Stable version 1.0.0 with new functions!

.Rbuildignore

@@ -7,3 +7,6 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^vignettes/articles$
+^doc$
+^Meta$

.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

@@ -6,3 +6,5 @@ docs
 .httr-oauth
 .DS_Store
 .quarto
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: REDCapDM
 Type: Package
 Title: 'REDCap' Data Management
-Version: 0.9.9.2000
+Version: 1.0.0
 Authors@R: c(
     person("João", "Carmezim", email = "jcarmezim@igtp.cat", role = c("aut", "cre")),
     person("Pau", "Satorra", role = c("aut")),
@@ -11,16 +11,15 @@ Authors@R: c(
     person("Cristian", "Tebé", role = c("aut"))
     )
 Maintainer: João Carmezim <jcarmezim@igtp.cat>
-Description: REDCap Data Management - REDCapDM is an R package that allows users to manage data exported directly from REDCap or using an API connection. This package includes several functions designed for pre-processing data, generating reports of queries such as outliers or missing values, and following up on the identified queries. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases and the REDCap API is an interface that allows external applications to connect to REDCap remotely, and is used to programmatically retrieve or modify project data or settings within REDCap, such as importing or exporting data.
+Description: REDCap Data Management - 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases and the REDCap API is an interface that allows external applications to connect to REDCap remotely, and is used to programmatically retrieve or modify project data or settings within REDCap, such as importing or exporting data. REDCapDM is an R package that allows users to manage data exported directly from REDCap or using an API connection. This package includes several functions designed for pre-processing data, generating reports of queries such as outliers or missing values, and following up on previously identified queries. 
 License: MIT + file LICENSE
 URL: https://bruigtp.github.io/REDCapDM/, https://doi.org/10.1186/s12874-024-02178-6
 BugReports: https://github.com/bruigtp/REDCapDM/issues
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports:
     dplyr,
     janitor,
-    magrittr,
     openxlsx,
     purrr,
     REDCapR,
@@ -33,12 +32,18 @@ Imports:
     utils,
     stringi,
     cli,
-    forcats
+    forcats,
+    lifecycle
 Suggests: 
     knitr,
     rmarkdown,
-    kableExtra
+    kableExtra,
+    testthat (>= 3.0.0),
+    mockery
 VignetteBuilder: knitr
 Depends: 
-    R (>= 3.6)
+    R (>= 4.1)
 LazyData: true
+Config/testthat/edition: 3
+Config/Needs/website: rmarkdown
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,15 +1,25 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(check_queries)
+export(rd_checkbox)
+export(rd_dates)
+export(rd_delete_vars)
+export(rd_dictionary)
 export(rd_event)
 export(rd_export)
+export(rd_factor)
 export(rd_insert_na)
 export(rd_query)
+export(rd_recalculate)
 export(rd_rlogic)
+export(rd_split)
 export(rd_transform)
 export(redcap_data)
 import(cli)
-importFrom(magrittr,"%>%")
+importFrom(lifecycle,deprecated)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
+importFrom(rlang,eval_tidy)
+importFrom(rlang,parse_expr)
+importFrom(stats,na.omit)
+importFrom(stats,setNames)

R/REDCapDM-package.R

@@ -0,0 +1,49 @@
+#' @name REDCapDM-package
+#' @keywords internal
+#' @aliases REDCapDM
+#'
+#' @title Managing REDCap Data: The R package REDCapDM / REDCapDM: A Toolkit for Managing REDCap Data in R
+#'
+#' @description
+#' The **REDCapDM** package provides tools to import, process, and manage REDCap data within R.
+#' It supports data retrieval through the REDCap API or directly from exported files and includes a robust
+#' set of functions for data transformation, validation, and discrepancy management. Designed for efficient
+#' workflow integration, **REDCapDM** simplifies the handling of REDCap datasets, making it easier to ensure
+#' data quality and consistency.
+#'
+#' Key Features:
+#'
+#' - **Flexible Data Import**: Import data directly from REDCap using API connections or process exported REDCap files.
+#' - **Data Transformation**: Streamline the cleaning and preparation of raw datasets for analysis.
+#' - **Query Management**: Identify and track data discrepancies, missing events, and manage resolution reports.
+#'
+#' Core Functions:
+#'
+#' - `redcap_data`: Reads data exported from REDCap or retrieved through the REDCap API into R.
+#' - `rd_transform`: One-step pipeline to clean and preprocess the raw REDCap data.
+#'    - `rd_dates`: Standardize date and datetime fields.
+#'    - `rd_delete_vars`: Remove specified variables (by name or pattern).
+#'    - `rd_recalculate`: Recompute calculated fields and compare with REDCap values.
+#'    - `rd_factor`: Replace numeric multiple-choice columns with their factor version.
+#'    - `rd_checkbox`: Expand checkbox responses with custom labels and rename 'var___1' columns (REDCap style) to 'var_option'.
+#'    - `rd_split`: Splits a REDCap dataset by form or event.
+#'    - `rd_insert_na`: Manually set specified variables to missing based on a logical filter.
+#'    - `rd_rlogic`: Translate REDCap branching or calculation logic into R syntax.
+#'    - `rd_dictionary`: Update dictionary (translation of REDCap logic into R syntax) to reflect transformed data and logic.
+#' - `rd_query`: Identifies discrepancies (queries) in the dataset for validation.
+#' - `rd_event`: Detects missing events in longitudinal datasets.
+#' - `check_queries`: Compares historical and current query reports to track changes and additions.
+#' - `rd_export`: Exports a summary report of identified queries to an Excel (.xlsx) file.
+#'
+#'
+#' @examples
+#' \dontrun{
+#' # Install REDCapDM from CRAN:
+#' install.packages("REDCapDM")
+#'
+#' # Install the latest version of REDCapDM from GitHub:
+#' remotes::install_github("bruigtp/REDCapDM")
+#' }
+#'
+#' @importFrom lifecycle deprecated
+NULL