Updated documentation (#24)

DESCRIPTION

@@ -36,7 +36,7 @@ Description: Partial R implementation of the BAPS software
 License: GPL-3
 BugReports: https://github.com/ocbe-uio/rBAPS/issues
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests:
     testthat (>= 2.1.0)
 Imports:

NAMESPACE

@@ -38,5 +38,6 @@ importFrom(methods,is)
 importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(utils,read.delim)
+importFrom(utils,read.table)
 importFrom(vcfR,read.vcfR)
 importFrom(zeallot,"%<-%")

R/greedyMix.R

@@ -19,8 +19,8 @@
 #' with high-throughput sequencing data. <http://www.htslib.org/>
 #' @export
 #' @examples
-#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
-#' greedyMix(data, "fasta")
+#' data <- system.file("extdata", "BAPS_format_clustering_diploid.txt", package = "rBAPS")
+#' greedyMix(data, "baps")
 greedyMix <- function(
   data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, npops = 1L,
   counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL,

R/logml2String.R

@@ -1,7 +1,6 @@
 #' @title Logml to string
 #' @description Returns a string representation of a logml
 #' @param logml input Logml
-#' @param
 #' @param leading_zeros_replacement string to replace leading zeros with
 #' @return String version of logml
 logml2String <- function(logml, leading_zeros_replacement = " ") {

R/rBAPS-package.R

@@ -1,6 +1,5 @@
 #' @title Bayesian Analysis of Population Structure
 #' @description This is a partial implementation of the BAPS software
-#' @docType package
 #' @name rBAPS
 #' @note Found a bug? Want to suggest a feature? Contribute to the scientific
 #' and open source communities by opening an issue on our home page.
@@ -11,4 +10,5 @@
 #' @importFrom stats runif
 #' @importFrom zeallot %<-%
 #' @importFrom matlab2r nargin log2
-NULL
+#' @importFrom utils read.table
+"_PACKAGE"