RE: Confidence intervals of PsN bootstrap output
Dear all,
Below you find the thread from the PsN mailing list that could not be
included with the e-mail I sent just before this one.
Best
Jakob
Preferably keep any discussion around the specific implementation in PsN
to the PsN mailing list, as of little interest to nmusers that are not
using PsN.
The previous discussion on the PsN list, regarding the R-script used in
the PsN bootstrap is found below:
Quoted reply history
-----Original Message-----
From: fengdubianbian [mailto:[email protected]]
Sent: 15 June 2011 08:30
To: [email protected]
Subject: [Psn-general] bootstrap problem
hey all,
There is .r file auto generated by psn 3.2.4 during bootstraping.
Some vertical lines will be plot on the distribution of parameters.
Actually the Median is Mean, the mean is median.
the R code is:
if (showmean) {
legend=paste(legend, "; Mean = ", sp[3], sep="")
}
if (showmedian) {
legend=paste(legend, "; Median = ", sp[4], sep="")
}
>sp
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0001998 0.0002994 0.0002994 0.0002967 0.0002994 0.0004768
Kun Wang Ph.D
-----Original Message-----
From: Kajsa Harling [mailto:[email protected]]
Sent: 23 June 2011 11:52
To: General Discussion about PsN.
Subject: Re: [Psn-general] bootstrap problem
Thank you for the error report. This will be fixed in the next release.
Best regards,
Kajsa
-----Original Message-----
From: Ribbing, Jakob
Sent: 24 June 2011 09:25
To: General Discussion about PsN.
Cc: '[email protected]'
Subject: RE: [Psn-general] bootstrap problem
Kajsa,
While you are looking at that R script in PsN; As I recall there are
additional bugs. For example, what bootstrap samples to use is hard
coded on the script, so no matter what you set in psn.conf or on the
command line to bootstrap; for histograms the R script will only use the
samples with successful terminations. I almost always want to use all bs
samples.
When you are ready to move bootstrap post-processing into Xpose I can
send you an R script that we use at Pfizer for the PsN bootstrap. This
provides a full summary of what you may get out of a bootstrap, with
nicer graphics, tables summarizing both the nonmem covstep and the
non-parametric bootstrap and including optional parameter
transformations and bs statistics for secondary parameters. Out script
would have to be in Xpose, though, because there are too many options
for PsN.
And I would have to find time to tweak it a bit; I have written the code
only for our ePharm environment in LINUX. Unfortunately I will not find
the time to do this in 2011, but it is worth waiting for :>)
Happy summer solstice!
Jakob
________________________________