em
allows this simplification?
- how can l(t) be constrained between 0 and 1 if both numerator and
denominator can vary between 0 and 1?
Any comment from nmusers will be greatly appreciated.
--
*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.biho...@c
on
of l(t) used by Dr. Beal starting from the previous expression of p(y |
y > LLQ)?
*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.biho...@cognigencorp.com
<mailto:sebastien.biho...@cognigencorp.com>
Phone: (716) 633-3463 ext. 323
Leonid Gibiansky
Hi Nele,
One possible reason of your Fortran compilation failure is that your
code does not respect the fortran 77 syntax standards. My guess is that
your should add 6 spaces before SUBROUTINE (look here for more info
http://www-teaching.physics.ox.ac.uk/unix+prog/hargrove/tutorial_77/03_basic
stopping the run at
different times, I found out that the content of the file is actually
overwritten at each sub-problem. Is there a option that would append the
new content to the file rather than overwriting it?
Thank you in advance for your feedback.
Sebastien Bihorel
Behalf Of Sebastien Bihorel
Sent: Wednesday, March 10, 2010 4:28 PM
To: nmusers@globomaxnm.com
Subject: [NMusers] Questions about the raw output file in NM7
Dear NMusers,
I would like to have your help on two issues regarding the raw output
file in NM7:
1- when using $ESTIMATION PRINT=0 with &quo
o the actual RES and WRES for the non-BLQ records?
Any feedback would be greatly appreciated.
Sebastien Bihorel
PS: this is the $ERROR block code we used for a simple proportional RV model
$ERROR (ONLY OBSERVATIONS)
;Information needed for BLQF and > BLQF samples
LOQ=5
SIG = THETA(3)
DFLG=0
martin.bergstr...@farmbio.uu.se
---
Work: +46 18 471 4639
Mobile: +46 709 994 396
Fax:+46 18 471 4003
-Original Message-
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Sebastien Biho
ally if Tlag is estimated.
Best,
Matt
-Original Message-
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Martin Bergstrand
Sent: Wednesday, April 07, 2010 1:02 PM
To: 'Sebastien Bihorel'; nmusers@globomaxnm.com
Subject: RE: [NMusers] RES an
Hi,
It looks like you are trying to derive the unknown values of KA, CL/F
and V/F from the known values of Tmax, Cmax and AUC (probably obtained
from a non compartmental analysis).
If that is really the case, you will need to know the values of the
half-life of elimination or the slope of el
little problem :the Ke.
Thank you for your generous help.
22 03:24:55??"Sebastien Bihorel" mailto:sebastien.biho...@cognigencorp.com>>Hi,
>
>It looks like you are trying to derive the unknown values of KA, CL/F
>and V/F from the known values of Tmax, Cmax and AUC (proba
d also be interested to know if a reference in the
literature would describe the properties of this particular RUV model.
Thank you
Sebastien Bihorel
$PROBLEM base-2cmt-sim
$DATA basedata.csv IGNORE=@
$INPUT ID TIME AMT RATE CMT EVID DV MDV STDY
$THETA
(0.,5.) ;1- clearance
(0.
--
Work: +46 18 471 4639
Mobile: +46 709 994 396
-Original Message-
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Sebastien Bihorel
Sent: Thursday, May 13, 2010 6:06 PM
To: nmusers; Martin Bergstrand
Subject: [NMusers] Unexpected differences i
Dear NMusers,
I always thought that the order in which parameters are declared in the
control stream has no impact on the estimation outcomes, but the following
results seem to contradict this.
The PK of drug X was modeled with a linear 3-compartment model using a
proportional residual variability
Hi Ethan,
You have reached the maximum number of function evaluation ( I
believe). Two solutions:
1- you create a copy of your control stream and update the initial
estimates with the 'final' estimates of your first run
2- you create a copy of your control stream and use an $MSFI statement
I am aware of the issues associated numerical representation in
computer memory but I must say that it is more than a bit surprising
(disturbing) that the order of the
parameters results in these pseudo-random outcomes in NONMEM
computations. As far as I know, this is not the case in R, despite
Behalf Of *Sebastien Bihorel
*Sent:* Wednesday, June 23, 2010 9:53 AM
*To:* Nick Holford
*Cc:* nmusers@globomaxnm.com
*Subject:* Re: [NMusers] Unexpected influence of parameter order on
estimation results
I am aware of the issues associated numerical representation in
computer memory but I
Dear Koen,
Depending on what type of work you want those add-ons to do (run
manager, graphing, reporting, etc...), different options are available
to you.
There a couple of free software packages that offer very nice wrapper
functions around NONMEM (for VPC, bootstrapping, simulation and mor
Dear NMusers,
I was wondering if there is a way to change the default format of output
tables in NONMEM7. I know that the FORMAT option allows the user to
override the default format at each $TABLE statement, but adding this
option in every control stream can become a very burdensome task. I'd
compartments by adding one compartment at a time
into the system.
As a starting point, you may want to try simulation in Berkeley Madonna.
It has a array notation that can be used to define arrays of
differential equations and therefore applies very nicely to this kind of
problem.
Sebastien Bihorel
PK/PD
nmfe72 is most likely included not in your path. Google is your best bet
here, as the inclusion operation is not specific to NONMEM but to your
operating system.
Batul Parta wrote:
Dear all,
I have installed nm72 with a successful test run (gfortran). However,
when I want to run it (nmfe72 .
Have a look at those two references:
J Pharmacokinet Pharmacodyn. 2009 Oct;36(5):381-405. Epub 2009 Aug 21.
Methods of utilizing baseline values for indirect response models. Woo
S, Pawaskar D, Jusko WJ.
J Pharmacokinet Pharmacodyn. 2008 Jun;35(3):269-83. Epub 2008 Apr 30.
Approaches to handli
Dear Hauke,
If I am not mistaken, the model that you are trying to reproduce is a
lifespan indirect response (LIDR) model. The direct implementation of
such models requires a solver of delay differential equations (DDE),
which is not available in NONMEM or Berkeley Madonna. Other software
pla
...@globomaxnm.com] *Im Auftrag von *Sebastien Bihorel
*Gesendet:* Freitag, 25. November 2011 12:14
*An:* Hauke Rühs
*Cc:* nmusers@globomaxnm.com
*Betreff:* Re: [NMusers] time dependant function
Dear Hauke,
If I am not mistaken, the model that you are trying to reproduce is a
lifespan indirect response
Dear NONMEM users,
A few month ago, a post by Li Li ("Question regarding Calculation
Process in $DES BLOCK") generated some interesting discussions about how
to implement abrupt changes in a model parameter in $DES. The original
problem proposed by Li Li was to implement a step function that t
: r.ter.he...@meandermc.nl
-Oorspronkelijk bericht-
Van: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com]
Namens Sebastien Bihorel
Verzonden: dinsdag 29 november 2011 17:05
Aan: nmusers
Onderwerp: [NMusers] How to implement a circadian reset of a step
function in $DES using
corrections (see attachment; checked in Berkeley Madonna over a large
range of SHIFT and DUR values).
Sebastien
Sebastien Bihorel wrote:
Thanks Rob for your reply.
I have tried something in the line of what you suggested (see
circadian4.ctl in attachment) but the integration is still not
complete in
Any chance that you are using a DOS file on a non-DOS system or vice versa?
Strother, R Matthew wrote:
The addition of carriage return after the $PK, as indicated in your
email, did not work.
I still get the same error --
AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
AN ERR
Hi,
I think that the introduction guide to NM7 mentions the following rules
for setting the options of numerical integration andestimation:
SIGL <= TOL
NSIG <= SIGL/3
Therefore, SIGL and TOL are conditioned on NSIG.
Sebastien
Wang, Xiaofeng wrote:
Hi all,
I wonder if there is an accept
Hi
Some things to consider:
- does your data support non-linear kinetics (perhaps all your actual
data are within the "linear" range of your MM kinetics)?
- are your estimates of Vmax and Km correlated?
- what about the estimates of IIV on Vmax and Km? Are they realistic?
Sebastien
fakrudeen
Hi,
Is there a reserve variable in $PK or $PRED that one can call in an
estimation run to know what it is current iteration number evaluated by
NONMEM?
Thank you
--
Sébastien Bihorel
Hi,
When one uses a typical PK ADVAN and a classical optimization method
(FO/FOCE/FOCEI), letting a model parameter (most notably CL) become negative or
forcing it to be a negative value will cause NONMEM 7.3 to stop and error out
of the optimization routine.
This is also the case with IMP a
Hi,
I would suggest the following solution which should also work if you want to
apply some covariate effect on bioavailability:
* On the dataset side, set your RATE variable to -1 and store the actual
infusion rates into another variable, eg IVRATE
* On the model side:
$PK
...
; assuming
Hi,
You may also have to define $BIND if your F1 expression is dependent on dataset
variables.
From: "Sebastien Bihorel"
To: "Bill Denney"
Cc: "NMUsers"
Sent: Tuesday, March 13, 2018 9:16:56 PM
Subject: Re: [NMusers] Time-Varying Bioavailability on Zero-
Hi,
As far as I know, F1 is set on dose records... any changes on sample records
should not affect how much drug will enter your system.
But I may be wrong...
From: "Bill Denney"
To: "Sebastien Bihorel"
Cc: "NMUsers"
Sent: Tuesday, March 13, 2018 9:2
So, you want F1 to change while the infusion is on-going. In that case, I would
use the same kind of MTIME-based code as you included in your original post.
From: "Bill Denney"
To: "Sebastien Bihorel"
Cc: "NMUsers"
Sent: Tuesday, March 13, 2018 9:21:00 P
Hi,
Two things:
- NONMEM does not require ID to be the first variable in $INPUT
- the headers of your csv file do not have to match the variable names used in
$INPUT
So you have 2 easy workarounds for your issue:
- as previously pointed out, you can use another first variable... a deletion
Hi,
As I already mentioned to you in a separate thread:
1. SAS and PsN have different methods to calculate percentiles, so
expecting these 2 pieces of softwares to give you the same answers is
unrealistic.
2. VPC statistics are very much dependent on your data and the binning
optio
Hi
The Introduction to NONMEM 7.x documents include a section entitled "Easier
Inter-occasion variability modeling" which describes a quicker way to code IOV.
$ABBR REPLACE ETA(OCC_CL)=ETA(4,7,10)
;when OCC=1, eta(4) to be used: when OCC=2, eta(7) to be used, etc.
...
$PK
CL=TVCL*EXP(ETA(1)+E
THE CHARACTERS IN ERROR ARE: ETA
484 SUBSCRIPT MUST BE AN INTEGER CONSTANT.
- Original Message -
From: "Jeroen Elassaiss-Schaap (PD-value B.V.)"
To: "Sebastien Bihorel" ,
nmusers@globomaxnm.com
Sent: Wednesday, January 16, 2019 3:14:53 AM
Subject: Re: [NMuser
Thank you so much Alison, that will be really helpful.
From: "Alison Boeckmann"
To: "Jeroen Elassaiss-Schaap, PD-value B.V." , "Sebastien
Bihorel"
Cc: nmusers@globomaxnm.com
Sent: Thursday, January 17, 2019 2:25:57 PM
Subject: Re: [NMusers] Easier IOV model
Hi,
Besides software-dedicated user lists like this one, are you aware about the
existence of a mailing list that discusses general pharmacometric questions?
--
Sebastien Bihorel
Thanks Bill
- Original Message -
From: "Bill Denney"
To: "Sebastien Bihorel" ,
nmusers@globomaxnm.com
Sent: Thursday, January 31, 2019 11:16:08 AM
Subject: RE: [NMusers] Mailing list about pharmacometrics
Hi Sebastien,
The best I know for general PMx questions
Hi,
I was wondering if there is a way to create "pure" csv file with $TABLE. I have
tried various things with the FORMAT option but always ended up with spaces in
between entries (in addition to the comma delimiters).
Is there a proper fortran format one can use in $TABLE to make this happen?
Thanks for the input but I already tried that (or things along the line of
FORMAT=,1PE11.4). Commas are indeed in the table file... but so are spaces.
From: "Emmanuel Chigutsa"
To: nmusers@globomaxnm.com, "Sebastien Bihorel"
Sent: Thursday, March 14, 2019 3:47:15 PM
S
9 10:33 AM
To: nmusers@globomaxnm.com
Cc: Sebastien Bihorel; Emmanuel Chigutsa; Paul Hutson
Subject: Re: [NMusers] How to format output table as purely comma-separated
file
Hi,
I am also wondering why NONMEM has this strange behavior. Is there any
possibility for the developer to fix tha
Hi,
Is it possible for NONMEM to generate a random number during an estimation run?
Thank you
Sebastien Bihorel
(VECTRA)
...
From: "Tingjie Guo"
To: "Sebastien Bihorel" ,
nmusers@globomaxnm.com
Sent: Monday, June 3, 2019 12:58:56 PM
Subject: Re: Random number generation
Hi Sebastien,
As far as I know, you could write verbatim code to generate random numbers
during estimation. E.
ERRATUM:
runif.f90:
FUNCTION FUNCA(X,X1,X2)
USE SIZES, ONLY: DPSIZE
REAL(KIND=DPSIZE) :: X,X1,X2,FUNCA
FUNCA = RAND()
RETURN
END
From: "Sebastien Bihorel"
To: "Tingjie Guo"
Cc: nmusers@globomaxnm.com
Sent: Monday, June 3, 2019 4:54:46 PM
Subject: [NMuser
Good to know!
Thanks for the follow up.
From: "Tingjie Guo"
To: "Sebastien Bihorel"
Cc: nmusers@globomaxnm.com
Sent: Wednesday, June 5, 2019 6:08:44 AM
Subject: Re: Random number generation
Hi Sebastien,
It worked perfectly for me in $ERROR, but I tested it on
Hi,
I am not 100% certain that a decrease in the IIV terms associated with the
covariate-parameter relationships is a criteria used in the automated selection
process implemented by the PsN scm command (at least I could not find any
reference in the documentation). You may want to implement a m
I would second that feature request!
From: owner-nmus...@globomaxnm.com on behalf of
Mark Tepeck
Sent: Monday, December 16, 2019 15:16
To: Nmusers
Subject: [NMusers] Use AND to ignore rows for input dataset
Hi Colleagues,
Although there are many workarounds to
@globomaxnm.com On Behalf Of
Sebastien Bihorel
Sent: Monday, December 16, 2019 12:39 PM
To: Mark Tepeck ; Nmusers
Subject: Re: [NMusers] Use AND to ignore rows for input dataset
I would second that feature request!
From: owner-nmus...@globomaxnm.com<mai
0769
robert.ba...@iconplc.com<mailto:robert.ba...@iconplc.com>
www.iconplc.com<http://www.iconplc.com/>
From: Sebastien Bihorel
Sent: Monday, December 16, 2019 5:02 PM
To: Bauer, Robert ; Nmusers
Subject: Re: [NMusers] Use AND to ignore rows for input dataset
Since nowadays most
53 matches
Mail list logo
