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
get_bad_ct(data, metacore, var, na_acceptable = NULL)Data to check
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.
Name of variable to check
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.
vector
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] ""