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Re: FDATA file bug

From: Mark Tepeck <mark.tepeck>
Date: Mon, 9 Dec 2019 13:48:36 -0800

Hi Alison,

Yes. You are right. This script went throug directly with NONMEM instead of
Psn,

However, this issue is considered a bug and has been acknowledged in the
NONMEM 7.4.3 bug list (
https://nonmem.iconplc.com/nonmem743/nm743_bug_list.pdf?token=6F99C315-1A=
CC-11ea-A323-005056911489&html).
It is described as:



*"7) For data sets with many items (columns), and when =DROP requests are
made onseveral of these items, the FDATA file may not be correctly
constructed. As awork-around, add the option WIDE to the $DATA record."*

Per the last NMuser email, this bug has been fixed in NONMEM 7.4.4*/7*.5. I
should have checked the bug list file at the very beginning. My oversight.

Thank you,

Mark



On Mon, Dec 9, 2019 at 11:11 AM Alison Boeckmann <
alisonboeckmann

> Hi Mark,
> You reported this message:
>
> The ERROR message is "There was an error when running nmfe, NMtran could
> not be initiated for model 1"
>
> I don't recognise this message as coming from the NONMEM system.
> If you are using 3d. party software to run NONMEM, it may be that the
> message is coming from that software.
> I used NONMEM 7.4.3 for my suggested control stream.
> It ought to work with all NONMEM 7.4 versions but I did not test them al=
l.
>
> If you have any more questions or comments, would you please start a new
> thread?
> "FDATA file bug" is misleading because there is no bug.
>
> Thanks,
>
> -- Alison
>
> On Mon, Dec 9, 2019, at 12:38 AM, Mark Tepeck wrote:
>
> Hi Alison,
>
> Thank you so much for your comprehensive suggestion, which is definitely
> helpful. This topic is like that we are still driving a manual transmissi=
on
> car in an era of self-driving car. Why could not NONMEM be updated to
> make the life easier for the end-users? A simple csv file with headings c=
an
> save us a lot of time.
>
> I still think that check of FDATA is the most intuitive and direct way to
> ensure correct input. Sometimes, plots may not sufficiently provide detai=
ls
> for every data point, especially when you have thousandths of points
> cluttered in one plot. Additionally, graphic evaluation can be highly
> dependent on the visual sensitivity of the investigator.
>
> Joel S. Owen and Jill Fiedler-Kelly also suggested examination of the
> FDATA file in the book "Introduction to Population Pharmacokinetic/
> Pharmacodynamic analysis with nonlinear mixed effects models". On page 33=
,
> it says "Such exclusions from the datafile can be confirmed by viewing th=
e
> FDATA output file"
>
> I followed your suggestion but got errors for the proposed model file as
> listed below.
>
> $PROBLEM INTRAVENOUS BOLUS STUDY
> $DATA CS1_IV1EST_PAR.CSV IGNORE=C CHECKOUT
> $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
>
> $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)"
>
>
> The ERROR message is "There was an error when running nmfe, NMtran could
> not be initiated for model 1"
>
>
> Thank you,
>
> Mark
>
>
>
>
> On Thu, Dec 5, 2019 at 12:14 PM Alison Boeckmann <
> alisonboeckmann
>
>
> 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 betwee=
n
> 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 Plo=
ts.
>
> 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 failur=
e
> 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
>
> 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 statemen=
t
> 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 <
> rikard.nordgren
>
> 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 4714308www.farmbio.uu.se/research/researchgroups/pharmacome=
trics/
>
>
>
>
>
>
>
>
>
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å innebär
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>
>
> --
> Rikard Nordgren
> Systems developer
>
> Dept of Pharmaceutical Biosciences
> Faculty of Pharmacy
> Uppsala University
> Box 591
> 75124 Uppsala
>
> Phone: +46 18 4714308www.farmbio.uu.se/research/researchgroups/pharmacome=
trics/
>
>
> --
> Alison Boeckmann
> alisonboeckmann
>
>
>
> --
> Alison Boeckmann
> alisonboeckmann
>
>
>

Received on Mon Dec 09 2019 - 16:48:36 EST

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