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Gets vector of control terminology which should be there

Source: R/checks.R
get_bad_ct.Rd

This function checks the column in the dataset only contains the control terminology as defined by the metacore specification. It will return all values not found in the control terminology

Usage

get_bad_ct(data, metacore, var, na_acceptable = NULL)

Arguments

data

Data to check

metacore

A metacore object to get the codelist from. If the variable has different codelists for different datasets the metacore object will need to be subsetted using select_dataset from the metacore package.

var

Name of variable to check

na_acceptable

Logical value, set to NULL by default, so the acceptability of missing values is 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.

Value

vector

Examples

library(haven)
library(metacore)
library(magrittr)
load(metacore_example("pilot_ADaM.rda"))
spec <- metacore %>% select_dataset("ADSL")
#> Warning: `core` from the `ds_vars` table only contains missing values.
#> Warning: `supp_flag` from the `ds_vars` table only contains missing values.
#> Warning: `common` from the `var_spec` table only contains missing values.
#> Warning: `where` from the `value_spec` table only contains missing values.
#> Warning: `dataset` from the `supp` table only contains missing values.
#> Warning: `variable` from the `supp` table only contains missing values.
#> Warning: `idvar` from the `supp` table only contains missing values.
#> Warning: `qeval` from the `supp` table only contains missing values.
#> ✔ ADSL dataset successfully selected
#> 
data <- read_xpt(metatools_example("adsl.xpt"))
get_bad_ct(data, spec, "DCSREAS")
#> character(0)
get_bad_ct(data, spec, "DCSREAS", na_acceptable = FALSE)
#> [1] ""