Merge pull request #44 from LotharukpongJS/master

Updates to package description and news.

DESCRIPTION

@@ -1,11 +1,12 @@
 Package: orthologr
 Type: Package
 Title: Comparative Genomics with R
-Version: 0.4.0
-Date: 2020-02-06
+Version: 0.4.1
+Date: 2023-09-08
 Authors@R: c(
             person("Hajk-Georg", "Drost", , "hajk-georg.drost@tuebingen.mpg.de", c("aut", "cre")),
-            person("Sarah", "Scharfenberg", , "Sarah.Scharfenberg@ipb-halle.de", role = "ctb")
+            person("Sarah", "Scharfenberg", , "Sarah.Scharfenberg@ipb-halle.de", role = "ctb"),
+            person("Jaruwatana Sodai", "Lotharukpong", , "jaruwatana.lotharukpong@tuebingen.mpg.de", role = "ctb", comment = c(ORCID = "0000-0002-3475-0980"))
             )
 Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
 Description: Genome-wide orthology inference and dN/dS estimation between multiple genomes. 
@@ -48,8 +49,8 @@ Suggests:
 Remotes: HajkD/metablastr
 RdMacros: Rdpack
 LinkingTo: Rcpp
-URL: https://github.com/HajkD/orthologr
-BugReports: https://github.com/HajkD/orthologr/issues
+URL: https://github.com/drostlab/orthologr
+BugReports: https://github.com/drostlab/orthologr/issues
 RoxygenNote: 7.2.3
 Config/testthat/edition: 3
 Encoding: UTF-8

NEWS.md

@@ -1,3 +1,9 @@
+## `orthologr` version 0.4.1
+
+### New Features
+
+- the `divergence_stratigraphy()` and `divergence_map()` functions now include the parameter `n_quantile`, which enables users to choose the number of quantiles to generate for the `divergence map`. This could allow users to get a higher-resolution `divergence map` if `n_quantile` is greater than 10. Alternatively, this can resolve the issue of empty divergence strata when deciling the dNdS values for closely related organisms with dNdS = 0 for over 10% of the genes.
+
 ## `orthologr` version 0.4.0
 
 ### New Functions

R/check_annotation.R

@@ -1,8 +1,8 @@
 #' @title Check whether an annotation file contains outlier lines
-#' @description Some annotation files include lines with character lengths greater than 65000. This causes problems when trying to import such annotation files into R using \code{\link[rtracklayer]{import}}.
+#' @description Some annotation files include lines with character lengths greater than 65000. This causes problems when trying to import such annotation files into R using \code{\href{https://rdrr.io/bioc/rtracklayer/man/export.html}{import}}.
 #' To overcome this issue, this function screens for such lines
 #' in a given annotation file and removes these lines so that
-#' \code{\link[rtracklayer]{import}} can handle the file.
+#' \code{\href{https://rdrr.io/bioc/rtracklayer/man/export.html}{import}} can handle the file.
 #' @param annotation_file a file path tp the annotation file.
 #' @param remove_annotation_outliers shall outlier lines be removed from the input \code{annotation_file}? 
 #' If yes, then the initial \code{annotation_file} will be overwritten and the removed outlier lines will be stored at \code{\link{tempdir}}