NONMEM Users Network Archive

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Re: PRED for BLQ-like observations

From: Fisher Dennis <fisher>
Date: Fri, 20 Nov 2015 13:14:33 -0800

Even better, take advantage of this (from NMHELP):

Values of MDV are:

      0 The DV data item is an observed value, i.e., DV is not miss-
           ing.

      1 The DV data item is not regarded an observed value, i.e., DV
           is missing. The DV data item is ignored. =
|

      100 Same as MDV=0, but this record is ignored during =
Estimation |
           and Covariance Steps. During other steps, MDV will changed =
|
           to 0. =
|

      101 Same as MDV=1, but this record is ignored during =
Estimation |
           and Covariance Steps. During other steps, MDV will changed =
|
           to 1. =
|

           Reserved variables MDVI1, MDVI2, MDVI3 can be used to over- =
|
           ride values of MDV>100. These variables are defined in =
|
           include file nonmem_reserved_general.

Dennis

Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com



> On Nov 20, 2015, at 12:38 PM, Nick Holford <n.holford
wrote:
>
> Pavel,
> Did you test the run time with double the records?
> I would expect that the MDV=1 records would be largely ignored in =
the estimation step and not contribute much to run time.
> Nick
>
> On 21-Nov-15 08:59, Pavel Belo wrote:
>> Thank you Bill,
>> In my case it exactly doubles the number of records... The records =
are daily measures and the code is running slow enough. I'll split the =
code into estimation part and one that that is redundant, but uses a =
larger file and creates an output. It will be something like
>> $EST MAXEVALS=9999 SIG=3 NOABORT PRINT=1 SORT CONSTRAIN=5
>> METHOD=SAEM NBURN=0 NITER=0 POSTHOC INTERACTION
>> LAPLACIAN GRD=TG(1-7):TS(8-9) CTYPE=3 CINTERVAL=10
>> I guess the best future way is modify something in NONMEM so there is =
an option to provide only PRED in the PRED column (version 7.4?).
>> Thanks!
>> Pavel
>> On Fri, Nov 20, 2015 at 01:06 PM, Denney, William S. wrote:
>>
>> Hi Pavel,
>>
>> The easiest way that I know is to generate your data file with one
>> set of rows for estimation with M3 and another row just above or
>> below with MDV=1. NONMEM will then provide PRED and IPRED in =
the
>> rows with MDV=1.
>>
>> Thanks,
>>
>> Bill
>>
>> *From:*owner-nmusers
>> [mailto:owner-nmusers
>> *Sent:* Friday, November 20, 2015 11:47 AM
>> *To:* nmusers
>> *Subject:* [NMusers] PRED for BLQ-like observations
>>
>> Hello The NONMEM Users,
>>
>> When we use M3-like approach, the outputs has PRED for non-missing
>> observations and something else for BLQ (is that PRED=CUMD?). =
As
>> in the diagnostic figures PRED for BLQs looks like noise, I remove
>> them. It is not always perfect, but OK in for most frequent =
cases.
>>
>> When we use count data such as a scale with few possible values
>> (for example, 0, 1, 2, 3, 4, 5), it makes more sense to use PHI
>> function (home-made likelihood) for all observations rather than
>> to treat the count as a continuous variable an apply M3-like
>> approach to 1 and 5 while only (as we know, they are like LLOQ and
>> ULOQ). In this case, all PRED values look like noise. A hard way
>> to replace the noise with PRED value is to simulate PRED for each
>> point and merge them with the DV and IPRED data. Is there an easy
>> way?
>>
>> (The model runs well and better than when the count is treated as
>> a continuous variable.)
>>
>> Thanks!
>>
>> Pavel
>>
>
> --
> Nick Holford, Professor Clinical Pharmacology
> Dept Pharmacology & Clinical Pharmacology, Bldg 503 Room 302A
> University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New =
Zealand
> office:+64(9)923-6730 mobile:NZ+64(21)46 23 53
> email: n.holford
> http://holford.fmhs.auckland.ac.nz/
>
> Holford SD, Allegaert K, Anderson BJ, Kukanich B, Sousa AB, Steinman =
A, Pypendop, B., Mehvar, R., Giorgi, M., Holford,N.H.G. =
Parent-metabolite pharmacokinetic models - tests of assumptions and =
predictions. Journal of Pharmacology & Clinical Toxicology. =
2014;2(2):1023-34.
> Holford N. Clinical pharmacology = disease progression + drug =
action. Br J Clin Pharmacol. 2015;79(1):18-27.
>


Received on Fri Nov 20 2015 - 16:14:33 EST

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