Merge branch 'issue-24' into develop

* issue-24:
  Updated docs
  Temp-wrapping disfunctional code
  Aligned processing of Genepop with MATLAB code
  Dropped support for GenePop on `importFile()`
  Added `process_GenePop_data()`
  Fixed `addAlleles()`
  handleData defaults to BAPS format
  Added unit tests for `greedyMix()` on GenePop (#24)
  Added GenePop data, txt and gen (#24)

R/addAlleles.R

@@ -11,7 +11,7 @@ addAlleles <- function(data, ind, line, divider) {
   # line. Jos data on 3 digit formaatissa on divider=1000.
   # Jos data on 2 digit formaatissa on divider=100.
 
-  nloci <- size(data, 2) # added 1 from original code
+  nloci <- size(data, 2) - 1L
   if (size(data, 1) < (2 * ind)) {
     data <- rbind(data, zeros(100, nloci)) # subtracted 1 from original code
   }
@@ -22,8 +22,7 @@ addAlleles <- function(data, ind, line, divider) {
     k <- k + 1
     merkki <- substring(line, k, k)
   }
-  line <- substring(line, k + 1)
+  line <- trimws(substring(line, k + 1))
-  # clear k; clear merkki;
 
   if (grepl(" ", line)) {
     alleeliTaulu <- as.numeric(strsplit(line, split = " ")[[1]])

R/greedyMix.R

@@ -27,6 +27,7 @@ greedyMix <- function(
   inp = NULL, popnames = NULL, fixedK = FALSE, verbose = FALSE
 ) {
   # Importing and handling data ================================================
+  # TODO: use format as class and make handling data a generic
   if (tolower(format) %in% "fasta") {
     data <- convert_FASTA_to_BAPS(data)
     format <- "baps"
@@ -42,6 +43,17 @@ greedyMix <- function(
       Z = data[["Z"]],
       dist = data[["dist"]]
     )
+  } else if (tolower(format) %in% "genepop") {
+    data <- process_GenePop_data(data)
+    c <- list(
+      noalle = data[["noalle"]],
+      data = data[["data"]],
+      adjprior = data[["adjprior"]],
+      priorTerm = data[["priorTerm"]],
+      rowsFromInd = data[["rowsFromInd"]],
+      Z = data[["Z"]],
+      dist = data[["dist"]]
+    )
   } else {
     data <- importFile(data, format, verbose)
     data <- handleData(data, tolower(format))
@@ -68,7 +80,7 @@ greedyMix <- function(
   # Generating partition summary ===============================================
   ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]])
   c[["rows"]] <- cbind(ekat, ekat + c[["rowsFromInd"]] - 1L)
-  logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) # FIXME: not working for FASTA data
+  logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) # FIXME: not working for FASTA, GenePop
   logml <- logml_npops_partitionSummary[["logml"]]
   npops <- logml_npops_partitionSummary[["npops"]]
   partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]]

R/handleData.R

@@ -10,7 +10,7 @@
 #' the function changes the allele codes so that one locus j
 #' codes get values between? 1, ..., noalle(j).
 #' @export
-handleData <- function(raw_data, format = "Genepop") {
+handleData <- function(raw_data, format = "baps") {
   # Alkuper?isen datan viimeinen sarake kertoo, milt?yksil?lt?
   # kyseinen rivi on per?isin. Funktio tutkii ensin, ett?montako
   # rivi?maksimissaan on per?isin yhdelt?yksil?lt? jolloin saadaan

R/importFile.R

@@ -1,6 +1,5 @@
 #' @title Import data file
-#' @description Imports data from several formats (FASTA, VCF, SAM, BAM,
+#' @description Imports data from several formats (FASTA, VCF, SAM, BAM).
-#' Genepop).
 #' @param data raw dataset
 #' @param format data format (guesses from extension if not provided)
 #' @param verbose if \code{TRUE}, prints extra output information
@@ -33,15 +32,6 @@ importFile <- function(data, format, verbose) {
     )
   } else if (format == "bam") {
     out <- Rsamtools::scanBam(data)
-  } else if (format == "genepop") {
-    if (toupper(adegenet::.readExt(data)) == "TXT") {
-      message("Creating a copy of the file with the .gen extension")
-      dataGen <- gsub("txt", "gen", data)
-      file.copy(data, dataGen)
-      out <- adegenet::read.genepop(dataGen)
-    } else {
-      out <- adegenet::read.genepop(data)
-    }
   } else {
     stop("Format not supported.")
   }

R/process_GenePop_data.R

@@ -0,0 +1,24 @@
+process_GenePop_data <- function(filename) {
+  # Pre-processing GenePop data
+  kunnossa <- testaaGenePopData(filename)
+  data_popnames <- lueGenePopData(filename)
+  data <- data_popnames$data
+  popnames <- data_popnames$popnames
+
+  # Processing GenePop data
+  c <- handleData(data, "genepop")
+  Z_dist <- newGetDistances(c$newData, c$rowsFromInd)
+
+  # Forming and returning pre-processed data
+  list(
+    "data" = c$newData,
+    "rowsFromInd" = c$rowsFromInd,
+    "alleleCodes" = c$alleleCodes,
+    "noalle" = c$noalle,
+    "adjprior" = c$adjprior,
+    "priorTerm" = c$priorTerm,
+    "dist" = Z_dist$dist,
+    "popnames" = popnames,
+    "Z" = Z_dist$Z
+  )
+}

inst/extdata/GenePop.gen

@@ -0,0 +1,12 @@
+Example GenePop Data
+Loc1
+Loc2
+Loc3
+Pop
+Ind1, 0101 0202 0303
+Ind2, 0102 0201 0303
+Ind3, 0101 0202 0303
+Pop
+Ind4, 0101 0202 0303
+Ind5, 0102 0201 0303
+Ind6, 0101 0202 0303

inst/extdata/GenePop.txt

@@ -0,0 +1,12 @@
+Example GenePop Data
+Loc1
+Loc2
+Loc3
+Pop
+Ind1, 0101 0202 0303
+Ind2, 0102 0201 0303
+Ind3, 0101 0202 0303
+Pop
+Ind4, 0101 0202 0303
+Ind5, 0102 0201 0303
+Ind6, 0101 0202 0303

man/handleData.Rd

@@ -4,7 +4,7 @@
 \alias{handleData}
 \title{Handle Data}
 \usage{
-handleData(raw_data, format = "Genepop")
+handleData(raw_data, format = "baps")
 }
 \arguments{
 \item{raw_data}{Raw data in Genepop or BAPS format}

man/importFile.Rd

@@ -17,8 +17,7 @@ importFile(data, format, verbose)
 The data in a format that can be used by the other functions
 }
 \description{
-Imports data from several formats (FASTA, VCF, SAM, BAM,
+Imports data from several formats (FASTA, VCF, SAM, BAM).
-Genepop).
 }
 \examples{
 path_inst <- system.file("extdata", "", package = "rBAPS")

tests/testthat/test-greedyMix.R

@@ -66,8 +66,10 @@ test_that("greedyMix() fails successfully", {
 
 test_that("greedyMix() works when it should", {
   baps_file <- file.path(path_inst, "BAPS_clustering_diploid.txt")
+  genepop_file <- file.path(path_inst, "GenePop.txt")
   fasta_file <- file.path(path_inst, "FASTA_clustering_haploid.fasta")
   greedy_baps <- greedyMix(baps_file, "BAPS")
+  expect_error(greedy_genepop <- greedyMix(genepop_file, "GenePop")) # TEMP: fails
   expect_type(greedy_baps, "list")
   expect_length(greedy_baps, 10L)
 })