CDISC datasets from R. Why not? [Software]

posted by Helmut Homepage – Vienna, Austria, 2019-03-21 16:43  – Posting: # 20066
Views: 1,716

Hi WhiteCoatWriter,

» While Phoenix needs an additional package to be purchased, I feel that the same can be done by creating tables on phoenix (or importing in .csv) and exporting it to .xpt without the specific package which I assume will only help with limited datasets.

[image]I did that myself before I got Certara’s CDISC-license. Never tried anything else than raw-data (scheduled & actual time points, concentrations) and NCA-results.

» » If you are an experienced R-coder, consider writing a package …
»
» I might not be an expert coder/programmer, but I have been working on this for quite some time. Thank you for the references, will definitely try doing something.

Needs patience and the learning curve is not flat. A coding environment like R-Studio and an account at GitHub greatly helps.

» It really has been a challenge to get it validated using pinnacle validator.

I believe it. Congratulations!

» Also, when it comes to Adam datasets it specially requires SAS date format which I assume is not possible to be created on R.

SAS’ date value (days since 1960-01-01) and datetime (seconds since 1960-01-01 midnight) are a pain in the ass. The format ddmmmyy:hh:mm:ss is just ugly. I played around in R a bit and see what you mean. I wouldn’t say it’s impossible, only tricky.*
The “origin” of date- and time-objects in R is (like the UNIX Epoch time) 1970-01-01 00:00:00 UTC. The timezone is important. Is National Language Support (NLS) part of SAS’ base installation? Without, everything is in local time. I found a funny document stating

The last counter is the datetime counter. This is the number of seconds since midnight, January 1, 1960. Why January 1, 1960? One story has it that the founders of SAS wanted to use the approximate birth date of the IBM 370 system, and they chose January 1, 1960 as an easy-to-remember approximation.

Heck, did they mean the timezone (EST = UTC-5) of Poughkeepsie, NY?
The man-page of as.POSIX() claims that the origin of SAS’ datetime is 1960-01-01 00:00:00 GMT but I prefer to avoid a second-hand reference.

» While No other regulatory mandates datasets for Bio equivalence study, I still keep wondering what really sparked the USFDA in the mid of Dec 2016 to make CDISC datasets mandate for regulatory submission.

Not the slightest idea.



Cheers,
Helmut Schütz
[image]

The quality of responses received is directly proportional to the quality of the question asked. ☼
Science Quotes

Complete thread:

Activity
 Mix view
Bioequivalence and Bioavailability Forum |  Admin contact
19,818 posts in 4,201 threads, 1,361 registered users;
online 8 (0 registered, 8 guests [including 5 identified bots]).
Forum time (Europe/Vienna): 19:05 CEST

If I find 10,000 ways something won’t work, I haven’t failed.
I am not discouraged, because every wrong attempt discarded
is another step forward.    Thomas Alva Edison

The BIOEQUIVALENCE / BIOAVAILABILITY FORUM is hosted by
BEBAC Ing. Helmut Schütz
HTML5