From 35f2530c0b5b368b7715a59d08b61deb8898b6cb Mon Sep 17 00:00:00 2001 From: Ian D Buller Date: Tue, 23 Jan 2024 09:13:10 -0500 Subject: [PATCH] Prepare for CRAN v0.1.15 release --- DESCRIPTION | 4 ++-- NEWS.md | 3 +++ R/package.R | 2 +- R/randCyto.R | 2 +- README.md | 6 +++--- cran-comments.md | 5 ++--- inst/CITATION | 4 ++-- man/gateR-package.Rd | 2 +- man/randCyto.Rd | 2 +- 9 files changed, 16 insertions(+), 14 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8d0981d..d4f0168 100644 --- 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 index 411cd42..d9818d0 100644 --- 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 index c2c94b8..8812452 100644 --- 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 index 0355c86..0d6fa2a 100644 --- 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 index 0bc6858..334a138 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,12 @@ gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation -**Date repository last updated**: January 22, 2024 +**Date repository last updated**: January 23, 2024

@@ -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 index 7bf576a..cf48f3d 100644 --- 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: * diff --git a/inst/CITATION b/inst/CITATION index 9113b3a..65df8ed 100755 --- a/inst/CITATION +++ b/inst/CITATION @@ -3,7 +3,7 @@ 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", @@ -11,7 +11,7 @@ bibentry(bibtype = "manual", 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 index c212b6a..39686ce 100644 --- a/man/gateR-package.Rd +++ b/man/gateR-package.Rd @@ -25,7 +25,7 @@ Key content of the 'gateR' package include:\cr \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. } \section{Dependencies}{ The 'gateR' package relies heavily upon \code{\link{sparr}}, \code{\link{spatstat.geom}}, and \code{\link{terra}}. For a two-level comparison, the spatial relative risk function uses the \code{\link[sparr]{risk}} function. The calculation of a Bonferroni correction for multiple testing accounting for the spatial correlation of the estimated surface uses the \code{\link[SpatialPack]{modified.ttest}} function. Basic visualizations rely on the \code{\link[fields]{image.plot}} function. diff --git a/man/randCyto.Rd b/man/randCyto.Rd index c99690d..2d78903 100644 --- a/man/randCyto.Rd +++ b/man/randCyto.Rd @@ -23,7 +23,7 @@ A data frame with 11763 rows and 7 variables: randCyto } \description{ -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. } \examples{ head(randCyto)