dear NM-community,
Is NONMEM reliably used for single-patient AUC-calculation in cases of
linear PK, or is e.g. WinNonLin (or similar software) preferred in such
cases?
best regards,
Markus
--
Markus Joerger MD PhD
Associate Professor
Medical Oncology&Clinical Pharmacology
Cantonal Hospital
9007 St. Gallen
Switzerland
[email protected]
[email protected]
Phone: +41-765591070
Fax: +41-714946325
single-patient AUC
Hi Markus,
Typically, AUCs are calculated using software like WinNonlin because it is both
simpler and more objective (the model is simple and specified a priori).
Generally, the model is just used as the linear-up, log-down trapezoidal rule
with personal (or corporate) preferences on handling BLQ and extrapolation to
infinity.
Thanks,
Bill
Quoted reply history
On Sep 1, 2012, at 11:13 PM, "markus joerger"
<[email protected]<mailto:[email protected]>> wrote:
dear NM-community,
Is NONMEM reliably used for single-patient AUC-calculation in cases of linear
PK, or is e.g. WinNonLin (or similar software) preferred in such cases?
best regards,
Markus
--
Markus Joerger MD PhD
Associate Professor
Medical Oncology&Clinical Pharmacology
Cantonal Hospital
9007 St. Gallen
Switzerland
[email protected]<mailto:[email protected]>
[email protected]<mailto:[email protected]>
Phone: +41-765591070
Fax: +41-714946325
Dear Markus,
I guess it depends on how you plan to make the estimation:
1) If it is by NCA, other programs will do this
2) If it is as model-based, non-linear regression, many programs will
do it (incl NONMEM)
3) If you want to analyse the individual data using a previous
population PK model as prior, NONMEM and other non-linear mixed effects
models are probably preferable.
Best regards,
Mats
Mats Karlsson, PhD
Professor of Pharmacometrics
FIRST WORLD CONFERENCE ON PHARMACOMETRICS, 5-7 September 2012, Seoul (
http://www.go-wcop.org/ www.go-wcop.org)
Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala
Phone: +46 18 4714105
Fax + 46 18 4714003
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of markus joerger
Sent: 02 September 2012 04:40
To: NONMEM
Subject: [NMusers] single-patient AUC
dear NM-community,
Is NONMEM reliably used for single-patient AUC-calculation in cases of
linear PK, or is e.g. WinNonLin (or similar software) preferred in such
cases?
best regards,
Markus
--
Markus Joerger MD PhD
Associate Professor
Medical Oncology&Clinical Pharmacology
Cantonal Hospital
9007 St. Gallen
Switzerland
[email protected]
[email protected]
Phone: +41-765591070
Fax: +41-714946325
Dear NM-Users,
I am doing a simulation using R, in which the within and between subject
variations, "EPSILON" and "OMEGA", are needed. They are automatically listed in
the ***.lst file of the NONMEM outputs. Is there a way I can read them from my
NONMEM output into R?
Thanks,
Shirley
Dr. Xiaoli Shirley Hou
Senior Biometrician, ECDS
351 N. Sumneytown Pike, UG1C36
North Wales, PA. 19454.
Phone (540) 381-9599
Fax (267) 305-6395
VoiceMailBox (800) 737-2088 ext 68134
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
http://www.merck.com/contact/contacts.html) 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.
Dear Shirley, If you have access in your group* to the Connect module of
Phoenix you will find that NONMEM jobs executed via this interface will
automatically extract certain information including these as tables for use in
other 'downstream' objects in your workflow which could include R. It also
supports PsN, Xpose, SAS, SigmaPlot and S-plus.
There are some webinars (e.g.
http://www.pharsight.com/events/eventsonline_archive.php#replay_049) that can
expand on my comments if you are interested and an example project in the User
Forum.
Best regards,
Simon.
*I know your organisation already has some float licenses for this.
Alterantively we could set you up with an evaluation license.
___________________________________
[email protected]<mailto:[email protected]>
Senior Scientific Consultant
Pharsight- A Certara(tm) Company
Get tips and discuss Pharsight products with other users;
www.pharsight.com/extranet
___________________________________
http://www.pharsight.com/training/training_upcoming.php
Satellite workshops at PAGE, 5 June 2012, Venice, Italy.
08:30 - 12:30 "Phoenix Connect: Linking Modeling and Simulation Tools,
including NONMEM, R, Xpose & PsN, in Phoenix Workflows"
https://pharsight.securesites.com/training/course_display_new.php?details_id=98.
13:00 - 17:00 "An Overview of the QRPEM Algorithm in Phoenix NLME"
https://pharsight.securesites.com/training/course_display_new.php?details_id=99.
Introduction to Phoenix WinNonlin 25-27 Sep. 2012 Amsterdam, The Netherlands
Population Modeling Methodology using Phoenix NLME 2-4 Oct. 2012 Paris, France
Introduction to Phoenix WinNonlin 4-6 Dec. 2012 London, UK
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Hou, Xiaoli Shirley
Sent: Sunday, September 02, 2012 10:50 PM
To: NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear NM-Users,
I am doing a simulation using R, in which the within and between subject
variations, "EPSILON" and "OMEGA", are needed. They are automatically listed in
the ***.lst file of the NONMEM outputs. Is there a way I can read them from my
NONMEM output into R?
Thanks,
Shirley
Dr. Xiaoli Shirley Hou
Senior Biometrician, ECDS
351 N. Sumneytown Pike, UG1C36
North Wales, PA. 19454.
Phone (540) 381-9599
Fax (267) 305-6395
VoiceMailBox (800) 737-2088 ext 68134
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
http://www.merck.com/contact/contacts.html) 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.
_________________________________________________________________
Dear Shirley,
If you dont have access to expensive software like Phoenix you can use this
R-script that reads your .lst file and extracts the EPSILON and ETAs. Note:
this script gives you the CORR matrix, if you want the COV matrix just
change it in the 2nd and 3rd row of the script.
#------ Extract EPSILON & ETAS from .lst ---
lst <- readLines(paste("YOUR_LIST_FILE.lst",sep="")) # Read in .lst file
row_startOMEGA <- grep("OMEGA - CORR MATRIX FOR RANDOM EFFECTS - ETAS
*******", lst, fixed=T) # Find the start of CORR MATRIX - ETAS
row_startSIGMA <- grep("SIGMA - CORR MATRIX FOR RANDOM EFFECTS - EPSILONS
***", lst, fixed=T) # Find the start of CORR MATRIX - EPSILON
n_ETAS <- (row_startSIGMA-row_startOMEGA-7)/3 # Find number of ETAs, 7
"emtpy" rows, 3 rows per ETA
CORRMATRIX_ETAS <- lst[row_startOMEGA:row_startSIGMA] # Extract the corr
matrix - ETA
CORRMATRIX_ETAS <- CORRMATRIX_ETAS[seq(7,(n_ETAS-1)*3+7,3)] # Extract the
numbers in the matrix
ETAS <- signif(as.numeric(gsub("\\D", "", CORRMATRIX_ETAS)),3)/1000 # Remove
correlations, signif to get 3 significant digits, /1000 to get %
ETA_character_vector <- paste(rep("ETA",n_ETAS),seq(1,n_ETAS,1),sep="") #
Create a character vector containing ETAn
ETAS <- data.frame(ETAS,ETA_character_vector) # Create data frame
CORRMATRIX_SIGMA <- lst[row_startSIGMA+6] # Extract the corr matrix -
EPSILON
EPS <- signif(as.numeric(gsub("\\D", "", CORRMATRIX_SIGMA)),3)/10000 #
/10000 to get %
#------ End of script ------------
Best regards,
Oskar Alskär
_____________________________________________
Description: uu logo red 60
Oskar Alskär, MSc Pharm
PhD Student
Pharmacometrics group
Department of Pharmaceutical Biosciences
Uppsala University
Box 591
75124 Uppsala
Sweden
[email protected]
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Simon Davis
Sent: den 3 september 2012 11:36
To: Hou, Xiaoli Shirley; NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear Shirley, If you have access in your group* to the Connect module of
Phoenix you will find that NONMEM jobs executed via this interface will
automatically extract certain information including these as tables for use
in other downstream objects in your workflow which could include R. It
also supports PsN, Xpose, SAS, SigmaPlot and S-plus.
There are some webinars (e.g.
http://www.pharsight.com/events/eventsonline_archive.php#replay_049) that
can expand on my comments if you are interested and an example project in
the User Forum.
Best regards,
Simon.
*I know your organisation already has some float licenses for this.
Alterantively we could set you up with an evaluation license.
___________________________________
[email protected]
Senior Scientific Consultant
Pharsight- A Certara Company
Get tips and discuss Pharsight products with other users;
www.pharsight.com/extranet
___________________________________
http://www.pharsight.com/training/training_upcoming.php
Satellite workshops at PAGE, 5 June 2012, Venice, Italy.
08:30 12:30 Phoenix Connect: Linking Modeling and Simulation Tools,
including NONMEM, R, Xpose & PsN, in Phoenix Workflows register
https://pharsight.securesites.com/training/course_display_new.php?details_i
d=98 .
13:00 17:00 An Overview of the QRPEM Algorithm in Phoenix NLME details
https://pharsight.securesites.com/training/course_display_new.php?details_i
d=99 .
Introduction to Phoenix WinNonlin 25-27 Sep. 2012 Amsterdam, The
Netherlands
Population Modeling Methodology using Phoenix NLME 2-4 Oct. 2012 Paris,
France
Introduction to Phoenix WinNonlin 4-6 Dec. 2012 London, UK
From: [email protected] [mailto:[email protected]] On
Behalf Of Hou, Xiaoli Shirley
Sent: Sunday, September 02, 2012 10:50 PM
To: NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear NM-Users,
I am doing a simulation using R, in which the within and between subject
variations, "EPSILON" and "OMEGA", are needed. They are automatically listed
in the ***.lst file of the NONMEM outputs. Is there a way I can read them
from my NONMEM output into R?
Thanks,
Shirley
Dr. Xiaoli Shirley Hou
Senior Biometrician, ECDS
351 N. Sumneytown Pike, UG1C36
North Wales, PA. 19454.
Phone (540) 381-9599
Fax (267) 305-6395
VoiceMailBox (800) 737-2088 ext 68134
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
http://www.merck.com/contact/contacts.html) 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.
_________________________________________________________________
Dear Simon,
Thanks for the information. I will check it.
Best!
Shirley
Quoted reply history
________________________________
From: Simon Davis [mailto:[email protected]]
Sent: Monday, September 03, 2012 5:36 AM
To: Hou, Xiaoli Shirley; NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear Shirley, If you have access in your group* to the Connect module of
Phoenix you will find that NONMEM jobs executed via this interface will
automatically extract certain information including these as tables for use in
other 'downstream' objects in your workflow which could include R. It also
supports PsN, Xpose, SAS, SigmaPlot and S-plus.
There are some webinars (e.g.
http://www.pharsight.com/events/eventsonline_archive.php#replay_049) that can
expand on my comments if you are interested and an example project in the User
Forum.
Best regards,
Simon.
*I know your organisation already has some float licenses for this.
Alterantively we could set you up with an evaluation license.
___________________________________
[email protected]<mailto:[email protected]>
Senior Scientific Consultant
Pharsight- A Certara(tm) Company
Get tips and discuss Pharsight products with other users;
www.pharsight.com/extranet
___________________________________
http://www.pharsight.com/training/training_upcoming.php
Satellite workshops at PAGE, 5 June 2012, Venice, Italy.
08:30 - 12:30 "Phoenix Connect: Linking Modeling and Simulation Tools,
including NONMEM, R, Xpose & PsN, in Phoenix Workflows"
https://pharsight.securesites.com/training/course_display_new.php?details_id=98.
13:00 - 17:00 "An Overview of the QRPEM Algorithm in Phoenix NLME"
https://pharsight.securesites.com/training/course_display_new.php?details_id=99.
Introduction to Phoenix WinNonlin 25-27 Sep. 2012 Amsterdam, The Netherlands
Population Modeling Methodology using Phoenix NLME 2-4 Oct. 2012 Paris, France
Introduction to Phoenix WinNonlin 4-6 Dec. 2012 London, UK
From: [email protected] [mailto:[email protected]] On
Behalf Of Hou, Xiaoli Shirley
Sent: Sunday, September 02, 2012 10:50 PM
To: NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear NM-Users,
I am doing a simulation using R, in which the within and between subject
variations, "EPSILON" and "OMEGA", are needed. They are automatically listed in
the ***.lst file of the NONMEM outputs. Is there a way I can read them from my
NONMEM output into R?
Thanks,
Shirley
Dr. Xiaoli Shirley Hou
Senior Biometrician, ECDS
351 N. Sumneytown Pike, UG1C36
North Wales, PA. 19454.
Phone (540) 381-9599
Fax (267) 305-6395
VoiceMailBox (800) 737-2088 ext 68134
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
http://www.merck.com/contact/contacts.html) 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.
_________________________________________________________________
Shirley,
The R package "metrumrg" has a function "rlog" that returns a
data.frame containing thetas, omegas, sigmas, mofv, etc for one or
more NONMEM runs. Available on CRAN. Contact me offline for any
additional help.
Kind regards,
Tim Bergsma
Metrum Research Group, LLC
[email protected]
Quoted reply history
On Sun, Sep 2, 2012 at 5:49 PM, Hou, Xiaoli Shirley
<[email protected]> wrote:
> Dear NM-Users,
>
> I am doing a simulation using R, in which the within and between subject
> variations, "EPSILON" and "OMEGA", are needed. They are automatically listed
> in the ***.lst file of the NONMEM outputs. Is there a way I can read them
> from my NONMEM output into R?
>
>
>
> Thanks,
>
> Shirley
>
>
>
> Dr. Xiaoli Shirley Hou
>
> Senior Biometrician, ECDS
>
> 351 N. Sumneytown Pike, UG1C36
>
> North Wales, PA. 19454.
>
> Phone (540) 381-9599
>
> Fax (267) 305-6395
>
> VoiceMailBox (800) 737-2088 ext 68134
>
>
>
>
>
>
>
>
>
> 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
> http://www.merck.com/contact/contacts.html) 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.
Shirley,
An interesting new possibility is the xml output. Using the XML package from
CRAN, this can be read in R as follows:
library(XML)
x <- xmlTreeParse("yourmodel.xml", getDTD=F)
r <- xmlRoot(x)
To see what is there:
names(r[['nonmem']][['problem']][['estimation']])
So for example:
xmlValue(r[['nonmem']][['problem']][['estimation']][['final_objective_function']])
Best regards,
Erik
Quoted reply history
________________________________________
From: [email protected] [[email protected]] on behalf of
Hou, Xiaoli Shirley [[email protected]]
Sent: Sunday, September 02, 2012 11:49 PM
To: NONMEM
Subject: RE: [NMusers] single-patient AUC
Dear NM-Users,
I am doing a simulation using R, in which the within and between subject
variations, "EPSILON" and "OMEGA", are needed. They are automatically listed in
the ***.lst file of the NONMEM outputs. Is there a way I can read them from my
NONMEM output into R?
Thanks,
Shirley
Dr. Xiaoli Shirley Hou
Senior Biometrician, ECDS
351 N. Sumneytown Pike, UG1C36
North Wales, PA. 19454.
Phone (540) 381-9599
Fax (267) 305-6395
VoiceMailBox (800) 737-2088 ext 68134
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
http://www.merck.com/contact/contacts.html) 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.