Re: [NMusers] Incomplete circles drawn in VPC plotted using R scripts generated by PsN

From: Jan-Stefan Van der Walt <janstefan.vanderwalt_at_gmail.com>
Date: Fri, 20 Nov 2015 14:20:48 +0100

Hi Matthew,

From many years back, I remember that a quick solution was to use CairoPDF
device. I've been doing it ever since... [old school].

Kind regards
Jan-Stefan

On 20 November 2015 at 11:33, Kajsa Harling <kajsa.harling_at_farmbio.uu.se>
wrote:

> Dear Matthew,
>
> I suggest you consult the xpose.VPC documentation ( ?xpose.VPC() ) for
> instructions on how to change how values are marked in the plot. The PsN
> -rplots script uses the default settings.
>
> Best regards,
> Kajsa
>
>
> On 11/19/2015 03:56 PM, HUI, Ka Ho wrote:
>
> Dear all,
>
>
>
> I was trying to generate VPC using the R scripts generated by PsN with th=
e
> following command line:
>
>
>
> *vpc*
>
> *-samples=200*
>
> *-stratify_on=…*
>
> *-rplots=1*
>
> *-idv=TIME*
>
> *-auto_bin=unique*
>
> *-predcorr*
>
> *-varcorr*
>
> *-dir=vpc_FINAL_MODEL*
>
> *FINAL_MODEL_vpc.mod*
>
>
>
> The R script generated looks like this:
>
>
>
> *#START OF AUTO-GENERATED PREAMBLE, WILL BE OVERWRITTEN WHEN THIS FILE IS
> USED AS A TEMPLATE*
>
> *#Created 2015-11-19 at 22:05*
>
>
>
> *rplots.level <- 1*
>
> *xpose.runno <- '1_vpc'*
>
> *toolname <- 'vpc'*
>
> *pdf.filename <- paste0('PsN_',toolname,'_plots.pdf')*
>
> *pdf.title <- 'vpc diagnostic plots run 1_vpc'*
>
> *working.directory<-'C:/…'*
>
> *raw.results.file <- 'raw_results_FINAL_MODEL1_vpc.csv'*
>
> *model.directory<-'C:/…'*
>
> *model.filename<-'FINAL_MODEL1_vpc.mod'*
>
> *subset.variable<-NULL*
>
> *mod.suffix <- '.mod'*
>
> *mod.prefix <- 'FINAL_MODEL'*
>
> *tab.suffix <- ''*
>
> *tool.results.file <- 'vpc_results.csv'*
>
> *theta.labels <- c('T1','T2','T3','T4','T5','T6')*
>
> *theta.fixed <- c(FALSE,FALSE,TRUE,FALSE,FALSE,FALSE)*
>
> *omega.labels <- c('O1','O2')*
>
> *omega.fixed <- c(FALSE,FALSE)*
>
> *sigma.labels <- c('S1')*
>
> *sigma.fixed <- c(FALSE)*
>
> *n.eta <- 2*
>
> *n.eps <- 1*
>
>
>
> *vpctab <- 'vpctab'*
>
> *have.loq.data <- FALSE*
>
> *have.censored <- FALSE*
>
> *is.categorical <- FALSE*
>
> *is.tte <- FALSE*
>
> *dv <- 'DV'*
>
> *idv <- 'TIME2'*
>
>
>
> *setwd(working.directory)*
>
>
>
>
> *########################################################################=
####*
>
> *#END OF AUTO-GENERATED PREAMBLE*
>
> *#WHEN THIS FILE IS USED AS A TEMPLATE THIS LINE MUST LOOK EXACTLY LIKE
> THIS*
>
>
>
>
>
> *library(xpose4)*
>
>
>
> *pdf(file=pdf.filename,width=10,height=7,title=pdf.title)*
>
>
>
> *done <- FALSE*
>
> *if (is.tte){*
>
> * #data is in the model directory, go there to read input*
>
> * setwd(model.directory)*
>
> * xpdb <- xpose.data(xpose.runno)*
>
> * plots <- kaplan.plot(object=xpdb,VPC=T)*
>
> * #go back to vpc directory *
>
> * setwd(working.directory)*
>
> * done <- TRUE*
>
> *} *
>
>
>
> *if (is.categorical & (!done)){*
>
> * plots<-xpose.VPC.categorical(vpc.info
> <http://vpc.info>=tool.results.file,vpctab=vpctab)*
>
> * done <- TRUE*
>
> *}*
>
>
>
> *if ((have.loq.data | have.censored) & (!done) ){*
>
> * plots<-xpose.VPC.both(vpc.info
> <http://vpc.info>=tool.results.file,vpctab=vpctab)*
>
> * done <- TRUE*
>
> *}*
>
>
>
> *if (!done){*
>
> * plots<-xpose.VPC(vpc.info
> <http://vpc.info>=tool.results.file,vpctab=vpctab)*
>
> * done <- TRUE*
>
> *}*
>
>
>
> *print(plots) *
>
>
>
> *dev.off()*
>
>
>
> However the “circles” (indicating raw Cp data) are incomp=
lete and take
> the shape of a “crescent moon” instead. When run with the=
 –lloq option, the
> 1st stratification has complete circles but the remaining 2 also has the
> crescent-moon circles instead. Other parts of the plots (Shades and plots
> of CI) look normal.
>
> Can anyone suggest any possible cause and solution?
>
>
>
> Thanks and regards,
>
> Matthew Hui
>
>
> --
> -----------------------------------------------------------------
> Kajsa Harling, PhD
> System Developer
> Department of Pharmaceutical Biosciences
> Uppsala University
> Kajsa.Harling_at_farmbio.uu.se+46-(0)18-471 4308
> http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
> -----------------------------------------------------------------
>
>

Received on Fri Nov 20 2015 - 08:20:48 EST

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