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

From: HUI, Ka Ho <matthew.hui_at_link.cuhk.edu.hk>
Date: Fri, 20 Nov 2015 15:30:37 +0000

Thanks all for the solutions provided!

Mannie and Joe, the tiff() or png() or jpeg() works well. But the use of "u=
seDingbats=F" suggested by Erik looks a bit better since it uses vector i=
nstead of pixel graphic.

Matthew


-----Original Message-----
From: Standing Joseph (GREAT ORMOND STREET HOSPITAL FOR CHILDREN NHS FOUNDA=
TION TRUST) [mailto:joseph.standing_at_nhs.net]
Sent: Friday, November 20, 2015 8:24 PM
To: Kajsa Harling <kajsa.harling_at_farmbio.uu.se>; HUI, Ka Ho <matthew.hui_at_li=
nk.cuhk.edu.hk>; nmusers_at_globomaxnm.com
Subject: RE: [NMusers] Incomplete circles drawn in VPC plotted using R scri=
pts 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

________________________________________
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 scri=
pts generated by PsN

Dear Matthew,

I suggest you consult the xpose.VPC documentation ( ?xpose.VPC() ) for inst=
ructions on how to change how values are marked in the plot. The PsN -rplot=
s 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 US=
ED 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,FAL=
SE,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=vpct=
ab)
        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 cresc=
ent-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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Received on Fri Nov 20 2015 - 10:30:37 EST

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