Adding a basic formatter CI and the empty renv

.Rbuildignore

@@ -0,0 +1,3 @@
+^renv$
+^renv\.lock$
+^\.github$

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/.gitignore

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

.github/workflows/format-suggest.yml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+    # Using `pull_request_target` over `pull_request` for elevated `GITHUB_TOKEN`
+    # privileges, otherwise we can't set `pull-requests: write` when the pull
+    # request comes from a fork, which is our main use case (external contributors).
+    #
+    # `pull_request_target` runs in the context of the target branch (`main`, usually),
+    # rather than in the context of the pull request like `pull_request` does. Due
+    # to this, we must explicitly checkout `ref: ${{ github.event.pull_request.head.sha }}`.
+    # This is typically frowned upon by GitHub, as it exposes you to potentially running
+    # untrusted code in a context where you have elevated privileges, but they explicitly
+    # call out the use case of reformatting and committing back / commenting on the PR
+    # as a situation that should be safe (because we aren't actually running the untrusted
+    # code, we are just treating it as passive data).
+    # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
+    pull_request_target:
+
+name: format-suggest.yml
+
+jobs:
+    format-suggest:
+        name: format-suggest
+        runs-on: ubuntu-latest
+
+        permissions:
+            # Required to push suggestion comments to the PR
+            pull-requests: write
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                  ref: ${{ github.event.pull_request.head.sha }}
+
+            - name: Install
+              uses: posit-dev/setup-air@v1
+
+            - name: Format
+              run: air format .
+
+            - name: Suggest
+              uses: reviewdog/action-suggester@v1
+              with:
+                  level: error
+                  fail_level: error
+                  tool_name: air

.github/workflows/lint-project.yml

@@ -0,0 +1,36 @@
+# 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: lint-project.yml
+
+permissions: read-all
+
+jobs:
+    lint-project:
+        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
+
+            - name: Install lintr
+              run: install.packages("lintr")
+              shell: Rscript {0}
+
+            - name: Install cyclocomp
+              run: install.packages("cyclocomp")
+              shell: Rscript {0}
+
+            - name: Lint root directory
+              run: lintr::lint_dir()
+              shell: Rscript {0}
+              env:
+                  LINTR_ERROR_ON_LINT: true

.lintr

@@ -1,15 +1,3 @@
-################################################################################
-## File: .lintr                                                               ##
-## Project: msm-nida-ctn                                                      ##
-## Created Date: 2025-08-28                                                   ##
-## Author: Matthew Carroll                                                    ##
-## -----                                                                      ##
-## Last Modified: 2025-11-05                                                  ##
-## Modified By: Dimitri Baptiste                                              ##
-## -----                                                                      ##
-## Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  ##
-################################################################################
-
 linters: all_linters(
     assignment_linter = assignment_linter(operator = c("<-"), allow_trailing = FALSE),
     backport_linter = backport_linter("4.0.0"),
@@ -19,8 +7,14 @@ linters: all_linters(
     object_name_linter = object_name_linter(styles = c("snake_case", "lowercase")),
     return_linter = return_linter(return_style = "explicit", allow_implicit_else = FALSE),
     cyclocomp_linter = cyclocomp_linter(complexity_limit = 10L),
-    object_usage_linter = object_usage_linter(interpret_glue = TRUE),
     unused_import_linter = unused_import_linter(interpret_glue = TRUE),
+    undesirable_function_linter = undesirable_function_linter(
+        fun = modify_defaults(
+            defaults = default_undesirable_functions,
+            source = NULL,
+            library = NULL,
+            require = NULL)),
+    object_usage_linter = NULL, # This doesn't work well with dplyr
     condition_call_linter = NULL,
     condition_message_linter = NULL,
     consecutive_mutate_linter = NULL,

R/utils.R

@@ -23,11 +23,18 @@
 #' @examples
 #' ensure_packages(c("dplyr", "here"))
 ensure_packages <- function(packages) {
-  sapply(packages, function(package) {
-    if (!(package %in%  rownames(installed.packages()))) {
-      install.packages(package, repos = "http://cran.us.r-project.org")
-    }
-    library(package, character.only = TRUE, warn.conflicts = FALSE)
-    return(require(package, character.only = TRUE))
-  })
+    return(vapply(
+        packages,
+        function(package) {
+            if (!(package %in% rownames(installed.packages()))) {
+                install.packages(
+                    package,
+                    repos = "http://cran.us.r-project.org"
+                )
+            }
+            library(package, character.only = TRUE, warn.conflicts = FALSE)
+            return(require(package, character.only = TRUE))
+        },
+        logical(length(packages))
+    ))
 }

renv.lock

@@ -0,0 +1,67 @@
+{
+  "R": {
+    "Version": "4.5.2",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "1.1.5",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Project Environments",
+      "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv",
+      "BugReports": "https://github.com/rstudio/renv/issues",
+      "Imports": [
+        "utils"
+      ],
+      "Suggests": [
+        "BiocManager",
+        "cli",
+        "compiler",
+        "covr",
+        "cpp11",
+        "devtools",
+        "generics",
+        "gitcreds",
+        "jsonlite",
+        "jsonvalidate",
+        "knitr",
+        "miniUI",
+        "modules",
+        "packrat",
+        "pak",
+        "R6",
+        "remotes",
+        "reticulate",
+        "rmarkdown",
+        "rstudioapi",
+        "shiny",
+        "testthat",
+        "uuid",
+        "waldo",
+        "yaml",
+        "webfakes"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Config/testthat/parallel": "true",
+      "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
+      "NeedsCompilation": "no",
+      "Author": "Kevin Ushey [aut, cre] (ORCID: <https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (ORCID: <https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
+      "Repository": "CRAN"
+    }
+  }
+}

renv/.gitignore

@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/