[NMusers] Error in parallel nonmem - related to file size?

2015-02-24 Thread Mark Sale
s, setting NREC = 10002 gives the above error. Doesn't seem related to the size of the file, just the number of records.? Perhaps this is related to the 4 digits assigned for the length of the data file in FCON (but then why 10001, not 1)? Anyone know of a work-around? thanks Mark

[NMusers] Re: Error in parallel nonmem - related to file size?

2015-02-25 Thread Mark Sale
?Bob, Thanks very much, setting computers = 2 solved it Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. (tm) 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 ms...@nuventra.com www.nuventra.com<http://www.nuventra.

[NMusers] Modeling accelerated phase of malignancy

2015-05-29 Thread Mark Sale
Dear Colleagues, I'm working on a model of a malignancy that, at some point in the course of the disease enters into an accelerated phase. I'm using a sort of standard serial compartment model, with a zero order input rate, then first order transit to the next compartment. I think the "corre

RE: [NMusers] Modeling accelerated phase of malignancy

2015-05-29 Thread Mark Sale
Thanks to Mannie, this is the correct way to solve this (and seems to work as well). Thanks Mark From: echigu...@yahoo.com [mailto:echigu...@yahoo.com] Sent: Friday, May 29, 2015 7:34 PM To: Mark Sale Subject: Re: [NMusers] Modeling accelerated phase of malignancy Hi Mark Have you tried

[NMusers] RE: Is it reasonable to add covarite to PD parameters kin or kout?

2015-07-27 Thread Mark Sale
Li, I'm going to go out on a limb (since I haven't seen your data or understand the biology) and suggest that the baseline value is not a covariate, but is just another observation (presumably with drug concentration = 0). The baseline value is sort of by definition a function of kin. So, you

[NMusers] Error in table step

2015-09-27 Thread Mark Sale
he $TABLE step). I assume it is crashing calculating the conditional ETAs (don't know why it does OK in estimation). PRDERR only has the small number of error from the estimation Anyone seen this error, any suggestions on how to get rid of it (other than removeing subject 51)? Ma

[NMusers] Re: Error in table step

2015-09-28 Thread Mark Sale
but crashed on tables). Tried FOCE, IMPMAP as well as SAEM. I did try removing the offending subjects, but just had the same problem with another (ultimately removed nearly 1/3 of the data, still had the error). So, ended up just going back to a simpler model. thank Mark Mark Sale M.D.

[NMusers] Pediatric brain scaling

2015-11-16 Thread Mark Sale
surprised that I can't find anything about dosing CNS drugs to peds, based on brain weight (and, ideally, brain clearance). Does anyone know of anything? thanks Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. (tm) 2525 Meridian Parkway, Suite 280 Research Tri

Re: [NMusers] setup of parallel processing and supporting software - help wanted

2015-12-08 Thread Mark Sale
WRT bootstrap, it makes much more sense to simply bootstrap the many nonmem runs (start 8 NONMEM runs at at time, rather than 1 run parallelized to 8 cores). So, no, don't use parallel NONMEM for bootstrap, run multiple bootstrap samples at the same time. Mark Mark Sale M.D.

Re: [NMusers] setup of parallel processing and supporting software - help wanted

2015-12-08 Thread Mark Sale
Nonmem 7.2 estimation methods and parallel ... Read more...<http://www.ncbi.nlm.nih.gov/pubmed/22101761> Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 ms...@nuventra.com www.nuventra

Re: [NMusers] setup of parallel processing and supporting software - help wanted

2015-12-09 Thread Mark Sale
e of the data set, except that the limit of parallelization is the number of subjects (the data set must be split up by subject). Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383

Re: [NMusers] setup of parallel processing and supporting software - help wanted

2015-12-09 Thread Mark Sale
es, but would look forward to learning about other peoples experience. Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 ms...@nuventra.com www.nuventra.com<http://www.nuventr

Re: [NMusers] setup of parallel processing and supporting software - help wanted

2015-12-09 Thread Mark Sale
completely agree, no reason to use FPI, Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 ms...@nuventra.com www.nuventra.com<http://www.nuventra.com> Empower your Pi

[NMusers] Mixture model with logistic regression

2016-02-19 Thread Mark Sale
it still gave me a very small difference in the intercept for the 2nd and 3rd populations. Is there an issue with using mixture models with logistic regression? I'm just using FOCE, Laplacian, without interaction, and LIKE. Any ideas? Mark Mark Sale M.D. Vice President, Modelin

[NMusers] Re: Mixture model with logistic regression

2016-02-20 Thread Mark Sale
imate for omega. If the data are population, and MAXE- VALS=0 is not coded, then METHOD=1 LAPLACE is required. Compare with PREDICTION option. Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 O

[NMusers] Re: Mixture model with logistic regression

2016-02-20 Thread Mark Sale
(s). If you have received this transmittal in error, please notify me immediately by reply email and destroy all copies of the transmittal. From: Bob Leary Sent: Saturday, February 20, 2016 9:24 AM To: Mark Sale; nmusers@globomaxnm.com Subject: RE: Mixture mod

Re: [NMusers] Mixture model with logistic regression

2016-02-20 Thread Mark Sale
o the apparent population in the data set. Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 ms...@nuventra.com www.nuventra.com<http://www.nuventra.com> Empower yo

Re: [NMusers] Mixture model with logistic regression

2016-02-20 Thread Mark Sale
Kudos to Jeroen, who solved this for me, needed the NOINTER option on $EST, then you can use SAEM, which gave a reasonable answer, unlike FOCE. Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office

[NMusers] Laplacian, BQL and initial estimates

2016-07-17 Thread Mark Sale
, LAPLACIAN ESTIMATION METHOD MUST BE USED It seems the Laplacian isn't used for the grid search for initial estimates (even though specified in $EST). any ideas? Mark Sale M.D. Vice President, Modeling and Simulation Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 280 Durham, NC

Re: [NMusers] Laplacian, BQL and initial estimates

2016-07-17 Thread Mark Sale
pretty standard $EST I think $ESTIMATION METH=1 NUMERICAL SLOW LAPLACIAN INTER NOTHETABOUNDTEST NOOMEGABOUNDTEST MAXEVAL= PRINT=1 NOABORT MSFO=MSF1 and just 1. Mark Sale M.D. Vice President, Modeling and Simulation Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 280

Re: [NMusers] Laplacian, BQL and initial estimates

2016-07-18 Thread Mark Sale
thanks Bob Mark Sale M.D. Vice President, Modeling and Simulation Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 280 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com CONFIDENTIALITY NOTICE The information in this transmittal (including attachments, if any) may be privileged

[NMusers] $PRIOR with normal for OMEGA?

2016-11-10 Thread Mark Sale
Is it possible to use a normal prior for OMEGA? The default is inverse Wishart, but I'd be interested in using Normal (insuring that it is positive definite) Any ideas? thanks Mark Sale M.D. Vice President, Modeling and Simulation Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway,

Re: [NMusers] $PRIOR with normal for OMEGA?

2016-11-11 Thread Mark Sale
l way to do it. I'll look into the TNPRI (didn't realize that stood for triple normal, but that makes sense). thanks Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 280 Durham, NC 27713 Phone (919)-973-0383 ms.

[NMusers] IMPMAP behavior question

2018-08-23 Thread Mark Sale
r than the LRT? But, basically, why is this happening? thanks Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com CONFIDENTIALITY NOTICE The information in this transmittal

Re: [NMusers] IMPMAP behavior question

2018-08-23 Thread Mark Sale
G JOB TO LOCAL STARTING SUBJECTS 9 TO 17 ON MANAGER: OK COLLECTING SUBJECTS 18 TO 32 ON WORKER2 and no mention of collecting subjects 33 to 85 on worker 3, or subjects 9 to 17 on worker 1. so, that could be the problem. Bob - thoughts? Mark Sale M.D. Senior

[NMusers] run NMFE without actually executing

2019-01-06 Thread Mark Sale
MFE73/74 batch file (for deployment reasons, would prefer not to have to edit the batch file, which would be easy enough to do, but again, I'd like a general/deployable solution, not a custom .bat file.). Can this be done, with the unedited version of NMFE??.bat or with PSN? thanks Mar

[NMusers] Different OBJ after covariance with parallel and IMPMAP

2019-02-04 Thread Mark Sale
EE etc. Can the SEE values in this case be believed? Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com

[NMusers] Microsoft MPI

2019-04-16 Thread Mark Sale
MS-MPI offers several benefits: we need to run this for another parallel application, and when we installed it, it broke parallel NONMEM. We're using Intel Fortran, 64 bit Window Server (2012). thanks Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Pharma Sciences, Inc. 25

Re: [NMusers] Microsoft MPI

2019-04-16 Thread Mark Sale
t clear there is a way to specify which mpiexec to use in a given application, along with lots of other stuff I don't understand. Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Pharma Sciences, Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nu

Re: [NMusers] Using evid 0 before dosing

2019-11-06 Thread Mark Sale
amount of information. That not withstanding, we also remove and pre-dose BQLs from the data set. Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com CONFIDENTIALITY NOTICE The information in

Re: [NMusers] Using evid 0 before dosing

2019-11-06 Thread Mark Sale
If >LLOQ has information, then !>LLOQ MUST also have information. and Yes, we evacuated for 6 days, back home now. Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com CONFIDENT

Re: [NMusers] Using evid 0 before dosing

2019-11-06 Thread Mark Sale
s of the transmittal. From: Stephen Duffull Sent: Wednesday, November 6, 2019 9:05 AM To: Dennis Fisher ; Mark Sale Cc: nmusers@globomaxnm.com Subject: RE: [NMusers] Using evid 0 before dosing WARNING: This email originated from outside of the company. Do not click links

[NMusers] LIBDECIMAL.LIB MISSING?

2019-11-29 Thread Mark Sale
e have any experience trying to run v7.4, ADVAN14 with old Intel Fortran? thanks Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com CONFIDENTIALITY NOTICE The information in this t

[NMusers] error message from xpose

2020-02-14 Thread Mark Sale
4 bytes free Base on a search for this error, it looks like it comes from dplyr. I'm running dplyr version 0.8.4, xpose version 0.4.7 and R version 3.6.2 with R Studio, under Windows 10. I've tried it with and without the NOAPPEND in the $TABLE records. Any suggestions would be apprecia

Re: [NMusers] error message from xpose

2020-02-14 Thread Mark Sale
Bill, thanks that may be it, seems to be working, thanks Mark Mark Sale M.D. Senior Vice President, Pharmacometrics Nuventra Inc. 2525 Meridian Parkway, Suite 200 Durham, NC 27713 Phone (919)-973-0383 ms...@nuventra.com Upcoming Events: Webinar:<https://www.nuventra.com/resources/eve

[NMusers] Open source package for AI/Machine learning model selection in NONMEM

2022-08-15 Thread Mark Sale
ffalo is a collaborator on this work and a co-investigator for this work. His laboratory has contributed sample datasets and suggestions on the strategies for model search Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM - 5

[NMusers] Simulate with parameter uncertainty

2022-12-17 Thread Mark Sale
lp me with the code to do this? Thanks Mark Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM - 5 PM Eastern Time +1 302-516-1684 www.certara.com This message (including any attachments) may contain confidential, propri

RE: [NMusers] Simulate with parameter uncertainty

2022-12-17 Thread Mark Sale
ation -keep_tables I'm thinking that may be easier than trying to use NWPRI. thanks Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM – 5 PM Eastern Time +1 302-516-1684 www.certara.com -Original Message- From:

RE: [NMusers] NONMEM Error on SAEM but not FOCEI

2024-01-26 Thread Mark Sale
does prohibit using PROTECT in automated methods to run models with/without BSV, or at least makes it a little more difficult. Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM - 5 PM Eastern Time +1 302-516-1684 www.certar

[NMusers] Announcement of Pre Conference workshop in RsNLME and machine learning with pyDarwin

2024-03-05 Thread Mark Sale
results using Darwin Reporter - hands on using AWS workspace. Registration fee: $275 Academic or Regulatory /$550 Industry Register here: https://www.certarauniversity.com/store/3646717-page2024-workshop-pmx-analysis-in-r-using-rsnlme-and-certara-toolsets Mark Sale M.D. Vice President Integrated

[NMusers] PyDarwin and RsNLME course at PAGE

2024-04-22 Thread Mark Sale
search results using Darwin Reporter - hands on using AWS workspace. Registration fee: $275 Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM - 5 PM Eastern Time +1 302-516-1684 www.certara.com [Certara Logo] This message

[NMusers] FREE - RsNLME and R tools at PAGE on June 25th

2024-06-04 Thread Mark Sale
ara-toolsets> Mark Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM - 5 PM Eastern Time +1 302-516-1684 www.certara.com [Certara Logo] This message (including any attachments) may contain confidential, proprietary, priv

RE: [NMusers] Sad news about Dr. Ludden

2024-08-03 Thread Mark Sale
esearch, a testament to both his technical knowledge and leadership skills. Like many others I personally benefited from my interactions with him. Mark Mark Sale M.D. Vice President Integrated Drug Development mark.s...@certara.com Remote-Forestville CA Office Hours 9 AM - 5 PM Eastern Time +1 30

[NMusers] Page course on Machine learning model selection in NONMEM and NLME still available

2025-04-21 Thread Mark Sale
Dear colleagues, There's still time to register for the Machine learning Model selection in NONMEM and NLME at the June Page meeting. Link below: https://www.certarauniversity.com/store/4230502-page2025-workshop-machine-learning-model-selection-in-nlme-nonmem-with-pirana-and-r Mark Mark

[NMusers] Machine learning course at PAGE

2025-04-04 Thread Mark Sale
Dear colleagues, Take a look at our Pre conference course at PAGE on PMX tools including Machine learning model selection https://www.certarauniversity.com/store/4230502-page2025-workshop-pmx-analysis-in-r-using-rsnlme-pirana-and-certara-toolsets Mark Mark Sale M.D. Vice President Integrated

[NMusers] Sample size/power in NONMEM

2007-02-07 Thread Mark Sale - Next Level Solutions
Dear Colleagues, In response to the recent discussion in this forum about sample size and power in NONMEM, Next Level Solutions has developed tools for formal "power" assessment in NONMEM using simulation (as described by Serge Guzy in this discussion). Essentially, one or more (preferably more)

RE: [NMusers] Simulation with covariates

2007-02-15 Thread Mark Sale - Next Level Solutions
nical Pharmacology > Medical Science Sweden > AstraZeneca R&D Lund > SE-221 87 Lund, Sweden > > > Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: [NMusers] Simulation with covariates > From: "Kriste

RE: [NMusers] WARNING 48

2007-02-26 Thread Mark Sale - Next Level Solutions
ct, the value of CONC is still left over from the last subject. This is all OK for the minimization, you just need to be aware of it when interpreting output, plots, tables etc. that the first value for CONC for a subject will not be correct. Mark Mark Sale MD Next Level Solutions, LLC www.Next

RE: [NMusers] create simulation file for 5000 patients ?

2007-02-28 Thread Mark Sale - Next Level Solutions
PROBS. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > > > > Original Message > > Subject: Re: [NMusers] create simulation file for 5000 patients ? > > From: "navin goyal" <[EMAIL PROTECTED]> > > Date: Tue, Februar

RE: [NMusers] Linear speedup of NONMEM on quad-core CPUs?

2007-03-12 Thread Mark Sale - Next Level Solutions
hey went out of business), and got zero parallelization for a single run of NONMEM. But this was a long time ago, maybe Intel figured out something new. Mark Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: Re: [NMusers] Linear sp

RE: [NMusers] Linear speedup of NONMEM on quad-core CPUs?

2007-03-12 Thread Mark Sale - Next Level Solutions
Brian, Windows will switch which processor/core it is running any executable on (unless you explicity tell it to run on a specific processor/core). But the total CPU time should be 100% (even if it is 25% on each of 4 processors). Mark Mark Sale MD Next Level Solutions, LLC

[NMusers] General question on modeling

2007-03-19 Thread Mark Sale - Next Level Solutions
point out that it is not nearly that linear a process, although in figure 11.1, Vol 5 of the NONMEM manuals, it is depicted as a step-by-step algorithm, without any looping back). Can anyone point me to any rigorous discussion of this model building strategy? Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com

RE: [NMusers] General question on modeling

2007-03-19 Thread Mark Sale - Next Level Solutions
once you've found it. I'm interest in how we find it. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: RE: [NMusers] General question on modeling > From: "Stephen Duffull" <[EMAIL PROTECTED]> > D

RE: [NMusers] General question on modeling

2007-03-19 Thread Mark Sale - Next Level Solutions
nly is no single criteria by which to evaluate the models, must be purpose specific. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: RE: [NMusers] General question on modeling > From: "Stephen Duffull" <[EMAIL PROTEC

RE: [NMusers] General question on modeling

2007-03-19 Thread Mark Sale - Next Level Solutions
g a label requiring them to do so would not result in an optimal outcome. (I won't defend ITT analysis, although I do appreciate that the origin of ITT is in another optimization issue, wherein type II errors are greatly prefered to type I errors in testing hypotheses, I likely would have a d

RE: [NMusers] General question on modeling

2007-03-20 Thread Mark Sale - Next Level Solutions
f mis-dosing drugs, and estimated the resulting fatalities. Making dosing more complicated is unlikely the help. In addition, each company very much wants their drug to be simpler to use than their competitors. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original

RE: [NMusers] General question on modeling

2007-03-20 Thread Mark Sale - Next Level Solutions
it is the structural model that drives pretty much everything. It matters more if you chose an Emax over an indirect response for your PD model than whether you put age as a predictor of Emax. Mark Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original

RE: [NMusers] General question on modeling

2007-03-20 Thread Mark Sale - Next Level Solutions
the structural model (which attempts to explain away the effect of time). Interesting insight from Allison on why the variance terms ended up last in the algorithm. Mark Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: Re: [NMus

RE: [NMusers] General question on modeling

2007-03-20 Thread Mark Sale - Next Level Solutions
> Subject: RE: [NMusers] General question on modeling > From: "Wang, Yaning" <[EMAIL PROTECTED]> > Date: Tue, March 20, 2007 1:33 pm > To: "Mark Sale - Next Level Solutions" <[EMAIL PROTECTED]>, > nmusers@globomaxnm.com > > In Marie Davidian

RE: [NMusers] General question on modeling

2007-03-20 Thread Mark Sale - Next Level Solutions
e certainly not true. But, evolutionary computation and machine learning is a very different approach (and IMHO a more rigorous approach) than what we currently do. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: Re: [NMusers] Ge

RE: [NMusers] input conversion error

2007-03-29 Thread Mark Sale - Next Level Solutions
you try to find the offending record in the data set (the NRECORDS option should help). Hopefully we'll hear from Alison (isn't it great to have her back?) Mark Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: [NMuse

RE: [NMusers] input conversion error

2007-03-29 Thread Mark Sale - Next Level Solutions
a set, and will only write legal data sets. If it makes it past NMTRAN, it has a legal (if not correct) data set. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: RE: [NMusers] input conversion error > From: "Bachman, Wil

RE: [NMusers] No Fit file

2007-05-22 Thread Mark Sale - Next Level Solutions
and saving. WRT plots, two options are Xpose from the Upsala group (R/Splus, http://xpose.sourceforge.net) or an excel macro from Next Level Solutions (www.nextlevelsolns.com) Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject:

RE: [NMusers] No Fit file

2007-05-22 Thread Mark Sale - Next Level Solutions
Thanks for clarifying this Alison, I think I did know this is a fortran I/O issue, not really a NMTRAN issue. Clearly we should all go back to MS-DOS edit ;-) (only us really old people even remember MS-DOS). Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Origi

RE: [NMusers] No Fit file -> bug or not a bug?

2007-05-23 Thread Mark Sale - Next Level Solutions
the first line of c:\nmvi\util\nmfe6.bat type c:\nmvi\util\end.txt >> %1 Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: RE: [NMusers] No Fit file -> bug or not a bug? > From: "Bill Bachman" <[EMAIL

RE: [NMusers] NONMEM ODE solver

2007-05-27 Thread Mark Sale - Next Level Solutions
: the Livermore solver, from the ODEPACK. and, no, I'm pretty sure there is no switching between algorithms. (does any software do this??) BTW, no one ever answered my question from 2 years ago. Mark Sale Next Level Solutions, LLC www.NextLevelSolns.com > Original

RE: [NMusers] NONMEM ODE solver

2007-05-28 Thread Mark Sale - Next Level Solutions
alty, 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]> > Date: Mon, May 28, 2007

RE: [NMusers] NONMEM ODE solver

2007-05-29 Thread Mark Sale - Next Level Solutions
here again (at least right away). Mark Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: RE: [NMusers] NONMEM ODE solver > From: "Alison Boeckmann" <[EMAIL PROTECTED]> > Date: Tue, May 29, 2007 2:09 pm &

RE: [NMusers] How to generate an output file with individual parameters at each iteration

2007-05-29 Thread Mark Sale - Next Level Solutions
d. It doesn't look like the iteration number is available in PK, but you have it in this file with the standard NONMEM output. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com > Original Message > Subject: [NMusers] How to generate an output file with individua

[NMusers] NONMEM output viewer

2007-07-07 Thread Mark Sale - Next Level Solutions
Dear Colleagues,  I've created a Windows application for summarizing NONMEM output file, called nmsee2 (after the original NMSEE).  I've put the setup files on the Next Level Solutions web site (http://www.nextlevelsolns.com/downloads.html, near the bottom).  This application was written to extrac

[NMusers] PD for monoclonal antibodies

2007-07-13 Thread Mark Sale - Next Level Solutions
Colleagues,  Is anyone aware of any data (general or specific) on pd relationships for monoclonal antibodies?  Especially things like AUC vs Cmax for drugs like anti TNF.thanksMark Sale MDNext Level Solutions, LLCwww.NextLevelSolns.com

RE: [NMusers] Simultaneous PK and Cell Life Span PD modeling

2007-07-16 Thread Mark Sale - Next Level Solutions
Wei-jian  The error message means exactly what it says, you have, in the $MODEL record more than one compartment labeled as DEFOBS (compartments 2 and 6).  Probably you don't want/need any compartment as the default dose or observation, but rather should be explicitly saying which compartment any d

RE: [NMusers] How to solve it? ERROR: PARAMETER ESTIMATE IS NEAR ITS BOUNDARY

2007-07-18 Thread Mark Sale - Next Level Solutions
SETUP.TXT, from the NONMEM home directory.The Introduction to NONMEM VI does alert the user that there are newerror messages but does not provide the details. This response will becopied to nmusers so that users are better informed.Thank you for your message.Tom Ludden Mark Sale MDNext Level

RE: [NMusers] Simultaneous PK and Cell Life Span PD modeling

2007-07-19 Thread Mark Sale - Next Level Solutions
t] or failure to converge) I don't hesitate to remove it. I don't see a reason to treat variance parameters any different from structural model parameters or co! variate parameters in this regard.Mark Mark Sale MDNext Level Solutions, LLCwww.NextLevelSolns.com Original Message

[NMusers] updated NONMEM output viewer

2007-07-20 Thread Mark Sale - Next Level Solutions
Dear Colleagues, The windows based NONMEM output viewer described earlier has been updated, with bug fixes.  Bug fixes are that it now correctly handles SAME blocks and handles missing files and files that are not NONMEM output files correctly.  Additional features include printing out SE of estim

RE: [NMusers] Minimization terminated ?

2007-07-20 Thread Mark Sale - Next Level Solutions
ecially if one checks both a point estimate (AUC, Cmax, Cmin) and some measure of variability (SE of AUC etc), since an artificially large variability can fool PPC.  Mark Sale MDNext Level Solutions, LLCwww.NextLevelSolns.com Original Message Subject: Re: [NMusers] Minimization

RE: [NMusers] PK analysis of data from different occasions

2007-07-31 Thread Mark Sale - Next Level Solutions
n't bother us to admit that sometimes we can't identify a compartment sometimes, when in reality we can only identify a tiny fraction of the true biological compartments. Mark Sale MDNext Level Solutions, LLCwww.NextLevelSolns.com Original Message Subject: [NMusers]

RE: [NMusers] Model Comparison and Viewing of Output

2007-08-14 Thread Mark Sale - Next Level Solutions
ions (http://www.nextlevelsolns.com/downloads.html) does delete records where MDV <> 0, if you include this in the $TABLE output.  Mark Sale MDNext Level Solutions, LLCwww.NextLevelSolns.com Original Message Subject: [NMusers] Model Comparison and Viewing of Output From: Nit

[NMusers] Data checking macro

2007-09-13 Thread Mark Sale - Next Level Solutions
Colleagues,  I suspect I'm not the only one who has, over the years had the experience of spending a week (or more) on an analysis only to find important errors in the data set.  I'm hoping for some feedback on what people do to try to find these errors (short of spending a week on an incorrect da

RE: [NMusers] Data checking macro

2007-09-13 Thread Mark Sale - Next Level Solutions
vel Solutions, LLCwww.NextLevelSolns.com919-846-9185 Original Message Subject: RE: [NMusers] Data checking macro From: "Bill Bachman" <[EMAIL PROTECTED]> Date: Thu, September 13, 2007 3:48 pm To: "'Mark Sale - Next Level Solutions'" <[EMAIL PROTEC

RE: [NMusers] Data checking macro

2007-09-13 Thread Mark Sale - Next Level Solutions
ale MDNext Level Solutions, LLCwww.NextLevelSolns.com919-846-9185 Original Message Subject: RE: [NMusers] Data checking macro From: "Bill Bachman" <[EMAIL PROTECTED]> Date: Thu, September 13, 2007 4:35 pm To: "'Mark Sale - Next Level Solutions'"

RE: [NMusers] permissible band matrix

2007-10-12 Thread Mark Sale - Next Level Solutions
Sam, I think you should have gotten the error:INITIAL ESTIMATE OF OMEGA HAS A NONZERO BLOCK WHICH IS NUMERICALLY NOT POSITIVE DEFINITEwhich is the case.  (you can check this in Excel, using the MDETERM function, the determinant is -2945).  When you get this message, try reducing the off-diagonal e

RE: [NMusers] Reporting Modeling Results

2007-10-25 Thread Mark Sale - Next Level Solutions
Nick,  I think, in the big picture, it is important to remember why we do all this.  It isn't for our own entertainment, or to congratulate each other on how insightful we are. It is to provide useful information to providers.  We are not (we hope) the real audience for our work.  It probably isn'

RE: [NMusers] Reporting Modeling Results

2007-10-25 Thread Mark Sale - Next Level Solutions
eignevalues are, allometric scaling is great, if it is people who have 12 minutes to examine, > diagnose and treat a patients, maybe we can keep it simple. Doing otherwise puts use are risk for > irrelevance. > > > > Mark Sal

RE: [NMusers] Reporting Modeling Results

2007-10-25 Thread Mark Sale - Next Level Solutions
-9185 Original Message Subject: RE: [NMusers] Reporting Modeling Results From: "Stephen Duffull" <[EMAIL PROTECTED]> Date: Thu, October 25, 2007 6:52 pm To: "'Mark Sale - Next Level Solutions'" <[EMAIL PROTECTED]> Cc: "'nmusers&

RE: [NMusers] Reporting Modeling Results

2007-10-26 Thread Mark Sale - Next Level Solutions
phen Duffull" <[EMAIL PROTECTED]> Date: Fri, October 26, 2007 2:56 pm To: "'James G Wright'" <[EMAIL PROTECTED]>, "'Mark Sale - Next Level Solutions'" <[EMAIL PROTECTED]> Cc: "'nmusers'" James, Mark I don't have tim

RE: [NMusers] Reporting Modeling Results

2007-10-26 Thread Mark Sale - Next Level Solutions
modeling to select dosing regimens, and finish with a purely regulatory and marketing piece of work that I'm familiar with:http://www.aesnet.org/Visitors/AnnualMeeting/A! bstracts/dsp_Abstract.cfm?id=2578(this got published as a real article, but I can't find a link to the paper).Mark Sa

RE: [NMusers] Reporting Modeling Results

2007-10-27 Thread Mark Sale - Next Level Solutions
Nick, Tacrine, My understanding (correct me if I'm wrong), was that the traditional analysis was unconvincing wrt efficacy and the model you developed ultimately helped justify approval.  Presumably, some patients had an improved outcome from the use of the drug.  My experience with end of phase I

[NMusers] Declining to do simulation bug/feature

2007-11-04 Thread Mark Sale - Next Level Solutions
I think I recently saw a thread about this, but is there a way to fix the bug/feature where NONMEM v6 gives this message:0THE SIMULATION TASK REQUIRES THAT A BETTER FINAL ESTIMATE BE AVAILABLE IN THE MODEL SPECIFICATION FILEand will do a simulation with an MSF regardless?thanksMarkMark Sale MD Nex

RE: [NMusers] error (157) forrtl: severe

2007-12-07 Thread Mark Sale - Next Level Solutions
Joachim, This is probably a file access error, from Fortan/OS, not from NONMEM.  Does NMTRAN run?  Does the compiler run?  Does nmlink6 run (do you get link.lnk)?  Do you get an executable? Does NONMEM start then stop?  If you get the executable (nonmem.exe or fsubs.exe), then the error is with fi

RE: [NMusers] error (157) forrtl: severe

2007-12-07 Thread Mark Sale - Next Level Solutions
ut, how do you explain that the same models reformulated with ANDAN6 run? Well, they take very long... and none of them has run to a successful minimization yet. Joachim Mark Sale - Next Level Solutions <[EMAIL PROTECTED]> 07.12.2007 13:44 To [EMAIL PROTECTED] cc nmusers@globomax

RE: [NMusers] error (157) forrtl: severe

2007-12-07 Thread Mark Sale - Next Level Solutions
annot open these file. It doesn't (usually) happen with the original data set, unless you try to run NMTRAN simultaneously. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com 919-846-9185 Original Message Subject: RE: [NMusers] error (157) forrtl: severe From: "

[NMusers] Why does covariance fail?

2008-01-29 Thread Mark Sale - Next Level Solutions
I'm thinking of doing a somewhat formal analysis of the meaning of a failed covariance step.  Some years ago Stu Beal explained that (as I recall), if the covariance step fails you cannot be sure that the minimum isn't a saddle point, which makes sense to me, and is consistent (I think), with the

RE: [NMusers] Why does covariance fail?

2008-01-29 Thread Mark Sale - Next Level Solutions
l? From: Leonid Gibiansky <[EMAIL PROTECTED]> Date: Tue, January 29, 2008 12:37 pm To: Mark Sale - Next Level Solutions <[EMAIL PROTECTED]> Cc: nmusers@globomaxnm.com Hi Mark I am pretty confident (although I do not have a proof) that all (or all reasonably good, meaning that you i

RE: RE : [NMusers] output SE of population PK parameters in Nonmem

2008-02-01 Thread Mark Sale - Next Level Solutions
Jin,  Another options it the Fortran app nmsee (ftp://ftp.globomaxnm.com/Public/nonmem/nmsee/)or a version of nmsee I recently put together (cleverly called nmsee2) at http://www.nextlevelsolns.com/downloads.html.   These are both post-processors that read the NONMEM output file (and so you only g

RE: [NMusers] output SE of population PK parameters in Nonmem

2008-02-06 Thread Mark Sale - Next Level Solutions
Rik, I don't know anything about the non-parametric estimates: 'expected value of ETA' and 'Covariance matrix of ETAI.  But, think the correlation matrix is CORRM in  COMMON /CM12/ COVM(LPAR3),COVINM(LPAR3),STHTA(LTH),SEN(LVR,LVR), 1  CORRM(LPAR3),NVLS,VLS(LPAR)and you can get

RE: [NMusers] output SE of population PK parameters in Nonmem

2008-02-06 Thread Mark Sale - Next Level Solutions
Heiner,  Your solution works really nicely - can't figure out why mine doesn't.  BTW, you can use (at least in Windows) an absolute reference to the SIZES file INCLUDE 'C:\NMVI\SIZES'also, I think you may need to assign a value to the filename  CHARACTER*16 FILECOV  FILECOV = 'COVOUT

RE: [NMusers] output SE of population PK parameters in Nonmem

2008-02-06 Thread Mark Sale - Next Level Solutions
Rik, It isn't pretty (but what Fortran is?, wouldn't be Fortran without a GOTO) but this seems to work.  The previous wasn't working because I didn't notice that the variables in COMMON /CM12/ are REAL, not the default DOUBLE PRECISION.$INFN"  FIRST"  INCLUDE 'C:\NMVI\SIZES'"  COMMON /CM12/ CO

RE: [NMusers] automating the writing of models

2008-03-31 Thread Mark Sale - Next Level Solutions
Carlos  I'm not sure what you want to do.  DruDevo (www.drudevo.com, don't know if they are still around) has a web site that seems to imply they do some of this:Ø  Automated structural model search Automated statistical model search Automated multi level covariate search Ø  Automated m

RE: [NMusers] automating the writing of models

2008-04-01 Thread Mark Sale - Next Level Solutions
e looking for, but I really don't know what that is. As Bill pointed out, PDx-Pop from Icon/globomax may be your best bet. Mark Sale MD Next Level Solutions, LLC www.NextLevelSolns.com 919-846-9185Mark Sale MDNext Level Solutions, LLCwww.NextLevelSolns.com919-846-9185

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