Merge pull request #8 from nanxstats/setup

Basic setup and style

.Rbuildignore

@@ -1,11 +1,9 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^data-raw$
+
 ^_pkgdown\.yml$
 ^pkgdown$
 ^docs$
-^LICENSE$
-^LICENSES_THIRD_PARTY$
+^LICENSE\.md$
+^LICENSE_THIRD_PARTY\.md$
 ^\.github$
-^codecov\.yml$
-^README\.Rmd$

.gitattributes

@@ -0,0 +1 @@
+*.rtf linguist-generated

.github/.gitignore

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

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

@@ -0,0 +1,50 @@
+# 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
+
+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/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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

.gitignore

@@ -3,6 +3,4 @@
 .RData
 .Ruserdata
 
-.DS_Store
 docs/
-docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: metalite.sl
 Title: Subject-level Analysis Using 'metalite'
 Version: 0.1.0
-Authors@R:c(
+Authors@R: c(
     person("Benjamin", "Wang", email = "[email protected]", role = c("aut", "cre")),
     person("Yujie", "Zhao", role = "aut"),
     person("Hiroaki", "Fukuda", role = "aut"),
@@ -12,19 +12,19 @@ Description: Provide subject-level analysis.
 Depends: R (>= 4.1.0)
 License: GPL (>= 3)
 Imports:
-    r2rtf,
+    glue,
     metalite,
     metalite.ae,
+    r2rtf,
     reactable,
-    glue,
     stringr
 Suggests:
     dplyr,
+    knitr,
     testthat (>= 3.0.0),
-    tidyr,
-    knitr
-Encoding: UTF-8
+    tidyr
 VignetteBuilder: knitr
+Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3

R/collect.R

@@ -33,17 +33,17 @@
 #'
 #' @examples
 #' meta <- meta_sl_example()
-#' meta |>
-#'   collect_baseline(
-#'     population = "apat",
-#'     parameter = "age"
-#'   )
-collect_baseline <- function(meta,
-                             population,
-                             parameter,
-                             type = "Subjects",
-                             use_na = c("ifany", "no", "always"),
-                             display_total = TRUE) {
+#' meta |> collect_baseline(
+#'   population = "apat",
+#'   parameter = "age"
+#' )
+collect_baseline <- function(
+    meta,
+    population,
+    parameter,
+    type = "Subjects",
+    use_na = c("ifany", "no", "always"),
+    display_total = TRUE) {
   use_na <- match.arg(use_na)
 
   title <- c(

R/format_base_char.R

@@ -19,10 +19,12 @@
 #' Prepare data for baseline characteristic table
 #'
 #' @param outdata A metadata object created by [prepare_base_char()].
-#' @param display_col Column wants to display on the table. Term could be selected from `c("n", "prop", "total")`.
+#' @param display_col Column wants to display on the table.
+#'   The term could be selected from `c("n", "prop", "total")`.
 #' @param digits_prop Number of digits for proportion columns.
 #' @param display_stat A vector of statistics term name.
-#'   The term name could be selected from c("mean", "sd", "se", "median", "q1 to q3", "range", "q1", "q3", "min", "max").
+#'   The term name could be selected from
+#'   `c("mean", "sd", "se", "median", "q1 to q3", "range", "q1", "q3", "min", "max")`.
 #'
 #' @return A list of analysis raw datasets.
 #'
@@ -34,10 +36,11 @@
 #' meta |>
 #'   prepare_base_char(parameter = "age;gender") |>
 #'   format_base_char()
-format_base_char <- function(outdata,
-                             display_col = c("n", "prop", "total"),
-                             digits_prop = 1,
-                             display_stat = c("mean", "sd", "se", "median", "q1 to q3", "range")) {
+format_base_char <- function(
+    outdata,
+    display_col = c("n", "prop", "total"),
+    digits_prop = 1,
+    display_stat = c("mean", "sd", "se", "median", "q1 to q3", "range")) {
   n_group <- length(outdata$group_label)
 
   # Select statistics want to display
@@ -56,7 +59,7 @@ format_base_char <- function(outdata,
     }
   }
 
-  # create output
+  # Create output
   tbl <- list()
 
   if ("n" %in% display_col) {
@@ -109,10 +112,10 @@ format_base_char <- function(outdata,
     (1 + n_group + ifelse("total" %in% display_col, 1, 0) + 1)
   )]
 
-
   rownames(within_tbl) <- NULL
   outdata$tbl <- within_tbl
   outdata$display_col <- display_col
   outdata$display_stat <- display_stat
+
   return(outdata)
 }

R/prepare_base_char.R

@@ -34,14 +34,13 @@
 #'
 #' @examples
 #' meta <- meta_sl_example()
-#'
-#' meta |>
-#'   prepare_base_char()
-prepare_base_char <- function(meta,
-                              population = "apat",
-                              observation = "wk12",
-                              analysis = "base_char",
-                              parameter = paste(names(meta$parameter), collapse = ";")) {
+#' meta |> prepare_base_char()
+prepare_base_char <- function(
+    meta,
+    population = "apat",
+    observation = "wk12",
+    analysis = "base_char",
+    parameter = paste(names(meta$parameter), collapse = ";")) {
   parameters <- unlist(strsplit(parameter, ";"))
 
   # obtain variables
@@ -77,18 +76,18 @@ prepare_base_char <- function(meta,
   n_pop <- n_pop[, c(length(group) + 2, 1:(length(group) + 1))]
   n_pop$var_label <- "-----"
 
-  # get the baseline characteristics variables in adsl
+  # Get the baseline characteristics variables in adsl
   # char_var <- collect_adam_mapping(meta, analysis)$var_name
   char_var <- do.call(c, lapply(parameters, function(x) {
     metalite::collect_adam_mapping(meta, x)$var
   }))
 
-  # get the baseline characteristics counts
+  # Get the baseline characteristics counts
   char_n <- lapply(parameters, function(x) {
     collect_baseline(meta, population, x)[[2]]
   })
 
-  # get the baseline characteristics propositions
+  # Get the baseline characteristics propositions
   char_prop <- lapply(parameters, function(x) {
     collect_baseline(meta, population, x)[[3]]
   })

R/react_base_char.R

@@ -18,20 +18,26 @@
 
 #' Display interactive baseline characteristic tables with AE subgroup analysis
 #'
-#' @param metadata_sl A metadata created by [metalite], which builds the baseline characteristic table
-#' @param metadata_ae A metadata created by [metalite], which builds the AE subgroup specific table
+#' @param metadata_sl A metadata created by [metalite],
+#'   which builds the baseline characteristic table
+#' @param metadata_ae A metadata created by [metalite],
+#'   which builds the AE subgroup specific table
 #' @param population A character value of population term name.
 #'   The term name is used as key to link information.
 #' @param observation A character value of observation term name.
 #'   The term name is used as key to link information.
 #' @param display_total Display total column or not.
-#' @param sl_parameter A character value of parameter term name for  the baseline characteristic table.
+#' @param sl_parameter A character value of parameter term name for
+#'   the baseline characteristic table.
 #'   The term name is used as key to link information.
-#' @param ae_subgroup A vector of strubf to specify the subgroups in the AE subgroup specific table
-#' @param ae_specific A string specifying the AE specific category
+#' @param ae_subgroup A vector of strubf to specify the subgroups
+#'   in the AE subgroup specific table.
+#' @param ae_specific A string specifying the AE specific category.
 #' @param width A numeric value of width of the table in pixels.
 #'
-#' @return An reactable combing both baseline characteristic table and AE subgroup specific tables
+#' @return An reactable combing both baseline characteristic table
+#'   and AE subgroup specific tables.
+#'
 #' @export
 #'
 #' @examples
@@ -48,15 +54,16 @@
 #'     width = 1200
 #'   )
 #' }
-react_base_char <- function(metadata_sl,
-                            metadata_ae,
-                            population = "apat",
-                            observation = "wk12",
-                            display_total = TRUE,
-                            sl_parameter = "age;gender;race",
-                            ae_subgroup = c("gender", "race"),
-                            ae_specific = "rel",
-                            width = 1200) {
+react_base_char <- function(
+    metadata_sl,
+    metadata_ae,
+    population = "apat",
+    observation = "wk12",
+    display_total = TRUE,
+    sl_parameter = "age;gender;race",
+    ae_subgroup = c("gender", "race"),
+    ae_specific = "rel",
+    width = 1200) {
   # ----------------------------------------- #
   #   total setting                           #
   # ----------------------------------------- #

R/react_subgroup_table.R

@@ -18,15 +18,16 @@
 
 #' Create interactive table for a subgroup
 #'
-#' @param tbl Tibble to create reactable
-#' @param group Treatment group label
-#' @param subgroup_name Subgroup label
+#' @param tbl A tibble to create reactable.
+#' @param group Treatment group label.
+#' @param subgroup_name Subgroup label.
 #'
-#' @return A reactable combing both baseline characteristic table
-#' and AE subgroup specific tables for a subgroup
-react_subgroup_table <- function(tbl,
-                                 group,
-                                 subgroup_name) {
+#' @return A reactable combining both baseline characteristic table
+#'   and AE subgroup specific tables for a subgroup.
+react_subgroup_table <- function(
+    tbl,
+    group,
+    subgroup_name) {
   names(tbl) <- tolower(names(tbl))
   subgroup_name <- tolower(subgroup_name)
   race_columns <- grep(tolower(subgroup_name), tolower(names(tbl)), value = TRUE)
@@ -80,7 +81,7 @@ react_subgroup_table <- function(tbl,
   )
 }
 
-# Borrow from metalite.ae
+# Borrowed from metalite.ae
 #' Format AE specific analysis
 #'
 #' @inheritParams metalite.ae::format_ae_specific