metatools (version 0.1.6)

check_ct_data: Check Control Terminology for a Dataset

Description

This function checks that all columns in the dataset only contains the control terminology as defined by the metacore specification

Usage

check_ct_data(data, metacore, na_acceptable = NULL, omit_vars = NULL)

Value

Given data if all columns pass. It will error otherwise

Arguments

data

Dataset to check

metacore

metacore object that contains the specifications for the dataset of interest. If any variable has different codelists for different datasets the metacore object will need to be subsetted using `select_dataset` from the metacore package.

na_acceptable

`logical` value or `character` vector, set to `NULL` by default. `NULL` sets the acceptability of missing values based on if the core for the variable is "Required" in the `metacore` object. If set to `TRUE` then will pass check if values are in the control terminology or are missing. If set to `FALSE` then NA will not be acceptable. If set to a `character` vector then only the specified variables may contain NA values.

omit_vars

`character` vector indicating which variables should be skipped when doing the controlled terminology checks. Internally, `omit_vars` is evaluated before `na_acceptable`.

Examples

library(haven)
library(metacore)
library(magrittr)
load(metacore_example("pilot_ADaM.rda"))
spec <- metacore %>% select_dataset("ADSL")
data <- read_xpt(metatools_example("adsl.xpt"))

check_ct_data(data, spec)
if (FALSE) {
# These examples produce errors:
check_ct_data(data, spec, na_acceptable = FALSE)
check_ct_data(data, spec, na_acceptable = FALSE, omit_vars = "DISCONFL")
check_ct_data(data, spec, na_acceptable = c("DSRAEFL", "DCSREAS"), omit_vars = "DISCONFL")
}