Merge pull request #2 from PersonalizedTransplantCare/testing

Testing

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+^docs$
+^test$
+^_pkgdown\.yml$
+^pkgdown$
+^doc$
+^Meta$
+^\.github$
+^README.Rmd
+^NEWS.Rmd
+^cran-comments\.md$
+^CRAN-SUBMISSION$

.github/.gitignore

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

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

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+# 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, testing]
+  pull_request:
+    branches: [main, master, testing]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -3,3 +3,11 @@
 .RData
 .Ruserdata
 banffIT.Rproj
+docs/
+tests/
+docs
+inst/doc
+/doc/
+/Meta/
+README.Rmd
+NEWS.Rmd

DESCRIPTION

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+Package: banffIT
+Type: Package
+Title: Automatize Diagnosis Standardized Assignation Using the Banff Classification
+Version: 1.0.0
+Authors@R: 
+    c(person(given = "Guillaume",
+             family = "Fabre",
+             role = c("aut","cre"),
+             email = "guijoseph.fabre@gmail.com",
+             comment = c(ORCID = "0000-0002-0124-9970")),
+      person(given = "Ruth",
+             family = "Sapir-Pichhadze",
+             role=c("fnd","cph","ctb"),
+             email="ruth.sapir-pichhadze@mcgill.ca"),
+      person(given = "Samuel",
+             family = "El Bouzaïdi Tiali",
+             role=c("ctb"),
+             email="sbtiali@maelstrom-research.org"),
+      person(given = "Jérôme",
+             family = "Laforme",
+             role=c("ctb"),
+             email="jlaforme@maelstrom-research.org"),
+      person(given = "Tina",
+             family = "Wey",
+             role=c("ctb"),
+             email="twey@maelstrom-research.org"))
+Maintainer: Guillaume Fabre <guijoseph.fabre@gmail.com>
+Description: Assigns standardized diagnoses using the Banff Classification
+    (Category 1 to 6 diagnoses, including Acute and Chronic active T-cell
+    mediated rejection as well as Active, Chronic active, and Chronic antibody
+    mediated rejection). The main function considers a minimal dataset
+    containing biopsies information in a specific format (described by a data
+    dictionary), verifies its content and format (based on the data dictionary),
+    assigns diagnoses, and creates a summary report. The package is developed on
+    the reference guide to the Banff classification of renal allograft pathology
+    Roufosse C, Simmonds N, Clahsen-van Groningen M, et al. A (2018) <doi:10.1097/TP.0000000000002366>.
+    The full description of the Banff classification is available at <https://banfffoundation.org/>.
+License: GPL-3
+Depends: R (>= 3.4)
+URL: https://github.com/PersonalizedTransplantCare/banffIT
+BugReports: https://github.com/PersonalizedTransplantCare/banffIT/issues
+Roxygen: list(markdown = TRUE)
+Imports: dplyr (>= 1.1.0),
+    rlang,
+    tools,
+    utils,
+    crayon,
+    stringr,
+    fs,
+    lubridate,
+    tidyr,
+    fabR,
+    madshapR
+Suggests: 
+    knitr,
+    rmarkdown,
+    usethis
+VignetteBuilder: knitr
+Encoding: UTF-8
+Language: en-US
+RoxygenNote: 7.2.3

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(add_diagnoses)
+export(banffIT_website)
+export(banff_dataset_evaluate)
+export(banff_launcher)
+export(calculate_adequacy)
+export(dataset_cat_as_labels)
+export(dataset_summarize)
+export(get_banff_dictionary)
+export(get_banff_example)
+export(get_banff_template)
+import(dplyr)
+import(fabR)
+import(fs)
+import(madshapR)
+import(stringr)
+import(tidyr)
+importFrom(crayon,bold)
+importFrom(lubridate,is.POSIXt)
+importFrom(madshapR,dataset_cat_as_labels)
+importFrom(madshapR,dataset_summarize)
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(tools,file_ext)
+importFrom(utils,browseURL)

NEWS.md

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+
+# banffIT 1.0.0
+
+The banffIT package provides functions to assign standardized diagnoses
+using the Banff Classification (Category 1 to 6 diagnoses, including
+Acute and Chronic active T-cell mediated rejection as well as Active,
+Chronic active, and Chronic antibody mediated rejection). The main
+function `banff_launcher()`considers a minimal dataset containing
+biopsies information in a specific format (described by a data
+dictionary), verifies its content and format (based on the data
+dictionary), assigns diagnoses, and creates a summary report.
+
+## Main functionality
+
+- `banff_launcher()` This function takes a path string identifying the
+  input file path. The function internally runs a series of tests that
+  assess the input dataset. If any of these tests fails, the user gets
+  information allowing them to correct the input dataset and rerun the
+  process. Once all tests pass, the dataset is given as an output with a
+  diagnosis for each observation (using the function `add_diagnoses()`
+  internally). The output dataset, along with its associated labels
+  (“label:en” by default) are provided to the user in an Excel format
+  file accessible in the output_folder specified. The output dataset
+  comes with a report that summarizes information about variable
+  distributions and descriptive statistics.
+
+## Additional functions (used in the main function, but can be used separately)
+
+- `banff_dataset_evaluate()` This function takes a dataset and evaluates
+  its format and content based on the accepted format specified in the
+  data dictionary.
+
+- `calculate_adequacy()` A tibble object with two variables: the
+  calculated adequacy (adequacy_calculated) and the adequacy specified
+  in input (adequacy_input).
+
+- `add_diagnoses()` This function takes a dataset and returns a
+  diagnosis for each observation. For the function to run, the dataset
+  must not contain any errors that `banff_launcher()`would have
+  detected. Please prefer using `banff_launcher()` to run additional
+  tests.
+
+## Helper functions
+
+- `get_banff_dictionary()`, `get_banff_example()`,
+  `get_banff_template()` This function gets the data dictionary used to
+  control the consistency of the input dataset, a example dataset and a
+  template.
+
+- function `banffIT_website()` This function sends the user to the
+  online documentation for the package, which includes a description of
+  the latest version of the package, vignettes, user guides, and a
+  reference list of functions and help pages.
+
+## Imported functions from madshapR
+
+- [dataset_cat_as_labels()](https://maelstrom-research.github.io/madshapR-documentation/reference/dataset_cat_as_labels.html)
+
+- [dataset_summarize()](https://maelstrom-research.github.io/madshapR-documentation/reference/dataset_summarize.html)

R/00-import-from-fabR.R

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+#' @importFrom madshapR dataset_cat_as_labels
+#' @name dataset_cat_as_labels
+#' @rdname dataset_cat_as_labels
+#' @keywords imported
+#' @export
+madshapR::dataset_cat_as_labels
+
+#' @importFrom madshapR dataset_summarize
+#' @name dataset_summarize
+#' @rdname dataset_summarize
+#' @keywords imported
+#' @export
+madshapR::dataset_summarize