NONMEM Users Network Archive

Hosted by Cognigen

Re: [NMusers] forest plots in Xpose?

From: Ron Keizer <ron_at_pirana-software.com>
Date: Wed, 16 Sep 2015 17:08:53 -0700

dear Pascal,

there seem to be copies of that library e.g. here
(*http://www2.uaem.mx/r-mirror/web/packages/popPK/index.html
<http://www2.uaem.mx/r-mirror/web/packages/popPK/index.html>*) and here (
https://cran.r-project.org/src/contrib/Archive/popPK/). You should be able
to download from there and install from the local zip file. I don't know
this library, so I'm not sure if it still works with current version of
Xpose. I also don't know of a different module that creates these plots,
but with the dplyr and ggplot2 libraries it shouldn't be more than 5-10
lines of code to create such a plot.

On a sidenote, I'm not a fan of the term "Forest plot" for these plots. The
"original" Forest plots show data across multiple studies (e.g. in a
meta-analysis), so calling it "Forest plot" could lead to confusion with
statisticians or clinicians. A more important reason, however, is that it
is not immediately clear what is actually shown in the plot. Various
covariate data can be summarized using the "Forest plot style", such as:

- uncertainty in covariate effect size (e.g. obtained from covariance step,
bootstrap, or posterior distribution from MCMC)
- inter-individual variability in covariate effect (distribution of
observed covariate values * covariate effect size)
- time-variance of the covariate effects
- a combination of 1 and 2?

So a covariate "Forest" covariate-plot should always be accompanied with a
description of what data is actually shown.
BTW, I think all of the above plots have utility in some way, either in
diagnosis, data checkout, or communicating modeling results. Would be great
if someone implemented an R package that could do all of the above :) I
assume the popPK package makes type 2, but it is not mentioned in the
manual.

best regards,
Ron


On Wed, Sep 16, 2015 at 12:57 AM, Pascal Girard <
pascal.girard_at_merckgroup.com> wrote:

> Dear NONMEM users, Dear Uppsala Folks, Dear Christopher
>
>
>
> I was looking for some Xpose function that would automatically create a
> forest plot from NONMEM output in order to present the results of covaria=
te
> analysis, assuming that all covariate models have been implemented the sa=
me
> way with same NULL value. The only thing I found was the Covariates
> function in the popPK package, which makes use of Xpose, developed by Chr=
istoffer
> Tornoe while he was at FDA.
> http://www2.uaem.mx/r-mirror/web/packages/popPK/popPK.pdf
>
>
>
> But this package looks like to be no longer supported and has been remove=
d
> from the CRAN.
>
>
>
> Has anyone developed such a package?
>
>
>
> *With best regards / Mit freundlichen Grüßen / Cordialement */=
 祝好 /
> よろしくお願いし=
ます
>
> Pascal
>
>
>
> Pascal Girard
>
> Director, Pharmacometry
>
> Merck Serono | Global Early Development
>
>
>
> * "Merck – Living Innovation" *
>
>
>
> Merck Institute for Pharmacometrics - Merck Serono S.A.
>
> EPFL Innovation Park - Building I, CH-1015 Lausanne, Switzerland
>
> Phone: +41 21 900 3702 | Mobile: +41 79 508 7898
>
> Email: pascal.girard_at_merckgroup.com | www.merckserono.com
>
> Mandatory information can be found at:
> http://www.merckgroup.com/mandatories
>
> *Please consider your environmental responsibility before printing this
> e-mail*
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipien=
t,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message an=
d
> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not guarantee that this message is free of viruses and do=
es
> not accept liability for any damages caused by any virus transmitted
> therewith.
>
>
>
> Click http://www.merckgroup.com/disclaimer to access the German, French,
> Spanish and Portuguese versions of this disclaimer.
>



-------------------------------
Pirana Software & Consulting BV
_at_ronpirana

Received on Wed Sep 16 2015 - 20:08:53 EDT

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: nmusers-request_at_iconplc.com. Once subscribed, you may contribute to the discussion by emailing: nmusers_at_globomaxnm.com.