Prepare for CRAN v0.1.15 release

lance-waller-lab · Jan 23, 2024 · 35f2530 · 35f2530
1 parent f95d530
commit 35f2530
Show file tree

Hide file tree

Showing 9 changed files with 16 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gateR
 Type: Package
 Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
-Version: 0.1.14
-Date: 2024-01-22
+Version: 0.1.15
+Date: 2024-01-23
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,8 @@
 # gateR (development version)
 
+## gateR v0.1.15
+* Fixed 'Moved Permanently' content by replacing the old URL with the new URL
+
 ## gateR v0.1.14
 * Fixed bug in calculation of False Discovery Rate in internal `pval_correct()` function
 * Argument `plot_cols` correctly renamed `cols` in `lrr_plot()` function

diff --git a/R/package.R b/R/package.R
@@ -18,7 +18,7 @@
 #' 
 #' \bold{Flow Cytometry Data}
 #' 
-#' \code{\link{randCyto}} A sample dataset containing information about flow cytometry data with two binary categorical variables. The data are a random subset of the 'extdata' data in the 'flowWorkspaceData' package found on Bioconductor \url{http://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html} and formatted for 'gateR' input.
+#' \code{\link{randCyto}} A sample dataset containing information about flow cytometry data with two binary categorical variables. The data are a random subset of the 'extdata' data in the 'flowWorkspaceData' package found on Bioconductor \url{https://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html} and formatted for 'gateR' input.
 #' 
 #' @name gateR-package
 #' @aliases gateR-package gateR

diff --git a/R/randCyto.R b/R/randCyto.R
@@ -1,6 +1,6 @@
 #' Subset of the 'extdata' data in the 'flowWorkspaceData' package
 #'
-#' A sample dataset containing information about flow cytometry data with two binary conditions and four markers. The data are a random subset of the 'extdata' data in the 'flowWorkspaceData' package found on Bioconductor \url{http://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html} and formatted for 'gateR' input. The selected markers are arcsinh transformed.
+#' A sample dataset containing information about flow cytometry data with two binary conditions and four markers. The data are a random subset of the 'extdata' data in the 'flowWorkspaceData' package found on Bioconductor \url{https://bioconductor.org/packages/release/data/experiment/html/flowWorkspaceData.html} and formatted for 'gateR' input. The selected markers are arcsinh transformed.
 #'
 #' @format A data frame with 11763 rows and 7 variables:
 #' \describe{

diff --git a/README.md b/README.md
@@ -7,12 +7,12 @@ gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation <img src
 [![CRAN version](https://www.r-pkg.org/badges/version-ago/gateR)](https://cran.r-project.org/package=gateR)
 [![CRAN RStudio mirror downloads total](https://cranlogs.r-pkg.org/badges/grand-total/gateR?color=blue)](https://r-pkg.org/pkg/gateR)
 [![CRAN RStudio mirror downloads monthly ](http://cranlogs.r-pkg.org/badges/gateR)](https://www.r-pkg.org:443/pkg/gateR)
-[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0/)
 ![GitHub last commit](https://img.shields.io/github/last-commit/lance-waller-lab/gateR)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5347892.svg)](https://doi.org/10.5281/zenodo.5347892)
 <!-- badges: end -->
 
-**Date repository last updated**: January 22, 2024
+**Date repository last updated**: January 23, 2024
 
 <h2 id="overview">
 
@@ -265,7 +265,7 @@ test_gating_fdr <- gateR::gating(dat = obs_dat,
 
 ### Funding
 
-This package was developed while the author was originally a doctoral student at in the [Environmental Health Sciences doctoral program](https://www.sph.emory.edu/departments/eh/degree-programs/phd/index.html) at [Emory University](https://www.emory.edu/home/index.html) and later as a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/). Any modifications since December 05, 2022 were made while the author was an employee of Social & Scientific Systems, Inc., a division of [DLH Corporation](https://www.dlhcorp.com).
+This package was developed while the author was originally a doctoral student at in the [Environmental Health Sciences doctoral program](https://sph.emory.edu/departments/eh/degree-programs/phd/index.html) at [Emory University](https://www.emory.edu/home/index.html) and later as a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/). Any modifications since December 05, 2022 were made while the author was an employee of Social & Scientific Systems, Inc., a division of [DLH Corporation](https://www.dlhcorp.com).
 
 ### Acknowledgments
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,8 +1,7 @@
-## This is the fourteenth resubmission
+## This is the fifteenth resubmission
 
 * Updates since previous submission:
-  * Fixed bug in calculation of False Discovery Rate in internal `pval_correct()` function
-  * Argument `plot_cols` correctly renamed `cols` in `lrr_plot()` function
+  * Fixed 'Moved Permanently' content by replacing the old URL with the new URL
 
 * Documentation for DESCRIPTION references the following DOIs that throw a NOTE in win-builder, Fedora Linux, and Ubuntu Linux but are valid URLs:
   * <https://doi.org/10.1002/sim.4780090616>

diff --git a/inst/CITATION b/inst/CITATION
@@ -3,15 +3,15 @@ bibentry(bibtype = "manual",
   author         = as.person("Ian D. Buller"),
   publisher      = "The Comprehensive R Archive Network",
   year           = "2024",
-  number         = "0.1.14",
+  number         = "0.1.15",
   doi            = "10.5281/zenodo.5347892",
   url            = "https://cran.r-project.org/package=gateR",
 
   textVersion    = 
   paste("Ian D. Buller (2024).",
         "gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation.",
         "The Comprehensive R Archive Network.",
-        "v0.1.14",
+        "v0.1.15",
         "DOI:10.5281/zenodo.5347892",
         "Accessed by: https://cran.r-project.org/package=gateR"),
 

diff --git a/man/gateR-package.Rd b/man/gateR-package.Rd
diff --git a/man/randCyto.Rd b/man/randCyto.Rd