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.
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.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.
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.