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Introduction to PKPDsim

Please use this thread to post all of your questions in this thread. @Ron_Keizer will monitor this page during his tutorial and answer all questions either during or after the session. The forum and twitter hashtag for asking questions on this webinar or in general about study groups is #askphmx. Please use this in every post to allow easy searches.

General Topic: PKPDsim, a library for simulation of systems of differential equations in the pharmacometric setting
Presenter: Ron Keizer
Date: Apr 29
Location: SF, CA
Time: 9am PT, noon EST
Webcast: http://www.youtube.com/watch?v=9JNW3YZ3f9k6
Background Resources for the Audience: https://github.com/ronkeizer/PKPDsim

1 Like

Can you add a loading + infusion dose?
In the sense, can type=“infusion” be a list

@Ron_Keizer, thanks for the webinar!
I see in the background materials on the github link above you have a shiny app. Does the pkpdsim package create the shiny code, or is that a standalone app you have created based on the package?

Brian - Ron has a shiny app that integrates into PKDPsim. you don’t have to write shiny code (for basic apps) if I am not wrong

install_github(“ronkeizer/PKPDsimShiny”)
the shiny part has its own package it is automatic. one caveat is that it is not compatible with shinyapps.io but we need to check.

one more tip if you gert annoying Rtools is not installed try to have this defined in your R session:
Sys.setenv(PATH="%PATH%;C:/Rtools/gcc-4.6.3/bin;c:/Rtools/bin")

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hi Brian,
the Shiny functionality was initially embedded into PKPDsim. However, too make development easier I recently split off that functionality into a separate package: PKPDsimShiny (also on my GitHub page). Using that package you can create a Shiny app on-the-fly. Instead of calling sim_ode() like I showed in the video, you would just call sim_ode_shiny(), with the same arguments.
One caveat is that that the PKPDsimShiny package at the moment is a bit less well developed than PKPDsim, so it might be that you will encounter an error. I hope to find some time soon to work on the Shiny part too.

2 Likes

Hi Ron,
I just tried it works !
https://isop.shinyapps.io/shiny-pkpd/
very nice introduction. Thank you
Bests,
Samer

1 Like

@Ron_Keizer Very nice tool. Thank you.
How to assign individual covariate to each ID?