Re: 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=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=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 1 st
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
[email protected]
+46-(0)18-471 4308
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/