test build

.Rbuildignore

@@ -4,4 +4,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-dev/*
+dev/*
+data-raw/*
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,52 @@
+# 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:
+    branches: [main, master]
+
+name: R-CMD-check
+
+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")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -10,7 +10,7 @@ URL: https://github.com/andreaczhang/ggehr
 BugReports: https://github.com/andreaczhang/ggehr/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     knitr,
     rmarkdown,

R/data_documentation.R

@@ -1,11 +1,38 @@
-#' Placeholder data x
+# antibiotics who----
+
+#' WHO antibiotics list
 #'
-#' This dataset contains one value, x
+#' This dataset contains information on antibiotics from WHO. More details to follow.
 #'
 #' @format
 #' \describe{
-#' \item{x}{The placeholder data x}
+#' \item{Antibiotic}{Name of the antibiotic}
+#' \item{Class}{Antibiotic class}
+#' \item{ATC code}{ATC code}
+#' \item{Category}{Access, watch or reserve}
+#' \item{Listed on EML/EMLc 2023}{Whether listed}
+#' \item{color_code}{Color code according to category}
 #' }
 #' @examples
-#' print(x)
-"x"
+#' head(ab_who)
+"ab_who"
+
+
+# antibiotics ahus ----
+#' AHUS antibiotics list
+#'
+#' This dataset contains information on antibiotics from AHUS. More details to follow.
+#'
+#' @format
+#' \describe{
+#' \item{Antibiotic}{Name of the antibiotic}
+#' \item{Category}{Access, watch or reserve}
+#' \item{Norsk_AHUS}{The Norwegian name, in AHUS hospital system}
+#' \item{color_code}{Color code according to category}
+#' }
+#' @examples
+#' head(ab_ahus)
+"ab_ahus"
+
+
+

README.md

@@ -2,4 +2,7 @@
 
 Visualize data from Electronic Health Records in a intuitive way.
 
-Status: early development
+<!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![R-CMD-check](https://github.com/andreaczhang/ggehr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andreaczhang/ggehr/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->

data-raw/load_data_ab.R

@@ -0,0 +1,60 @@
+library(readxl)
+library(data.table)
+
+
+# antibiotics who ----
+# this list also has data on the AHUS
+# list.files(system.file('extdata', package = 'ggehr'))
+# 
+# fs::path_package('ggehr')
+# system.file("extdata", "ab_list_who.xlsx", 
+#             package = "ggehr")
+# dir(system.file("extdata", "ab_list_who.xlsx", 
+#                 package = "ggehr"))
+# getwd()
+ablist <- readxl::read_xlsx('./inst/extdata/ab_list_who.xlsx')
+
+# ablist <- readxl::read_xlsx(system.file("extdata", "ab_list_who.xlsx", 
+#                                             package = "ggehr"))
+ablist <- setDT(ablist)
+head(ablist)
+colnames(ablist)
+
+# code colors
+# access: green
+# watch: yellow
+# reserve: red
+
+ablist[Category == 'Access', color_code := 'green']
+ablist[Category == 'Watch', color_code := 'yellow']
+ablist[Category == 'Reserve', color_code := 'red']
+
+head(ablist)
+
+# for who, drop the one for ahus
+ab_who <- copy(ablist)
+ab_who[, Norsk_AHUS := NULL]
+
+# save
+save(ab_who, file = 'data/ab_who.rda', compress = 'xz')
+
+
+
+# ahus specific ----
+# keep the ahus ones 
+ab_ahus <- ablist[!is.na(Norsk_AHUS), .(Antibiotic, Category, Norsk_AHUS, color_code)]
+
+ab_ahus$Category |> table()
+# 21 access, 2 reserve, 16 watch
+
+
+ab_ahus[Category == 'Reserve']
+# Aztreonam, Linezolid (very rare)
+ab_ahus[Category == 'Watch']
+
+
+# save
+save(ab_ahus, file = 'data/ab_ahus.rda', compress = 'xz')
+
+
+

dev/ab_list_who.R

@@ -16,7 +16,7 @@ ablist_who[Category == 'Access', color_code := 'green']
 ablist_who[Category == 'Watch', color_code := 'yellow']
 ablist_who[Category == 'Reserve', color_code := 'red']
 
-
+head(ablist_who)
 
 
 # ahus specific ----