Package app

.Rbuildignore

@@ -2,3 +2,6 @@
 ^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^data-raw$
+^LICENSE\.md$
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -7,4 +7,5 @@ renv/library/
 renv/staging/
 renv/cache/
 inst/doc
+.Rprofile
 .Renviron

DESCRIPTION

@@ -8,31 +8,45 @@ Authors@R:
            email = "[email protected]",
            role = c("aut"),
            comment = c(ORCID = "0000-0003-3759-2911")),
-    person(given = "Scott",
-           family = "Chamberlain",
-           email = "sachamber@fredhutch.org",
+    person(given = "Sean",
+           family = "Kross",
+           email = "skross@fredhutch.org",
            role = c("ctb", "cre"),
-           comment = c(ORCID = "0000-0003-1444-9135")),
+           comment = c(ORCID = "0000-0001-5215-0316")),
     person(given = "Monica",
            family = "Gerber",
            email = "[email protected]",
-           role = "ctb",
+           role = c("ctb"),
            comment = c(ORCID = "0000-0001-9878-9166")),
-    person(given = "Sean",
-           family = "Kross",
-           email = "skross@fredhutch.org",
+    person(given = "Scott",
+           family = "Chamberlain",
+           email = "sachamber@fredhutch.org",
            role = c("ctb"),
-           comment = c(ORCID = "0000-0001-5215-0316")))
+           comment = c(ORCID = "0000-0003-1444-9135"))
+    )
 Description: Oncarto (Oncology Cartographer) is an R package / Shiny dashboard
     developed by the Fred Hutch Data Science Lab (DaSL) for the
     automated integration and visualization of publicly available cancer
     incidence data for the Fred Hutch Cancer Center catchment area.
-License: MIT
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Imports:
+    dplyr,
+    htmltools,
+    leaflet,
+    sf,
+    shiny,
+    shinycssloaders,
+    shinydashboard,
+    tigris
+Depends: 
+    R (>= 2.10)
+Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: oncarto authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 oncarto authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1 +1,41 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(example_callback)
+export(oncarto_file)
+export(run_app)
+importFrom(dplyr,filter)
+importFrom(dplyr,left_join)
+importFrom(htmltools,HTML)
+importFrom(htmltools,a)
+importFrom(htmltools,tags)
+importFrom(leaflet,addLegend)
+importFrom(leaflet,addPolygons)
+importFrom(leaflet,addTiles)
+importFrom(leaflet,colorNumeric)
+importFrom(leaflet,highlightOptions)
+importFrom(leaflet,labelOptions)
+importFrom(leaflet,leaflet)
+importFrom(leaflet,leafletOutput)
+importFrom(sf,st_transform)
+importFrom(shiny,NS)
+importFrom(shiny,addResourcePath)
+importFrom(shiny,column)
+importFrom(shiny,fluidRow)
+importFrom(shiny,includeMarkdown)
+importFrom(shiny,moduleServer)
+importFrom(shiny,renderUI)
+importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
+importFrom(shiny,uiOutput)
+importFrom(shinycssloaders,withSpinner)
+importFrom(shinydashboard,box)
+importFrom(shinydashboard,dashboardBody)
+importFrom(shinydashboard,dashboardHeader)
+importFrom(shinydashboard,dashboardPage)
+importFrom(shinydashboard,dashboardSidebar)
+importFrom(shinydashboard,menuItem)
+importFrom(shinydashboard,sidebarMenu)
+importFrom(shinydashboard,tabItem)
+importFrom(shinydashboard,tabItems)
+importFrom(tigris,counties)
+importFrom(utils,read.table)

R/example-callback.R

@@ -0,0 +1,22 @@
+#' A function that provides an example dataframe for testing.
+#' @param key A string used internally (in a specific shiny server module
+#' implementation) to indicate which data to return.
+#' @export
+#' @importFrom utils read.table
+#' @examples
+#' example_callback("county-incidence")
+#'
+example_callback <- function(key) {
+  stopifnot(key %in% c("county-incidence", "contact-info"))
+
+  if (key == "county-incidence") {
+    utils::read.table(
+      header = TRUE,
+      system.file(file.path("test", "example-incidence.tsv"), package = "oncarto"),
+      sep = "\t"
+    )
+  } else if (key == "contact-info") {
+    oncarto_file("fh-contact-info.md")
+  }
+}
+

R/get-county-boundaries.R

@@ -0,0 +1,14 @@
+# Get the right county boundaries for the desired choropleth visualization
+#' @importFrom tigris counties
+#' @importFrom sf st_transform
+#'
+get_county_boundaries <- function(state_abbr, county_col_name) {
+  # Get county boundaries for the choropleth visualization using the tigris package
+  out <- sf::st_transform(
+    tigris::counties(state = state_abbr, class = "sf"),
+    crs = 4326
+  )
+
+  out[[county_col_name]] <- out[['NAMELSAD']]
+  out
+}

R/global.R

@@ -0,0 +1 @@
+utils::globalVariables(c("NAMELSAD", "cancer_type", "race", "sex", "age", "stage", "year"))

R/make-leaflet.R

@@ -0,0 +1,41 @@
+# Make the choropleth map
+#' @importFrom leaflet leaflet addTiles addPolygons addLegend labelOptions
+#' highlightOptions
+#'
+make_leaflet <- function(in_data, in_palette, incidence_col_name,
+                         county_col_name, legend_title) {
+
+  leaflet::leaflet(data = in_data) |>
+    leaflet::addTiles() |>
+    leaflet::addPolygons(
+      fillColor = ~in_palette(
+        in_data[[incidence_col_name]]
+      ),
+      weight = 1,
+      opacity = 1,
+      color = "white",
+      dashArray = "3",
+      fillOpacity = 0.7,
+      highlightOptions = leaflet::highlightOptions(
+        weight = 3,
+        color = "#666",
+        dashArray = "",
+        fillOpacity = 0.7,
+        bringToFront = TRUE
+      ),
+      label = ~paste(in_data[[county_col_name]], ": ",
+                     in_data[[incidence_col_name]]),
+      labelOptions = leaflet::labelOptions(
+        style = list("font-weight" = "normal", padding = "3px 8px"),
+        textsize = "15px",
+        direction = "auto"
+      )
+    ) |>
+    leaflet::addLegend(
+      pal = in_palette,
+      values = ~in_data[[incidence_col_name]],
+      opacity = 0.7,
+      title = legend_title,
+      position = "topright"
+    )
+}

R/make-palette.R

@@ -0,0 +1,12 @@
+# Generate palette for choropleth map
+#' @importFrom leaflet colorNumeric
+#'
+make_palette <- function(in_data, col_name, lower_color, upper_color,
+                         na_color) {
+
+  leaflet::colorNumeric(
+    c(lower_color, upper_color),
+    domain = in_data[[col_name]],
+    na.color = na_color
+  )
+}

R/oncarto-body.R

@@ -0,0 +1,6 @@
+# This function fills in the body of the shiny dashboard
+#' @importFrom shinydashboard dashboardBody
+#'
+oncarto_body <- function() {
+
+}

R/oncarto-file.R

@@ -0,0 +1,23 @@
+#' Get the paths to files installed with oncarto
+#'
+#' This function allows you to quickly access files that are installed with
+#' oncarto.
+#'
+#' @param path The name of the file. If no argument is provided then
+#' all of the example files will be listed.
+#'
+#' @return A vector of file paths
+#' @export
+#' @examples
+#' oncarto_file()
+#'
+oncarto_file <- function(path = NULL){
+  if(is.null(path)) {
+    list.files(
+      system.file(c("app"), package = "oncarto"),
+      full.names = TRUE)
+  } else {
+    system.file(c("app"), path, package = "oncarto",
+                mustWork = TRUE)
+  }
+}

R/oncarto-header.R

@@ -0,0 +1,14 @@
+# This function fills in the header of the shiny dashboard
+#' @importFrom shinydashboard dashboardHeader
+#' @importFrom htmltools tags
+#'
+oncarto_header <- function(title, logo_src, logo_href, logo_width, logo_height) {
+  shinydashboard::dashboardHeader(
+    title = htmltools::tags$a(
+      href = logo_href,
+      tags$img(
+        src = logo_src, height = logo_height, width = logo_width
+      )
+    )
+  )
+}

R/oncarto-sidebar.R

@@ -0,0 +1,19 @@
+# This function fills in the sidebar of the shiny dashboard
+#' @importFrom shinydashboard dashboardSidebar sidebarMenu menuItem
+#'
+oncarto_sidebar <- function() {
+  shinydashboard::dashboardSidebar(
+    shinydashboard::sidebarMenu(
+      # Multiple tabs, each correspond to a different type of map / info
+      shinydashboard::menuItem(
+        "Cancer Incidence by County",
+        tabName = "county-incidence"
+      ),
+
+      shinydashboard::menuItem(
+        "Background",
+        tabName = "background"
+      )
+    )
+  )
+}