Prepare for CRAN v0.2.7 Release

* Migrated R-spatial dependency
* Replaced `raster` and `sp` in Imports with `terra` because of imminent package retirement
* `geojsonsf`, `ggmap`, `ggplot2`, `sf`, `tidyterra` are now Suggests because they are used in the vignette
* Updated vignette and documentation throughout
* Added GitHub R-CMD-check
* Updated citation style for CITATION file

.github/workflows/R-CMD-check.yaml

@@ -27,6 +27,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      DISPLAY: 99.0
 
     steps:
       - uses: actions/checkout@v3
@@ -43,6 +44,16 @@ 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:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sparrpowR
 Title: Power Analysis to Detect Spatial Relative Risk Clusters
-Version: 0.2.7.9000
-Date: 2022-12-16
+Version: 0.2.7
+Date: 2023-02-01
 Authors@R:
     c(person(given = "Ian D.",
              family = "Buller",
@@ -35,7 +35,7 @@ Description: Calculate the statistical power to detect clusters using kernel-bas
 License: Apache License (>= 2.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 3.5.0)
 Imports: 

NEWS.md

@@ -1,42 +1,43 @@
 # sparrpowR (development version)
 
-# sparrpowR v0.2.7.9000
+## sparrpowR v0.2.7
 * Migrated R-spatial dependency
 * Replaced `raster` and `sp` in Imports with `terra` because of imminent package retirement
 * `geojsonsf`, `ggmap`, `ggplot2`, `sf`, `tidyterra` are now Suggests because they are used in the vignette
 * Updated vignette and documentation throughout
 * Added GitHub R-CMD-check
+* Updated citation style for CITATION file
 
-# sparrpowR v0.2.6
+## sparrpowR v0.2.6
 * Replaced `if()` conditions comparing `class()` to string with `inherits()`
 * Added `future::plan(future::multisession)` in tests to remove the files in temp directory
 * Updated maintainer contact information
 
-# sparrpowR v0.2.5
+## sparrpowR v0.2.5
 * 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` and `spatstat.random` are now Imports
   * `spatstat.data` is now Suggests
   * [See the GitHub merge pull request](https://github.com/machiela-lab/sparrpowR/commit/4df5d85343dd222c9d4b1ae30f894ed6482bcb52).
 * Fixed annotation typos in the `pval_correct()` function
 
-# sparrpowR v0.2.4
+## sparrpowR v0.2.4
 * Addressed ERROR on R-devel CRAN environments by setting `parallelly.makeNodePSOCK.setup_strategy = sequential` for all CRAN tests as suggested by the maintainer for the `future` and `parallelly` packages who is actively working on a solution. [See the GitHub issue](https://github.com/HenrikBengtsson/parallelly/issues/65).
 
-# sparrpowR v0.2.3
+## sparrpowR v0.2.3
 * Following advice from `future` package maintainer, now `spatial_power()` and `jitter_power()` functions reset future strategy when exiting
 * Addressed ERROR in MacOS CRAN environments by setting the `parallelly.makeNodePSOCK.setup_strategy = sequential` for MacOS environments running `tcltk` until `parallelly` (>=1.26.1-9002) is on CRAN. This workaround was suggested by the `parallelly` maintainer. [See the GitHub issue](https://github.com/HenrikBengtsson/parallelly/issues/62#issuecomment-880665390).
 
-# sparrpowR v0.2.2
+## sparrpowR v0.2.2
 * Removed `LazyData: true` from 'DESCRIPTION' file because the package has no data accessed via a `data()` command and has no `data/` directory (in response to CRAN NOTE: 'LazyData' is specified without a 'data' directory)
 * Changed hyperlink for Stamen basemap in 'vignette' file with a Hypertext Transfer Protocol Secure destination
 * Added 'CITATION' file
 * Deprecation badges in 'jitter_power.Rd' and 'spatial_power.Rd' files now hyperlink to `lifecycle` r-lib.org site
 
-# sparrpowR v0.2.1
+## sparrpowR v0.2.1
 * Updated vignette with appropriate hyperlinks
 
-# sparrpowR v0.2.0
+## sparrpowR v0.2.0
 * Updates to dependencies
   * Updated `spatstat` package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). `spatstat.geom` and `spatstat.core` packages replace `spatstat` package in Depends
   * Imports `lifecycle` package to document deprecated argument `cascon` in `spatial_power()` and `jitter_power()` functions

R/package.R

@@ -28,8 +28,7 @@
 #' 
 #' @section Dependencies: The 'sparrpowR' package relies heavily upon \code{\link{sparr}}, \code{\link{spatstat.random}}, \code{\link{spatstat.geom}}, and \code{\link{terra}} for computing the statistical power and visualizing the output. Computation can be performed in parallel using \code{\link{doFuture}}, \code{\link[future]{multisession}}, \code{\link{doRNG}}, and \code{\link[foreach]{foreach}}. Basic visualizations rely on the \code{\link[spatstat.geom]{plot.ppp}} and \code{\link[fields]{image.plot}} functions.
 #' 
-#' @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.} \cr\cr
-#' Derek W. Brown\cr \emph{Integrative Tumor 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 (original)}\cr
 #' 
 #' Maintainer: I.D.B. \email{ian.buller@@alumni.emory.edu.gov}
 #'

README.md

@@ -10,10 +10,9 @@ sparrpowR: Power analysis to detect spatial relative clusters <img src="man/figu
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 ![GitHub last commit](https://img.shields.io/github/last-commit/machiela-lab/sparrpowR)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5347997.svg)](https://doi.org/10.5281/zenodo.5347997)
-
 <!-- badges: end -->
 
-**Date repository last updated**: December 16, 2022
+**Date repository last updated**: February 01, 2023
 
 <h2 id="overview">
 
@@ -45,8 +44,8 @@ Available functions
 
 <table>
 <colgroup>
-<col width="30%" />
-<col width="70%" />
+<col width="30%"/>
+<col width="70%"/>
 </colgroup>
 <thead>
 <tr class="header">
@@ -79,9 +78,9 @@ Authors
 
 </h2>
 
-* **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 (original)* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582)
 
-* **Derek W. Brown** - *Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland* - [GitHub](https://github.com/derekbrown12) - [ORCID](https://orcid.org/0000-0001-8393-1713)
+* **Derek W. Brown** - *Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (original)* - [GitHub](https://github.com/derekbrown12) - [ORCID](https://orcid.org/0000-0001-8393-1713)
 
 See also the list of [contributors](https://github.com/machiela-lab/sparrpowR/graphs/contributors) who participated in this package, including:
 
@@ -195,7 +194,7 @@ sparrpowR::spatial_plots(foo, cascon = TRUE)
 
 ### Funding
 
-This package was developed while the authors were postdoctoral fellows 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 authors were originally postdoctoral fellows 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 I.D.B. was an employee of Social & Scientific Systems, Inc., a division of [DLH Corporation](https://www.dlhcorp.com).
 
 ### Acknowledgments
 

cran-comments.md

@@ -5,6 +5,7 @@
   * Replaced `raster` and `sp` in Imports with `terra` because of imminent package retirement
   * `geojsonsf`, `ggmap`, `ggplot2`, `sf`, `tidyterra` are now Suggests because they are used in the vignette
   * Updated vignette and documentation throughout
+  * Updated citation style for CITATION file
 
 * Documentation for `pval_correct()` references a doi <https://doi.org/10.2307/2283989> that throws a NOTE but is a valid URL
 

inst/CITATION

@@ -1,24 +1,24 @@
-citHeader("To cite sparrpowR in publications use:")
-
-citEntry(entry = "Article",
-  title        = "{sparrpowR}: a flexible {R} package to estimate statistical power to identify spatial clustering of two groups and its application",
-  author       = personList(as.person("I. D. Buller"),
-                   as.person("D. W. Brown"),
-                   as.person("T. A. Myers"),
-                   as.person("R. R. Jones"),
-                   as.person("M. J. Machiela")),
-  journal      = "International Journal of Health Geographics",
-  year         = "2021",
-  volume       = "20",
-  number       = "1",
-  pages        = "1--7",
-  doi          = "10.1186/s12942-021-00267-z",
-  url          = "https://ij-healthgeographics.biomedcentral.com/articles/10.1186/s12942-021-00267-z",
-  publisher    = "BioMed Central",
+bibentry(bibtype = "Article",
+  title          = "{sparrpowR}: a flexible {R} package to estimate statistical power to identify spatial clustering of two groups and its application",
+  author         = c(as.person("I. D. Buller"),
+                     as.person("D. W. Brown"),
+                     as.person("T. A. Myers"),
+                     as.person("R. R. Jones"),
+                     as.person("M. J. Machiela")),
+  journal        = "International Journal of Health Geographics",
+  year           = "2021",
+  volume         = "20",
+  number         = "1",
+  pages          = "1--7",
+  doi            = "10.1186/s12942-021-00267-z",
+  url            = "https://ij-healthgeographics.biomedcentral.com/articles/10.1186/s12942-021-00267-z",
+  publisher      = "BioMed Central",
 
-  textVersion  =
+  textVersion    =
   paste("I. D. Buller, D. W. Brown (co-first), T. A. Myers, R. R. Jones, M. J. Machiela (2021).",
         "sparrpowR: a flexible R package to estimate statistical power to identify spatial clustering of two groups and its application.",
         "International Journal of Health Geographics 20(1), 1-7.",
-        "DOI 10.1186/s12942-021-00267-z.")
+        "DOI 10.1186/s12942-021-00267-z."),
+
+  header         = "To cite sparrpowR in publications use:"
 )