RE: Incomplete circles drawn in VPC plotted using R scripts generated by PsN
I think it is a problem with R making pdfs. Workaround: try using tiff() or png() instead - then you can save the image as a pdf.
Joe
Quoted reply history
________________________________________
From: owner-nmusers_at_globomaxnm.com [owner-nmusers_at_globomaxnm.com] On Behalf Of Kajsa Harling [kajsa.harling_at_farmbio.uu.se]
Sent: 20 November 2015 10:33
To: HUI, Ka Ho; nmusers_at_globomaxnm.com
Subject: Re: [NMusers] Incomplete circles drawn in VPC plotted using R scripts generated by PsN
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 the following command line:
vpc
-samples 0
-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,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=tool.results.file,vpctab=vpctab)
done <- TRUE
}
if ((have.loq.data | have.censored) & (!done) ){
plots<-xpose.VPC.both(vpc.info=tool.results.file,vpctab=vpctab)
done <- TRUE
}
if (!done){
plots<-xpose.VPC(vpc.info=tool.results.file,vpctab=vpctab)
done <- TRUE
}
print(plots)
dev.off()
However the circles (indicating raw Cp data) are incomplete 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<mailto:Kajsa.Harling_at_farmbio.uu.se>
+46-(0)18-471 4308
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
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