for both types of records.
Best regards
Jakob
Jakob Ribbing, Ph.D.
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does PsN need to do
this).
Best wishes
Jakob
Jakob Ribbing, Ph.D.
Principal Consultant, Pharmetheus AB
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acceptable?
Best regards
Jakob
Jakob Ribbing, Ph.D.
Principal Consultant, Pharmetheus AB
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> On 19 Dec 2
writing a few lines of code, or preparing a whole set of control
streams with different fixed values for the parameter in question, but maybe
someone else can suggest a PsN command for this?
Best regards
Jakob
Jakob Ribbing, Ph.D.
Principal Consultant, Pharmetheus AB
> On 7 Feb 2023, at
).
And for summary stats I believe what Leonid suggests (off-diagonal omega) is
the more useful correlation, whereas e.g for a diagnostic plot EBE etas may be
useful.
Cheers
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile: +46 (0)70 514 33 77
jakob.ribb
irrelevant, but I do
not think that is what you mean.
Best regards
Jakob
Jakob Ribbing, Ph.D.
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Hi Mark,
I am assuming that you problem is a little more complex than only one theta,
e.g. that you would like to simulate typical CL for a number of subgroups,
where several covariate values (impactful on CL) are different across sub
groups.
In that case Leoid’s nonmem code would be a quick way
much value in joint modelling
(simultaneous estimation of the two models), since no subject has observations
of both endpoints.
Or maybe I missed your point?
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile: +46 (0)70 514 33 77
jakob.ribb
Dear Niurys,
It would be down to distributional assumptions in that case.
For example if you have a very strong predictor (covariate) of either
elimination or absorption rate (but not both) - data could be informative to
discriminate between flip-flop or not.
Had your therapeutic been IgG monoc
Dear Andre,
Since nonmem warns for the same lines as before it is quite clear the nonmem is
reading the old datafile.
Did you update the datafile name in the nonmem control stream?
Or, if you did not change the name of the datafile, are you sure the datafile
is updated on the server where nonmem
Dear all,
For simulation, the EXP(EPS(1)) would be a log-normal distribution as intended,
so either or would work in simulation mode and it is only in estimation (FOCE)
the log-transform is necessary.
Cheers
Jakob
> On 19 Jul 2021, at 18:10, Leonid Gibiansky wrote:
>
> yes, it does at e
Dear Monia,
Yes, that is correct.
So if one were to use this parameterization for FOCE then one would effectively
get a proportional (symmetric) error distribution, exactly according to what
you suggested:
Y=F*(1+EPS(1))
For this reason, the standard approach in NONMEM (for FOCE and exponential
could
include the log of T and in that case you would use:
DEL = 1E-12
...LOG((T+DEL)...
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
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Dear Matts,
Did you get funny results in the way that using T_DAY did now work as intended?
If you are unsure you could set up a simple test where you have the analytical
solution to the output, as an initial confirmation.
Otherwise, for models integrating forward in time, a covariate value at t
find e.g. psn.mod. If on a LINUX system
you can just run diff or ’sdiff -s’ to compare this file between the two runs
with execute
Did you change anything else in the configuration of PsN or NONMEM, e.g. the
compiler?
Best wishes
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
tps://ascpt.onlinelibrary.wiley.com/doi/abs/10.1016/j.clpt.2003.11.158>
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile: +46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
www.pharmetheus.com
Phone, Office: +46 (0)18 513 328
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jects with multiple
observations?
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
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observations per subject it will be difficult to find support
for more than one level.
And for a model with only residual error (no IIV), would not the FO Estimation
method be sufficient, so why would you need to use SAEM for this data/model?
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior
limited. Sign up as soon as possible
to give us a chance to help you tackle your challenges!
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Hope to meet with you during ACoP!
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile: +46
;=vpcPlot@plotList[[3]],
“Dose C"=vpcPlot@plotList[[5]],layout = c(3,1))
That last step one has to be careful, as it is a bit error prone: you manually
set the labels and if you get it wrong it will be mislabelled.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
ariates are added during the forward path.
>
> Best Regards,
>
> Emeric Sibieude
>
> Student trainee in Master's degree
>
> Biopharma | R&D | Global Development | Translational Medicine
>
> Merck
>
> Lausanne , Switzerland
>
> emer
Dear Emeric,
The code has negative PD, maybe PsN has problems interpreting this?
I am not sure how PD=-100 would be interpreted by NONMEM, but try PD=100,
instead.
I think this is what you intended to do?
As a side note, PsN (mainly to handle old nonmem versions) has functionality
for dropping
Great to hear it is now working.
If you want to set the same limits for all power models, you can even write
this in a more generic form:
*:*-5 = -5
And if you want to apply only for one parameter or one covariate that is
possible as well, e.g.:
V2:*-5 = -5
Best regards
Jakob
> On 21 Nov 20
e value, I thought it doesnt make sense, and instead I provided median
> BMI in place of missing values. Didn’t work that way either.
>
> Regards,
> Sumeet Singla
>
>
>
>> On Nov 19, 2019, at 11:10 PM, Jakob Ribbing
>> wrote:
>>
>> Hi Sumeet,
&
Hi Sumeet,
It is great that you have considered already that covarite values do not
include zero or negative values, as that would not work with the power model.
Did you have any missing values, and how were they coded?
I would recommend to code these (in your data file) using the default -99 in
Hi Sumeet,
If you have rich sampling (and rich information on all parameters of interest)
then one would not expect much difference between the individual parameter
estimates with/without covariates in the model.
This does not make the covariate model meaningless, since future patients may
be s
AGE%20_2014_tte_sim_joakim_nyberg_with_code.pdf>
These include the log-normal distribution, as well as Gompertz and Weibull.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
www.pharmetheus.com <http://www.pharmetheus.com
services later - this
is open to everyone.
Please use this link to get in contact with us for this matter:
Pharmetheus.com/speed-consulting <http://pharmetheus.com/speed-consulting>
Looking forward to seeing you at PAGE!
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
good to check manually.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
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these questions?
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
www.pharmetheus.com <http://www.pharmetheus.com/>
Phone, Office: +46 (0)18 513 328
Uppsala Science Park, Dag Hammarskjöl
on and
instead specify p-values for forward and backward selection.
The gof option is only used in special cases, where one does not want to assume
that delta-OFV follows a chi-square distribution (or if one wants to use
p-values lower than 0.0001).
Best regards
Jakob
Jakob Ribbing
possible on these covariate-parameter data.
Best wishes
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
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Phone, Office: +46 (0)18 513 328
Uppsala Scienc
Hi Ruben,
I think I misread Tingjies original posting as taking ABS(ETA), whereas his
initial attempt was actually ABS(1+ETA), which is less problematic.
The latter would not bias simulations much if IIV is e.g. 30% CV, agreed.
However, as Tingjies is mainly interested in estimation, I believe t
Hi Tingjie,
It does not: Sigma squared is the sum of all error variances, and assay error
in most cases is only a small contribution to this sum.
There are exceptions, but when applying a previous model to new data it is
rarely the first modification that comes to my mind.
Given your objectives
PARA = TVPARA * (1+ETA(1))
ENDDO
ENDIF
;Etas that do not need resampling should be declared after the above DO WHILE
block. They should follow below
[…]
$SIMULATION (123456 NEW) (7891011 UNIFORM) ONLYSIMULATION […] ; The SIMETA
requires an additional seed number, see nmhelp for more info
).
DS.
Example code for estimating additive error model with sigma estimated.
IPRED = [Model specific equation, or F]
IRES = DV-IPRED
ADD= SQRT(SIGMA(1,1))
SD = ADD
IWRES = IRES/SD
Y = IPRED + EPS(1)
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:
Dear all,
The Pharmetheus team is expanding!
Pharmetheus is a pharmacometrics consultancy company supporting drug
development of compounds in all phases and in most therapeutic areas, through
strategic support as well as hands on modelling and simulation performed within
a reproducible report
covariate effects so that a covariate may not reduce by more
than 100%, or use e.g. a power model, if covariate values are >0.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
www.pharmetheus.
:
10.1007/s10928-012-9274-0. Epub 2012 Sep 23.
Longitudinal FEV1 dose-response model for inhaled PF-00610355 and salmeterol in
patients with chronic obstructive pulmonary disease.
Nielsen JC, Hutmacher MM, Cleton A, Martin SW, Ribbing J.
DS.
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Hi Hanna,
I did not check the whole model code, but could it be a typo in the rate for
re-distribution that produces the difference?
DADT(3) = K23*A(2) - K23*A(3)
Kind regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb
und
limitations/features with NWPRI, since that is clearly out of scope for the
topic in this tread :>)
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
www.pharmetheus.com
Phone, Office: +46 (0)
what you need from this
variable is the previous DV value?
I did not find time to check your control steam, but if there is any obvious
error I am sure someone else will spot that.
Best wishes
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33
Sorry, an error in what I wrote below: It should be EXP(0)=1 concentration unit
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
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www.pharmetheus.com
Phone, Office: +46 (0)18 513 328
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our problem.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile:+46 (0)70 514 33 77
jakob.ribb...@pharmetheus.com
www.pharmetheus.com
Phone, Office: +46 (0)18 513 328
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T
Dear all,
I agree, implementing the actual PK model (i.e. IPP) or using linear
interpolation to describe the individual PK profiles as suggested by Juergen
and David is necessary in this example.
However, for understanding when input concentrations can be used directly as
a reasonable approximati
Hi Huadong,
You say that you do not think that the allometry law should be fixed to 1
for volume-based parameters. I think that we all agree to that the apparent
volumes are sometimes not proportional to body weight. However, when this
happens it is because something else is confounded with body si
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