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Compute Facts Over Time

Source: R/fact_loops.R
compute_fot.Rd

This function will loop through a time series and execute a user-provided function against only the data within the time period of interest. It will also ensure that only patients whose start date has passed but whose end date has not passed are included in the analysis for any given time period. This means that, for example, a patient who has a cohort period 1/1/2020 to 1/1/2025 would be included when looking at the year of 2024, but they would not be included when looking at the year of 2019 as they had not yet entered the cohort.

Usage

compute_fot(
  cohort,
  check_func,
  site_col,
  reduce_id = NULL,
  time_period = "year",
  time_span = c("2012-01-01", "2020-12-31"),
  site_list
)

Arguments

cohort

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

Note that the start and end dates included in this table will be used to limit the search window for the analyses in this module.

check_func

function || required

The function that should be executed within each time period in the loop. This parameter should be structured as the following, where dat is the input data for the function:

function(dat){check_function(param1 = dat, param2 = param2_input, ..., paramX = paramX_input)}

Make sure to include all parameters required for the original function where default values are not being used.

site_col

string || required

The name of the column in the cohort table that contains the site names. This will typically be either site or site_summ

reduce_id

string || defaults to NULL

If the function provided in check_func returns a list of tables, this parameter should be the name of the column that should be used to reduce the tables into one dataframe (via dplyr::bind_rows)

time_period

string || defaults to year

A string indicating the distance between dates within the specified time_span. Defaults to year, but other time periods such as month or week are also acceptable

time_span

vector - length 2 || defaults to c('2012-01-01', '2020-01-01')

A vector indicating the lower and upper bounds of the time series for longitudinal analyses

site_list

list || required

A list of sites for which you would like to examine clinical facts. Can be one site (single-site) or multiple (multi-site). Ensure that all sites listed here exist in the provided cohort table.

Value

This function will return a dataframe where the output of the provided check_func has been executed once for each time_period in the provided time_span for each of the sites included in site_list

Examples