Re: AW: $Error log transformed
Katrin,
It is not good practice to add a small quantity to the prediction to avoid numerical errors. Stuart Beal (the original developer of NONMEM) wrote this comment in 2004:
"..., this will very often alter the results, especially when during the
Estimation Step parameter
values are considered that lead to smaller values of F than might be
imagined."
http://www.cognigencorp.com/nonmem/nm/98feb112004.html
He supplies some workarounds which you may wish to consider.
You may also wish to use a more realistic error model that includes an additive component that would be appropriate for a concentration approaching zero. All real measurements will have some noise when the true value is zero.
Best wishes,
Nick
Quoted reply history
On 18-Dec-16 07:46, Katrin Volz wrote:
> Hey Rob,
>
> Thank a lot. It seems to work well.
>
> I´m quite happy with this log transformation :)
>
> And yes, thanks for clarifying that I have to take the natural logarithm.
>
> Cheers
>
> Katrin
>
> *Von:* [email protected] [ mailto: [email protected] ] *Im Auftrag von * [email protected]
>
> *Gesendet:* 16 December 2016 11:24
> *An:* [email protected]; [email protected]
> *Betreff:* RE: [NMusers] $Error log transformed
>
> Hi Katrin,
>
> You’ll have to take the natural logarithm of your DVs
>
> I would change your error block to:
>
> $ERROR
>
> IPRED=LOG(F+1E-16) ; Protection against LOG(0) in case of dosing events etc
>
> Y=IPRED+ERR(1) ; FOR PROPORTIAL ERROR
>
> Cheers!
>
> Rob
>
> *Van:* [email protected] < mailto: [email protected] > [ mailto: [email protected] ] *Namens *Katrin Volz
>
> *Verzonden:* vrijdag 16 december 2016 10:35
> *Aan:* [email protected] <mailto:[email protected]>
> *Onderwerp:* [NMusers] $Error log transformed
>
> Dear All,
>
> I would like to model my data log transformed.
>
> So far, I already found some suggestions for this problem here but none of them worked in my case - probably I did sth. wrong.
>
> I would be very happy if someone could help me with changing my error model, which I assume has to be changed.
>
> (I also assume that the dataset has to be changed from DV to LOG(DV)?)
>
> So, here is the code I used so far (not log transformed):
>
> $ERROR
>
> IPRED = F ;IPRED drug in the central compartment
>
> IF (CMT.EQ.5) IPRED = A(5) ;IPRED second drug in 5th compartment
>
> DEL=0
>
> IF (IPRED.EQ.0) DEL=0.0001
>
> W = F
>
> IRES = DV - IPRED
>
> IWRES = IRES /(W + DEL)
>
> Y = IPRED + IPRED * EPS(1) ; error drug in the central compartment
>
> IF (CMT.EQ.5) Y = IPRED + IPRED * EPS(2) ; error second drug in 5th compartment
>
> It would be great to get some help.
>
> Thanks!
>
> Katrin
>
> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology, Bldg 503 Room 302A
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