Generate a web-based visual report for a harmonized dossier

Source: R/05-harmonized_data_visualize.R

Generates a visual report of a harmonized dossier in an HTML bookdown document, with summary figures and statistics for each harmonized variable. The report outputs can be grouped by a categorical variable.

harmonized_dossier_visualize(
  harmonized_dossier,
  bookdown_path,
  harmonized_dossier_summary = NULL
)

Arguments

harmonized_dossier

A list containing the harmonized dataset(s).

bookdown_path

A character string identifying the folder path where the bookdown report files will be saved.

harmonized_dossier_summary

A list which identifies an existing summary produced by harmonized_dossier_summarize() of the harmonized variables. Using this parameter can save time in generating the visual report.

Value

A folder containing files for the bookdown document. To open the bookdown document in a browser, open 'docs/index.html', or use bookdown_open() with the folder path.

Details

A harmonized dossier is a named list containing one or more data frames, which are harmonized datasets. A harmonized dossier is generally the product of applying processing to a dossier object. The name of each harmonized dataset (data frame) is taken from the reference input dataset. A harmonized dossier also contains the DataSchema and Data Processing Elements used in processing as attributes.

Examples

{

library(fs)

# Use Rmonize_examples to run examples.
# Perform data processing

harmonized_dossier <- Rmonize_examples$`harmonized_dossier`
harmonized_dossier_summary <- Rmonize_examples$`summary_report_harmonized_dossier`

# Create a folder where the visual report will be placed

if(dir_exists(tempdir())) dir_delete(tempdir())
bookdown_path <- tempdir()

# Generate the visual report
harmonized_dossier_visualize(
  harmonized_dossier = harmonized_dossier,
  bookdown_path = bookdown_path,
  harmonized_dossier_summary = harmonized_dossier_summary)
  
# To open the file in a browser, open 'bookdown_path/docs/index.html'.
# Or use bookdown_open(bookdown_path) function.

}
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