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Prepare Cohort

Source: R/cohort_prep.R
prepare_cohort.Rd

For the cohort table input into any of the *_process functions, this function will prepare that cohort for the rest of the analysis. This includes computing follow-up based on start and end dates and computing age at cohort entry categorized into user-provided groups.

Usage

prepare_cohort(cohort_tbl, age_groups = NULL, omop_or_pcornet)

Arguments

cohort_tbl

tabular input || required

The cohort to be used for data quality testing. This table should contain, at minimum:

  • site | character | the name(s) of institutions included in your cohort

  • person_id / patid | integer / character | the patient identifier

  • start_date | date | the start of the cohort period

  • end_date | date | the end of the cohort period

age_groups

tabular input || defaults to NULL

If you would like to stratify the results by age group, create a table or CSV file with the following columns and use it as input to this parameter:

  • min_age | integer | the minimum age for the group (i.e. 10)

  • max_age | integer | the maximum age for the group (i.e. 20)

  • group | character | a string label for the group (i.e. 10-20, Young Adult, etc.)

If you would not like to stratify by age group, leave as NULL

omop_or_pcornet

string || required

A string, either omop or pcornet, indicating the CDM format of the data

Value

This function will return the same input cohort table with the addition of the column fu, which includes the length of patient follow-up based on the provided start & end dates. Optionally, if age_groups is not NULL, the output will also include age_ce (patient age at cohort entry) and age_grp (the user-provided age group category)

Examples