NONMEM Users Network Archive

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Re: Updating xpose4 stratification headers in VPCs

From: Jakob Ribbing <jakob.ribbing>
Date: Thu, 24 Sep 2020 08:57:59 +0200

Hi Rik,

Indeed, you can make it prettier, more informative and more ggplot-like =
(but it is still a lattice plot).
You can change the xposeVPC object (vpcPlot, in my example), e.g. =
setting size of strip labels, y-label, etc, by updating the plot list.
vpcPlot
arguments, like ylab=list(“Your y-label",cex=2)])

Then, you can select what panels you want to include, and give them the =
appropriate strip-label text:
PrettierPlot <- c(“Dose A"=vpcPlot
                  “Dose B"=vpcPlot
                  “Dose C"=vpcPlot
c(3,1))

That last step one has to be careful, as it is a bit error prone: you =
manually set the labels and if you get it wrong it will be mislabelled.

Best regards

Jakob



Jakob Ribbing, Ph.D.

Senior Consultant, Pharmetheus AB


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> On 24 Sep 2020, at 08:34, Rik Schoemaker <rik.schoemaker
wrote:
>
> Dear all,
>
> I realise that xpose4 is perceived as getting a bit old, but as far as =
I can tell it is still very widely used in the community, and =
auto-generated R-code from PsN still uses xpose4. My own hesitation has =
always been in the perceived lack of options to customise the output, =
but it has so many handy features 😊. Currently I'm running =
VPCs with multi-level stratification implemented using the STRT variable =
in NONMEM code, and my resulting VPCs have 4 graphs. However, the =
headings of these graphs are the pretty ugly "STRT==0.5", =
"STRT==101" etc. Is there a way to change this to a nice factor with =
customisable layout? And while we're at it: is there a way to =
access/extract the individual graphs so these can be formatted and/or =
printed separately?
>
> Thanks very much in advance!
>
> Kind regards,
>
> Rik
>
>
> xpose4::xpose.VPC(pc.info <http://pc.info/>='vpc_results.csv',
> vpctab='vpctab008',#xlim=c(0,42),
> =
PI='lines',type='n',PI.identify.outliers=FALSE,#by='STRT',
> PI.x.median=TRUE,
> PI.ci.area.smooth=TRUE,
> PI.rug=FALSE,
> PI.ci.up.arcol="dodgerblue",
> PI.ci.down.arcol="dodgerblue",
> PI.real.med.col="brown",
> PI.real.up.col="brown",
> PI.real.down.col="brown",col="brown",
> main="VPC final model",ylb="Drug X =
(ng/mL)",xlb="Time (h)",ylim=c(0.01,120),logy=TRUE,
> scales = list(x = list(at = =
seq(0,36,3))))
>
>
> Rik Schoemaker, PhD
> Occams Coöperatie U.A.
> Malandolaan 10
> 1187 HE Amstelveen
> The Netherlands
> www.occams.com <http://www.occams.com/>
> +31 20 441 6410
> rik.schoemaker
>
> <image001.png>


Received on Thu Sep 24 2020 - 02:57:59 EDT

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