This function checks the column in the dataset only contains the control terminology as defined by the metacore specification
check_ct_col(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
FALSEthen NA will not be acceptable.
Given data if column only contains control terms. If not, will error given the values which should not be in the column
library(metacore)
library(haven)
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"))
check_ct_col(data, spec, TRT01PN)
#> # A tibble: 254 × 51
#> STUDYID USUBJID SUBJID SITEID SITEGR1 ARM TRT01P TRT01PN TRT01A TRT01AN
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> <dbl>
#> 1 CDISCPILOT… 01-701… 1015 701 701 Plac… Place… 0 Place… 0
#> 2 CDISCPILOT… 01-701… 1023 701 701 Plac… Place… 0 Place… 0
#> 3 CDISCPILOT… 01-701… 1028 701 701 Xano… Xanom… 81 Xanom… 81
#> 4 CDISCPILOT… 01-701… 1033 701 701 Xano… Xanom… 54 Xanom… 54
#> 5 CDISCPILOT… 01-701… 1034 701 701 Xano… Xanom… 81 Xanom… 81
#> 6 CDISCPILOT… 01-701… 1047 701 701 Plac… Place… 0 Place… 0
#> 7 CDISCPILOT… 01-701… 1097 701 701 Xano… Xanom… 54 Xanom… 54
#> 8 CDISCPILOT… 01-701… 1111 701 701 Xano… Xanom… 54 Xanom… 54
#> 9 CDISCPILOT… 01-701… 1115 701 701 Xano… Xanom… 54 Xanom… 54
#> 10 CDISCPILOT… 01-701… 1118 701 701 Plac… Place… 0 Place… 0
#> # ℹ 244 more rows
#> # ℹ 41 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>,
#> # AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>,
#> # AGEGR2 <chr>, AGEGR2N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>,
#> # SEX <chr>, ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>,
#> # COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>,
#> # DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, …
check_ct_col(data, spec, "TRT01PN")
#> # A tibble: 254 × 51
#> STUDYID USUBJID SUBJID SITEID SITEGR1 ARM TRT01P TRT01PN TRT01A TRT01AN
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> <dbl>
#> 1 CDISCPILOT… 01-701… 1015 701 701 Plac… Place… 0 Place… 0
#> 2 CDISCPILOT… 01-701… 1023 701 701 Plac… Place… 0 Place… 0
#> 3 CDISCPILOT… 01-701… 1028 701 701 Xano… Xanom… 81 Xanom… 81
#> 4 CDISCPILOT… 01-701… 1033 701 701 Xano… Xanom… 54 Xanom… 54
#> 5 CDISCPILOT… 01-701… 1034 701 701 Xano… Xanom… 81 Xanom… 81
#> 6 CDISCPILOT… 01-701… 1047 701 701 Plac… Place… 0 Place… 0
#> 7 CDISCPILOT… 01-701… 1097 701 701 Xano… Xanom… 54 Xanom… 54
#> 8 CDISCPILOT… 01-701… 1111 701 701 Xano… Xanom… 54 Xanom… 54
#> 9 CDISCPILOT… 01-701… 1115 701 701 Xano… Xanom… 54 Xanom… 54
#> 10 CDISCPILOT… 01-701… 1118 701 701 Plac… Place… 0 Place… 0
#> # ℹ 244 more rows
#> # ℹ 41 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>,
#> # AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>,
#> # AGEGR2 <chr>, AGEGR2N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>,
#> # SEX <chr>, ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>,
#> # COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>,
#> # DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, …