Review pass: citation files with the concept DOI, shorter title, site from gh-pages, CI

.Rbuildignore

@@ -9,3 +9,4 @@
 ^pkgdown$
 ^\.github$
 ^references
+^package_processing\.R$

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

@@ -1,10 +1,13 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# R CMD check on every push and pull request, written by washr::setup_ci().
+# Derived from https://github.com/r-lib/actions/tree/v2/examples (check-standard),
+# with the dev branch in the triggers as the openwashdata review standard requires.
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
+  workflow_dispatch:
 
 name: R-CMD-check
 
@@ -47,4 +50,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          build_args: 'c("--no-manual")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,47 @@
+# 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@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - 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/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -4,3 +4,4 @@
 .httr-oauth
 .DS_Store
 .quarto
+docs

CITATION.cff

@@ -1,16 +1,16 @@
-# -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v1.0.0
+# ------------------------------------------------
+# CITATION.cff file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# -----------------------------------------------------------
+# ------------------------------------------------
 
 cff-version: 1.2.0
 message: 'To cite package "rwpfunctionality" in publications use:'
-type: software
+type: dataset
 license: CC-BY-4.0
-title: 'rwpfunctionality: Water point functionality assessment in nine sub-Saharan
-  Africa and South Asia countries'
+title: 'rwpfunctionality: Water point functionality in sub-Saharan Africa and South
+  Asia'
 version: 0.0.1
-doi: 10.5281/zenodo.10878635
+doi: 10.5281/zenodo.10878634
 abstract: 'Water point monitoring data associated with the paper "[Rural water point
   functionality estimates and associations: evidence from nine countries in sub-Saharan
   Africa and South Asia](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023WR034679)"
@@ -38,9 +38,34 @@ authors:
 - family-names: Kayser
   given-names: Georgia L.
   orcid: https://orcid.org/0000-0002-3273-184X
-date-released: '2024-03-26'
+repository-code: https://github.com/openwashdata/rwpfunctionality
+url: https://github.com/openwashdata/rwpfunctionality
+date-released: '2024-03-11'
 contact:
 - family-names: Götschmann
   given-names: Margaux
   email: margauxg@ethz.ch
   orcid: https://orcid.org/0009-0002-2567-3343
+keywords:
+- open data
+- washdata
+- water points
+- functionality
+- rural water supply
+- water committees
+- Ethiopia
+- India
+- Malawi
+- Mali
+- Mozambique
+- Nepal
+- Niger
+- Rwanda
+- Uganda
+- management
+- open-data
+- r
+- wash
+- water
+- waterpoint
+

DESCRIPTION

@@ -1,6 +1,5 @@
 Package: rwpfunctionality
-Title: Water point functionality assessment in nine sub-Saharan Africa and South
-    Asia countries
+Title: Water point functionality in sub-Saharan Africa and South Asia
 Version: 0.0.1
 Authors@R: c(
     person("Margaux", "Götschmann", , "margauxg@ethz.ch", role = c("aut", "cre"),
@@ -18,9 +17,15 @@ Description: Water point monitoring data associated with the paper "[Rural water
 License: CC BY 4.0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
 Depends: 
     R (>= 2.10)
 LazyData: true
 Language: en-GB
 Date: 2024-03-11
+Config/Needs/website: rmarkdown, tidyverse, kableExtra
+URL: https://github.com/openwashdata/rwpfunctionality
+BugReports: https://github.com/openwashdata/rwpfunctionality/issues
+X-schema.org-keywords: open data, washdata, water points, functionality, rural water supply, water committees, Ethiopia, India, Malawi, Mali, Mozambique, Nepal, Niger, Rwanda, Uganda
+X-schema.org-spatialCoverage: Ethiopia, India, Malawi, Mali, Mozambique, Nepal, Niger, Rwanda, Uganda
+X-schema.org-temporalCoverage: 2017-05-22/2020-12-19
+Config/roxygen2/version: 8.0.0

R/rwpfunctionality.R

@@ -1,12 +1,12 @@
-#' Water point functionality assessment in nine sub-Saharan Africa and South
-#' Asia countries
+#' Water point functionality in sub-Saharan Africa and South Asia
 #'
 #' Water point monitoring data associated with the paper "[Rural water point
 #' functionality estimates and associations: evidence from nine countries in sub-Saharan
 #' Africa and South Asia](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023WR034679)" (Murray, Anna L et al., 2024).
 #'
 #' @format A tibble with 1793 rows and 52 variables
 #' \describe{
+#'   \item{id}{Row number assigned during processing}
 #'   \item{country}{Name of the country}
 #'   \item{admin1}{Administrative unit 1}
 #'   \item{admin2}{Administrative unit 2}

README.Rmd

@@ -17,6 +17,7 @@ knitr::opts_chunk$set(
   fig.path = "man/figures/README-",
   out.width = "100%"
 )
+knitr::opts_chunk$set(screenshot.force = FALSE)
 
 library(tidyverse)
 ```
@@ -68,7 +69,7 @@ Sustained functionality of rural water systems is a global challenge. Addressing
 
 The dataset includes observations of water point functionality and management committee questionnaires. Displayed on the map are the locations of the water points.
 
-![](man/figures/map.png)
+<img src="man/figures/map.png" alt="Map of the water point locations in the nine countries" width="100%"/>
 
 The package provides access to one single dataset.
 
@@ -115,11 +116,9 @@ rwpfunctionality |>
   scale_fill_manual(values = custom_colors) +  # Set custom colors
   labs(title = "Functionality rating for water points", fill = NULL,
        x = "",  # Empty x-axis label
-       y = "Count") +  # y-axis label
-  scale_fill_manual(labels = c("Functional", "Partially functional", "Abandoned or not functional"),
-                    values = custom_colors)  # Custom legend labels
+       y = "Count")  # y-axis label
 ```
-Based on this pie chart, it could be interesting to redefine the category "Partially functional" to gain insights and precision on this aspect of the data. However, we still clearly see that only a small part of the water points are functional.
+Based on this pie chart, it could be interesting to redefine the category "Partially functional" to gain insights and precision on this aspect of the data. Most water points are functional: `r sum(rwpfunctionality$functional3 == "Functional")` of `r nrow(rwpfunctionality)`.
 
 ### Water Points Types
 
@@ -146,7 +145,7 @@ This plot provides insight into the distribution of different types of water poi
 ## License
 
 Data are available as 
-[CC-BY](https://github.com/openwashdata/rwpfunctionality/LICENSE.md).
+[CC-BY](https://github.com/openwashdata/rwpfunctionality/blob/main/LICENSE.md).
 
 ## Citation