[NMusers] FW: Output File Format for NONMEM 7

From: Bauer, Robert Sent: Tuesday, December 16, 2008 2:25 PM To: nmusers Cc: Bauer, Robert Subject: Output File Format for NONMEM 7 Dear NONMEM Users: ICON Development Solutions (IDS) is in the process of upgrading NONMEM to incorporate new analysis methods, as well as additional output files

RE: [NMusers] NONMEM 7 Update

Allow me to respond to questions 2 and 3 regarding source code legacy. 2. The new methods were originally written by me for S-ADAPT, so as author, I was free to use them for other purposes. The reworking of the code to fit NONMEM was then performed by me as a paid employee of ICON. This code fo

RE: [NMusers] method=ITS, OPTIMIZATION NOT TESTED (?!)

Pavel: The objective function progress looks good. You should expect some Monte Carlo fluctuations. You should also run more iterations (perhaps NITER=200), and set CTYPE=3, which turns on the termination tester. To resume where you left off, rename your new control stream file, and put in the f

RE: [NMusers] $COV UNCONDITIONAL PRINT=E

as below. How can I get around this problem? === $SUBROUTINES ADVAN13 TOL=6 $EST METHOD=BAYES NBURN=100 NSAMPLE=3000 SIGL=6 NOABORT FILE=RUN136.TXT Best regards, Sam From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Bauer, Robe

RE: RE: [NMusers] method=ITS, OPTIMIZATION NOT TESTED (?!)

...@iconplc.com Web: www.icondevsolutions.com From: non...@optonline.net [mailto:non...@optonline.net] Sent: Tuesday, October 27, 2009 9:23 AM To: Bauer, Robert Cc: nmusers@globomaxnm.com Subject: Re: RE: [NMusers] method=ITS, OPTIMIZATION NOT TESTED (?!) Hello

RE: RE: RE: [NMusers] method=ITS, OPTIMIZATION NOT TESTED (?!)

) 286-0769 Email: robert.ba...@iconplc.com Web: www.icondevsolutions.com From: non...@optonline.net [mailto:non...@optonline.net] Sent: Friday, October 30, 2009 11:03 AM To: Bauer, Robert Cc: nmusers@globomaxnm.com Subject: Re: RE: RE: [NMusers] metho

RE: [NMusers] NM7 Question on METHOD=IMP

Dear Thuy: The OBJ of the IOV model is clearly incorrect. You may want to inspect several things: 1) Is the IOV modeled and mu referenced in a similar manner as the example 7 in the intro7.pdf manual 2) Based on your GRD setting, it appears that your original, non-IOV code has Thetas 10 and 11 as s

RE: [NMusers] NM7 ISODA error code -1 and -6

If you get this error only occasionally, and the problem still runs, it may not be in issue. Alternatively, you can try different TOL settings. Finally, if these do not work, you should fall back on advan9. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel:

RE: [NMusers] advan8 vs. advan13

Pavel: Regarding your statement: Another thing I noted is that when IMP is used, the lower boundary for bioavailability cannot be 0 Typically, Monte Carlo methods try a large number of etas, from negative infinity to positive infinity. You may want to remodel your bioavailability to something li

RE: [NMusers] NM7 question

Yes Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.icondevsolutions.com From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@glob

RE: [NMusers] NM7 question

: Sam Liao [mailto:sl...@pharmaxresearch.com] Sent: Wednesday, November 04, 2009 9:04 PM To: Bauer, Robert; 'nmusers' Subject: RE: [NMusers] NM7 question Dear Robert: Thanks for your kindly reply. I tried either one of the following two methods to run M3 method to handle BQL samples,

RE: [NMusers] Standard errors using SAEM

Try $COVARIANCE UNCONDITIONAL This will give you a standard error from the METHOD=IMP EONLY=1 step even if there is some positive indefiniteness. But, be cautious about its quality when such a message occurs. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions

RE: [NMusers] Questions about the raw output file in NM7

I would recommend the following: 1. Set PRINT= This way, iteration 0 is printed, as well as the final results. Unlikely you will have more than iterations to have any intervening iterations printed. 2. Do not specify the FILE= in a multi-problem statement such as the $SIML NSUB=3 type.

RE: [NMusers] nm7 IMP method question

Ethan: We have noticed this occurs with IMP on a few other problems. We have modified the code so this occurs less often, and the change will be in NONMEM 7.2, scheduled for January. Meanwhile, as Sebastian suggested, only SAEM needs an IMP EONLY=1 step. The importance sampler itself produces it

RE: [NMusers] NONMEM 7 Bug with Verbatim Code

Bill: I investigated the problem and found that not verbatimizing the code allows NM7/NMTRAN to properly construct the PRINT statement and set up the connection of ID to EVTREC(): PRINT*,ID When verbatimizing: " PRINT*,ID NM7/NMTRAN does not connect ID with EVTREC()/DATREC(),

RE: [NMusers] negative ETA shrinkage

Navin: Could you please send me an example of where your manually evaluated eta shrinkage differs from that outputted by NM7? Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.ico

RE: [NMusers] How serious are negative eigenvalues?

Dieter: You can trust the fit. The negative eignvalue diagnostic arises from evaluating the information matrix of the estimates evaluated after the fit. Because this was constructed with Monte Carlo components, on occasion the slight imprecision from calculating obscure off-diagonal elements r

RE: [NMusers] Differences in Covariance analysis between FOCE vs. IMPMAP

Andreas: The IMP/IMPMAP method of standard error assessment for OMEGA band matrices may be less reliable. I am presently investigating if there is a bug pertaining to it, and if so, I shall have it fixed for the next version. Meanwhile, Monte Carlo EM methods do quite well with full OMEGA matr

RE: [NMusers] is there a way to change fit to csv

This is Fortran format that is trying to keep within the alloted spaced for the number while expressing values less than 1e-100. Users may select the following format to express the exponent over 3 digits instead of the usual 2: FORMAT=s,1PE16.8E3 the FORMAT option may be used on $EST or $TABL

RE: [NMusers] is there a way to change fit to csv

: Fidler,Matt,FORT WORTH,R&D [mailto:matt.fid...@alconlabs.com] Sent: Tuesday, September 14, 2010 5:14 PM To: Bauer, Robert Cc: nmusers@globomaxnm.com Subject: RE: [NMusers] is there a way to change fit to csv Bob, I was looking further into the FORMAT statement. In the NONMEM 7 hel

RE: [NMusers] quality of SE estimate by IMP method

At this point the SE may be unreliable. Try using IMPMAP (and EONLY=1) and see if that helps. Let it run for 20 iterations. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.icond

RE: [NMusers] quality of SE estimate by IMP method

From: Ethan Wu [mailto:ethan.w...@yahoo.com] Sent: Thursday, September 16, 2010 12:19 PM To: Bauer, Robert; nmusers@globomaxnm.com Subject: Re: [NMusers] quality of SE estimate by IMP method Hi Bob, Is there a way to pick up from the last run with SAEM/IMP so to only run the additional step

RE: [NMusers] quality of SE estimate by IMP method

From: Ethan Wu [mailto:ethan.w...@yahoo.com] Sent: Friday, September 17, 2010 9:13 AM To: Bauer, Robert; nmusers@globomaxnm.com Subject: Re: [NMusers] quality of SE estimate by IMP method Hi Bob, IMP/MAP also came back with pretty similar OBJ like IMP. Below is the

RE: [NMusers] bug list

Leonid: Here is the the bug list of 7.1.0 that were fixed in nm 7.1.2. The particular bug you mentioned is item 5, and has been fixed in nm 7.1.2. Several bugs have been found in nm 7.1.2, which have appeared in the last couple of months. As they appear, we have corrected them for the next majo

[NMusers] FW: NM7.2 Parallelization and Virtualization

lutions.com From: Denney, William S. [mailto:william_den...@merck.com] Sent: Tuesday, September 21, 2010 10:02 AM To: Bauer, Robert Subject: NM7.2 Parallelization and Virtualization Hi Bob, I hope that you're doing well these days. I have a cou

RE: [NMusers] FW: NM7.2 Parallelization and Virtualization

evsolutions.com From: Denney, William S. [mailto:william_den...@merck.com] Sent: Wednesday, September 22, 2010 9:58 PM To: Bauer, Robert; nmusers Subject: RE: [NMusers] FW: NM7.2 Parallelization and Virtualization Hi Bob, Thanks for the detailed response. I'm thinking of

RE: [NMusers] What does "Second Error signal from LINV1PD: 129" mean?

Nick: It means that a positive definiteness correction on the eta Hessian matrix of a particular individual at a particular iteration was not successful, but NONMEM goes ahead anyway. If it happened on an intermediate iteration, and the error signal was not continually repeated, then NONMEM manage

RE: [NMusers] Suppress output to *.phi for $EST

Dieter: It is not possible to redirect or suppress output sent to the *.phi file. The FILE= option only redirects estimated parameter outputs. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com

RE: [NMusers] NONMEM 7: Problems with example10.ctl and example10l.ctl

Dear Dr. Frede: I too obtain an error from the Laplace method when correcting example10.ctl with a FIX option on the prior to $OMEGA. This does not reflect an installation issue, only an issue with the Laplace method, in that it occasionally is very sensitive to starting positions. In our next

RE: [NMusers] error message 0VAR-COV OF SOME OBS ESTIMATED TO BE 0 - a bug?

Pavel: If you do not mind sharing your control stream file, and if necessary, your data file (or a truncated version of it), perhaps you could send it to me. I may be able to determine if there is a way to modify the control stream code to avoid these errors, or if there is a bug. Robert J. Bauer

RE: [NMusers] Output of each chain in Bayses and ISAMPLE >1

MCMC automatically sets ISAMPLE=1 for its run. ISAMPLE>1 is only for SAEM. To perform multiple chains, you must run separate control stream problems with different initial SEED settings. -Original Message- From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf

[NMusers] NONMEM 7.2.0 release Notice

Dear nmusers: This past week we have begun shipping CD's of NONMEM 7.2.0 to all users with up-to-date licenses. Some of the new features of NONMEM 7.2.0 include: Dynamic Memory Allocation: No need to modify SIZES for unusually large problems. Memory is automatically sized according to the number

RE: [NMusers] simulation problem or bug

Leonid: Could you please try this problem also with NONMEM 7.1.2 and nonmem 7.2.0 Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.icondevsolutions.com -Original Message-

FW: FW: [NMusers] simulation problem or bug

On 5/25/2011 9:43 PM, Bauer, Robert wrote: > Leonid: > Tom reminded me of our solution, shown below, which you have indeed > experienced with the more verbose error message in nm7.2. NONMEM's > classic design regarding MSF is that everything from the analysis is > captured

RE: [NMusers] simulation problem or bug

26, 2011 8:13 AM To: Bauer, Robert Cc: nmusers Subject: Re: [NMusers] simulation problem or bug Bob, Tom: Thanks for sharing this explanation. Users might actually be interested in conducting simulations from a model that terminates with rounding errors for diagnostic or other purposes. I

RE: [NMusers] NM7.2 with MPI on 64bit linux and ifort 12

All: I appreciate your efforts in working out the MPI installations for various platforms, and disseminating the information to NONMEM users. I will keep track of this information and add to the documentation to make things clearer. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Dev

RE: [NMusers] Re: MPI error when run directory is a Windows network drive

Nick and Andreas: I do not have an appropriate windows network drive available for testing, but I think I know what is going on. On Windows, when mpiexec is loaded and begins executing through the call to nmmpi.bat, which is right after the statement > Starting MPI version of nonmem execution

RE: [NMusers] Re: MPI error when run directory is a Windows network drive

Nick and Andreas: I managed to get MPI work when running from a windows network drive by placing -mapall on every command line to mpiexec. For example, 1:mpiexec -mapall -wdir "%cd%" -hosts 1 localhost 1 nonmem.exe %* 2-[nodes]:-mapall -wdir "%cd%\worker{#-1}" -hosts 1 localhost 1 nonmem.exe

RE: [NMusers] How to Increase Maximum NO. of Evaluations of Differential Equation in NONMEM 7

If you are using NONMEM 7.2, IMAX can be increased by setting MAXFCN, by inserting as the first executable line in the control stream file: $SIZES MAXFCN=10 Keep in mind that as a 4 byte integer, MAXFCN cannot exceed 2**31=2147483648. Robert J. Bauer, Ph.D. Vice President, Pharmacome

RE: [NMusers] SETUP72 on linux system -- why does gfortran give these compile errors?

Nick: I recommend that you download and install a later version of the gfortran compiler: gcc-trunk-i686.tar.gz available at ftp://nonmem.iconplc.com/Public/nonmem7/compilers/ Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON Development Solutions Tel: (215) 616-6428 Mob: (925) 28

RE: [NMusers] Epsilon shrinkage and IWRES

riginal Message- From: Leonid Gibiansky [mailto:lgibian...@quantpharm.com] Sent: Thursday, September 22, 2011 1:20 PM To: Andrew Hooker Cc: Rik Schoemaker; nmusers; Bauer, Robert Subject: Re: [NMusers] Epsilon shrinkage and IWRES Hi Andy, Could you, please, provide an example of the mod

RE: [NMusers] "ERROR IN LSODA: CODE -1"

The source code of LSODA is supplied in the ..\source directory of NONMEM for NONMEM 7.1.2 and earlier. For NONMEM 7.2, the ..pr directory has the PREDDPP source code available for viewing. Typically when LSODA errors occur, is is corrected by modifying TOL. However, sometimes LSODA errors occur

RE: [NMusers] NM7 Importance Sampling: Objective function goes to zero, but results look reasonable

Dear Filip: You may wish to try using NONMEM 7.2, which has an improved transition process between SAEM and IMP EONLY=1. Add the extra option MAPITER=0: $EST METHOD=IMP LIKE NITER=20 CTYPE=3 ISAMPLE=300 NOABORT EONLY=1 MAPITER=0 Robert J. Bauer, Ph.D. Vice President, Pharmacometrics ICON D

RE: [NMusers] NM7 Importance Sampling: Objective function goes to zero, but results look reasonable

) 286-0769 Email: robert.ba...@iconplc.com Web: www.icondevsolutions.com From: De Ridder, Filip [JRDBE] [mailto:fdrid...@its.jnj.com] Sent: Thursday, December 08, 2011 5:32 AM To: Bauer, Robert; nmusers@globomaxnm.com Subject: RE: [NMusers] NM7

[NMusers] Bug list for NONMEM 7.2.0

Dear Nmusers: A list of bugs for NONMEM 7.2 are located as file nm720_bug_list.pdf ftp://nonmem.iconplc.com/Public/nonmem720/ An interim version of NONMEM will not be issued as these bugs have work-arounds. These issues are being corrected for version NONMEM 7.3, to be released in June 2013.

[NMusers] RE: Set initial values for PHIs

Sven: You cannot easily bring in individual phi values externally. But, suitable optimal phi values can be supplied to the BAYES method if you perform an ITS analysis just before that. For example, $EST METHOD=ITS INTERACTION NITER=0 (plus additional options) $EST METHOD=BAYES INTERACTION NBUR

[NMusers] RE: NM7.2 Importance Sampling Termination Testing

This is an erroneous statement by NONMEM given that convergence is not tested when EONLY=1, even when CTYPE>0, which you may ignore. It has been corrected for NM7.2. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover,

[NMusers] NONMEM Workshop May 15-17, 2012

ICON Development Solutions is pleased to announce workshops on NONMEM: May 15-16 & 17, 2012 Howard Community College - Gateway Campus 6751 Columbia Gateway Drive (First Floor) Columbia, Maryland 21046 Lab A / Classroom 3 May 15-16 - 2-Day Beginners Course Introductory NONMEM & PDx-Pop Hands-on Wo

RE: [NMusers] NM72 compilation using MinGW64

Paul: Your g95 compiler is interfering with gfortran. Open a DOS window, then set PATH=c:\program files\gfortran;%PATH% set LIBRARY_PATH= or wherever the proper gfortran460 is. Then, rebuild your NONMEM, and test it. This PATH statement must be re-specified each time you initiate a DOS window

RE: [NMusers] NM72 compilation using MinGW64

Web: www.iconplc.com<http://www.iconplc.com/> From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Bauer, Robert Sent: Friday, May 04, 2012 4:42 PM To: prhut...@pharmacy.wisc.edu; nmusers@globomaxnm.com Subject: RE: [NMu

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

You should read the next several paragraphs in the guide, stating how you can alternatively control NONMEM if the control keys do not work in certain environments. This is done using the sig.exe program supplied with NONMEM. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Deve

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

1076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com -Original Message- From: Paolo Denti [mailto:paolo.de...@uct.ac.za] Sent: Monday, May 28, 2012 4:54 AM To: Bauer, Robert Cc: Fidler,Matt,FORT WORTH,R&D; nmusers Subject: Re: SPAM:

[NMusers] QRPEM matters

Dear users: Some of you who attended the PAGE meeting in Venice last week asked me about the quasi-random parametric expectation maximization method (QRPEM) that was being presented by Bob Leary. This quasi-random sampling method used in QRPEM is the Sobol method, and is available in NONMEM 7.2

RE: [NMusers] omega matrix - friendly suggestion

Thank you all for your suggestions. The more flexible OMEGA element entries will not be easy to implement in NONMEM's structure, but I will look into it. A couple of things need to be noted. 1) Regarding Matt's suggestions, to enter initial Omega elements in Cholesky format in NM 7.2, $OMEGA

RE: [NMusers] Simulation: MAX no of observations per individual exceed

In NONMEM 7.2, you may set: $SIZES NO=500 or whatever size you need. This is described in nm720.pdf, section I.5 Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Emai

[NMusers] nmusers test

This is a test of the nmusers list-serve. Please discard. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com

RE: [NMusers] Error files when using multicore runs and psn

Pascal: I cannot help regarding having all console messages sent to the proper files in the PSN environment, but I can assist in avoiding your present NONMEM error. If you insert at the beginning of the control stream file $SIZES LIM1=?? and insert a large enough value for ??, then file buffer 1

[NMusers] RE: Error in NONMEM 7.2 run

Rebecca: As there is no precise information about the error, it is possible that NONMEM flagged it because a predictive value of F returned an Infinity or Not a number. This could have been cause by a divide by 0 somewhere, or log of a negative number, etc. You should check your code. Robert

[NMusers] RE: NM7.2 SAEM with LIKE

Filip: The $TABLE results are obtained from a "post-hoc" assessment at the best fit eta values (modal, EBE), regardless of the method used. To evaluate $TABLE parameters at the conditional mean positions, you may select FNLETA=0. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON

[NMusers] RE: NM7.2 SAEM with LIKE

August 07, 2012 3:08 PM To: Bauer, Robert; nmusers@globomaxnm.com Subject: RE: NM7.2 SAEM with LIKE Hi Bob, Thanks for the clarification. Would you agree that the conditional means are more trustworthy, in case there is a relevant difference? In my specific dataset, there are 5 subjects fo

[NMusers] FW: NONMEM 7.2 maximum parallelization nodes

(925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com<http://www.iconplc.com/> From: Manjunatha Shivaiah (BLR GSS) [mailto:manjunat...@nousinfo.com] Sent: Thursday, August 23, 2012 7:03 AM To: Bauer, Robert Subject: FW: NONMEM 7.2 maximum paral

[NMusers] FW: November Workshop

Hello Users: Beginners and advanced PDX-POP and NONMEM workshops presented by ICON Development Solutions are now open for enrollment. See the links below for information 2-Day Beginner's Course - November 13 & 14, 2012 http://www.iconplc.com/news-events/events/workshops/ids-nonmem-pdx-pop-hand

[NMusers] Suitable subject headers

Hello all: I would like to remind everyone using nmusers to place appropriate subject headers so that the archived e-mails can be easily searched for content. For example, the most recent e-mail under RE: [NMusers] single-patient AUC (see e-mail trail below) has nothing to do with singe-patient

RE: [NMusers] restart NONMEM

Yes, restarting NONMEM using the MSF system for a multi $EST methods problem is sufficiently complex, that it is best to leave it to the user to decide what needs to be done (that is, modifying the control stream file for the appropriate re-start action), rather than trying to make an intelligen

RE: [NMusers] Obtain current estimation method index

You may access the following: IEST_COUNTER, which is the estimation number for a given problem (it restarts to 1 on the next $PROB ITABLE, which continues incrementing on the next $PROB The fortran code for access is, if you are inserting in $PK or $ERROR for example: "FIRST " USE NMBAYES_IN

RE: [NMusers] MPI on linux Exit status=1

The exit status=1 just means MPI is selected rather than FPI. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com

[NMusers] RE: THETA numbering

Andreas: NMTRAN has a a limit of accepting 2 digits for indexing etas, thetas, or sigmas. This limitation has been removed for nm73, which is presently in beta preparation. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Ha

[NMusers] RE: RANMETHOD also for $SIM

Sven: It would be mathematically incorrect to create simulated values using a Sobol quasi-random method. You would obtain eta and eps values that are not truly normally distributed. The Sobol technique is specifically designed to improve the efficiency of Monte Carlo integration in multi-dimens

RE: [NMusers] What does MU_WARNING 24 mean?

Nick: The MU warnings are completely passive. I do not know what your control stream would have. Any MU_X declarations? Link errors are caused by your intel compiler may not be set up properly. It has nothing to do with NMTRAN errors and warnings. Robert J. Bauer, Ph.D. Vice President, Pharm

RE: [NMusers] What does MU_WARNING 24 mean?

NM6. Therefore there are no MU_X declarations (see question 1). The intel and g95 compilers works fine with all other problems I've tried. Its only with this strange warning/error situation that there seems to be a difference between them. Nick On 13/10/2012 1:35 p.m., Bauer, Robert wrote: > Ni

RE: [NMusers] What does MU_WARNING 24 mean?

769 Email: robert.ba...@iconplc.com Web: www.iconplc.com -Original Message- From: Alison Boeckmann [mailto:alisonboeckm...@fastmail.fm] Sent: Saturday, October 13, 2012 1:53 AM To: Bauer, Robert; Nick Holford; nmusers Subject: Re: [NMusers] What does MU_WARNING 24 mean? Nick, The subroutin

[NMusers] RE: installation of both NONMEM 7.2 and Phoenix WinNonLin 6.2

An alternative is to use the self-install versions of NONMEM for Windows using gfortran that Bill and I have provided, which are located at: ftp://nonmem.iconplc.com/Public/nonmem720 32 bit: NONMEM720_gfortran460.exe README_NONMEM720_gfortran460.exe 64 bit: NONMEM720_64gfortran463.exe Installat

[NMusers] RE: installation of both NONMEM 7.2 and Phoenix WinNonLin 6.2

kway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com<http://www.iconplc.com/> From: Kevin Dykstra [mailto:kevin.dyks...@qpharmetra.com] Sent: Thursday, November 15, 2012 1:04 PM To: Bau

RE: [NMusers] Different EBE estimation between original and enriched dataset with MDV=1

My receipt of Bill Denney's e-mail lagged somewhat. My explanation is similar to his. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.co

RE: [NMusers] Different EBE estimation between original and enriched dataset with MDV=1

Pascal: There is one more consideration. If your model depends on the use of covariate data, then during the numerical integration from time t1 to t2, where t1 and t2 are times of two contiguous records, which have values of the covariate c1 and c2, respectively, NONMEM uses the covariate at ti

RE: [NMusers] Mixture model simulation

I have studied the code and here is what I have found, and is based on the ICALL value: ICALL=2 (Estimation) MIXNUM is sequentially set by NONMEM during optimization, so the user's model may be called with each of the sub-population possibilities, so NONMEM may calculate objective function valu

[NMusers] FW: ICON workshops for 2013

Dear NMusers: ICON Development Solutions is presenting several workshops throughout the year. Two workshops will be hosted in Ellicott City, Maryland, April 9-11, and September 10-12. These are 3 day workshops, first two days are beginner/intermediate workshops, and the third day is for new and

[NMusers] RE: ICON workshops for 2013

Dear NMusers: ICON Development Solutions is presenting several workshops throughout the year. Two workshops will be hosted in Ellicott City, Maryland, April 9-11, and September 10-12. These are 3 day workshops, first two days are beginner/intermediate workshops, and the third day is for Monte C

RE: [NMusers] M3 method and multiple LOQ values

Actually, the ability to use SIGMA(1,1) on the right side has been around since NONMEM VI release 2. In the case of: PROP=THETA(1)*F ; proportional part ADD=THETA(2) ; additive part SD=SQRT(PROP*PROP + ADD*ADD) ; Standard deviation using proportional This could be transposed to: PROP=SQRT(SIGM

[NMusers] RE: William Bachman's retirement

Dear nmusers: After a long and fruitful career in the pharmaceutical sciences and pharmacometrics, William Bachman is retiring. While at ICON Bill has been the primary technical support person for NONMEM and PDxPOP, as well as the primary developer of PDx-POP. ICON will continue provide suppor

nmusers@globomaxnm.com

The following is an advertisement for an omployment opportunity at ICON Development Solutions. Director, Pharmacometrics R&D Location- Anywhere in the US (office or home-based) This is an exciting opportunity to work within a fast paced, busy environment for a leading global provider of outs

RE: [NMusers] command prompt windows opening with -parafile option

There are several ways to do this. Read about PARATYPE=2 in nm720.pdf Or, instead of using psexec as the loader, use the native WINDOWS start command. Here is an alternative fpiwini8.pnm using start: $DEFAULTS [nodes]=8 $GENERAL NODES=[nodes] PARSE_TYPE=2 PARSE_NUM=34 TIMEOUTI=300 TIMEOUT

[NMusers] RE: Where to download the Linux installation file of NONMEM7

At present we do not have an easy install system for Linux, because of the inconsistent environment. You will need to install from the CD. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428

[NMusers] RE: SUBPROBLEM > 9999?

Unfortunately there is a hard-coded limit for this option to 4 digits in NTMRAN. I will raise to 12 digits for nm73 Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Em

RE: [NMusers] a potential bug

Your problem may be resolved by looking at item 4) in ftp://nonmem.iconplc.com/Public/nonmem720/nm720_bug_list.pdf Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Ema

RE: [NMusers] NONMEM 7.2 and Pirana/Xpose4

I made a quick check with nonmem 7.2, and I have no problem creating table files even after two $TABLE statements that do not specify table files. Maggie: It appears specific to your control stream file. Please send me your control stream and data file so I can determine if there is a bug in NO

RE: [NMusers] NONMEM 7.2 and Pirana/Xpose4

Hello all: New bug item in nm7.2.0, which will be resolved in nm73: When a series of $TABLE statements without FILE= specification is followed by $TABLE statements with FILE= specification, not all tables print out, and an error is issued in the NONMEM report file: "0ERROR IN WRITING FILE : TAB

RE: [NMusers] NONMEM 7.2 and Pirana/Xpose4

50 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com<mailto:robert.ba...@iconplc.com> Web: www.iconplc.com<http://www.iconplc.com/> From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Bauer, Robert Sent: Tuesday

[NMusers] NONMEM/TMDD Workshops in Maryland

Dear NMusers: ICON Development Solutions is presenting a 4-day workshop which will be hosted in Howard County, Maryland, September 10-13. First two days are beginner/intermediate NONMEM / PDxPoP workshops, and the third day is for Monte Carlo Expectation/Maximization and full Bayesian analyses

RE: [NMusers] Access to iteration number if $PK or $PRED

If you mean the iteration number of the estimation, this is accessed through ITER_REPORT by inserting: $PK "FIRST "USE NMBAYES_INT, ONLY: ITER_REPORT Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (2

[NMusers] NONMEM web site

Dear Beta Testers: An eighth release of the beta version of NONMEM 7.3.0 is now available for testing. The complete list of changes from NONMEM 7.2 to NONMEM 7.3, with references to their descriptions in ..\guides\nm730.pdf, is given in readme_nm730.pdf, readme_nm730.txt, and .

[NMusers] NONMEM/TMDD Workshops in Maryland, week of April 8, 2014

Dear NMusers: ICON Development Solutions is presenting a 4-day workshop which will be hosted in Howard County, Maryland, April 8-11. First two days are beginner/intermediate NONMEM / PDxPoP workshop The third day is for Monte Carlo Expectation/Maximization and full Bayesian analyses. In addit

[NMusers] NONMEM 7.3.0 is now available

Dear NMUSERS: NONMEM 7.3.0 is now available. Please visit the site ftp://nonmem.iconplc.com/Public/nonmem730 and view readme_730.pdf. This file lists new features of NONMEM 7.3.0 and bug fixes. The guide nm730.pdf contains a more detailed description of the new features. Lisa Wilhelm has been

RE: [NMusers] negative time values

Andreas: Presently and historically, NONMEM (actually PREDPP) has a restriction against negative time. Removing this restriction by commenting out a piece of code in PREDPP and running a test problem indicates that the differential equation solvers are set up in NONMEM to be able to handle thi

RE: [NMusers] backward integration from t-a to t

t;http://www.iconplc.com/> From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Pavel Belo Sent: Tuesday, January 14, 2014 1:45 PM To: Bauer, Robert Cc: nmusers@globomaxnm.com Subject: [NMusers] backward integration from t-a to t Dear Robert, Efficacy is freq

[NMusers] Advanced NONMEM/Modeling of Biologics with Target Mediated Disposition Workshops

Dear nmusers: Continuing the workshop topic, ICON and QuantPharm will team up again to present two Workshop series that will combine NONMEM course with the course on TMDD modeling: April 8-11, 2014, Maryland, US (near Baltimore): Days 1-2: Beginner/intermediate NONMEM / PDxPoP workshops (ICON

[NMusers] RE: Slow PRED in tables?

Douglas: Thank you for sharing your code and data with me. When PRED, WRES, or RES are requested, NONMEM calls the weighted residual routine PRRES, which calculates PRED, WRES, and RES together. Your problem has a large number of data per subject (up to 1544) , and evaluating WRES requires some

[NMusers] RE: Slow PRED in tables?

Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com -Original Message- From: Bob Leary [mailto:bob.le...@certara.com] Sent: Wednesday, January 29, 2014 7:03 PM To: Bauer, Robe

[NMusers] RE: Slow PRED in tables?

2014 3:52 AM To: Bauer, Robert; nmusers@globomaxnm.com Subject: RE: Slow PRED in tables? Hi Robert, Thank you very much for your feedback! Indeed, I only saw this phenomenon with large numbers of observations per individual, so that makes sense. However, to get back to the original problem, I

[NMusers] testing nmusers: please ignore

Testing nmusers. Please ignore Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: robert.ba...@iconplc.com Web: www.iconplc.com

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