Type:	Package
Title:	Automated Standardized Assignment of the Banff Classification
Version:	2.0.0
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
Imports:	dplyr (≥ 1.1.0), rlang, tools, utils, crayon, stringr, fs, lubridate, tidyr, fabR, madshapR (≥ 2.0.0)
Suggests:	knitr, rmarkdown, usethis
VignetteBuilder:	knitr
Encoding:	UTF-8
Language:	en-US
RoxygenNote:	7.2.3
NeedsCompilation:	no
Packaged:	2025-07-05 12:17:59 UTC; guill
Author:	Guillaume Fabre [aut, cre], Ruth Sapir-Pichhadze [fnd, cph, ctb], Jan Ulrich Becker [ctb], Samuel El Bouzaïdi Tiali [ctb], Jérôme Laforme [ctb], Tina Wey [ctb], Edden Gitelman [ctb]
Repository:	CRAN
Date/Publication:	2025-07-05 12:40:06 UTC

Add diagnoses to the input dataset

Description

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.

Usage

add_diagnoses(banff_dataset, version = NULL)

Arguments

Value

A tibble object that contains additional variables with the diagnoses results.

Examples

{

banff_dataset <- get_banff_template()
add_diagnoses(banff_dataset)

}

Call the online documentation

Description

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.

Usage

banffIT_website()

Value

Nothing to be returned. The function opens a web page.

Examples

{

banffIT_website()

}

Evaluates the format and content of the input dataset

Description

This function takes a dataset and evaluates its format and content based on the accepted format specified in the data dictionary. It applies a series of checks to make sure the dataset is ready to be processed by the add_diagnoses() function which assigns diagnoses to each observation of the dataset. The function evaluates whether:

• The input file is a dataset

• All mandatory variables are present in the dataset

• Missing values (NA) are present in variables where they are not allowed

• Data types are correct.

• The combination of ID, center, and biopsy date is unique

• There are duplicated variable in the dataset

• Dates are valid

• Content values follow the category values as specified in the data dictionary

• Constraints specified in the data dictionary are respected

Usage

banff_dataset_evaluate(banff_dataset, version = NULL)

Arguments

Value

A list of tibble objects giving information on the assessment of the dataset.

Examples

{

banff_dataset <- get_banff_template()
banff_dataset_evaluate(banff_dataset)

}

Launch the program

Description

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.

Usage

banff_launcher(
  input_file,
  output_folder,
  language = "label:en",
  version = NULL,
  option_filter,
  detail = FALSE
)

Arguments

Value

Nothing to be returned. The function generates a folder (if not already existing) where Excel files are stored.

Examples

{

version <- get_banff_version()
input_file <- system.file("extdata",
   paste0(version,"/banff_template.xlsx"), package = "banffIT")
banff_launcher(input_file, output_folder = tempdir())

}

Calculate adequacy of each biopsy from glomeruli and arteries variables

Description

This function calculates adequacy of each biopsy (i.e., each observation) based on glomeruli and arteries variables (if provided).

Usage

calculate_adequacy(banff_dataset)

Arguments

Value

A tibble object with two variables: the calculated adequacy (adequacy_calculated) and the adequacy specified in input (adequacy_input).

Examples

{

banff_dataset <- get_banff_template()
calculate_adequacy(banff_dataset)

}

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

madshapR

dataset_cat_as_labels

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

madshapR

dataset_summarize

Get the Banff data dictionary

Description

This function gets the data dictionary used to control the consistency of the input dataset.

Usage

get_banff_dictionary(
  version = NULL,
  which = NULL,
  language = "label:en",
  detail = FALSE
)

Arguments

Value

A list of tibbles representing meta data used in the process. The metadata are the list of variables used, and their associated categories, if any.

Examples

{

  get_banff_dictionary()

}

Get a dataset example

Description

This function gets the dataset used in the vignette as an example.

Usage

get_banff_example(version = NULL)

Arguments

Value

A tibble representing the dataset used in the the vignette as an example.

Examples

{

  get_banff_example()

}

Get a dataset template

Description

This function gets the empty dataset with variables that are mandatory in the process.

Usage

get_banff_template(version = NULL)

Arguments

Value

A tibble representing the empty dataset.

Examples

{

  get_banff_template()

}

Extract version of the Banff classification

Description

This internal function extracts for user input the version of the Banff classification.

Usage

get_banff_version(version = NULL)

Arguments

Value

A character string which is the version of Banff classification.

Examples

{

get_banff_version()

}