NONMEM Users Network Archive

Hosted by Cognigen

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
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>
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 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,


"Mats Karlsson" <mats.karlsson>


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


14/02/2013 08:50


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

Sent by:


Eisai Limited
Registered in England No. 2242511
Registered Address: European Knowledge Centre, Mosquito Way, Hatfield,
Hertfordshire, AL10 9SN
Please note our new telephone no. is +44 (0) 845 676 1400 and the fax is
+44 (0) 845 676 1401

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 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
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?
Jos Lommerse
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555

Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.

This email has been scanned by the Symantec Email service.
For more information please visit

If you are not the intended recipient you are notified that any
disclosure, reproduction,copying, distribution, or action taken in
reliance on the contents of this information is strictly prohibited. If
you have received this transmission in error please notify the sender
immediately and then delete this email. Email transmission cannot be
guaranteed to be secure or error free as information could be intercepted,
corrupted, lost, destroyed,arrive late or incomplete, or contain viruses.
The company/sender accepts no liability for any changes made to this email
during transmission or any damage caused by any virus transmitted by this
email. Any views or opinions expressed in this email are solely those of
the author and do not necessarily represent those of the company. The
company/sender accepts no liability for the content of this email, or for
the consequences of any actions taken on the basis of the information
provided, unless that information is subsequently confirmed in writing.
[attachment "graycol.gif" deleted by Pascal Girard/SINT/Merck] [attachment
"ecblank.gif" deleted by Pascal Girard/SINT/Merck]

This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith.

Click to access the German, French, Spanish and Portuguese versions of this disclaimer.

(image/gif attachment: 01-part)

(image/gif attachment: 02-part)

(image/gif attachment: 03-part)

(image/gif attachment: 04-part)

(image/gif attachment: 05-part)

(image/gif attachment: 06-part)

(image/gif attachment: 07-part)

(image/gif attachment: 08-part)

(image/gif attachment: 09-part)

(image/gif attachment: 10-part)

(image/gif attachment: 11-part)

Received on Thu Feb 14 2013 - 08:11:49 EST

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to:

Once subscribed, you may contribute to the discussion by emailing: