Dear NONMEM users
Has anyone ever tried to include analytical expressions within a control file
in NOMEM? I guess that would obviously imply the use of a routine alternative
to the $DES.
I'd appreciate if you could provide me with some tips or a short example on
that.
Many thanks in advance,
Georgios
Georgios Vlasakakis, BEng
Post-Doctoral Fellow
GlaxoSmithKline, Middlesex, UB11 1BT, Stockley Park
CPMS Development and
https://connect.gsk.com/sites/cpms/TandD/Pages/default.aspx
Quantitative Sciences, R&D
Internal Phone Number: 792 2047
External: +44 (0) 208 990 2047
email: [email protected]
Inclusion of Analytical Expressions in NONMEM control file
Georgios The most straightforward way (and the only way I know of) to do this is to call an external fortran subroutine. Pretty easy to call it (just include it in the $SUBS). I've never done a real analytical solution (like root finding or something), but I've done simple search algorithms. I'm sure I don't have the code anymore though, it really is pretty easy. Mark Dear NONMEM users Has
anyone ever tried to include analytical expressions within a control
file in NOMEM? I guess that would obviously imply the use of a routine
alternative to the $DES. I’d appreciate if you could provide me with some tips or a short example on that. Many thanks in advance, Georgios Mark Sale MD President, Next Level Solutions, LLC www.NextLevelSolns.com 919-846-9185 A carbon-neutral company See our real time solar energy production at: http://enlighten.enphaseenergy.com/public/systems/aSDz2458
you can use ADNVAN9 $AES (see manual) although it is much better (quicker and more stable) to solve them (if possible) analytically.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Quoted reply history
On 2/3/2011 11:50 AM, Georgios Vlasakakis wrote:
> Dear NONMEM users
>
> Has anyone ever tried to include analytical expressions within a control
> file in NOMEM? I guess that would obviously imply the use of a routine
> alternative to the $DES.
>
> I’d appreciate if you could provide me with some tips or a short example
> on that.
>
> Many thanks in advance,
>
> Georgios
>
> /Georgios Vlasakakis, BEng///
>
> Post-Doctoral Fellow
>
> GlaxoSmithKline, Middlesex, UB11 1BT, Stockley Park
>
> CPMS Development and Technologies
> https://connect.gsk.com/sites/cpms/TandD/Pages/default.aspx
>
> Quantitative Sciences, R&D
>
> Internal Phone Number: 792 2047
>
> External: +44 (0) 208 990 2047
>
> email: [email protected]
Georgios,
Leonid has already asked you to make it clearer what you are trying to do.
Coding "analytical expressions" that do not involve $DES or other PREDPP subroutines in NONMEM may be done using $PRED e.g.
$INPUT ID DOSE DV
$THETA 1
$OMEGA 1
$SIGMA 1
$PRED
D50=THETA(1)*EXP(ETA(1)
Y=DOSE/(DOSE+D50) + EPS(1)
This estimates the D50 for a dose-response relationship with an exponential random effects model for D50 and an additive random effect for the residual error. The dose response is assumed to have a maximum of 1 in this very simple example.
Nick
Quoted reply history
On 4/02/2011 6:49 a.m., Leonid Gibiansky wrote:
> Addition:
>
> I assumed that you need to use analytical equations; if you need just expressions, you can do it in the error block like
>
> TEMP=A(1)/V1
> Y=(TEMP**2+1)**0.5 + EPS(1)
>
> If you need something else, please, give an example of what exactly you are trying to implement
>
> Regards,
> Leonid
>
> On 2/3/2011 12:39 PM, Leonid Gibiansky wrote:
>
> > you can use ADNVAN9 $AES (see manual) although it is much better
> > (quicker and more stable) to solve them (if possible) analytically.
> > Leonid
> >
> > --------------------------------------
> > Leonid Gibiansky, Ph.D.
> > President, QuantPharm LLC
> > web: www.quantpharm.com
> > e-mail: LGibiansky at quantpharm.com
> > tel: (301) 767 5566
> >
> > On 2/3/2011 11:50 AM, Georgios Vlasakakis wrote:
> >
> > > Dear NONMEM users
> > >
> > > Has anyone ever tried to include analytical expressions within a control
> > >
> > > file in NOMEM? I guess that would obviously imply the use of a routine
> > > alternative to the $DES.
> > >
> > > I’d appreciate if you could provide me with some tips or a short example
> > >
> > > on that.
> > >
> > > Many thanks in advance,
> > >
> > > Georgios
> > >
> > > /Georgios Vlasakakis, BEng///
> > >
> > > Post-Doctoral Fellow
> > >
> > > GlaxoSmithKline, Middlesex, UB11 1BT, Stockley Park
> > >
> > > CPMS Development and Technologies
> > > https://connect.gsk.com/sites/cpms/TandD/Pages/default.aspx
> > >
> > > Quantitative Sciences, R&D
> > >
> > > Internal Phone Number: 792 2047
> > >
> > > External: +44 (0) 208 990 2047
> > >
> > > email: [email protected]
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology& Clinical Pharmacology
University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email:[email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Dear all
Many thanks for your feedback and apologies for my late reply.
Maybe my first message wasn't clear enough but I'm interested in "bypassing"
the existing libraries in PREDPP in order to include the model's analytical
solution instead of an ADVAN or set of differential equations ($DES).
I think I got the solution through Leonid's & Nick's replies. Thank you all for
your valuable feedback.
Best
Georgios
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Nick Holford
Sent: 03 February 2011 18:39
To: nmusers
Subject: Re: [NMusers] Inclusion of Analytical Expressions in NONMEM control
file
Georgios,
Leonid has already asked you to make it clearer what you are trying to do.
Coding "analytical expressions" that do not involve $DES or other PREDPP
subroutines in NONMEM may be done using $PRED e.g.
$INPUT ID DOSE DV
$THETA 1
$OMEGA 1
$SIGMA 1
$PRED
D50=THETA(1)*EXP(ETA(1)
Y=DOSE/(DOSE+D50) + EPS(1)
This estimates the D50 for a dose-response relationship with an exponential
random effects model for D50 and an additive random effect for the residual
error. The dose response is assumed to have a maximum of 1 in this very simple
example.
Nick
On 4/02/2011 6:49 a.m., Leonid Gibiansky wrote:
Addition:
I assumed that you need to use analytical equations; if you need just
expressions, you can do it in the error block like
TEMP=A(1)/V1
Y=(TEMP**2+1)**0.5 + EPS(1)
If you need something else, please, give an example of what exactly you are
trying to implement
Regards,
Leonid
On 2/3/2011 12:39 PM, Leonid Gibiansky wrote:
you can use ADNVAN9 $AES (see manual) although it is much better
(quicker and more stable) to solve them (if possible) analytically.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: http://www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
On 2/3/2011 11:50 AM, Georgios Vlasakakis wrote:
Dear NONMEM users
Has anyone ever tried to include analytical expressions within a control
file in NOMEM? I guess that would obviously imply the use of a routine
alternative to the $DES.
I'd appreciate if you could provide me with some tips or a short example
on that.
Many thanks in advance,
Georgios
/Georgios Vlasakakis, BEng///
Post-Doctoral Fellow
GlaxoSmithKline, Middlesex, UB11 1BT, Stockley Park
CPMS Development and Technologies
https://connect.gsk.com/sites/cpms/TandD/Pages/default.aspx https://connect.gsk.com/sites/cpms/TandD/Pages/default.aspx
Quantitative Sciences, R&D
Internal Phone Number: 792 2047
External: +44 (0) 208 990 2047
email: [email protected]<mailto:[email protected]>
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology
University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]<mailto:[email protected]>
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford