Re: FDATA file bug

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 transmission > 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 can 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 details > 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 the 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 > <[email protected]> wrote: >> __ >> 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 >> >> 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] >> >> -- Alison Boeckmann [email protected]