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Introduction to PKNCA: Automation of Noncompartmental Analysis in R (May 25th, Noon EDT)

studygroup
#1

Title: Introduction to PKNCA: Automation of Noncompartmental Analysis in R
General Topic: Introduction to PKNCA: Automation of Noncompartmental Analysis in R
Presenter: William S. Denney
Date(s): 25-May-2016, 1-June-2016
Time: Noon EDT
Livelink Feed: http://www.youtube.com/watch?v=WCmFrheYtcc
Background Resources and Code for the Audience: https://cran.r-project.org/web/packages/PKNCA/

https://github.com/isop-phmx/studyGroup/issues/17

Background

The PKNCA R package is designed to perform all noncompartmental analysis (NCA) calculations for pharmacokinetic (PK) data. The package is broadly separated into two parts (calculation and summary) with some additional housekeeping functions.

The primary and secondary goals of the PKNCA package are to 1) only give correct answers to the specific questions being asked and 2) automate as much as possible to simplify the task of the analyst. When automation would leave ambiguity or make a choice that the analyst may have an alternate preference for, it is either not used or is possible to override.

Note that backward compatibility will not be guaranteed until version 1.0. Argument and function changes will continue until then. These will be especially noticable around the inclusion of IV NCA parameters and additional specifications of the dosing including dose amount and route.

1 Like
#2

@bdenney , let me know when you have the livelink feed and I will add it here

#3

@isoplinks - @bdenney needs orientation of setting up the live link. The instructional video is on they way and will make it into the general instructions here on discuss soon.

1 Like
#4

@bdenney Looking forward to the talk next week, and even starting to prepare beforehand.

When I load the package initially, I get the following error

 ERROR: dependency 'digest' is not available for package 'PKNCA'
* removing 'C:/Users/corrigb/Documents/R/win-library/3.2/PKNCA'
 Error: Command failed (1)

Any thoughts on what I am doing wrong/need to add beforehand?

#5 
 install.packages("digest")

Seemed to fix it :slight_smile:

#6

I’m glad that

install.packages("digest")

worked for you. I’ve seen problems with incorrect installations of the digest package before where it required removing current installations and then running install.packages. If others have the issue, try the following:

  1. Find your library locations (run .libPaths() at the R prompt)
  2. Go to each of the listed directories and delete the subdirectory named “digest”
  3. Reinstall the digest package with install.packages(“digest”)
#7

You knew that I was going to ask this…any plans for a nice shiny app wrapper for the package? Should someone in our community be working on this?

#8

There is a group working on a CDISC standard for NCA pk datasets. Was wondering i fyou are aware of it and if the package is being planned with the standards in mind?

#9

Thanks for this. Will the webinar be made available on Youtube as a video as well? I might miss the live version.

#10

@isoplinks A Shiny app wrapper is in the future plans. I want to get the underlying calculations completed before starting on any form of graphical interface.

#11

@isoplinks There is a consortium of people and companies working on NCA validation in addition to the CDISC standardization for NCA PK datasets. One of the members of the consortium is also working on the CDISC NCA standard (ADaM NCA or ADNCA). These will be briefly mentioned during today’s webinar.

One goal of PKNCA is to take any input data set and make it more standardized. Currently, the calculation engine for PKNCA is dataset agnostic (you tell the columns to use, it’ll figure out the rest). In future versions, I intend to make connectors so that there is almost no effort to input standardized datasets. If you provide SDTM EX and PC domains, ADaM NCA, or ADaM PC (ADPC) data, PKNCA will simplify the selection of options to do the calculations.

On the output side, PKNCA is SDTM PP-ready. What I mean by that is: The raw outputs from PKNCA are very similar to the SDTM PP domain, and a simple wrapper (which will come in a future version) will format the output for the PP domain. I don’t force PP domain output because there are many scenarios where the users may not want the full PP domain output (like exploratory or academic analyses).

2 Likes
#12

@henrik The webinar will be available on YouTube at the following link: https://www.youtube.com/watch?v=WCmFrheYtcc

Also, the slides from the webinar will be in the vignettes section of the PKNCA GitHub repository: https://github.com/billdenney/pknca/blob/master/vignettes/PKNCA-ISoP_Study_Group-2016-05-25.pptx?raw=true

If you have any questions, please let me know-- either here, on GitHub, or by email.

#13

Hi @bdenney ,

Could you please mention how to calculate partial AUC’s while conducting the : Introduction to PKNCA presentation.

Thanks

#14

Bill can you check the sound. We are not hearing anything

#15

I am testing sound now.

#16

excellent, we can hear now. thanks

#17

@bdenney - can you comment on the speed of the NCA routines in PKNCA especially with large datasets e.g. model simulated datasets that can run up to 100-1000 simulation reps.

#18

Thank you Bill. I forgot to ask, is there a built in reporting function?

#19

Thanks Bill,

Is there an option to calculate % predicted AUC0-inf?

#20

Can you set individual terminal point selection?