metadata_map — metadata_map • mapmetadata

This function will read in the metadata file for a chosen dataset and create a summary plot. It will ask a user to select a table from this dataset to process, and loop through all the variables in this table, asking the user to map (categorise) each variable to one or more domains. The domains will appear in the Plots tab for the user's reference.

These categorisations will be saved to a csv file, alongside a log file which summarises the session details. To speed up this process, some auto-categorisations will be made by the function for commonly occurring variables, and categorisations for the same variable can be copied from one table to another.

Example inputs are provided within the package data, for the user to run this function in a demo mode. Refer to the package website for more guidance.

Usage

metadata_map(
  metadata_file = NULL,
  domain_file = NULL,
  look_up_file = NULL,
  output_dir = getwd(),
  table_copy = TRUE,
  long_output = TRUE,
  demo_number = 5,
  quiet = FALSE
)

Arguments

metadata_file: This should be a csv download from HDRUK gateway (in the form of ID_Dataset_Metadata.csv). Run '?mapmetadata::metadata' to see how the metadata_file for the demo was created.
domain_file: This should be a csv file created by the user, with two columns (Domain_Code and Domain_Name). Run '?mapmetadata::domain_list' to see how the domain_file for the demo was created.
look_up_file: The lookup file makes auto-categorisations intended for variables that appear regularly in health datasets. It only works for 1:1 mappings right now, i.e. variable should only be listed once in the file. Run '?mapmetadata::look_up' to see how the default look_up was created.
output_dir: The path to the directory where the two csv output files will be saved. Default is the current working directory.
table_copy: Turn on copying between tables (default TRUE). If TRUE, categorisations you made for all other tables in this dataset will be copied over (if 'OUTPUT_' files are found in output_dir). This can be useful when the same variables appear across multiple tables within one dataset; copying from one table to the next will save the user time, and ensure consistency of categorisations across tables.
long_output: Run map_convert.R to create a new longer output. Default is TRUE.
demo_number: How many table variables to loop through in the demo. Default is 5. 'L-OUTPUT_' which gives each categorisation its own row. Default is TRUE.
quiet: Default is FALSE. Change to TRUE to quiet the cli_alert_info and cli_alert_success messages.

Value

A html plot summarising the dataset. Various csv and png outputs to summarise the user's mapping session for a specific table in the dataset.

Examples

# Demo run requires no function inputs but requires user interaction.
# See package documentation to guide user inputs.
if(interactive()) {
    temp_output_dir <- tempdir()
    metadata_map(output_dir = temp_output_dir)
}