R/Pharma ADaM Workshop

Fanny Gautier Cytel

Ben Straub GSK

Edoardo Mancini Roche

Sadchla Mascary Gilead

Friday, October 25, 2024

Objectives

• By the end of this workshop you will have:
  • Updated code for ADaMs ADSL and ADVS using pharmaverse packages, tidyverse packages, base R and Pinnacle21-like specs.
  • Gained an understanding of how to use pharmaverse packages
  • Gained an understanding of how to use resources for building ADaMs in R.

Assumptions

• Basic knowledge of CDISC Standards (ADaM and SDTM Domains)
• Basic background in R and its packages
• Basic familiarity with RStudio IDE (So much Pane!!)
• %>% chaining functions together
• Dual Screens - Workshop and “Coding along”
• 🦺 But even lacking all this we still think you will gain some good knowledge! 🦺

Play by Play

• 🕙10:05 - 10:15 Introductions and Setup

• 🕙10:15 - 10:30 Overview of pharmaverse packages and functions

• 🕥10:30 - 11:20 ADSL

• 🕚11:20 - 11:30 Break

• 🕦11:30 - 12:30 ADVS

• 🕐12:30 - 1:00 Questions and Resources

Introductions and Setup

🕙10:05 - 10:15

Who will help you achieve the workshop’s objectives!

• Fanny Gautier - presenting on ADVS 📣
• Ben Straub - presenting on ADSL and pharmaverse packages 📣
• Edoardo Mancini - Chat Support 💻
• Sadchla Mascary - Chat Support 💻

Setting up your Workspace to “code”

• Preferred:
  • Sign up for a free Posit Account
  • Share Link for R/Pharma: ADaM Workshop
    • Everything loaded (data, packages, specs) and ready to go!
• Quick and Dirty
  • Grab files from Repo
  • Files are in exercises, metadata and solutions folders
• Advanced:
  • Clone Repo and set up yourself
• Sit back and Relax
  • 🏖️🏖️🍷🍷

How we will “code” today

• Fanny and I will walk you through coding ADSL and ADVS
  • Lite Discussion on each function and function arguments
  • A few fill in the blanks!
  • Occasional Check-in Poll
• Important to move along quickly
  • Please post questions to chat
  • Full scripts are available in solutions folder

Overview of pharmaverse packages and functions

🕥10:15 - 10:30

The core pharmaverse packages

• metacore
• metatools
• xportr
• admiral

The core tidyverse packages

• dplyr
• stringr
• haven
• lubridate

Hello pharmaverse Functions!

Package	Function	Purpose
admiral	derive_vars_merged()	left_join on steroids
admiral	derive_param_computed()	Core function for wrappers used in ADVS
admiral	convert_blanks_to_na()	SAS blanks versus R NAs
admiral	derive_vars_dtm()	Take a ---DTC variable and turn it into a ---DTM variable
admiral	derive_vars_duration()	Duration between timepoints
admiral	derive_vars_extreme_event()	🤯

Hello pharmaverse Functions!

Package	Function	Purpose
metatools	combine_supp()	Join Parent and Supplementary Datasets
metatools	create_var_from_codelist()	Numeric Vars from Specs!
metatools	drop_unspec_vars()	Easily drop variables not in Spec
xportr	xportr_label()	Apply labels from Spec
xportr	xportr_write()	Write out an xpt file

Hello Specs!

• Pinnacle21-like Specs

• Not fit for purpose - just a helpful guide

• What is in the the Specs:

  • Two datasets, dataset labels and variable keys
  • Variables - labels, lengths, types, linked to method
  • Codelists!!
  • No VLMs

ADSL

🕥10:30 - 11:20

ADSL Quizzes

Check-in 1

Which admiral function can be used to turn a ---DTC variable into a ---DTM variable

1. derive_vars_dtc()
2. derive_var_trtdurd()
3. derive_vars_dtm()
4. derive_vars_exsdtc()

• Correct Answer: c) derive_vars_dtm()

Check-in 2

How many arguments does derive_vars_merged() have?

Hint: Go to the documentation ?fcn_name or F1

1. 15 arguments
2. 4 argruments
3. 1 argrument
4. 10 arguments

• Correct Answer: a) 15 arguments

Check-in 3

Which function did I use to load the adams_little_helpers.R?

1. load_all()
2. install.functions()
3. source()
4. callr()

• Correct Answer: c) source()

Check-in 4

How many packages did I load using library() to create ADSL today?

1. 15
2. 4
3. 8
4. 10

• Correct Answer: c) 8

Break

🕦11:20 - 11:30

ADVS

🕦11:30 - 12:30

ADVS Quizzes

Check-in 1

Have a look to admiraldiscovery: Which admiral function could be used to derive “BMI” parameter at any time point?

• 1. compute_bmi()
• 2. derive_param_bmi()
• 3. derive_params_growth_age()

• Correct answer:
• b) the wrapper function derive_param_bmi()

• We could also use derive_param_computed()

Check-in 2

Have a look to admiraldiscovery: Which admiral wrapper function could be used to derive “BSA” parameter at any time point?

• 1. derive_param_bsa()
• 2. compute_bsa()

• Correct answer:
• a) the wrapper function derive_param_bsa()

• We could also use derive_param_computed()

Check-in 3

With the help of admiraldiscovery: Which admiral function could be used to derive ONTRTFL variable?

• 1. derive_var_trtemfl()
• 2. derive_var_trtdurd()
• 3. derive_var_ontrtfl()

• Correct answer:
• c) the function derive_var_ontrtfl()

Check-in 4

Execute the derivation of PCHG on a subset of the input dataset: Post-baseline records only. Which admiral functions will you use? Get some hints on the Reference page

• Correct answer:
• restrict_derivation()
• derive_var_pchg()

Check-in 5

With the help of the Reference page: which admiral function could be used to compute the Analysis Sequence Number (Numbering the Observations Within Each Group)?

• Correct answer:
• derive_var_obs_number()

Questions and Resources

• admiraldiscovery
• pharmaverse examples
• pgkdown sites for xportr, metatools, metacore and admiral
• Extension packages for admiral: admiralophtha, admiralonco, admiralpeds

Closing Thoughts

• We were only able to show a small number of pharmaverse packages and functions today, but please delve deeper to explore the full breadth
• If you’d like to contribute to pharmaverse, check out options at pharmaverse.org
• Finally, be sure to join our community on Slack!

Pacakges and Session Information

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8 
[2] LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] link_2024.4.0   countdown_0.4.0 glue_1.8.0     

loaded via a namespace (and not attached):
 [1] rappdirs_0.3.3    sass_0.4.9        utf8_1.2.4        generics_0.1.3   
 [5] tidyr_1.3.1       xml2_1.3.6        stringi_1.8.4     hms_1.1.3        
 [9] digest_0.6.37     magrittr_2.0.3    evaluate_1.0.1    timechange_0.3.0 
[13] fastmap_1.2.0     cellranger_1.1.0  jsonlite_1.8.9    backports_1.5.0  
[17] admiraldev_1.1.0  purrr_1.0.2       fansi_1.0.6       xportr_0.4.1     
[21] httr2_1.0.5       jquerylib_0.1.4   cli_3.6.3         rlang_1.1.4      
[25] withr_3.0.1       cachem_1.1.0      yaml_2.3.10       tools_4.3.3      
[29] tzdb_0.4.0        memoise_2.0.1     checkmate_2.3.2   dplyr_1.1.4      
[33] forcats_1.0.0     curl_5.2.3        vctrs_0.6.5       R6_2.5.1         
[37] lifecycle_1.0.4   metacore_0.1.3    lubridate_1.9.3   stringr_1.5.1    
[41] pkgconfig_2.0.3   admiral_1.1.1     pillar_1.9.0      bslib_0.8.0      
[45] metatools_0.1.6   haven_2.5.4       xfun_0.48         tibble_3.2.1     
[49] tidyselect_1.2.1  rstudioapi_0.17.0 knitr_1.48        htmltools_0.5.8.1
[53] rmarkdown_2.28    readr_2.1.5       compiler_4.3.3    downlit_0.4.4    
[57] readxl_1.4.3     

R/Pharma ADaM Workshop Starting at 10:02 US EST