# radiator 1.3.5 2024-11-06

* Fix the one column matrices in dplyr::filter warning.
* Fix the error when dplyr::select couldn't find the column STRATA.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: radiator
 Type: Package
 Title: RADseq Data Exploration, Manipulation and Visualization using R
-Version: 1.3.4
-Date: 2024-06-05
+Version: 1.3.5
+Date: 2024-11-06
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "thierrygosselin@icloud.com", role = c("aut", "cre")),
@@ -57,7 +57,7 @@ License: GPL-3
 LazyLoad: yes
 VignetteBuilder:
     knitr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 ByteCompile: TRUE
 URL: https://thierrygosselin.github.io/radiator/
 BugReports: https://github.com/thierrygosselin/radiator/issues

NEWS.md

@@ -1,3 +1,10 @@
+# radiator 1.3.5 2024-11-06
+
+* Fix the one column matrices in dplyr::filter warning.
+* Fix the error when dplyr::select couldn't find the column STRATA.
+
+
+
 # radiator 1.3.4 2024-06-05
 
 * Open the `parallel.core` argument for some internal functions to help windows users with parallel processing problems in R. #188

R/filter_genotyping.R

@@ -190,7 +190,6 @@ filter_genotyping <- function(
   if (interactive.filter) message("\nStep 1. Missing visualization and helper table\n")
 
   # Generate coverage stats---------------------------------------------------
-  if (verbose) message("Generating statistics")
   info <- generate_stats(
     gds = data,
     individuals = FALSE,
@@ -205,7 +204,8 @@ filter_genotyping <- function(
     plot = FALSE,
     path.folder = path.folder,
     file.date = file.date,
-    parallel.core = parallel.core
+    parallel.core = parallel.core,
+    verbose = verbose
   )
 
   stats <- info$m.stats

R/filter_ma.R

@@ -438,7 +438,7 @@ filter_ma <- function(
       choices = c("MAC_GLOBAL_CORR", "MAF_GLOBAL_COUNT_CORR", "MAF_GLOBAL_DEPTH_CORR", "MAD_GLOBAL_CORR"),
       several.ok = FALSE
     )
-  if (rlang::has_name(x, stats)) nrow(dplyr::filter(.data = x, x[stats] >= threshold))
+  if (rlang::has_name(x, stats)) nrow(dplyr::filter(.data = x, x[[stats]] >= threshold))
   }#End how_many_markers
 
   end.seq <- ceiling(0.2 * n.diplo.samples)
@@ -453,7 +453,8 @@ filter_ma <- function(
     ) %>%
     readr::write_tsv(
       x = .,
-      file = file.path(path.folder, "mac.helper.table.tsv"))
+      file = file.path(path.folder, "mac.helper.table.tsv")
+      )
 
   # if (verbose) message("File written: mac.helper.table.tsv")
 

R/filter_rad.R

@@ -786,7 +786,7 @@ filter_rad <- function(
       filter.long.ld = filter.long.ld.bk,
       parallel.core = parallel.core,
       filename = NULL,
-      iiiiverbose = verbose,
+      verbose = verbose,
       long.ld.missing = long.ld.missing.bk,
       ld.method = ld.method.bk,
       parameters = filters.parameters,
@@ -895,7 +895,7 @@ filter_rad <- function(
             path = path.folder,
             filename = "strata.filtered.tsv",
             tsv = TRUE,
-            write.message = "Writing the filtered strata: strata.filtered.tsv",
+            write.message = "Writing the filtered strata: ",
             verbose = verbose)
 
 

R/radiator_tidy.R

@@ -426,7 +426,8 @@ tidy_genomic_data <- function(
   # Strata----------------------------------------------------------------------
   strata.df <- read_strata(
     strata = strata,
-    pop.id = TRUE,
+    pop.id = FALSE,
+    # pop.id = TRUE,
     blacklist.id = blacklist.id,
     verbose = verbose) %$% strata
 

README.md

@@ -5,8 +5,8 @@
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![packageversion](https://img.shields.io/badge/Package%20version-1.3.4-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--06--05-brightgreen.svg)](/commits/master)
+[![packageversion](https://img.shields.io/badge/Package%20version-1.3.5-orange.svg)](commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--11--06-brightgreen.svg)](/commits/master)
 [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060)
 <!-- badges: end -->