Merge develop into main

.Rbuildignore

@@ -11,4 +11,5 @@
 ^docs$
 ^pkgdown$
 ^README.html$
-^extras$
+^extras$
+^vignettes/articles$

.github/workflows/pkgdown.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, develop]
+    branches: [main, master]
   pull_request:
   release:
     types: [published]

.gitignore

@@ -10,3 +10,5 @@ README.html
 SRS.*
 extras/SRS.qmd
 extras/SRS.docx
+docs
+inst/doc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: studyGenerics
 Type: Package
 Title: A centralised repository of tested and frequently used methods for OMOP-CDM studies
-Version: 0.0.0.9000
+Version: 0.0.0.9002
 Authors@R: c(
     person(
       "Cesar", "Barboza",
@@ -37,7 +37,13 @@ Imports:
     fs,
     usethis
 Config/roxygen2/version: 8.0.0
-Suggests: 
+Suggests:
+    gert,
+    gh,
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 URL: https://mi-erasmusmc.github.io/studyGenerics/
+VignetteBuilder: knitr
+Config/Needs/website: rmarkdown

NAMESPACE

@@ -3,8 +3,11 @@
 export(arrangeCdmNames)
 export(assertCdmNames)
 export(createResultsDir)
+export(developCheckout)
 export(getPkgZips)
 export(insertStructure)
+export(issueOpen)
+export(pullRequest)
 export(setLoggers)
 export(unZipStudyFiles)
 export(zipStudyFiles)
@@ -16,6 +19,8 @@ importFrom(checkmate,assertCharacter)
 importFrom(checkmate,assertDirectoryExists)
 importFrom(checkmate,assertFileExists)
 importFrom(checkmate,assertLogical)
+importFrom(checkmate,assertTRUE)
+importFrom(checkmate,checkClass)
 importFrom(cli,cli_abort)
 importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)

NEWS.md

@@ -1,3 +1,15 @@
+# studyGenerics 0.0.9002
+
+* New article about `insertStructure()`
+
+* New `updateColumnValues()`
+
+* 'macOS solves' article
+
+# studyGenerics 0.0.9001
+
+* Version control functions: `issueOpen()`, `pullRequest`, `developCheckout`
+
 # studyGenerics 0.0.9000
 
-* readme and initial functions.
+* readme and initial functions.

R/getPkgZips.R

@@ -411,3 +411,33 @@ mockLock <- function() {
   return(lockfile)
 }
 
+suppPackages <- function() {
+  list(
+    Packages = list(
+      devtools = list(
+        Package = "devtools",
+        Version = "2.5.2"
+      ), # 2.5.2 exists in multiple releases, should pick from the newest (R v4.6)
+      dplyr = list(
+        Package = "dplyr",
+        Version = "0.6"
+      ), # there is no 0.6 in any of the releases, should get v1.2.1 as alternate from R v4.4
+      tidyrr = list(
+        Package = "tidyr",
+        Version = "1.3.2"
+      ), # tidyrr does not exist
+      RPostgres = list(
+        Package = "RPostgres",
+        Version = NULL
+      ), # no version provided, should get v1.4.10 as alternate from R v4.4
+      renv = list(
+        Package = "renv",
+        Version = "1.0.7"
+      ), # renv already exists in lockfile, if override_lock = TRUE, should get v1.0.7 from R v4.2
+      xfun = list(
+        Package = "xfun",
+        Version = NULL
+      )
+    )
+  ) # xfun already exists in lockfile, if override_lock = TRUE, should get v0.57 from R v4.4
+}

R/updateColumnValues.R

@@ -0,0 +1,27 @@
+#' Update values in a summarised result
+#'
+#' @description
+#' Updates the character values of specific column(s) in a summarised result object
+#' (e.g., changing cohort names to a more polished version for Shiny app labels)
+#' according to a given name mapping.
+#'
+#' @param summarised_result The summarised result with values to update.
+#' @param names_map A named vector containing the mapping between old and new names.
+#' @param variable The column name(s) containing the values to be updated in the
+#' summarised result object.
+#'
+#' @returns The summarised result itself with updated values.
+#'
+updateColumnValues <- function(
+    summarised_result,
+    names_map,
+    variable
+) {
+
+  summarised_result[[variable]] <- dplyr::recode(
+    summarised_result[[variable]],
+    !!!names_map
+  )
+
+  return(summarised_result)
+}

R/versionControl.R

@@ -8,15 +8,24 @@
 #'
 #' @returns A message with the link of the PR
 #' @importFrom checkmate assertCharacter assertLogical assertTRUE checkClass
-#' @importFrom gh gh gh_tree_remote gh_token_exists
-#' @importFrom gert git_branch_create git_branch
 #' @export
-#' @examples
 issueOpen <- function(
   title, 
   body,
   newBranch = FALSE
 ) {
+  if (!requireNamespace("gh", quietly = TRUE)) {
+    stop(
+      "Package \"gh\" must be installed to use this function.",
+      call. = FALSE
+    )
+  }
+  if (!requireNamespace("gert", quietly = TRUE)) {
+    stop(
+      "Package \"gert\" must be installed to use this function.",
+      call. = FALSE
+    )
+  }
   checkmate::assertCharacter(
     title,
     len = 1,
@@ -85,15 +94,24 @@ issueOpen <- function(
 #'
 #' @returns A message with the link of the issue
 #' @importFrom checkmate assertCharacter assertLogical assertTRUE checkClass
-#' @importFrom gh gh gh_tree_remote gh_token_exists
-#' @importFrom gert git_branch_create git_branch
 #' @export
-#' @examples
 pullRequest <- function(
   title,
   body,
   base = "develop"
 ) {
+  if (!requireNamespace("gh", quietly = TRUE)) {
+    stop(
+      "Package \"gh\" must be installed to use this function.",
+      call. = FALSE
+    )
+  }
+  if (!requireNamespace("gert", quietly = TRUE)) {
+    stop(
+      "Package \"gert\" must be installed to use this function.",
+      call. = FALSE
+    )
+  }
   checkmate::assertCharacter(
     title,
     len = 1,
@@ -136,10 +154,14 @@ pullRequest <- function(
 #' and pull latest changes
 #'
 #' @returns Git log messages after checking out and pulling 'develop'
-#' @importFrom gert git_branch_exists git_branch_checkout git_pull
 #' @export
-#' @examples
 developCheckout <- function() {
+  if (!requireNamespace("gert", quietly = TRUE)) {
+    stop(
+      "Package \"gert\" must be installed to use this function.",
+      call. = FALSE
+    )
+  }
   branch <- "develop"
   if (gert::git_branch_exists(branch)) {
     gert::git_branch_checkout(

studyGenerics.Rproj

@@ -1,4 +1,4 @@
-Version: 1.0
+sVersion: 1.0
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

tests/testthat/test-cdmNames.R

@@ -1,5 +1,5 @@
 test_that("assertCdmNames works", {
-  # Assert a group of acryonims
+  # Assert a group of acronyms
   labels <- c(
     "BCR",
     "IQVIA LPD Belgium",
@@ -9,9 +9,9 @@ test_that("assertCdmNames works", {
   )
   assertCdmNames(labels = labels) |>
     expect_invisible()
-  # Error acronim do not match
+  # Error acronym do not match
   labels <- c(
-    "BCRX", # Mispelled acronym
+    "BCRX", # Misspelled acronym
     "IQVIA LPD Belgium",
     "NLHR@UiO:PERINATAL",
     "IQVIA US - AmbEMR",
@@ -22,7 +22,7 @@ test_that("assertCdmNames works", {
 })
 
 test_that("assertCdmNames against expected acronyms", {
-  # Assert a group of acryonims
+  # Assert a group of acronyms
   labels <- c(
     "BCR",
     "IQVIA LPD Belgium",
@@ -42,7 +42,7 @@ test_that("assertCdmNames against expected acronyms", {
     expect_error()
   # Incorrect acronym
   labels <- c(
-    "BCRX", # Mispelled acronym
+    "BCRX", # Misspelled acronym
     "IQVIA LPD Belgium",
     "NLHR@UiO:PERINATAL",
     "IQVIA US - AmbEMR",
@@ -78,9 +78,9 @@ test_that("arrangeCdmNames returns required acronyms in order", {
       "IQVIA US - AmbEMR",
       "IQVIA US - PMTX+"
     ))
-  # Error acronim do not match
+  # Error acronym do not match
   labels <- c(
-    "BCRX", # Mispelled acronym
+    "BCRX", # Misspelled acronym
     "IQVIA LPD Belgium",
     "NLHR@UiO:PERINATAL",
     "IQVIA US - AmbEMR",