diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..1b8ff8a 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -43,6 +43,16 @@ jobs: with: extra-packages: any::rcmdcheck needs: check + + - name: Install XQuartz on macOS + if: runner.os == 'macOS' + run: brew install xquartz --cask + + - name: Install system dependencies + if: runner.os == 'Linux' + run: | + sudo apt-get update -y + sudo apt-get install -y tk-dev tcl-dev - uses: r-lib/actions/check-r-package@v2 with: diff --git a/DESCRIPTION b/DESCRIPTION index 4c5f361..d48dd84 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: gateR Type: Package Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation -Version: 0.1.13.9000 -Date: 2022-12-16 +Version: 0.1.13 +Date: 2023-02-01 Authors@R: c(person(given = "Ian D.", family = "Buller", @@ -41,7 +41,7 @@ License: Apache License (>= 2.0) Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.2 +RoxygenNote: 7.2.3 Depends: R (>= 3.5.0) Imports: diff --git a/NEWS.md b/NEWS.md index 3750f76..b82cb85 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,15 +1,16 @@ # gateR (development version) -# gateR v0.1.13.9000 +## gateR v0.1.13 * Migrated R-spatial dependency * Replaced `raster` in Imports with `terra` because of imminent package retirement * Updated documentation throughout * Added GitHub R-CMD-check + * Updated citation style for CITATION file -# gateR v0.1.12 +## gateR v0.1.12 * Updated maintainer contact information -# gateR v0.1.11 +## gateR v0.1.11 * Updated package URL and BugReports to renamed GitHub account "lance-waller-lab" (previously "Waller-SUSAN") * Replaced `if()` conditions comparing `class()` to string with `inherits()` in functions * `tools` is no longer Imports @@ -18,24 +19,24 @@ * Added CITATION file * Fixed typos in documentation throughout -# gateR v0.1.10 +## gateR v0.1.10 * Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random` * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends * `spatstat.geom` is now Imports * `dplyr`, `ncdfFlow`, `flowWorkspaceData`, and `usethis` now Suggests (for generating random data set `randCyto`) * Fixed annotation typos in the vignette. Removed packages no longer used in the vignette -# gateR v0.1.9 -* Now `rlang` is in Depends. -* Output for `gating()` now includes a diagnostic message saved as a character string for reference in a slot called `note` -* A diagnostic message can be viewed running `rlang::last_error()$out$note` after the unsuccessful run of `gating()` -* Removed redundant `@importFrom fields image.plot` in 'package.R' +## gateR v0.1.9 + * Now `rlang` is in Depends. + * Output for `gating()` now includes a diagnostic message saved as a character string for reference in a slot called `note` + * A diagnostic message can be viewed running `rlang::last_error()$out$note` after the unsuccessful run of `gating()` + * Removed redundant `@importFrom fields image.plot` in 'package.R' -# gateR v0.1.8 +## gateR v0.1.8 * Updated `spatstat` package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). Now `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>= 2.0-0)` are in Depends * Fixed check for `vars` in `dat` within the `gating()` function -# gateR v0.1.7 +## gateR v0.1.7 * Updated `spatstat` package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). `spatstat.geom` package replaces `spatstat` package in Imports * Added additional multiple testing corrections, including False Discovery Rate, spatially dependent Sidak correction, independent Sidak correction, and two corrections based on Random Field Theory (Adler and Hasofer or Friston) * The latter two corrections required a new argument `bandw` to be added to `gating()`, `lotrrs()`, and `rrs()` functions to allow users to specify bandwidth for the kernel density estimation @@ -45,11 +46,11 @@ * Removed `maptools` and `sp` packages from Imports * Updated links in 'gateR-package.Rd' for package updates -# gateR v0.1.6 +## gateR v0.1.6 * Updated URLs in 'gateR-package.Rd' * Updated year in DESCRIPTION -# gateR v0.1.5 +## gateR v0.1.5 * Added arguments `save_gate`, `name_gate`, and `path_gate` in `lotrrs()`, `rrs()`, and `gating()` to save plots as PNG files as output * Renamed `doplot` argument as `plot_gate` for consistency with new plotting arguments * Added a stop (and return no results) if no significant clusters detected during first gate @@ -59,12 +60,12 @@ * Removed fullstop in error messages * Added a `make.names()` check for `vars` and `colnames(dat)` in `gating()` -# gateR v0.1.4 +## gateR v0.1.4 * Added documentation to `lotrrs()`, `rrs()`, and `gating()` about the levels of condition(s) * Fixed bug in `lotrrs()` that was mislabeling numerator and denominator levels of second condition * Added parameters `c1n` and `c2n` in `lotrrs()`, `rrs()`, and `gating()` to specify the numerator level -# gateR v0.1.3 +## gateR v0.1.3 * Removed `ncdFlow`, `flowWorkspaceData`, and `knitr` packages from Suggests * Created a random data set `randCyto` and all documentation * Updated examples and testthat to use `randCyto` data diff --git a/R/package.R b/R/package.R index 5ea6724..c2c94b8 100644 --- a/R/package.R +++ b/R/package.R @@ -26,7 +26,7 @@ #' #' @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. #' -#' @author Ian D. Buller\cr \emph{Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA.} +#' @author Ian D. Buller\cr \emph{Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland, USA (current); Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA (former); Environmental Health Sciences, James T. Laney School of Graduate Studies, Emory University, Atlanta, Georgia, USA. (original)}\cr #' #' Maintainer: I.D.B. \email{ian.buller@@alumni.emory.edu} #' diff --git a/README.md b/README.md index 9f2bff2..8a00fc9 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation -**Date repository last updated**: December 16, 2022 +**Date repository last updated**: February 01, 2023

@@ -60,8 +60,8 @@ Available functions --++ @@ -101,8 +101,8 @@ Available sample data sets
--++ @@ -123,7 +123,7 @@ Authors -* **Ian D. Buller** - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582) +* **Ian D. Buller** - *Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland (current)* - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (former)* - *Environmental Health Sciences, James T. Laney School of Graduate Studies, Emory University, Atlanta, Georgia. (original)* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582) See also the list of [contributors](https://github.com/lance-waller-lab/gateR/graphs/contributors) who participated in this project. Main contributors include: @@ -254,7 +254,7 @@ test_lotrrs <- gateR::lotrrs(dat = obs_dat[ , -5:-4]) ### Funding -This package was developed while the author was 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 a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/). +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). ### Acknowledgments diff --git a/cran-comments.md b/cran-comments.md index b123264..509dadd 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -4,6 +4,7 @@ * Migrated R-spatial dependency * Replaced `raster` in Imports with `terra` because of imminent package retirement * Updated documentation throughout + * Updated citation style for CITATION file * 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 e903514..ad15928 100755 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,19 +1,19 @@ -citHeader("To cite gateR in publications, please use the following and include the version number and DOI:") - -citEntry(entry = "manual", - title = "gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation", - author = personList(as.person("Ian D. Buller")), - publisher = "The Comprehensive R Archive Network", - year = "2022", - number = "0.1.13.9000", - doi = "10.5281/zenodo.5347892", - url = "https://cran.r-project.org/package=gateR", +bibentry(bibtype = "manual", + title = "gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation", + author = as.person("Ian D. Buller"), + publisher = "The Comprehensive R Archive Network", + year = "2023", + number = "0.1.13", + doi = "10.5281/zenodo.5347892", + url = "https://cran.r-project.org/package=gateR", - textVersion = - paste("Ian D. Buller (2022).", + textVersion = + paste("Ian D. Buller (2023).", "gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation.", "The Comprehensive R Archive Network.", - "v0.1.13.9000.", + "v0.1.13", "DOI:10.5281/zenodo.5347892", - "Accessed by: https://cran.r-project.org/package=gateR") + "Accessed by: https://cran.r-project.org/package=gateR"), + + header = "To cite gateR in publications, please use the following and include the version number and DOI:" ) diff --git a/man/gateR-package.Rd b/man/gateR-package.Rd index 183513b..c212b6a 100644 --- a/man/gateR-package.Rd +++ b/man/gateR-package.Rd @@ -32,7 +32,7 @@ Key content of the 'gateR' package include:\cr } \author{ -Ian D. Buller\cr \emph{Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA.} +Ian D. Buller\cr \emph{Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland, USA (current); Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA (former); Environmental Health Sciences, James T. Laney School of Graduate Studies, Emory University, Atlanta, Georgia, USA. (original)}\cr Maintainer: I.D.B. \email{ian.buller@alumni.emory.edu} } diff --git a/vignettes/vignette.html b/vignettes/vignette.html index 58529c5..1c654e6 100644 --- a/vignettes/vignette.html +++ b/vignettes/vignette.html @@ -12,7 +12,7 @@ - + gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation @@ -31,23 +31,23 @@ +code{white-space: pre-wrap;} +span.smallcaps{font-variant: small-caps;} +span.underline{text-decoration: underline;} +div.column{display: inline-block; vertical-align: top; width: 50%;} +div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} +ul.task-list{list-style: none;} +