This function checks that all columns in the dataset only contains the control terminology as defined by the metacore specification
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, 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.
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)
#> # A tibble: 254 × 49
#> 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 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>,
#> # AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <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>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …