Merge pull request #1 from InsightRX/RXR-2949

RXR-2949: Clean up package

Author: roninsightrx

.Rbuildignore

@@ -0,0 +1,9 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^codecov\.yml$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^LICENSE\.md$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# 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, 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

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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: test-coverage.yaml
+
+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")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: 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

.gitignore

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

DESCRIPTION

@@ -3,27 +3,33 @@ Title: Forging data for pharmacometric analyses
 Version: 0.0.0.9000
 Authors@R: c(
     person("Ron", "Keizer", email = "[email protected]", role = c("cre", "aut")),
+    person("Michael", "McCarthy", email = "[email protected]", role = "ctb"),
     person("InsightRX", role = "cph")
   )
-Author: Ron Keizer
-Maintainer: Ron Keizer <[email protected]>
 Description: Functions for parsing, converting, and generating data for pharmacometric analyses.
+License: MIT + file LICENSE
+Depends: 
+    R (>= 3.5)
 Imports:
+    admiral,
     dplyr,
+    irxutils,
     lubridate,
+    mice (>= 3.7.5),
+    mvtnorm,
     rlang,
     stringr,
+    tibble,
     tidyr,
-    jsonlite,
-    irxutils
+    tidyselect
 Suggests:
     testthat (>= 3.2.0),
     withr
-License: file LICENSE
+Remotes:
+  InsightRX/irxutils
+Config/testthat/edition: 3
 Encoding: UTF-8
+LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
-Config/testthat/edition: 3
-Depends: 
-    R (>= 3.5)
-LazyData: true
+URL: https://insightrx.github.io/irxforge/

LICENSE

@@ -1 +1,2 @@
-Copyright 2023 InsightRX. All rights reserved.
+YEAR: 2025
+COPYRIGHT HOLDER: InsightRX

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2025 InsightRX
+
+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

@@ -2,8 +2,6 @@
 
 export(add_nominal_timepoints)
 export(create_demographics_table)
-export(get_data_for_modelfit)
-export(get_data_for_nca)
 export(get_nominal_timepoints)
 export(get_route_from_data_column)
 export(reformat_data)

NEWS.md

@@ -0,0 +1,3 @@
+# irxforge (development version)
+
+* Initial CRAN submission.

R/add_nominal_timepoints.R

@@ -3,31 +3,27 @@
 #' @param data `data.frame` or `tibble` with at least a time column
 #' @param time_var variable name for time vector in dataset
 #' @param nominal_time_var variable name for new nominal time vector
-#' @param ... passed as argument to `get_nominal_timepoints()` and
-#' to `stats::density()`.
+#' @param verbose Logical.
+#' @param ... passed as argument to [get_nominal_timepoints()] and to
+#'   `stats::density()`.
 #' 
 #' @returns data.frame or tibble
+#' 
+#' @seealso [get_nominal_timepoints()]
 #'
 #' @export
 add_nominal_timepoints <- function(
-    data,
-    time_var = "time",
-    nominal_time_var = "NOMINAL_TIME",
-    verbose = FALSE,
-    ...
+  data,
+  time_var = "time",
+  nominal_time_var = "NOMINAL_TIME",
+  verbose = FALSE,
+  ...
 ) {
-  t_nom <- get_nominal_timepoints(
-    data[[time_var]], 
-    ...
-  )
+  rlang::check_dots_used()
+  t_nom <- get_nominal_timepoints(data[[time_var]], ...)
   if(verbose) {
     message("Nominal times identified: ", paste0(t_nom, collapse=", "))
   }
   data[[nominal_time_var]] <- t_nom[match.closest(data[[time_var]], t_nom)]
   data
 }
-
-match.closest <- function(x, y) {
-  cuts <- c(-Inf, y[-1] - diff(y)/2, Inf)
-  idx <- findInterval(x, cuts)
-}