NONMEM Users Network Archive

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Re: FDATA file missing

From: Mark Tepeck <mark.tepeck>
Date: Wed, 27 Nov 2019 09:19:03 -0800

The most simple way would be NONMEM to generate a CSV file with headings to
replace FDATA. Although many auxiliary tools can help, it would save the
end-users huge efforts of looking for third-party tools for
post-processing. This would also minimize the chance of errors due to
software incompatibilities issues. An idea scenario is like the windows 10
that comes with many essentials tools pre-installed.

Thanks

On Tue, Nov 26, 2019 at 9:22 AM Mahmoud Tareq Abdelwahab <
mah.tareq87

> Hello Mark,
>
> in addition to Sarah's suggestions, you could run NONMEM via psn using
> option clean=0 which will stop psn from cleaning the temp files generated
> by NONMEM.
>
> for the data issues, it refers to the actual data that's read into NONMEM
> i.e after excluding all ignore statements and dropped columns, a workaround
> is to filter out the dataset in the same way it's being filtered in the
> NMtran control stream or kill the run before it crashes and you should have
> the FDATA file in the NM folder.
>
> Mahmoud
>
> On Tue, Nov 26, 2019 at 7:10 PM Cook, Sarah <sfcook
>
>> Hi Mark,
>>
>>
>> I'm guessing that you are probably running NONMEM via PsN. The default
>> behavior of PsN is to suppress some output files, including the FDATA file.
>> To request that the FDATA file be retained, you can include the option
>> -extra_output=fdata on your PsN execute command line.
>>
>>
>> I don't think there is any way to include the column headings (since they
>> are ignored and not actually read into NONMEM), but having the FDATA file
>> should help you troubleshoot your problem. As far as I know, the warnings
>> relate to the location in the FDATA file, again, because the ignored rows
>> are not actually being read in.
>>
>>
>> Best of luck,
>>
>> Sarah
>>
>>
>>
>> Sarah F. Cook, PhD
>> Adjunct Assistant Professor
>> University at Buffalo
>> Department of Pharmaceutical Sciences
>> E-mail: sfcook
>> Phone: (570) 362-2981
>> ------------------------------
>> *From:* owner-nmusers
>> behalf of Mark Tepeck <mark.tepeck
>> *Sent:* Tuesday, November 26, 2019 11:13 AM
>> *To:* nmusers
>> *Subject:* [NMusers] FDATA file missing
>>
>>
>> During my troubleshooting of a failed NONMEM run, I want to confirm the
>> correct exclusion of some records (e.g., IGNORE CMT=2) for the input file.
>> However, I could not find the FDATA file in the run directory. Is there any
>> way to force NONMEM to generate a FDATA? I am also wondering about the
>> possible causes of missing FDATA.
>>
>> Even the FDATA file is available, is it possible to include the column
>> heads (e.g., ID, DV) on the top of the numbers? So, I can confirm which
>> column is excluded or retained.
>>
>> In addition, I am not sure whether the dataset related warnings (e.g.,
>> DATA WARING 1, RECORD 100, DATA ITEM 11, THE DV IS NULL BUT MDV IS 0) is
>> refereeing to the FDATA file or the raw input CSV file. In other words, the
>> problematic record 100 represents the row 100 in the FDATA file or the CSV
>> file?
>>
>> Thank you,
>>
>> Mark
>>
>
>
> --
>
>
>
>
>
>
>
>
>
>
> *Mahmoud Tareq AbdelwahabPhD StudentPharmacometrics Research GroupDivision
> of Clinical PharmacologyDepartment of MedicineUniversity of Cape TownK45
> Old Main BuildingGroote Schuur HospitalObservatory, Cape Town 7925, South
> Africa.*
>
>
> *Tel: +27 21 650 4861Email: Abdmah009
>
>

Received on Wed Nov 27 2019 - 12:19:03 EST

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