NONMEM Users Network Archive

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RE: Bootstrap, re-using inital model run results

From: pascal.girard
Date: Thu, 14 Feb 2013 14:11:49 +0100

Dear Anuhbia,

Since bootstrap is performed to replace the estimation of precision that
is performed in the $COV step, you definitively do not need the $COV
option when you do a bootstrap.

Then CI are obtained based on the quantiles of the bootstrap estimates.

Kind regards,

Pascal Girard, PhD
pascal.girard
Head of Modeling & Simulation - Oncology
Global Exploratory Medicine
Merck Serono S.A. · Geneva
Tel: +41.22.414.3549
Cell: +41.79.508.7898




From: <Anubha_Gupta
To: "Mats Karlsson" <mats.karlsson armbio.uu.se>
Cc: <jos.lommerse
Date: 14/02/2013 10:33
Subject: RE: [NMusers] Bootstrap, re-using inital model run results
Sent by: owner-nmusers



Dear Mats

My question is more related to boot strapping itself.

if data set and model I am working with takes long time to run, then
during bootstrap run I only run $EST and skip $COV step. We will get
confidence interval for parameter from bootstrap results.

What is your opinion on that?

Best regards

Anubha

...................................
Anubha Gupta, PhD
Associate Director,
Modeling and Simulation
Clinical Pharmacology
Scientific and Clinical Support CFU
European Knowledge Centre
Mosquito Way, Hatfield, Herts.
AL10 9SN
United Kingdom


"Mats Karlsson" ---14/02/2013 08:50:29---Dear Jos,


From:

"Mats Karlsson" <mats.karlsson rmbio.uu.se>

To:

"'Lommerse, JPM \(Jos\)'" <jos.lommerse
<nmusers

Date:

14/02/2013 08:50

Subject:

RE: [NMusers] Bootstrap, re-using inital model run results

Sent by:

owner-nmusers


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Registered Address: European Knowledge Centre, Mosquito Way, Hatfield,
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Dear Jos,
 
If you haven’t run the original model (indicated by absence of lst-file
with the same prefix) psn will run it before the bootstrap. If you have
run it, PsN will not rerun it. It will use the results in the
corresponding lst file. If you have run it and called it something else,
you could use the “-out=xxx.yyy” to point to the correct file if that does
not follow naming conventions. If you have not run it and really don’t
want to run it, you could substitute xxx.yyy for some other output file
with similar structure.
 
Best regards,
Mats
 
Mats Karlsson, PhD
Professor of Pharmacometrics
 
Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala
 
Phone: +46 18 4714105
Fax + 46 18 4714003
 
From: owner-nmusers
On Behalf Of Lommerse, JPM (Jos)
Sent: 14 February 2013 08:29
To: nmusers
Subject: [NMusers] Bootstrap, re-using inital model run results
 
Hi
 
I would like to ask to NONMEM community whether it is possible to re-use
the results of a nonmem model run when starting bootstrapping.
As I understand, a bootstrap run using PsN starts with a single
calculation of the model of interest and data set as is. Once this initial
model run
has completed, the actual bootstrapping starts by sampling from the
initial data set to the requested number of samples.
However, the initial run often has been carried out already, and the
bootstrap method this seems to be repeated.
 
I am dealing with a rather time consuming model / data set. Therefore I
was wondering whether it is possible the re-use the results of a nonmem
model run and start the bootstrapping directly without repeating this
initial nonmem model run. I was not able to find any option to do so.
Perhaps there
is way around?
 
Thanks,
 
Jos
 
Jos Lommerse
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555
jos.lommerse

MSD
Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands
  
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Received on Thu Feb 14 2013 - 08:11:49 EST

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