bug fix in the compilation results section when not using pop.id.star…

…t and pop.id.end (bug introduced in version 0.2.2)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: assigner
 Type: Package
 Title: Assignment Analysis with GBS/RADseq Data using R
-Version: 0.2.2
-Date: 2016-04-15
+Version: 0.2.3
+Date: 2016-04-23
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "[email protected]", role = c("aut", "cre")))

NAMESPACE

@@ -5,6 +5,7 @@ export(assignment_mixture)
 export(assignment_ngs)
 export(dlr)
 export(gsi_sim_binary)
+export(import_subsamples)
 export(install_gsi_sim)
 export(plot_assignment)
 export(plot_assignment_dlr)

R/assignment_ngs.R

@@ -2211,7 +2211,7 @@ package and update your whitelist")
                 METHOD = rep(sampling.method, n()),
                 MISSING_DATA = rep(missing.data, n())
               ) %>%
-              select(INDIVIDUALS, ANALYSIS, CURRENT, INFERRED, SCORE, SECOND_BEST_POP, SECOND_BEST_SCORE, MARKER_NUMBER, METHOD, MISSING_DATA) %>%
+              select(INDIVIDUALS, CURRENT, INFERRED, SCORE, SECOND_BEST_POP, SECOND_BEST_SCORE, MARKER_NUMBER, METHOD, MISSING_DATA) %>%
               arrange(CURRENT)
           )
         }

R/import_subsamples.R

@@ -0,0 +1,46 @@
+# Write a dataframe containing all the subsample individual assignment
+
+#' @name import_subsamples
+#' @title Import individual's assignment results of different subsample folder.
+#' @description This function will import all the individual's assignment results 
+#' of different subsample folder into R.
+#' @param dir.path The path to the directory containing the subsample folders.
+#' @param imputations (logical) Was the data imputed or not. 
+#' Default: \code{imputations = FALSE}
+#' @return A data frame of all the individual's assignment, with iterations and subsample.
+
+#' @export
+#' @rdname import_subsamples
+#' @import dplyr
+#' @import stringi
+
+
+#' @examples
+#' \dontrun{
+#' subsamples.data <- import_subsamples(
+#' dir.path = "assignment_analysis_method_random_imputations_rf_populations",
+#' imputations = TRUE
+#' )
+#' }
+
+#' @author Thierry Gosselin \email{thierrygosselin@@icloud.com}
+
+import_subsamples <- function(dir.path, imputations){
+  if (missing (dir.path)) stop("dir.path argument missing")
+  if (missing (imputations)) imputations <- FALSE
+
+  subsample.folders <- list.files(path = dir.path, pattern = "subsample_", full.names = FALSE)
+  data <- list()
+  for (i in subsample.folders) {
+    sub.name <- stri_replace_all_fixed(str = i, pattern = "_", replacement = ".", vectorize_all = FALSE)
+    if (imputations == TRUE){
+      filename <- stri_paste(i, "/","assignment.random.imputed.results.individuals.iterations.", sub.name, ".tsv")
+    } else {
+      filename <- stri_paste(i, "/","assignment.random.no.imputation.results.individuals.iterations.", sub.name, ".tsv")
+    }
+    subsample.data <- read_tsv(file = filename, col_names = TRUE) #%>% filter (MISSING_DATA == 'no.imputation')
+    data[[i]] <- subsample.data
+  }
+  data <- as_data_frame(bind_rows(data))
+  return(data)
+}

README.md

@@ -140,6 +140,9 @@ The Amazon image can be imported into Google Cloud Compute Engine to start a new
 
 ## New
 
+**v.0.2.3**
+* bug fixed in the compilation results section when no pop.id.start and end are used.
+
 **v.0.2.1**
 * updated the function `assignment_mixture` with `sampling.method = "ranked"` and 
 `assignment.analysis = "adegenet"`.

inst/CITATION

@@ -7,5 +7,5 @@ year = "2016",
 author = personList(as.person("Thierry Gosselin")),
 url = "https://github.com/thierrygosselin/stackr",
 doi = "http://dx.doi.org/10.5281/zenodo.46723",
-textVersion = paste("Gosselin T (2016). assigner: Assignment Analysis with GBS/RAD Data using R. R package version 0.1.9. https://github.com/thierrygosselin/assigner. doi : 10.5281/zenodo.46723")
+textVersion = paste("Gosselin T (2016). assigner: Assignment Analysis with GBS/RAD Data using R. R package version 0.2.3. https://github.com/thierrygosselin/assigner. doi : 10.5281/zenodo.47452")
 )