Description
Automatize Diagnosis Standardized Assignation Using the Banff Classification.
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/>.
README.md
banffIT
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
Download section
also available in R using get_banff_dictionary()
also available in R using get_banff_template()
also available in R using get_banff_example()
Get started
Install the package and use the example file
# To install banffIT
install.packages('banffIT')
library(banffIT)
# If you need help with the package, please use:
banffIT_website()
# use example
input_file = system.file("extdata", "example.xlsx", package = "banffIT")
banff_launcher(
input_file = input_file,
output_folder = tempdir(), # 'folder_path/example'
language = 'label:en',
option_filter = adequacy == 1,
detail = TRUE)