r cmd check fix + cleaning

.Rbuildignore

@@ -13,3 +13,5 @@ book
 ^cran-comments\.md$
 ^\.github$
 Dockerfile
+y_hap_pred
+tests/shiny*

NAMESPACE

@@ -24,6 +24,7 @@ export(get_ld_gp)
 export(pca_mds_Server)
 export(pca_mds_UI)
 export(plotPCA)
+export(plot_hap_dist)
 export(plot_hap_div)
 export(plot_ld)
 export(popgen_UI)
@@ -91,6 +92,7 @@ importFrom(stats,cov)
 importFrom(stats,frequency)
 importFrom(stats,hclust)
 importFrom(stats,ks.test)
+importFrom(stats,median)
 importFrom(stats,p.adjust)
 importFrom(stats,qqplot)
 importFrom(stats,qunif)

R/helpers.R

@@ -426,7 +426,7 @@ get_hw_gp <- function(fname, n_iter) {
 #' @keywords internal
 plot_hap_div <- function(df) {
   hap_1 <- hap_2 <- value <- NULL
-  midpoint <- median(df$value)
+  midpoint <- stats::median(df$value)
   plt <- ggplot2::ggplot(data = df, aes(hap_1, hap_2, fill = value)) +
     ggplot2::geom_tile(color = "white") +
     ggplot2::scale_fill_gradient2(low = "#ffffff", mid = "#fdae6b", high = "#e6550d", 

R/helpers_haplo_stats.R

@@ -41,15 +41,15 @@ getHaploStatsFromGenind <- function(data) {
       flag = "0"
     )
   )
-  hap_data <- tibble::tibble(
+  hap_data <- data.frame(
     haplotype_id = hap_labels,
     h_count = h_count,
     h_freq = h_freq,
     h_value = gsub("_", "|", names(h_count))
   )
 
   ## population level table
-  hap_pop_data <- tibble::tibble(
+  hap_pop_data <- data.frame(
     h_div = h_div
   )
 

R/straf.R

@@ -31,7 +31,7 @@
 #' @importFrom reshape2 acast
 #' @importFrom shinycssloaders withSpinner
 #' @importFrom shinyWidgets awesomeCheckbox pickerInput
-#' @importFrom stats as.dist cmdscale cov frequency hclust ks.test qqplot qunif p.adjust
+#' @importFrom stats as.dist cmdscale cov frequency hclust ks.test median qqplot qunif p.adjust
 #' @importFrom tidyr gather
 #' @importFrom utils read.table write.table count.fields
 NULL

scripts/generate_expectations.R

@@ -1,21 +1,21 @@
 library(straf)
 
-input_diploid <- list(datapath="./tests/input_files/exampleSTRAFdiplo.txt")
+input_diploid <- list(datapath="./tests/testthat/exampleSTRAFdiplo.txt")
 dat_diploid <- straf::createGenind(input_diploid, ploidy = 2)
 freq_diploid <- straf::getFreqAllPop(dat_diploid)
 indices_diploid <- straf::getIndicesAllPop(dat_diploid)
 
 
-input_haploid <- list(datapath="./tests/input_files/exampleSTRAFhaplo.txt")
+input_haploid <- list(datapath="./tests/testthat/exampleSTRAFhaplo.txt")
 dat_haploid <- straf::createGenind(input_haploid, ploidy = 1)
-freq_haploid <- straf::getFreqAllPop(dat_diploid)
-indices_haploid <- straf::getIndicesAllPop(dat_diploid)
+freq_haploid <- straf::getFreqAllPop(dat_haploid)
+indices_haploid <- straf::getIndicesAllPop(dat_haploid)
 
 
-input_haploid_point <- list(datapath="./tests/input_files/exampleSTRAFhaplo_point.txt")
+input_haploid_point <- list(datapath="./tests/testthat/exampleSTRAFhaplo_point.txt")
 dat_haploid_point <- straf::createGenind(input_haploid_point, ploidy = 1)
-freq_haploid_point <- straf::getFreqAllPop(dat_diploid)
-indices_haploid_point <- straf::getIndicesAllPop(dat_diploid)
+freq_haploid_point <- straf::getFreqAllPop(dat_haploid_point)
+indices_haploid_point <- straf::getIndicesAllPop(dat_haploid_point)
 
 expectations <- list(
   dat_diploid=dat_diploid,
@@ -29,4 +29,4 @@ expectations <- list(
   indices_haploid_point=indices_haploid_point
 )
 
-saveRDS(expectations, file = "./tests/expectations.rds")
+saveRDS(expectations, file = "./tests/testthat/expectations.rds")