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Re: FDATA file bug

From: Alison Boeckmann <alisonboeckmann>
Date: Thu, 05 Dec 2019 12:13:44 -0800

Hi Richard and others:
Thanks for explaining FDATA. There is no bug.
FDATA would have a simpler, space delimited format if there were fewer c=
haracters per line.
It only uses a dense format when it has not got enough room to keep the =
length of lines in FDATA to 80.
If you add "WIDE" to the $DATA record, then FDATA will have spaces betwe=
en data items and will be easier to read.

Mark wrote: "I want to confirm the right input dataset into NONMEM. "

I see no reason to look into NONMEM internal files such as FDATA.
The best way to check the data was suggested by Lewis Sheiner in NONMEM =
Users Guide V, Introductory Guide,
Chapter 11 Model Building, section 3 *3 *3. Check-out — Index Pl=
ots.

I took the control stream and data file from Mark's email and made three=
 changes
to the control stream, following the spirit of Sheiner's suggestions.

Add CHECKOUT to the $DATA record. This tells NONMEM not to try to comput=
e the objective function.
It may not be able to do this if the data or model is faulty.

Delete the $ESTIM record. Why waste computer time and risk another failu=
re if the data is faulty?

Sheiner suggested index plots, but right now we are just checking the ba=
sic set up rather than
hunting for errors in the data.

Replace $TABLE with the following. I would not ordinarily use LFORMAT/RF=
ORMAT
but I put them in so as to generate something scrunched that I can copy =
and paste into this email:

$TABLE ID TIME DV AMT DOSE MDV AGE WT SCR ISM CLCR AA BB CC DD EE FF
NOAPPEND NOPRINT FILE=test.tab
LFORMAT="(' ',20A6)"
RFORMAT="(20F6.1)"

When I run this, test.tab is generated.

 ID TIME DV AMT DOSE MDV AGE WT SCR ISM CLCR AA BB CC DD EE FF
 1.0 0.0 0.0 100.0 100.0 1.0 34.8 38.2 1.1 0.0 42.6 42.6 42.6 42.6 42.6 =
42.6 42.6 * *

Its easy to see that this matches the original data.* *
1, 0 , 0, 100, 100, 1, 34.823, 38.212, 1.1129, 0 , 42.635, 42.635, 42.63=
5, 42.635, 42.635, 42.635, 42.635

With WIDE option of $DATA, the table is unchanged, though FDATA is easie=
r to examine visually and
the format in FCON is simper.

Hope this helps,
Alison

On Wed, Dec 4, 2019, at 11:54 PM, Rikard Nordgren wrote:
> Hi Mark,
>
> I tested your model and dataset and checked the FORM section of the FC=
ON file:
>
> FORM
> (E3.0,E4.0,E8.0,2E3.0,E1.0,2E6.0,E7.0,E1.0,5E6.0/2E6.0,1F2.0)
> and the FDATA, first record here:
> 1 0 0100100134.82338.212 1.1129042.63542.63542.63542.63542.635
> 42.63542.635 1
>
> It seems to be fine. Please refer to how fortran uses the format state=
ment to parse strings using field sizes rather than delimiters.
>
> Best regards,
> Rikard
>
>
>
>
>
> On 2019-12-05 08:23, Mark Tepeck wrote:
>> Hi Nordgren and Denny,
>>
>> Thanks for your tips. Here are the NONMEM script, input CSV file row =
1, and FDATA row 1. I also attached the original model file, CSV input f=
ile as well as the FDATA (not sure NMuser allows attachment) for trouble=
shooting. I did observe that multiple columns from input were combined t=
o fewer columns in the FDATA file. I also found occasional generation of=
 *fdata-1* file but not sure its role.
>> * *
>> *The input CSV file (17 columns) *
>> CID, TIME, CONC, AMT, DOSE, MDV, AGE, WT, SCR, ISM, CLCR, AA, BB, CC =
, DD, EE, FF
>> 1, 0 , 0, 100, 100, 1, 34.823, 38.212, 1.1129, 0 , 42.635, 42.635, 42=
.635, 42.635, 42.635, 42.635, 42.635
>>
>> *FDATA (6 columns):* 1, 0, 0100100134.82338.212, 1.1129042.63542.6354=
2.63542.63542.635, 42.63542.635,1
>>
>> *NONMEM script:*
>>
>> $PROBLEM Test Fdata
>> $DATA CS1_IV1EST_PAR.CSV IGNORE=C
>> $INPUT ID TIME DV AMT DOSE MDV AGE WT SCR ISM CLCR AA BB CC DD EE FF
>> $SUBROUTINE ADVAN1 TRANS2
>> $PK
>> CL = THETA(1)*EXP(ETA(1))
>> V= THETA(2)*EXP(ETA(2))
>> S1 = V
>>
>> $ERROR
>> IPRED = F
>> Y=F+F*ERR(1)+ERR(2)
>>
>> $THETA
>> (0.1,1)
>> (1,10,20)
>>
>> $OMEGA
>> 0.09
>> 0.09
>>
>> $SIGMA
>> 0.09
>> 1
>> $ESTIMATION METH=1 MAXEVAL=9999 PRINT=5 POSTHOC
>> $TABLE ID TIME DV FILE=CS1_IV1ESTFPDF.fit
>>
>>
>> I really appreciate your input.
>>
>> Mark
>>
>>
>>
>>
>>
>> On Tue, Dec 3, 2019 at 11:57 PM Rikard Nordgren <rikard.nordgren
bio.uu.se> wrote:
>>> Hi,
>>>
>>> NM-TRAN will not add columns not listed in $INPUT or dropped/skipped=
 to FDATA. Could that be the reason?
>>>
>>> Best regards
>>> Rikard Nordgren
>>>
>>>
>>>
>>> On 2019-12-04 01:27, Mark Tepeck wrote:
>>>> Hi All,
>>>>
>>>> I am using NONMEM 7.4.3. I want to confirm the right input dataset =
into NONMEM. However, I found that the FDATA file can save only around t=
he beginning 9 columns of the original CSV file. The ending columns (e.g=
., column 10-20) are either missing or combined into a single column in =
the FDATA file.
>>>>
>>>> I am not sure other people encountered the same problem.
>>>>
>>>> Thank you,
>>>>
>>>> Mark
>>>
>>> --
Rikard Nordgren
Systems developer

Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala

Phone: +46 18 4714308
>>> www.farmbio.uu.se/research/researchgroups/pharmacometrics/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> När du har kontakt med oss på Uppsala universitet med e-po=
st så innebär det att vi behandlar dina personuppgifter. Fö=
r att läsa mer om hur vi gör det kan du läsa här:htt=
p://www.uu.se/om-uu/dataskydd-personuppgifter/
>>>
>>> E-mailing Uppsala University means that we will process your persona=
l data. For more information on how this is performed, please read here:=
 http://www.uu.se/en/about-uu/data-protection-policy
>
> --
Rikard Nordgren
Systems developer

Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala

Phone: +46 18 4714308
> www.farmbio.uu.se/research/researchgroups/pharmacometrics/

--
 Alison Boeckmann
 alisonboeckmann


Received on Thu Dec 05 2019 - 15:13:44 EST

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