Package 'banffIT'

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)

Arguments

banff_dataset

A tibble object.

Value

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

Examples

{

banff_dataset <- get_banff_template()
add_diagnoses(banff_dataset)

}

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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)

Arguments

banff_dataset

A tibble object.

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",
  option_filter,
  detail = FALSE
)

Arguments

input_file	A character string identifying the path of the input file (must be a CSV or a one sheet Excel file) to be processed.
output_folder	A character string identifying the folder path where the output files will be saved.
language	Optional argument allowing the user to get the diagnoses in a specific language. Options are "label:en" (default), "label:fr", "label:de", "label:sp", "label:nl", "label:jp", "label:in".
option_filter	Optional argument allowing the user to filter the dataset using dplyr::filter() syntax. The variable used to filter must exist.
detail	Optional argument indicating whether the output should include temporary variables generated in the process or not. FALSE by default.

Value

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

Examples

{

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

}

---

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()

}

---

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

banff_dataset

A tibble object.

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

Arguments

which	Indicates which variables to get from the Banff data dictionary. If NULL both input and output variables are provided.*
language	Optional input allowing the user to get the diagnoses in a specific language. Options are "label:en" (default), "label:fr", "label:de", "label:sp", "label:nl", "label:jp", "label:in".
detail	Optional argument indicating whether the data dictionary should include temporary variables generated in the process or not. FALSE by default.

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()

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()

Value

A tibble representing the empty dataset.

Examples

{

  get_banff_template()

}

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