Small updates and convenience stuff (#8)

* Documentation and pkgdown addition

* Adding datapaths as entry

* 🚀 negated in function

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -13,7 +13,7 @@ Authors@R:
       )
 Description: What the package does (one paragraph).
 License: MIT + file LICENSE
-URL: https://github.com/iiasa/BNRTools
+URL: https://github.com/iiasa/BNRTools, https://iiasa.github.io/BNRTools/
 BugReports: https://github.com/iiasa/BNRTools/issues
 Depends: R (>= 3.6)
 Imports:
@@ -27,3 +27,4 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Config/testthat/edition: 3
+LazyData: true

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%notin%")
 export(misc_sanitizeNames)
+export(sp_replaceGriddedNA)
 export(sp_resampleRas)
-export(sp_replaceGriddedNA)

R/data.R

@@ -0,0 +1,24 @@
+#' Table with default paths to commonly used spatial input files
+#'
+#' @description
+#' This dataset contains path names to commonly-used spatial data files. Given that
+#' those files are usually quite large, we here only describe where to find them internally
+#' and not upload the data itself.
+#' Medium-long-term this could be improved by relying on github LFS systems or our own gitlab
+#' instance.
+#'
+#' @details
+#' The file has the following columns:
+#'
+#' [*] 'drive': The path to drive where the data is stored (Default: \code{'P:/bnr/'}). Can be system dependent (Windows/Linux).
+#' [*] 'access': A non-structured field containing the list of people that have access (for example \code{'IBF'} or \code{'bnr'}).
+#' [*] 'group': A field entry describing to what this file belongs to (i.e. \code{"EPIC"}).
+#' [*] 'filename': The actual filename
+#'
+#' @note
+#' To update or overwrite, load the file and update, then apply
+#' \code{usethis::use_data(bnr_datapaths, overwrite = TRUE) }.
+#'
+#' @format A [data.frame] containing paths to key spatial data sources.
+#' @source Manually updated and curated by BNR researchers
+"bnr_datapaths"

R/misc_notIn.R

@@ -0,0 +1,19 @@
+#' Inverse of 'in' call
+#'
+#' @description
+#' Calculates the set of entries not present in the second vector.
+#' Added for convenience since this is not supported by default in R.
+#'
+#' @param a First [`vector`] object.
+#' @param b Second [`vector`] object.
+#'
+#' @returns A [`vector`] of [`logical`] entries of \code{'a'} not present in \code{'b'}.
+#' @examples
+#' # example code
+# lu <- c("Forest", "Cropland", "Wetland", "OtherLand")
+# lu2 <- c("Forest", "Wetland", "otherland")
+# which(lu %notin% lu2)
+#' @keywords utils
+#' @author Martin Jung
+#' @export
+`%notin%` = function(a, b){!(a %in% b)}

R/spl_replaceGriddedNA.R

@@ -17,10 +17,10 @@
 #'
 #' @examples
 #' # Example
-#' s <- rast(system.file("ex/logo.tif", package="terra"))
+#' s <- terra::rast(system.file("ex/logo.tif", package="terra"))
 #' s[sample(1:terra::ncell(s), 100)] <- NA
 #' sfill <- sp_replaceGriddedNA(s, value = 100)
-#' plot(sfill)
+#' terra::plot(sfill)
 #'
 #' @returns A object of the same type as the input but with no-data values replaced with \code{'value'}.
 #' @author Martin Jung

README.md

@@ -24,3 +24,37 @@ See this [website](https://r-pkgs.org/) for more general help and examples in de
 ## Code of Conduct
 
 Please note that the BNRTools project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+
+## Contributors
+
+
+<!--- Added via allcontributors::add_contributors(type = "code") --->
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+
+All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
+
+<table>
+
+<tr>
+<td align="center">
+<a href="https://github.com/Martin-Jung">
+<img src="https://avatars.githubusercontent.com/u/3788377?v=4" width="100px;" alt=""/>
+</a><br>
+<a href="https://github.com/iiasa/BNRTools/commits?author=Martin-Jung">Martin-Jung</a>
+</td>
+<td align="center">
+<a href="https://github.com/mhesselbarth">
+<img src="https://avatars.githubusercontent.com/u/29225293?v=4" width="100px;" alt=""/>
+</a><br>
+<a href="https://github.com/iiasa/BNRTools/commits?author=mhesselbarth">mhesselbarth</a>
+</td>
+</tr>
+
+</table>
+
+<!-- markdownlint-enable -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://iiasa.github.io/BNRTools/
+template:
+  bootstrap: 5
+

tests/testthat/test-misc_tests.R

@@ -1,3 +1,9 @@
-test_that("Basic unit tests for misc functions", {
+test_that("Basic unit tests for small misc functions", {
   expect_equal(misc_sanitizeNames("Climate-temperature2015"), "Climate_temperature2015")
+
+  # Not in function\
+  lu <- c("Forest", "Cropland", "Wetland", "OtherLand")
+  lu2 <- c("Forest", "Wetland", "otherland")
+  test <- which(lu %notin% lu2)
+  expect_equal(test, c(2,4))
 })