teal.builder.checks

Overview

teal.builder.checks is a package for checking the data integrity of ADaM datasets

[Package website] - (https://github.com/teal.builder.checks/index.html)

Installation

You can install the development version from Github with:

# remotes::install_github(
#  "https://<github.com>/teal.builder.checks",
#  auth_token = Sys.getenv("GITHUB_PAT"),
# upgrade = "never"
# )

Usage

teal.builder.checks checks the following ADaM datasets:

ADaM datasets	ADaM datasets contd.
adam	adrs
adsl	adqs
adae	adlb
adtte

teal.builder.checks can perform the following data integrity checks by column on those datasets:

Column Checks	Column Checks contd.
existence	is date
is character	is datetime
is integerish	has values
is double	lacks values
is logical	has one record per subject
is factor	has one record per subject per param

Example usage

library(purrr)
library(dplyr)    
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(lubridate)
#> 
#> Attaching package: 'lubridate'
#> The following objects are masked from 'package:base':
#> 
#>     date, intersect, setdiff, union
library(stringr)
library(checkmate)
library(vctrs)
#> 
#> Attaching package: 'vctrs'
#> The following object is masked from 'package:dplyr':
#> 
#>     data_frame
library(random.cdisc.data)

# Load adam datasets for checking
adsl <- random.cdisc.data::radsl(N = 10, seed = 1, na_percentage = .1)
adtte <- random.cdisc.data::radtte(adsl, seed = 1, na_percentage = .1)

Successful check of adsl

This check returns a logical TRUE with an attribute data which contains the original ADaM dataset checked

library(teal.builder.checks)
check_adsl(adsl)
#> [1] TRUE
#> attr(,"data")
#> # A data frame: 10 × 55
#>    STUDYID USUBJID    SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
#>    <chr>   <chr>      <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
#>  1 AB12345 AB12345-C… id-10  CHN-3     NA YEARS M     <NA>  NOT H… CHN     N    
#>  2 AB12345 AB12345-J… id-7   JPN-4     30 YEARS <NA>  ASIAN NOT H… JPN     N    
#>  3 AB12345 AB12345-U… id-3   USA-13    35 YEARS F     AMER… NOT H… USA     N    
#>  4 AB12345 AB12345-B… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y    
#>  5 AB12345 AB12345-C… id-2   CHN-11    35 YEARS M     BLAC… NOT H… CHN     N    
#>  6 AB12345 AB12345-C… id-1   CHN-11    35 YEARS F     WHITE NOT H… CHN     Y    
#>  7 AB12345 AB12345-C… id-5   CHN-3     36 YEARS F     ASIAN NOT H… CHN     N    
#>  8 AB12345 AB12345-R… id-4   RUS-1     36 YEARS M     BLAC… NOT H… RUS     N    
#>  9 AB12345 AB12345-R… id-6   RUS-1     36 YEARS F     ASIAN NOT H… RUS     N    
#> 10 AB12345 AB12345-B… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N    
#> # ℹ 44 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
#> #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
#> #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
#> #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
#> #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
#> #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>,
#> #   AP01SDTM <dttm>, AP01EDTM <dttm>, AP02SDTM <dttm>, AP02EDTM <dttm>, …

Unsuccessful check of adsl

check for non-existence of columns

This check returns a logical FALSE with two attributes

msg contains a character vector describing the reason for failure, if the check failed
data which contains the ADaM dataset checked

adsl |>
  dplyr::select(-STUDYID) |> 
  check_adsl()
#> [1] FALSE
#> attr(,"msg")
#> [1] "Dataset must have columns 'STUDYID', 'USUBJID', but is missing 'STUDYID'."
#> [2] "Column 'STUDYID' must have data type 'factor', but is data type 'NULL'."  
#> attr(,"data")
#> # A data frame: 10 × 54
#>    USUBJID      SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL INVID
#>    <chr>        <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct> <chr>
#>  1 AB12345-CHN… id-10  CHN-3     NA YEARS M     <NA>  NOT H… CHN     N     INV …
#>  2 AB12345-JPN… id-7   JPN-4     30 YEARS <NA>  ASIAN NOT H… JPN     N     INV …
#>  3 AB12345-USA… id-3   USA-13    35 YEARS F     AMER… NOT H… USA     N     INV …
#>  4 AB12345-BRA… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y     INV …
#>  5 AB12345-CHN… id-2   CHN-11    35 YEARS M     BLAC… NOT H… CHN     N     INV …
#>  6 AB12345-CHN… id-1   CHN-11    35 YEARS F     WHITE NOT H… CHN     Y     INV …
#>  7 AB12345-CHN… id-5   CHN-3     36 YEARS F     ASIAN NOT H… CHN     N     INV …
#>  8 AB12345-RUS… id-4   RUS-1     36 YEARS M     BLAC… NOT H… RUS     N     INV …
#>  9 AB12345-RUS… id-6   RUS-1     36 YEARS F     ASIAN NOT H… RUS     N     INV …
#> 10 AB12345-BRA… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N     INV …
#> # ℹ 43 more variables: INVNAM <chr>, ARM <fct>, ARMCD <fct>, ACTARM <fct>,
#> #   ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>, TRT02A <fct>,
#> #   REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>,
#> #   ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>, AEWITHFL <fct>,
#> #   RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>, TRT01SDTM <dttm>,
#> #   TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, AP01SDTM <dttm>,
#> #   AP01EDTM <dttm>, AP02SDTM <dttm>, AP02EDTM <dttm>, EOSSTT <fct>, …

Creation of your own multichecker

Successful check of adtte

In the following example, the checks are performed:

the existence of certain columns
specific values in one column
one record per subject per parameter

my_adtte_checker <- make_multi_checker(
  check_has_cols(
    column_names = c("STUDYID", "USUBJID", "PARAMCD")
  ),
  check_has_values(
    column_name = "ARM",
    values = c("A: Drug X", "B: Placebo", "C: Combination")
  ),
  check_has_one_record_per_subject_per_param
)

my_adtte_checker(adtte) 
#> [1] TRUE
#> attr(,"data")
#> # A data frame: 50 × 67
#>    STUDYID USUBJID    SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
#>    <chr>   <chr>      <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
#>  1 AB12345 AB12345-B… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N    
#>  2 AB12345 AB12345-B… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N    
#>  3 AB12345 AB12345-B… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N    
#>  4 AB12345 AB12345-B… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N    
#>  5 AB12345 AB12345-B… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N    
#>  6 AB12345 AB12345-B… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y    
#>  7 AB12345 AB12345-B… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y    
#>  8 AB12345 AB12345-B… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y    
#>  9 AB12345 AB12345-B… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y    
#> 10 AB12345 AB12345-B… id-8   BRA-9     31 YEARS F     ASIAN NOT H… BRA     Y    
#> # ℹ 40 more rows
#> # ℹ 56 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
#> #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
#> #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
#> #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
#> #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
#> #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, …

Unsuccessful check of adtte

This check returns a msg attribute with multiple error messages.

adtte |>
  dplyr::slice_head(n = 12) |>
  dplyr::select(-STUDYID) |>
  dplyr::filter(ARM != "A: Drug X") |>
  my_adtte_checker() 
#> [1] FALSE
#> attr(,"msg")
#> [1] "Dataset must have columns 'STUDYID', 'USUBJID', 'PARAMCD', but is missing 'STUDYID'."                                       
#> [2] "Column 'ARM' must have values 'A: Drug X', 'B: Placebo', 'C: Combination', but is missing values 'A: Drug X', 'B: Placebo'."
#> attr(,"data")
#> # A data frame: 7 × 66
#>   USUBJID       SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL INVID
#>   <chr>         <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct> <chr>
#> 1 AB12345-BRA-… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N     INV …
#> 2 AB12345-BRA-… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N     INV …
#> 3 AB12345-BRA-… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N     INV …
#> 4 AB12345-BRA-… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N     INV …
#> 5 AB12345-BRA-… id-9   BRA-1     35 YEARS F     BLAC… UNKNO… BRA     N     INV …
#> 6 AB12345-CHN-… id-1   CHN-11    35 YEARS F     WHITE NOT H… CHN     Y     INV …
#> 7 AB12345-CHN-… id-1   CHN-11    35 YEARS F     WHITE NOT H… CHN     Y     INV …
#> # ℹ 55 more variables: INVNAM <chr>, ARM <fct>, ARMCD <fct>, ACTARM <fct>,
#> #   ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>, TRT02A <fct>,
#> #   REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>,
#> #   ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>, AEWITHFL <fct>,
#> #   RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>, TRT01SDTM <dttm>,
#> #   TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, AP01SDTM <dttm>,
#> #   AP01EDTM <dttm>, AP02SDTM <dttm>, AP02EDTM <dttm>, EOSSTT <fct>, …

Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
R		R
man-roxygen		man-roxygen
man		man
tests		tests
vignettes		vignettes
.gitignore		.gitignore
DESCRIPTION		DESCRIPTION
LICENSE.md		LICENSE.md
NAMESPACE		NAMESPACE
README.Rmd		README.Rmd
README.md		README.md

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Repository files navigation

teal.builder.checks

Overview

Installation

Usage

Example usage

Successful check of adsl

Unsuccessful check of adsl

check for non-existence of columns

Creation of your own multichecker

Successful check of adtte

Unsuccessful check of adtte

About

Releases 1

Packages

Languages

License

Sanofi-Public/teal.builder.checks

Folders and files

Latest commit

History

Repository files navigation

teal.builder.checks

Overview

Installation

Usage

Example usage

Successful check of adsl

Unsuccessful check of adsl

check for non-existence of columns

Creation of your own multichecker

Successful check of adtte

Unsuccessful check of adtte

About

Resources

License

Stars

Watchers

Forks

Releases 1

Packages 0

Languages

Packages