Merge 13e8fd4 into edf8cd1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: corehunter
 Title: Multi-Purpose Core Subset Selection
-Version: 3.0.1
-Date: 2016-10-04
+Version: 3.1.0
+Date: 2017-01-27
 Authors@R: c(person("Herman", "De Beukelaer", email = "herman.debeukelaer@gmail.com", role = c("aut", "cre")),
              person("Guy", "Davenport", email = "daveneti@gmail.com", role = "aut"),
              person("Veerle", "Fack", email = "veerle.fack@ugent.be", role = "ths"))

NEWS.md

@@ -1,6 +1,14 @@
 Core Hunter 3
 =============
 
+Version 3.1.0 (27/01/2017)
+--------------------------
+
+ - More informative output when printing Core Hunter data objects.
+ - It is now required to explicitly specify the format when reading genotype data. Moreover, a warning is raised in case it seems that the wrong format may have been selected, through an inspection of the data that was read.
+ - Fixed issues when reading files with single or double quoted values.
+ - Improved test coverage.
+
 Version 3.0.1 (04/10/2016)
 --------------------------
 

R/corehunter.R

@@ -12,33 +12,43 @@
 #'
 #' @examples
 #' \dontrun{
-#' # sample core based on genetic marker data
+#' # sample core based on genetic marker data (default format)
 #' geno.file <- system.file("extdata", "genotypes.csv", package = "corehunter")
-#' geno <- genotypes(file = geno.file)
-#' sampleCore(geno)
+#' geno <- genotypes(file = geno.file, format = "default")
+#' core <- sampleCore(geno)
+#'
+#' # sample core based on genetic marker data (biparental format)
+#' geno.file <- system.file("extdata", "genotypes-biparental.csv", package = "corehunter")
+#' geno <- genotypes(file = geno.file, format = "biparental")
+#' core <- sampleCore(geno)
+#'
+#' # sample core based on genetic marker data (frequency format)
+#' geno.file <- system.file("extdata", "genotypes-frequency.csv", package = "corehunter")
+#' geno <- genotypes(file = geno.file, format = "frequency")
+#' core <- sampleCore(geno)
 #'
 #' # sample core based on phenotypic traits
 #' pheno.file <- system.file("extdata", "phenotypes.csv", package = "corehunter")
 #' pheno <- phenotypes(file = pheno.file)
-#' sampleCore(pheno)
+#' core <- sampleCore(pheno)
 #'
 #' # sample core based on precomputed distance matrix
 #' dist.file <- system.file("extdata", "distances.csv", package = "corehunter")
 #' dist <- distances(file = dist.file)
-#' sampleCore(dist)
+#' core <- sampleCore(dist)
 #'
 #' # sample core from genotypes with custom objective (allelic richness)
-#' sampleCore(geno, obj = objective("HE"))
+#' core <- sampleCore(geno, obj = objective("HE"))
 #'
 #' # sample core from genotypes with custom size and objective (representativeness)
-#' sampleCore(geno, obj = objective("AN", "MR"), size = 0.1)
+#' core <- sampleCore(geno, obj = objective("AN", "MR"), size = 0.1)
 #'
 #' # sample core from genotypes with custom size and stop condition
-#' sampleCore(geno, size = 0.1, impr.time = 2)
+#' core <- sampleCore(geno, size = 0.1, impr.time = 2)
 #'
 #' # sample core based on both genotypes and phenotypes
 #' geno.pheno <- coreHunterData(geno, pheno)
-#' sampleCore(geno.pheno)
+#' core <- sampleCore(geno.pheno)
 #' }
 #'
 #' @seealso \code{\link{coreHunterData}}, \code{\link{genotypes}},