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Clinical Fact Documentation – Processing

Source: R/clinical_fact_documentation.R
process_cfd.Rd

Intakes the combined output of check_cfd from all relevant institutions in order to apply additional processing. It will compute overall counts/proportions across all sites included in the input and tidy some of the descriptive metadata.

Usage

process_cfd(cfd_results, rslt_source = "remote", csv_rslt_path = NULL)

Arguments

cfd_results

tabular input || required

The tabular output of check_cfd. This table should include results for all institutions that should be included in the computation of overall / "network level" statistics.

rslt_source

string || defaults to remote

A string that identifies the location of the cfd_results table. Acceptable values are

  • local - table is stored as a dataframe in the local R environment

  • csv - table is stored as a CSV file

  • remote - table is stored on a remote database

csv_rslt_path

string || defaults to NULL

If rslt_source has been set to csv, this parameter should indicate the path to the result file(s). Otherwise, this parameter can be left as NULL

Value

This function will return all columns from the cfd_results input with additional rows where site = total that reflect the combined results of all institutions provided in the input data.

Examples

# This function should be run after check_cfd has been executed for all
# network institutions and results have been combined into a common table

## When results are kept locally:
if (FALSE) { # \dontrun{
my_cfd_process <- process_cfd(cfd_results = my_cfd_rslts,
                              rslt_source = 'local')
} # }

## When results are kept in CSV files:
if (FALSE) { # \dontrun{
my_cfd_process <- process_cfd(cfd_results = 'my_cfd_rslts',
                              rslt_source = 'csv',
                              csv_rslt_path = 'path/to/my/results')
} # }

## When results are kept on a remote database:
if (FALSE) { # \dontrun{
my_cfd_process <- process_cfd(cfd_results = 'my_cfd_rslts',
                              rslt_source = 'remote')
} # }