Moved used datasets to /isnt/extdata (#25)

.Rbuildignore

@@ -4,7 +4,6 @@ PITFALLS.md
 CHANGELOG.md
 CITATION.cff
 .travis.yml
-inst/ext/ExamplesDataFormatting
+inst/testdata
 .github
 aux
-

R/greedyMix.R

@@ -9,6 +9,9 @@
 #' @references Samtools: a suite of programs for interacting
 #' with high-throughput sequencing data. <http://www.htslib.org/>
 #' @export
+#' @examples
+#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
+#' greedyMix(data)
 greedyMix <- function(data, format, verbose = TRUE) {
   # Parsing data format ------------------------------------------------------
 

R/load_fasta.R

@@ -9,7 +9,7 @@
 #' @return A character matrix with filtered SNP data
 #'
 #' @examples
-#' msa <- system.file("ext", "seqs.fa", package = "rBAPS")
+#' msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
 #' snp.matrix <- load_fasta(msa)
 #' @author Gerry Tonkin-Hill, Waldir Leoncio
 #' @seealso rhierbaps::load_fasta

man/greedyMix.Rd

@@ -16,6 +16,10 @@ greedyMix(data, format, verbose = TRUE)
 \description{
 Clustering of individuals
 }
+\examples{
+data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
+greedyMix(data)
+}
 \references{
 Samtools: a suite of programs for interacting
 with high-throughput sequencing data. <http://www.htslib.org/>

man/load_fasta.Rd

@@ -19,7 +19,7 @@ Loads a fasta file into matrix format ready for
 running the hierBAPS algorithm.
 }
 \examples{
-msa <- system.file("ext", "seqs.fa", package = "rBAPS")
+msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
 snp.matrix <- load_fasta(msa)
 }
 \seealso{

tests/testthat/test-greedyMix.R

@@ -1,11 +1,11 @@
 context("Auxiliary functions to greedyMix")
 
 # Defining the relative path to current inst -----------------------------------
-path_inst <- system.file("ext", "", package = "rBAPS")
+path_inst <- system.file("extdata", "", package = "rBAPS")
 
 # Reading datasets -------------------------------------------------------------
 baps_diploid <- read.delim(
-  file = paste(path_inst, "BAPS_format_clustering_diploid.txt", sep = "/"),
+  file = file.path(path_inst, "BAPS_format_clustering_diploid.txt"),
   sep = " ",
   header = FALSE
 )

tests/testthat/test-spatialMixture.R

@@ -79,7 +79,7 @@ test_that("lakseKlitik() and subfunctions produce expected output", {
 })
 
 test_that("testFastaData() produces same output as on MATLAB", {
-  msa <- system.file("ext", "seqs.fa", package = "rBAPS")
+  msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
   test_msa <- testFastaData(msa)
   expect_equal(test_msa$ninds, 515)
   expect_equal(dim(test_msa$data), c(515, 745))