pkgdown github workflow addition and updated based on js package

Author: worthyc51

.Rbuildignore

@@ -1,2 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^vignettes/articles$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,57 @@
+# 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, any::readr, any::webshot2, local::.
+          needs: website
+
+      - name: Render README.Rmd for GitHub
+        run: rmarkdown::render("README.Rmd")
+        shell: Rscript {0}
+
+      - name: Render index.Rmd for site
+        run: rmarkdown::render("index.Rmd")
+        shell: Rscript {0}
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

DESCRIPTION

@@ -15,3 +15,5 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.3
+Config/Needs/website: rmarkdown
+URL: https://grunwaldlab.github.io/metaMapWidgetR/

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(df_to_tsv)
 export(meta_map_widget)
 export(meta_map_widgetOutput)
 export(renderMeta_map_widget)

R/meta_map_widget.R

@@ -1,28 +1,23 @@
-#' <Add Title>
-#'
-#' <Add Description>
-#'
-#' @param df dataframe
-#' @export
+#' @keywords internal
 df_to_tsv <- function(df) {
   paste(
-    paste(colnames(df), collapse = "\t"),
-    apply(df, 1, function(row) paste(row, collapse = "\t")),
-    sep = "\n",
+    c(paste(colnames(df), collapse = "\t"),
+      apply(df, 1, function(row) paste(row, collapse = "\t"))),
     collapse = "\n"
   )
 }
 
-
 #' @param input A `data.frame`, `tibble`, or a path to tabular data.
 #' @param width   Width of the widget (CSS units or number).
 #' @param height  Height of the widget (CSS units or number).
 #' @param elementId Optional element ID for the widget.
+#' @param sizeVar Size factor rendered by default.
+#' @param colorVar Color factor rendered by default.
 #'
 #' @import htmlwidgets
 #'
 #' @export
-meta_map_widget <- function(input, width = NULL, height = NULL, elementId = NULL) {
+meta_map_widget <- function(input, width = NULL, height = NULL, elementId = NULL, sizeVar = '', colorVar = '') {
 
   # Parse input to table
   if (is.data.frame(input)) {
@@ -39,14 +34,24 @@ meta_map_widget <- function(input, width = NULL, height = NULL, elementId = NULL
     stop(call. = FALSE, 'Input must be a path to a file or a data.frame/tibble.')
   }
 
+  #Convert NAs to empty strings for all columns
+  table[] = lapply(table, function(x) {
+    x[is.na(x)] = ''
+    return(x)
+  })
+
   # create widget
   createWidget(
     name = 'meta_map_widget',
-    x = df_to_tsv(table),
+    x = list(
+      tsv = df_to_tsv(table),
+      sizeVar = sizeVar,
+      colorVar = colorVar
+    ),
     width = width,
     height = height,
     package = 'metaMapWidgetR',
-    elementId = 'map'
+    elementId = elementId,
   )
 }
 

README.Rmd

@@ -2,36 +2,21 @@
 output: github_document
 ---
 
-## metaMapWidget: R Wrapper for the meta-map-widget Leaflet widget
-
-```{r}
-library(metaMapWidgetR)
-df <- tibble::tibble(
-  latitude = runif(20, min = 34.0, max = 45.0),
-  longitude = runif(20, min = -120.0, max = -75.0),
-  name = paste("Sample", 1:20),
-  color_by = c(rep('type;proportion_infected;comically_small_test_column', 10), rep('type', 10)),
-  type = sample(c("Nursery", "Forest", "Urban", "Farm"), 20, replace = TRUE),
-  proportion_infected = runif(20),
-  comically_small_test_column = sample(c(0.000001898, 0.0000000023678876, 0.0024), 20, replace = TRUE)
-)
-print(df)
-
-example_data_path <- system.file('extdata', 'data.csv', package = 'metaMapWidgetR')
-
-meta_map_widget(df)
-meta_map_widget(example_data_path)
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(message = FALSE, warning = FALSE)
 ```
 
+# metaMapWidget: R Wrapper for the meta-map-widget Leaflet widget
 
+This package allows users to view the locations of custom data samples and their various attributes using an interactive map widget. The widget may be embedded in Rmd/Quarto documents.
 
+## Installation
 
-```{r}
-library(rgbif)
-occ_data <- occ_search(scientificName = "Bombus franklini")
-occ_table <- occ_data$data
-occ_table$latitude <- occ_table$decimalLatitude
-occ_table$longitude <- occ_table$decimalLongitude
-meta_map_widget(occ_table)
+For now, metaMapWidgetR is only available on Github and can be installed with devtools:
+
+```{r eval=FALSE}
+devtools::install_github('grunwaldlab/metaMapWidgetR')
 ```
 
+```{r child='vignettes/articles/quickstart.Rmd'}
+```

README.md

@@ -0,0 +1,44 @@
+
+# metaMapWidget: R Wrapper for the meta-map-widget Leaflet widget
+
+This package allows users to view the locations of custom data samples
+and their various attributes using an interactive map widget. The widget
+may be embedded in Rmd/Quarto documents.
+
+## Installation
+
+For now, metaMapWidgetR is only available on Github and can be installed
+with devtools:
+
+``` r
+devtools::install_github('grunwaldlab/metaMapWidgetR')
+```
+
+## Quick start
+
+This package includes multiple example data sets that are automatically
+loaded with the package. After installation, simply run the lines below
+to test randomly generated data and customized test columns:
+
+``` r
+library(metaMapWidgetR)
+
+example_data_path <- system.file('extdata', 'data.csv', package = 'metaMapWidgetR')
+
+meta_map_widget(example_data_path)
+```
+
+![](README_files/figure-gfm/unnamed-chunk-7-1.png)<!-- -->
+
+Or, to get an idea of how this would work with real data:
+
+``` r
+library(rgbif)
+occ_data <- occ_search(scientificName = "Bombus franklini")
+occ_table <- occ_data$data
+occ_table$latitude <- occ_table$decimalLatitude
+occ_table$longitude <- occ_table$decimalLongitude
+meta_map_widget(occ_table, sizeVar='individualCount', colorVar='county')
+```
+
+![](README_files/figure-gfm/unnamed-chunk-8-1.png)<!-- -->