Re: FDATA file bug
Hi Richard and others:
Thanks for explaining FDATA. There is no bug.
FDATA would have a simpler, space delimited format if there were fewer
characters 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 between 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 Plots.
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 compute 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 failure if
the data is faulty?
Sheiner suggested index plots, but right now we are just checking the basic set
up rather than
hunting for errors in the data.
Replace $TABLE with the following. I would not ordinarily use LFORMAT/RFORMAT
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, 42.635,
42.635, 42.635, 42.635, 42.635
With WIDE option of $DATA, the table is unchanged, though FDATA is easier to
examine visually and
the format in FCON is simper.
Hope this helps,
Alison
Quoted reply history
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 FCON 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 statement 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 file as well
>> as the FDATA (not sure NMuser allows attachment) for troubleshooting. I did
>> observe that multiple columns from input were combined to 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,
>> 1.1129042.63542.63542.63542.63542.635, 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
>> <[email protected]> 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 the
>>>> 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-post så innebär det
>>> att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det
>>> kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>>>
>>> E-mailing Uppsala University means that we will process your personal 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
[email protected]