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Domain Concordance – Processing

Source: R/domain_concordance.R
process_dcon.Rd

Intakes the output of check_dcon in order to apply additional processing. This includes computing the following cohort overlap counts and proportions:

  • cohort_1_only: overall, patients in just cohort 1

  • cohort_2_only: overall, patients in just cohort 2

  • combined: overall, patients in both 1 and 2

  • cohort_1_denom: patients in cohort 1 not cohort 2

  • cohort_2_denom: patients in cohort 2 not cohort 1

  • cohort_1_in_2: patients in cohort 2 who are also in 1 (use cohort 2 as denominator)

  • cohort_2_in_1: patients in cohort 1 who are also in 2 (use cohort 1 as denominator)

Usage

process_dcon(dcon_results, rslt_source = "remote", csv_rslt_path = NULL)

Arguments

dcon_results

tabular input || required

The dcon_counts output of check_dcon. 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 dcon_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 a dataframe that, for each cohort pair, contains one row for each cohort overlap computation type listed in the description, including the associated raw counts and proportions

Details

Note that cohort_1_in_2 and cohort_2_in_1 will have the same raw count, but different proportions since the denominator is different

Examples

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

# Once the labels have been applied, the function can be executed
## When results are kept locally:
if (FALSE) { # \dontrun{
my_dcon_process <- process_dcon(dcon_results = my_dcon_rslts,
                                rslt_source = 'local')
} # }

## When results are kept in CSV files:
if (FALSE) { # \dontrun{
my_dcon_process <- process_dcon(dcon_results = 'my_dcon_rslts',
                                rslt_source = 'csv',
                                csv_rslt_path = 'path/to/my/results')
} # }

## When results are kept on a remote database:
if (FALSE) { # \dontrun{
my_dcon_process <- process_dcon(dcon_results = 'my_dcon_rslts',
                                rslt_source = 'remote')
} # }