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 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
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/
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: [email protected] [[email protected]] On Behalf Of
Kajsa Harling [[email protected]]
Sent: 20 November 2015 10:33
To: HUI, Ka Ho; [email protected]
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=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 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
[email protected]<mailto:[email protected]>
+46-(0)18-471 4308
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
-----------------------------------------------------------------
********************************************************************************************************************
This message may contain confidential information. If you are not the intended
recipient please inform the
sender that you have received the message in error before deleting it.
Please do not disclose, copy or distribute information in this e-mail or take
any action in reliance on its contents:
to do so is strictly prohibited and may be unlawful.
Thank you for your co-operation.
NHSmail is the secure email and directory service available for all NHS staff
in England and Scotland
NHSmail is approved for exchanging patient data and other sensitive information
with NHSmail and GSi recipients
NHSmail provides an email address for your career in the NHS and can be
accessed anywhere
********************************************************************************************************************
I'm not sure if this is related, but I always use the "useDingbats=F" option
when creating pdfs in R.
Erik
Quoted reply history
________________________________________
From: [email protected] [[email protected]] on behalf of
Standing Joseph (GREAT ORMOND STREET HOSPITAL FOR CHILDREN NHS FOUNDATION
TRUST) [[email protected]]
Sent: Friday, November 20, 2015 1:23 PM
To: Kajsa Harling; HUI, Ka Ho; [email protected]
Subject: RE: [NMusers] 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
________________________________________
From: [email protected] [[email protected]] On Behalf Of
Kajsa Harling [[email protected]]
Sent: 20 November 2015 10:33
To: HUI, Ka Ho; [email protected]
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=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 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
[email protected]<mailto:[email protected]>
+46-(0)18-471 4308
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
-----------------------------------------------------------------
********************************************************************************************************************
This message may contain confidential information. If you are not the intended
recipient please inform the
sender that you have received the message in error before deleting it.
Please do not disclose, copy or distribute information in this e-mail or take
any action in reliance on its contents:
to do so is strictly prohibited and may be unlawful.
Thank you for your co-operation.
NHSmail is the secure email and directory service available for all NHS staff
in England and Scotland
NHSmail is approved for exchanging patient data and other sensitive information
with NHSmail and GSi recipients
NHSmail provides an email address for your career in the NHS and can be
accessed anywhere
********************************************************************************************************************
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
Quoted reply history
On 20 November 2015 at 11:33, Kajsa Harling <[email protected]>
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 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
> 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 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
> [email protected]+46-(0)18-471 4308
> http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
> -----------------------------------------------------------------
>
>
Thanks all for the solutions provided!
Mannie and Joe, the tiff() or png() or jpeg() works well. But the use of
"useDingbats=F" suggested by Erik looks a bit better since it uses vector
instead of pixel graphic.
Matthew
Quoted reply history
-----Original Message-----
From: Standing Joseph (GREAT ORMOND STREET HOSPITAL FOR CHILDREN NHS FOUNDATION
TRUST) [mailto:[email protected]]
Sent: Friday, November 20, 2015 8:24 PM
To: Kajsa Harling <[email protected]>; HUI, Ka Ho
<[email protected]>; [email protected]
Subject: RE: [NMusers] 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
________________________________________
From: [email protected] [[email protected]] On Behalf Of
Kajsa Harling [[email protected]]
Sent: 20 November 2015 10:33
To: HUI, Ka Ho; [email protected]
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=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 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
--
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Kajsa Harling, PhD
System Developer
Department of Pharmaceutical Biosciences Uppsala University
[email protected]<mailto:[email protected]>
+46-(0)18-471 4308
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
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