Re: forest plots in Xpose?
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
Quoted reply history
On Wed, Sep 16, 2015 at 12:57 AM, Pascal Girard <
[email protected]> 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 covariate
> analysis, assuming that all covariate models have been implemented the same
> 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
> Christoffer
> 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 removed
> 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
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