# assigner 0.5.6 2019-05-01

* included 2 simulated datasets * updated documentation of `assignment_ngs` * vignette to get started with assigner, finally! * this is really starting to smell like a CRAN release * work on travis CI * work on pkgdown
thierrygosselin · May 1, 2019 · 5936459 · 5936459
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@
 ^docs$
 ^pkgdown$
 ^_pkgdown\.yml$
+^\.github
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: assigner
 Type: Package
 Title: Assignment Analysis with RADseq Data
-Version: 0.5.5
-Date: 2019-04-25
+Version: 0.5.6
+Date: 2019-05-01
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "[email protected]", role = c("aut", "cre")),
@@ -40,6 +40,7 @@ Remotes:
     github::thierrygosselin/radiator
 License: GPL (>=2)
 LazyLoad: yes
+LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1
 URL: http://thierrygosselin.github.io/assigner/, https://github.com/thierrygosselin/assigner

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# assigner 0.5.6 2019-05-01
+
+* included 2 simulated datasets
+* updated documentation of `assignment_ngs`
+* vignette to get started with assigner, finally!
+* this is really starting to smell like a CRAN release
+* work on travis CI
+* work on pkgdown
+
+
 # assigner 0.5.5 2019-04-25
 
 * cosmetic changes to the package: using `pkgdown`

diff --git a/R/assignment_ngs.R b/R/assignment_ngs.R
@@ -256,6 +256,8 @@
 # Return ------------------------ ----------------------------------------------
 #' @return Depending on arguments selected, several folders and files are written:
 #' \enumerate{
+#' \item \code{01_radiator_tidy_genomic} this is the result of importing the data
+#' with radiator import module \href{https://thierrygosselin.github.io/radiator/reference/tidy_genomic_data.html}{tidy_genomic_data}.
 #' \item \code{[email protected]}: For reproducibility,
 #' the function call, arguments and values used along the default arguments.
 #' \item \code{assignment.plot.pdf}: The assignment figure.
@@ -306,7 +308,7 @@
 #' is used, for the iteration.
 #' }
 #' The output in your global environment is a list. To view the assignment results
-#' \code{$assignment} to view the ggplot2 figure \code{$plot.assignment}. 
+#' \code{$assignment} to view the ggplot2 figure \code{$assignment.plot}. 
 #' See example below.
 
 
@@ -327,7 +329,7 @@
 #' assignment <- assignment.treefrog$assignment
 #' 
 #' # To plot the assignment using ggplot2 and facet 
-#' fig <- assignment.treefrog$plot.assignment
+#' fig <- assignment.treefrog$assignment.plot
 #' 
 #' # To view the full range of y values = Assignment success(%): 
 #' fig + ggplot2::scale_y_continuous(limits = c(0,100)) 
@@ -604,7 +606,7 @@ assignment_ngs <- function(
   res.list$assignment <- res
 
   # Assignment plot ------------------------------------------------------------
-  res.list$plot.assignment <- plot_assignment(x = res, path.folder = directory)
+  res.list$assignment.plot <- plot_assignment(x = res, path.folder = directory)
 
   # Return results --------------------------------------------------------------------
   return(res.list)
@@ -657,10 +659,7 @@ generate_subsamples <- function(
   )
 
   # keep track of subsampling individuals and write to directory
-  if (is.null(subsample)) {
-    message("Subsampling: not selected")
-  } else {
-    message("Subsampling: selected")
+  if (!is.null(subsample)) {
     readr::write_tsv(
       x = dplyr::bind_rows(subsample.list), 
       path = file.path(path.folder, "subsampling_individuals.tsv"), 

diff --git a/R/data.R b/R/data.R
@@ -0,0 +1,62 @@
+#' Simulated dataset to test assigner
+#'
+#' A dataset of genotypes containing 500 bi-allelic SNPs, simulated 
+#' for 250 individuals, 5 populations.
+#'
+#' @format A tibble with 125000 rows (genotypes) and 4 variables:
+#' \describe{
+#'   \item{MARKERS}{SNPs markers}
+#'   \item{POP_ID}{Populations/strata for the samples}
+#'   \item{INDIVIDUALS}{Samples id)}
+#'   \item{GT}{Genotypes coded \emph{a la genepop} format}
+#' }
+#' @details 
+#' Dataset simulation caracteristics:
+#' \itemize{
+#' \item num.pops: 5
+#' \item num.loci: 1000
+#' \item div.time: 25e3
+#' \item ne: 200
+#' \item nm: 0.5
+#' \item theta: 0.2
+#' \item mig.type: island
+#' \item mut.rate: 2.5e-4
+#' \item mig.rate: 0.0025
+#' }
+#' From this simulated dataset, 500 SNPs and 250 individuals (50 ind/pop) were
+#' randomly selected.
+#' @source The data was simulated with grur
+#' \url{https://thierrygosselin.github.io/grur/reference/simulate_rad.html}
+
+"data_assigner_sim_01"
+
+#' Simulated dataset to test assigner
+#'
+#' A dataset of genotypes containing 500 bi-allelic SNPs, simulated 
+#' for 250 individuals, 5 populations.
+#'
+#' @format A tibble with 125000 rows (genotypes) and 4 variables:
+#' \describe{
+#'   \item{MARKERS}{SNPs markers}
+#'   \item{POP_ID}{Populations/strata for the samples}
+#'   \item{INDIVIDUALS}{Samples id}
+#'   \item{GT}{Genotypes coded \emph{a la genepop} format}
+#' }
+#' @details 
+#' Dataset simulation caracteristics:
+#' \itemize{
+#' \item num.pops: 5
+#' \item num.loci: 1000
+#' \item div.time: 25e3
+#' \item ne: 200
+#' \item nm: 0.5
+#' \item theta: 0.2
+#' \item mig.type: island
+#' \item mut.rate: 2.5e-4
+#' \item mig.rate: 0.0025
+#' }
+#' From this simulated dataset, 500 SNPs and 250 individuals (50 ind/pop) were
+#' randomly selected.
+#' @source The data was simulated with grur
+#' \url{https://thierrygosselin.github.io/grur/reference/simulate_rad.html}
+"data_assigner_sim_02"
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ Status](https://travis-ci.org/thierrygosselin/assigner.svg?branch=master)](https
 state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![DOI](https://zenodo.org/badge/14548/thierrygosselin/assigner.svg)](https://zenodo.org/badge/latestdoi/14548/thierrygosselin/assigner)
-[![packageversion](https://img.shields.io/badge/Package%20version-0.5.5-orange.svg)](commits/master)
+[![packageversion](https://img.shields.io/badge/Package%20version-0.5.6-orange.svg)](commits/master)
 [![Last-changedate](https://img.shields.io/badge/last%20change-2019--05--01-brightgreen.svg)](/commits/master)
 <!-- badges: end -->
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -23,13 +23,17 @@ navbar:
     href: index.html
   - text: Features
     href: FEATURES.html
+  - text: Get started
+    href: articles/get_started.html
   - text: Reference
     href: reference/index.html
   - text: Articles
     href: articles/index.html
     menu:
     - text: Life cycle
       href: articles/life_cycle.html
+    - text: Get started
+      href: articles/get_started.html
     - text: Fst analysis
       href: articles/fst_confidence_intervals.html
     - text: Using whitelists in assignment

diff --git a/data/.DS_Store b/data/.DS_Store
diff --git a/data/data_assigner_sim_01.rda b/data/data_assigner_sim_01.rda
diff --git a/data/data_assigner_sim_02.rda b/data/data_assigner_sim_02.rda
diff --git a/docs/FEATURES.html b/docs/FEATURES.html
diff --git a/docs/articles/assignment.whitelists.html b/docs/articles/assignment.whitelists.html
diff --git a/docs/articles/assignment_loo_test4.png b/docs/articles/assignment_loo_test4.png
diff --git a/docs/articles/assignment_thl_test1.png b/docs/articles/assignment_thl_test1.png
diff --git a/docs/articles/assignment_thl_test1_full_range.png b/docs/articles/assignment_thl_test1_full_range.png
diff --git a/docs/articles/assignment_thl_test2.png b/docs/articles/assignment_thl_test2.png
diff --git a/docs/articles/assignment_thl_test3.png b/docs/articles/assignment_thl_test3.png
diff --git a/docs/articles/fst_confidence_intervals.html b/docs/articles/fst_confidence_intervals.html