{number of individuals}
+
+\item{rowsFromInd}{a list of rows for each individual}
+
+\item{noalle}{number of alleles}
+
+\item{adjprior}{ajuster prior probabilities}
+
+\item{npops}{number of populations}
+
+\item{priorTerm}{prior terms}
+
+\item{counts}{counts}
+
+\item{sumcounts}{sumcounts}
+
+\item{max_iter}{maximum number of iterations}
+
+\item{alleleCodes}{allele codes}
+
+\item{inp}{input file}
+
+\item{popnames}{population names}
+
+\item{fixedK}{if \code{TRUE}, the number of populations is fixed}
+
 \item{verbose}{if \code{TRUE}, prints extra output information}
 }
 \description{