Check Variable Names

Source: R/checks.R

This function checks the variables in the dataset against the variables defined in the metacore specifications. If everything matches the function will print a message stating everything is as expected. If there are additional or missing variables an error will explain the discrepancies

check_variables(data, metacore, dataset_name = deprecated(), strict = TRUE)

Arguments

data

Dataset to check

metacore

metacore object that only contains the specifications for the dataset of interest.

dataset_name

[Deprecated] Optional string to specify the dataset. This is only needed if the metacore object provided hasn't already been subsetted.
Note: Deprecated in version 0.2.0. The dataset_name argument will be removed in a future release. Please use metacore::select_dataset to subset the metacore object to obtain metadata for a single dataset.

strict

A logical value indicating whether to perform strict validation on the input dataset. If TRUE (default), errors will be raised if validation fails. If FALSE, warnings will be issued instead, allowing the function execution to continue event with invalid data.

Value

message if the dataset matches the specification and the dataset, and error otherwise

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"))
check_variables(data, spec)
#> No missing or extra variables
#> # 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>, …
data["DUMMY_COL"] <- NA
check_variables(data, spec, strict = FALSE)
#> Warning: In: [check_variables(data, spec, strict = FALSE)]
#> 
#> The following variables do not belong: DUMMY_COL
#> # A tibble: 254 × 52
#>    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 42 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>, …