Perform data checks on IDDO-SDTM data

Provides a variety of checks and summaries on IDDO-SDTM data including summarising the number of rows by study ID (STUDYID), the number of participants under 6 month, 18 years and over 90 years, and the number of units used by each test (TESTCD) and study ID.

Usage

check_data(data, age_in_years = FALSE)

Arguments

data

A dataset using IDDO-SDTM columns

age_in_years

Boolean. Is the AGE column in years. Default is FALSE, and function will call convert_age_to_years if FALSE, otherwise will not convert age.

Value

A list with various summaries/checks, the number of which is dependent on what variables are present in the input data. A plot is also returned showing the missingness in each variable.

Examples

check_data(DM_RPTESTB)

#> $studyid
#> # A tibble: 1 × 2
#>   STUDYID     n
#>   <chr>   <int>
#> 1 RPTESTB     3
#> 
#> $sex
#>    SEX n
#> 1    F 2
#> 2    M 1
#> 3 <NA> 0
#> 
#> $age
#> # A tibble: 1 × 7
#>   n_USUBJID AGE_min AGE_max n_missing_AGE n_AGE_under_6M n_AGE_under_18Y
#>       <int>   <dbl>   <dbl>         <int>          <int>           <int>
#> 1         3       4      67             0              0               1
#> # ℹ 1 more variable: n_AGE_over_90Y <int>
#> 
#> $missingness
#> STUDYID  DOMAIN USUBJID  SUBJID RFSTDTC  DTHDTC   DTHFL  SITEID   INVID  INVNAM 
#>   0.000   0.000   0.000   0.000   0.000   0.667   0.667   0.000   1.000   1.000 
#> BRTHDTC     AGE  AGETXT     SEX    RACE  ETHNIC   ARMCD     ARM COUNTRY   DMDTC 
#>   1.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000 
#>    DMDY 
#>   0.000 
#> 

check_data(LB_RPTESTB)

#> $studyid
#> # A tibble: 1 × 2
#>   STUDYID     n
#>   <chr>   <int>
#> 1 RPTESTB    10
#> 
#> $testcd
#> # A tibble: 3 × 17
#>   STUDYID TESTCD   min    q5   q25   q50   q75   q95   max n_UNITS UNITS   n_LOC
#>   <chr>   <chr>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>   <int> <chr>   <int>
#> 1 RPTESTB HCG       NA  NA    NA    NA     NA    NA     NA       0 ""          0
#> 2 RPTESTB HGB       88  89.8  95.8  98.5  100.  102.   102       1 "g/L"       0
#> 3 RPTESTB PLAT      90  91    95   100    140.  173.   181       1 "10^9/…     0
#> # ℹ 5 more variables: LOC <chr>, n_METHOD <int>, METHOD <chr>, n_SPEC <int>,
#> #   SPEC <chr>
#> 
#> $missingness
#>  STUDYID   DOMAIN  USUBJID    LBSEQ LBTESTCD   LBTEST  LBORRES LBMODIFY 
#>      0.0      1.0      0.0      0.0      0.0      0.0      0.0      1.0 
#> LBORRESU LBSTRESC LBSTRESN LBSTRESU VISITNUM    VISIT  VISITDY    EPOCH 
#>      0.1      0.9      0.1      0.1      0.0      0.0      0.1      0.0 
#>    LBDTC     LBDY LBEVINTX 
#>      0.1      0.1      1.0 
#>