Re: [NMusers] T in $DES

T ADVANCE TO) AN EVENT > TIME OF THE PRIOR INDIVIDUAL RECORD. > > The wording is arcane but the basic message is that, for each subject, the > first values for DES computed entries are not what you expect. > Despite this, NONMEM is "doing the right thing". > I defer to

Re: [NMusers] FDATA file bug

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,

Re: [NMusers] FDATA file bug

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 alisonboeckm...@fastmail.fm

Re: [NMusers] ERROR NUMBER OF BASIC PK PARAMETERS EXCEEDS VALUE OF NPARAM IN $MODEL

LOCK > > > > $DES > > > > CC=A(1)/V1 > > > > RT=0 > > > > IF(CC.GT.MIC) RT=1 > > > > DADT(1) = - A(1) * (K10 + K12 + K13) + A(2) * K21  + A(3)*K31 > > > > DADT(2) = A(1) * K12 - A(2) * K21 > > > > D

Re: [NMusers] How do I access the total number of subject?

nk it is accessible. Could you please > tell me how to access the variable from PRED subroutine? > > Regards > > Ryota Jin > Chiba university, Japan. > email: ryot...@chiba-u.jp > > > -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Easier IOV modeling

... REPLACE. -- Alison Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Easier IOV modeling

he above code >> snippets are>> heavily leaning on the userguide examples and completely >> untested. >> Please test before use. >> >> Hope this helps, >> >> Jeroen >> >> http://pd-value.com >> jer...@pd-value.com >> @PD_value >> +31 6 23118438 >> -- More value out of your data! >> >> On 16-01-19 04:06, Sebastien Bihorel wrote: >>> Hi >>> >>> The Introduction to NONMEM 7.x documents include a section entitled >>> "Easier Inter-occasion variability modeling" which describes a >>> quicker way to code IOV. >>> >>> $ABBR REPLACE ETA(OCC_CL)=ETA(4,7,10) ;when OCC=1, eta(4) to be >>> used: when OCC=2, eta(7) to be used, etc. >>> >>> ... >>> >>> $PK CL=TVCL*EXP(ETA(1)+ETA(OCC_CL)) >>> >>> When this approach is used, OCC must be a data item defined in >>> $INPUT. >>> >>> Is there a similar way to code ETAs using a dynamic variable defined >>> in $PK? >>> >>> Thanks >>> >>> Sebastien >>> >>>>> -- Alison Boeckmann alisonboeckm...@fastmail.fm Links: 1. http://pd-value.com/ 2. tel:+31%206%2023118438

[NMusers] Time After Dose example in help/html

om to report a match, or to report a discrepancy in values of TAD. We will try to resolve the discrepancy. Alison Boeckmann Dec 17, 2018 === ++ || |

[NMusers] Time After Dose example in help/html

a discrepancy in values of TAD. We will try to resolve the discrepancy. Alison Boeckmann Nov 18, 2018 === ++ || | TIME AFTER DOSE (TAD

Re: [NMusers] Time-Varying Bioavailability on Zero-Order Infusion

> > >ENDIF > > > >MTIME(1)=TDOSE > > > >MTIME(2)=DOSEEND > > > >F1 = 0 ; Bioavailability is zero so that the $DES block has full > > control over the rate. > > > >RATEADJTAU=THETA(10) > > > >RATEADJMAX=THETA(11) > > > > $DES > > > >; Manually control the infusion > > > >RATEIN = 0 > > > >IF (MTIME(1).LE.T .AND. T.LE.MTIME(2)) THEN > > > > RATEADJCALC = RATEADJMAX * EXP(-(T – MTIME(1)) * RATEADJTAU) > > > > RATEIN = DOSERATE - RATEADJCALC > > > >ENDIF > > > >DADT(1) = RATEIN - K10*A(1) - K12*A(1) + K21*A(2) - K13*A(1) + > > K31*A(3) > > > >DADT(2) = K12*A(1) - K21*A(2) > > > >DADT(3) = K13*A(1) - > > K31*A(3) > > > > Thanks, > > > > Bill > > > > > -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] DEFDOSE/DEFOBS Required for Many Compartments?

+1-617-899-8123. Please then delete the e-mail and any copies of it. Thank you. --   Alison Boeckmann   alisonboeckm...@fastmail.fm

Re: [NMusers] Steady-state (SS) and $DES veeeery slow

Schuur > Hospital Observatory, Cape Town 7925 South Africa phone: +27 21 404 > 7719 fax: +27 21 448 1989 email: paolo.de...@uct.ac.za > > Disclaimer - University of Cape Town This e-mail is subject to UCT > policies and e-mail disclaimer published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable > from +27 21 650 9111. If this e-mail is not related to the business of > UCT, it is sent by the sender in an individual capacity. Please report > security incidents or abuse via cs...@uct.ac.za -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Time varying volume of distribution implementation

"Declarative languages are a form of dementia -- they have no memory of > events" > > Holford SD, Allegaert K, Anderson BJ, Kukanich B, Sousa AB, Steinman A, > Pypendop, B., Mehvar, R., Giorgi, M., Holford,N.H.G. Parent-metabolite > pharmacokinetic models - tests of assumptions and predictions. Journal of > Pharmacology & Clinical Toxicology. 2014;2(2):1023-34. > Holford N. Clinical pharmacology = disease progression + drug action. Br > J Clin Pharmacol. 2015;79(1):18-27. > -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Markov model dataset

Here iis an explanation of why the error messages were being produced by PREDPP. At my request, Achim send me the $MODEL statement from the control stream. $MODEL NCOMP = 4 COMP=(G0) COMP=(G1) COMP=(G2) COMP=(G3) Compartment 1 is the default compartment for doses and observations, because no

Re: [NMusers] unbalanced data set

ries considerably between these individuals." -- Alison Boeckmann On Tue, Jan 5, 2016, at 06:03 PM, Zheng Liu wrote: > Dear all, > > I recently have a data set for pk parameters fitting. The issue is > some patients have far more measurement points than others (i.e. a few >

Re: [NMusers] Saving solution to differential equation from previous time point and carry over to next time point

nt variables such that my > > code would work as intended? > > > > Thank you Tommy Li > > -- > Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & > Clinical Pharmacology, Bldg 503 Room 302A University of Auckland,85 > Park Rd,Private Bag 92019,Aucklan

Re: [NMusers] RE: Implementing a Kalman Filter based optimization in NONMEM

erential Equations in NONMEM®: > Implementation, Application,  and Comparison with Ordinary > Differential Equations  Pharmaceutical Research, Vol. 22, No. 8, > August 2005 2005) > > > > John H. Warner, PhD, MBA > Director, Biostatistics > CHDI Management / CHDI Foundation > 155 Village Boulevard, Suite 200 > Princeton, NJ, 08540 > (609) 945-9644: office > (609) 751-7345: cell > (609) 452-2160: fax > john.war...@chdifoundation.org > -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Is “DOSE=0” accepted by NONMEM?

s NONMEM only accepts DOSE is a positive number. If > DOSE=0, NONMEM can't perform the fitting. Can anyone kindly give me > some suggestions to solve this problem? Thanks a lot in advance! > > PTIDDVAMTtimeEVID2.126.821.13263.131.0830.16330.03639 > > Zheng -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] $MIX variable from $PK

t; NONMEM read what is defined in $PK into $MIX? > > Much thanks, > > Mannie -- Alison Boeckmann alisonboeckm...@fastmail.fm

[NMusers] Output-type compartments in PREDPP

relying on the fact that the compartment was initally on by default. No existing problem specification that avoided the error message by using extra event records is incorrect. It is simply that the data files could have been left as-is and the $MODEL statements changed instead. -- Alison Boeckmann

Re: [NMusers] Cross-validation script in NM

: there is no point running $ESTIM till you are sure you've got the model right! Instead, *each* problem should display items of interest $TABLE ID TIME IND_DIA DIALYSIS TDM etc. Now you can make sure you are getting the correct data items from the correct records. Alison Boeckmann On Fri, Dec 5, 2014, at 02:03

Re: [NMusers] Logic Expression in $DATA: ACCEPT or IGNORE

and in the mean time, B are less than 100. NONMEM manual VIII did not specify this type of acceptance. Could anybody please tell me how to write this kind expression using ACCEPT, or IGNORE in nonmem? Thanks a lot for your help. Best Regards -- Xinting -- Xinting -- Alison

Re: [NMusers] Logic Expression in $DATA: ACCEPT or IGNORE

; This is the problem that should have $ESTIMATION or ; other tasks using the selected portion of the data set. -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] RE: Slow PRED in tables?

and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). Thank you. buSp9xeMeKEbrUze -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Transit Absorption Model in NONMEM

+EPS2, and let the program to estimate EPS1 and EPS2? 2. What's the purpose of SIMEPS(EPS) here? From my understanding is that if ICALL equals 4, then conduct a limited number of Y=CP*(1+RUV_CV*EPS1)+RUV_SD*EPS2. Thanks to you all for your kind support. -- Xinting -- Alison Boeckmann

Re: [NMusers] Time-varing covariate

have never found the need to use PCMT. I usually do not rely on the default compartment with complex models but use the compartment explicitly in $ERROR to define the prediction I want to output. Best wishes, Nick On 27/08/2013 10:45 p.m., Alison Boeckmann wrote: There have been a number

Re: [NMusers] When will NONMEM UsersNet Archive be searchable again?

of this message is not permitted and may be unlawful. References 1. http://www.cognigencorp.com/index.php/cognigen/resources_nonmem -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] What does MU_WARNING 24 mean?

arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835 -- Alison Boeckmann alisonboeckm...@fastmail.fm

[NMusers] Files for multiple dose superimpositon into transit compartment

: ftp://nonmem.iconplc.com/Public/nonmem/transit_compartment/ The paper is: Implementation of dose superimposition to introduce multiple doses for a mathematical absorption model (transit compartment model) Jun Shen, Alison Boeckmann Andrew Vick Journal of Pharmacokinetics and Pharmacodynamics

Re: SPAM: [NMusers] Interactive Control of NONMEM runs

, please reply to the sender, so that ICON plc can arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835 -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] COMPARTMENT INITIALIZATION: A_0

of a compartment when SS=2 or SS=3 given and also comment on the information does that parameter give more than the trough concentration measured at the clinical visit? Regards, Ayyappa -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Steady state dose

(second attempt) From: Alison Boeckmann alisonboeckm...@fastmail.fm To: Joanna Lewis joanna.le...@ucl.ac.uk Cc: Nick Holford n.holf...@auckland.ac.nz, nmusers@globomaxnm.com Date: Mon, 24 Oct 2011 15:38:44 -0700 Subject: Re: [NMusers] Steady state dose My remarks are attached lewis.ss.nmusers2

Re: [NMusers] Steady state dose

the value of 1 during the calculation of the steady state solution -- although that would be a reasonable assumption that could be confirmed by someone such as Alison Boeckmann. Nick PS NONMEM calculates steady state amounts in compartments -- it does not calculate steady state doses

RE: [NMusers] lagged absorption and empirical input function

, Pierre-Olivier -- Alison Boeckmann alisonboeckm...@fastmail.fm mpast.ctl Description: Binary data mpast.out Description: Binary data

Re: [NMusers] Question regarding Calculation Process in $DES BLOCK

(716) 633-3463 ext. 236 Alison Boeckmann wrote: Here is a little background on how it works. ADVAN routines such as ADVAN6 use a subroutine from third party sources to do the integration. For example, ADVAN6 calls DVERK from IMSL, ADVAN13 calls LSODA, etc. These subroutines

Re: [NMusers] Question regarding Calculation Process in $DES BLOCK

result is produced for the TABLE file? If the code is in fact too complicated for anyone to understand anymore at least one can have an empirical attempt to see if this change has any effect -- other then producing the correct value in the TABLE file. Nick On 2/06/2011 5:29 a.m., Alison Boeckmann

Re: [NMusers] Question about warning 68 in NONMEM

understand that there might be multiple situations/explanations for this warning. I just want to get the general concepts. Thank you. best regards, Li li -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Question regarding Calculation Process in $DES BLOCK

(in the $DES block) are set to the values defined at the end time, not the start time. I'm afraid that I can't give you a good explanation for this design decision. Kind regards, -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Problem with predicted values for peripherial compartment

$TABLE C ID TIME CMT EVID DV IPRE NOPRINT ONEHEADER FILE=benzopred.tab István Németh PhD Biostatistician Developmental Drug Metabolism Pharmacokinetics Pharmacological and Drug Safety Research Gedeon Richter Plc Tel: 00 36 1 505 7082 Fax: 00 36 1 889 8526 -- Alison Boeckmann

Re: [NMusers] Speeding up code with explicit, piecewise ODE solutions

://gaps.cpb.ouhsc.edu/nm/58sep2496.html 2. mailto:svanw...@icpd.com 3. mailto:owner-nmus...@globomaxnm.com 4. mailto:owner-nmus...@globomaxnm.com 5. mailto:nmusers@globomaxnm.com -- Alison Boeckmann alisonboeckm...@fastmail.fm

RE: RE: [NMusers] how to implement AR residual error model in Nonmem with FOCE INT routine

Registered number: 145835 -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Weird behavior (or poor understanding on my side) of the SS=2 option

-- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] OMEGA off-diagonal elements parameterized as correlations

(9)923-6730 fax:+64(9)373-7090 mobile: +33 64 271-6369 (Apr 6-Jul 20 2009) http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford -- Alison Boeckmann alisonboeckm...@fastmail.fm

RE: [NMusers] OMEGA BLOCK with mixture model?

://www.actelion.com -- Alison Boeckmann alisonboeckm...@fastmail.fm

Re: [NMusers] Code for EHC

show double peaks but even in fasting state. Can we expect EHC in fasting state? Can anybody provide some coding help in modeling intermittent episodes of EHC rather than continuous mode? Thank you. Regards, Ayyappa Chaturvedula -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] Code for EHC

but even in fasting state. Can we expect EHC in fasting state? Can anybody provide some coding help in modeling intermittent episodes of EHC rather than continuous mode? Thank you. Regards, Ayyappa Chaturvedula -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] archive of this list

of models? Is it included in wings? (where). Thanks, Carlos Hoyo [EMAIL PROTECTED] -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] Is the use of II, SS, and ADDL allowed simultaneously

but I wish to know if there is an easier method available -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] Modeling a concentration curve with secondary peaks?

. -- -- Alison Boeckmann [EMAIL PROTECTED]

RE: [NMusers] different COMRES statements

PROTECTED] -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] Modeling compartment initial conditinns using ETA()= EPS(1) and CPZERO measure

) EN CSS IPR1 IPR2 NOPRINT FILE=VER1.TAB $TABLE ID TIME IAGE K12 K21 K R1 IDIF NOPRINT FILE=VER1.TAB $SCAT CP VS IPR1 UNIT -- Alison Boeckmann [EMAIL PROTECTED]

RE: [NMusers] Interindividual variability in residual variance

471 4105 fax +46 18 471 4003 [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:owner- [EMAIL PROTECTED] On Behalf Of Alison Boeckmann Sent: Thursday, July 12, 2007 02:04 To: Samtani, Mahesh [PRDUS]; nmusers@globomaxnm.com Subject: Re: [NMusers

RE: [NMusers] Interindividual variability in residual variance

) in the model for eta on eps. On Thu, 12 Jul 2007 13:24:00 -0700, Alison Boeckmann [EMAIL PROTECTED] said: Dear Mats, thanks for the explanation. Very helpful. You and others have said that INTERACTION is needed when there is an eta on EPS. Some people may wonder why. Perhaps I can help

Re: [NMusers] Interindividual variability in residual variance

regards, Vladimir Cut here -- Alison Boeckmann [EMAIL PROTECTED]

RE: [NMusers] NONMEM ODE solver

based just on the first and second derivative (with some penalty, to keep it out of that range again)? Mark Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com Original Message Subject: Re: [NMusers] NONMEM ODE solver From: Alison Boeckmann [EMAIL PROTECTED

Re: [NMusers] NONMEM ODE solver

for your help in this matter. Benjamin Ribba Therapeutic Targeting in Oncology (EA3738) University Claude Bernard Lyon 1 Faculty of Medicine Lyon-Sud 165, chemin du grand revoyet 69921 Oullins cedex Tel: +33 4 26 23 59 57 / +33 6 66 06 15 21 -- Alison Boeckmann [EMAIL PROTECTED

RE: [NMusers] Indirect response model

in computing your COEF parameter (must be in $DES block). I hope this helps, David Salinger RFPK, Univ. of Washington -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] modeling the circadian baseline

of Pharmaceutical Sciences University at Buffalo, SUNY C237 Cooke Hall, Buffalo, NY 14260 Tel: 716 645 2828 ext 275 Fax: 716 645 3693 E-mail: [EMAIL PROTECTED] -- Alison Boeckmann [EMAIL PROTECTED]

Re: [NMusers] batches with different half-life - linear PK

or publications which can help? Thanks! Pavel -- Alison Boeckmann [EMAIL PROTECTED] $PROB batch1 $DATA dat1.txt IGNORE=# $INPUT ID TIME AMT RATE CMT DV $SUBR ADVAN1 $PK F1=1 D1=1 ALAG1=1 K=1 S1=1+ETA(1) $ERROR Y=F+ERR(1) $OMEGA 1 $SIGMA 1 $TABLE TIME CMT FILE=tab1.txt $PROB batch2

Re: [NMusers] batches with different half-life - linear PK

. Theoretically, it is easy to model if PKis linear because NONMEM superimposes single-dose processes to obtain predicted concentrations for multiple doses. Does enyone know how to implement it in NONMEM? Are there any classes or publications which can help? Thanks! Pavel -- Alison

Re: [NMusers] batches with different half-life - linear PK

, it is easy to model if PKis linear because NONMEM superimposes single-dose processes to obtain predicted concentrations for multiple doses. Does enyone know how to implement it in NONMEM? Are there any classes or publications which can help? Thanks! Pavel -- Alison Boeckmann [EMAIL PROTECTED

Re: [NMusers] Absorption delay NOT completed before the next dose is given

the depot compartment. Will this circumvent the problem stated above? In other words does ALAG always have to be smaller than II and why? Please advice#8230;MNS -- Alison Boeckmann [EMAIL PROTECTED] Mahesh Samtani raised two questions about the restrictions

Re: [NMusers] coding data at steady-state

St.Jude Children's Research Hospital 332 North Lauderdale street Memphis, TN 38105 Danny Thomas Research Center Room D1034 Mail Stop 314 Phone: (901)-495-5938 E-mail: [EMAIL PROTECTED] -- Alison Boeckmann [EMAIL PROTECTED]