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Example of SDTM and ADaM datasets from the CDISC

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Here is to present a set of SDTM and ADaM datasets from CDISC pilot projects as resources for R develpment and programming.

If you want to review the full datsets for pilot project, I would recommand it's better to clone the cdisc-org/sdtm-adam-pilot-project git repository, as following:

clone https://github.com/cdisc-org/sdtm-adam-pilot-project.git

If neccessary, otherwise you can aslo get CDISC pilot projects from the phuse-scripts repository.

clone https://github.com/phuse-org/phuse-scripts.git

Supposed you just want to get SDTM and ADaM datasets and run some tests in R, I would like to import those datasets from R packages, like admiral package. And install and try it right here.

library(admiral)
data(admiral_adsl)
adsl <- admiral_adsl
head(adsl[1:5,1:5])

# A tibble: 5 × 5
  STUDYID      USUBJID     SUBJID RFSTDTC    RFENDTC   
  <chr>        <chr>       <chr>  <chr>      <chr>     
1 CDISCPILOT01 01-701-1015 1015   2014-01-02 2014-07-02
2 CDISCPILOT01 01-701-1023 1023   2012-08-05 2012-09-02
3 CDISCPILOT01 01-701-1028 1028   2013-07-19 2014-01-14
4 CDISCPILOT01 01-701-1033 1033   2014-03-18 2014-04-14
5 CDISCPILOT01 01-701-1034 1034   2014-07-01 2014-12-30

You can also find the function list directly right here, to see which ADaM datsets are avaiable for use, such as adae, adeg, advs and so on.

If you want to import SDTM datasets, you should use the function like data(admiral_ae) from admiral.test package.

library(admiral.test)
data(admiral_ae)
ae <- admiral_ae
head(ae[1:5,1:5])

# A tibble: 5 × 5
  STUDYID      DOMAIN USUBJID     AESEQ AESPID
  <chr>        <chr>  <chr>       <dbl> <chr> 
1 CDISCPILOT01 AE     01-701-1015     1 E07   
2 CDISCPILOT01 AE     01-701-1015     2 E08   
3 CDISCPILOT01 AE     01-701-1015     3 E06   
4 CDISCPILOT01 AE     01-701-1023     3 E10   
5 CDISCPILOT01 AE     01-701-1023     1 E08

I find it quite practical, don't you? In addition to the admiral package, I aslo find that r2rtf and clinUtils R packages contain the exmaple datasets for CDISC pilot projects. But both of them are not quite complete, so this is just a alternative option.

Overall, from my persepctive, these example datasets are a great resource for developing R packages or Shiny dashboards for pharmaceutical use.

Reference

https://github.com/phuse-org/phuse-scripts
https://pharmaverse.github.io/admiral/index.html
https://github.com/pharmaverse/pharmaverse
https://github.com/atorus-research/CDISC_pilot_replication
https://cran.r-project.org/web/packages/admiral.test/admiral.test.pdf
https://rdrr.io/cran/clinUtils/f/vignettes/clinUtils-vignette.Rmd

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