chore(repo): initialize reproducible research workspace

2026-09-20 05:17:11 +12:00
commit 1e7cc2a71b
36 changed files with 9169 additions and 0 deletions
@@ -0,0 +1,48 @@
+command_args <- commandArgs(trailingOnly = FALSE)
+script_path <- sub("^--file=", "", grep("^--file=", command_args, value = TRUE)[1])
+script_dir <- dirname(normalizePath(script_path, winslash = "/"))
+project_root <- normalizePath(file.path(script_dir, "..", ".."), winslash = "/")
+library_path <- file.path(project_root, ".r-library", "4.6")
+dir.create(library_path, recursive = TRUE, showWarnings = FALSE)
+.libPaths(c(library_path, .libPaths()))
+
+required_packages <- c(
+  "survey", "srvyr",
+  "mirt",
+  "lavaan", "semTools", "psych",
+  "data.table", "jsonlite", "arrow", "haven", "readr",
+  "dplyr", "tidyr", "purrr", "stringr",
+  "digest", "renv", "targets", "withr"
+)
+
+installed <- rownames(installed.packages(lib.loc = .libPaths()))
+missing <- setdiff(required_packages, installed)
+
+if (length(missing) > 0L) {
+  install.packages(
+    missing,
+    lib = library_path,
+    repos = c(CRAN = "https://cloud.r-project.org"),
+    dependencies = c("Depends", "Imports", "LinkingTo"),
+    type = "binary",
+    Ncpus = max(1L, parallel::detectCores(logical = TRUE) - 2L)
+  )
+}
+
+installed_after <- rownames(installed.packages(lib.loc = .libPaths()))
+still_missing <- setdiff(required_packages, installed_after)
+if (length(still_missing) > 0L) {
+  stop("Missing R packages after installation: ", paste(still_missing, collapse = ", "))
+}
+
+versions <- vapply(
+  required_packages,
+  function(package) as.character(packageVersion(package, lib.loc = library_path)),
+  character(1)
+)
+writeLines(
+  jsonlite::toJSON(as.list(versions), pretty = TRUE, auto_unbox = TRUE),
+  file.path(script_dir, "r-package-versions.json"),
+  useBytes = TRUE
+)
+cat("Installed and verified", length(required_packages), "required R packages.\n")