v0.1.0

.Rbuildignore

@@ -13,3 +13,8 @@
 ^README.html$
 ^extras$
 ^vignettes/articles$
+^\.posit/assistant$
+^cran-comments\.md$
+^doc$
+^Meta$
+^AGENTS\.md$

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

@@ -65,7 +65,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            github::OHDSI/ROhdsiWebApi
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -31,7 +31,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: |
+            any::pkgdown
+            github::OHDSI/ROhdsiWebApi
+            local::.
           needs: website
 
       - name: Build site

.gitignore

@@ -12,3 +12,6 @@ extras/SRS.qmd
 extras/SRS.docx
 docs
 inst/doc
+.posit/assistant
+/doc/
+/Meta/

.posit/assistant/settings.json

@@ -0,0 +1,6 @@
+{
+  "sandbox": {
+    "enabled": false
+  },
+  "model.webSearch": true
+}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: studyGenerics
 Type: Package
-Title: A centralised repository of tested and frequently used methods for OMOP-CDM studies
-Version: 0.0.0.9002
+Title: A Centralised Repository of Tested and Frequently Used Methods for OMOP-CDM Studies
+Version: 0.1.3
 Authors@R: c(
     person(
       "Cesar", "Barboza",
@@ -10,23 +10,28 @@ Authors@R: c(
     ),
     person(
       "Cristiana", "Di Tullio",
-      email = "a.alamshahi@mi-erasmusmc.nl",
+      email = "c.ditullio@mi-erasmusmc.nl",
       role = c("aut")
     ),
     person(
       "Arianna", "Alamshahi",
       email = "a.alamshahi@mi-erasmusmc.nl",
       role = c("aut")
+    ),
+    person(
+      "Erasmus MC",
+      role = "cph"
     )
   )
-Description: This set of generic functions wraps routine and basic functions required to run an OMOP-CDM study. 
-  But besides testing this recurrent methods, studyGenerics aims to centralise colaboration to speed-up development of this type of projects. 
+Description: Provides generic functions for routine tasks required to run OMOP-CDM studies.
+  In addition to testing these recurring methods, studyGenerics aims to centralise
+  collaboration and speed up the development of these types of projects. The optional
+  ROhdsiWebApi package is available from <https://github.com/OHDSI/ROhdsiWebApi>.
 License: Apache License (>= 2)
 Encoding: UTF-8
 LazyData: true
 Imports: 
     cli,
-    httr,
     renv,
     ParallelLogger,
     checkmate,
@@ -35,15 +40,25 @@ Imports:
     zip,
     here,
     fs,
-    usethis
-Config/roxygen2/version: 8.0.0
+    usethis,
+    dplyr,
+    jsonlite,
+    withr
+Config/roxygen2/version: 8.1.0
 Suggests:
+    desc,
     gert,
     gh,
+    jsonvalidate,
     knitr,
+    omopgenerics,
+    purrr,
     rmarkdown,
+    ROhdsiWebApi,    
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
-URL: https://mi-erasmusmc.github.io/studyGenerics/
+URL: https://mi-erasmusmc.github.io/studyGenerics/, https://github.com/mi-erasmusmc/studyGenerics
 VignetteBuilder: knitr
 Config/Needs/website: rmarkdown
+Roxygen: list(markdown = TRUE)
+BugReports: https://github.com/mi-erasmusmc/studyGenerics/issues

NAMESPACE

@@ -3,37 +3,64 @@
 export(arrangeCdmNames)
 export(assertCdmNames)
 export(createResultsDir)
-export(developCheckout)
-export(getPkgZips)
+export(devCheckout)
 export(insertStructure)
+export(installCellar)
 export(issueOpen)
+export(packageCellar)
+export(pullConceptsAtlas)
 export(pullRequest)
 export(setLoggers)
 export(unZipStudyFiles)
+export(updateColumnValues)
 export(zipStudyFiles)
-importFrom(ParallelLogger,createFileAppender)
-importFrom(ParallelLogger,createLogger)
-importFrom(ParallelLogger,layoutParallel)
-importFrom(ParallelLogger,registerLogger)
-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)
-importFrom(cli,cli_alert_success)
-importFrom(cli,cli_alert_warning)
+importFrom(ParallelLogger,
+  createFileAppender,
+  createLogger,
+  layoutParallel,
+  logInfo,
+  registerLogger
+)
+importFrom(checkmate,
+  assertCharacter,
+  assertChoice,
+  assertDirectoryExists,
+  assertDouble,
+  assertFileExists,
+  assertList,
+  assertLogical,
+  assertTRUE,
+  checkClass
+)
+importFrom(cli,
+  cli_abort,
+  cli_alert_info,
+  cli_alert_success
+)
+importFrom(dplyr,
+  bind_rows,
+  tibble
+)
 importFrom(fs,path_ext_set)
-importFrom(glue,glue)
-importFrom(glue,glue_collapse)
+importFrom(glue,
+  glue,
+  glue_collapse
+)
 importFrom(here,here)
-importFrom(httr,HEAD)
-importFrom(renv,lockfile_read)
-importFrom(stats,setNames)
-importFrom(stringr,str_detect)
-importFrom(utils,download.file)
-importFrom(zip,unzip)
-importFrom(zip,zip)
+importFrom(jsonlite,toJSON)
+importFrom(renv,
+  lockfile_read,
+  lockfile_validate,
+  retrieve
+)
+importFrom(stringr,
+  str_detect,
+  str_remove,
+  str_replace_all,
+  str_to_lower
+)
+importFrom(usethis,proj_set)
+importFrom(zip,
+  unzip,
+  zip
+)

NEWS.md

@@ -1,15 +1,15 @@
-# studyGenerics 0.0.9002
+# studyGenerics 0.1.3
 
-* New article about `insertStructure()`
+* Initial CRAN release.
 
-* New `updateColumnValues()`
+# studyGenerics 0.1.2
 
-* 'macOS solves' article
+* `packageCellar()` documentation fixed and exported.
 
-# studyGenerics 0.0.9001
+# studyGenerics 0.1.1
 
-* Version control functions: `issueOpen()`, `pullRequest`, `developCheckout`
+* `packageCellar()` now tries to find default `renv.lock` and `cellarDir` if parameters are missing. 
 
-# studyGenerics 0.0.9000
+# studyGenerics 0.1.0
 
-* readme and initial functions.
+* Initial version.

R/cdmNames.R

@@ -1,8 +1,8 @@
-#' `assertCdmNames()` verifies if data partner's names are correct and display an error if incorrect
+#' `assertCdmNames()` verifies whether data partner names are valid and displays an error if they are not.
 #'
 #' @param labels A character vector of data partner acronyms
 #' @param expected A character vector of expected data partner acronyms. If omitted, the package's built-in CDM names are used.
-#' @returns Invisible if labels are correct
+#' @returns Returns invisibly if all labels are valid.
 #' @importFrom checkmate assertCharacter
 #' @importFrom cli cli_abort
 #' @importFrom glue glue glue_collapse
@@ -41,10 +41,10 @@ assertCdmNames <- function(labels, expected) {
     }
   }
 
-#' `arrangeCdmNames()` verifies if data partner's acronyms are valie
-#' and returns a vector ordered by country alphabetical order
+#' `arrangeCdmNames()` verifies whether data partners' acronyms are valid
+#' and returns a vector ordered alphabetically by country.
 #'
-#' @param labels A character vector of data partners acronyms
+#' @param labels A character vector of data partners' acronyms
 #'
 #' @returns A character vector
 #' @importFrom checkmate assertCharacter

R/createResultsDir.R

@@ -48,22 +48,14 @@ createResultsDir <- function(
       )
   } else {
     if (!dir.exists(outputDir)) {
-      dir.create(
-        outputDir
-        )
-      checkmate::assertDirectoryExists(
-        outputDir
-        )
+      dir.create(outputDir)
+      checkmate::assertDirectoryExists(outputDir)
     } else {
-      outputDir <- normalizePath(
-        outputDir
-        )
-      checkmate::assertDirectoryExists(
-        outputDir
-        )
+      outputDir <- normalizePath(outputDir)
+      checkmate::assertDirectoryExists(outputDir)
     }
   }
-  resultsDirName <- glue::glue(
+resultsDirName <- glue::glue(
     "results_{dbname}"
     )
   resultsDir <- file.path(
@@ -73,14 +65,12 @@ createResultsDir <- function(
   if (!dir.exists(resultsDir)) {
     dir.create(resultsDir)
   }
-  checkmate::assertDirectoryExists(
-    resultsDir
-    )
+  checkmate::assertDirectoryExists(resultsDir)
   return(
     list(
       outputDir = outputDir,
       resultsDir = resultsDir,
       resultsDirName = resultsDirName
     )
   )
-}
+}