[NMusers] PhD position in pharmacometrics at Uppsala University, Sweden
Hi All, Interested in getting a PhD in pharmacometrics? We have a PhD position available in the Pharmacometrics Research Group at the Department of Pharmacy, Uppsala University with a focus on developing pharmacometric methods to demonstrate treatment effectiveness in very small clinical trials (N-of-1 and N-of-few). The doctoral position is part of an EU funded Marie Sklodowska-Curie Action (MSCA) "doctoral network" called Medicines Made to Measure. Deadline for applying is November 27th, 2023. For more information visit https://lnkd.in/dvqKRyVu. Best regards, Andy Andrew Hooker, Ph.D. Professor of Pharmacometrics Dept. of Pharmacy Uppsala University Box 580, 751 23, Uppsala, Sweden Phone: +46 18 471 4355 https://katalog.uu.se/profile/?id=N4-631 <https://katalog.uu.se/profile/?id=N4-631> <http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/> N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: 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
Re: [NMusers] Distribution of CWRESI as a diagnostic
Hi Rik, In some investigations that Joakim Nyberg and I did at PAGE a while back, we saw that CWRESI were less likely to be N(0,1) even if the model is correct, compared to CWRES (Nyberg, Bauer, Hooker, PAGE, 2010). So I might recommend creating the plot with CWRES. Otherwise, you could do multiple simulation-evaluations with the model that you have to get an empirical understanding of the expected CWRESI distribution, if the model you are currently using was the model that generated the data. This could be done using the “simeval” tool in NONMEM and “tricking” PsN into thinking that the CWRESI are actually the CWRES by setting (CWRES=CWRESI) in the table file (not tested, but I suspect this will work). On a side note, I think my NMUSERS account is associated with my old “farmbio” email address, so maybe you could forward this to note to NMUSERS? Best regards, Andy Andrew Hooker, Ph.D. Professor of Pharmacometrics Dept. of Pharmacy Uppsala University Box 580, 751 23, Uppsala, Sweden Phone: +46 18 471 4355 https://katalog.uu.se/profile/?id=N4-631 <https://katalog.uu.se/profile/?id=N4-631> <http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/> On 15 Nov 2022, at 09:53, Rik Schoemaker mailto:rik.schoema...@occams.com>> wrote: Dear all, I have routinely generated a histogram of CWRESI residuals as a model diagnostic, expecting the standard deviation to be close to one, and then commenting 'the SD is close to one as would be expected in a well behaved model'. However, I have now run into a situation where the SD is 0.887 which I consider a lot lower than I'd expect, but I have no clue what that tells me... Any ideas? Should I stop making the plot? ;) Kind regards, Rik Rik Schoemaker, PhD Occams Coöperatie U.A. Malandolaan 10 1187 HE Amstelveen The Netherlands www.occams.com<http://www.occams.com/> +31 20 441 6410 rik.schoema...@occams.com<mailto:rik.schoema...@occams.com> 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
[NMusers] Open positions in methodological research at the Pharmacometrics Group, Uppsala University.
Dear all, We are looking for enthusiastic colleagues in Pharmacometrics with a methodological focus (decision making using pharmacometric models and automation of pharmacometric approaches through the use of AI, machine learning and/or other methods)! Right now we have open positions at either the post-doc or researcher level: - Post-doc, 2 years, application deadline 30 July: https://www.uu.se/en/about-uu/join-us/details/?positionId=415947 - Researcher, 1 year, application deadline 30 July: https://www.uu.se/en/about-uu/join-us/details/?positionId=415960 Please contact us if you have questions. Andrew Hooker andrew.hoo...@farmaci.uu.se<mailto:andrew.hoo...@farmaci.uu.se> Mats Karlsson mats.karls...@farmaci.uu.se<mailto:mats.karls...@farmaci.uu.se> Best regards, Andy Andrew Hooker, Ph.D. Professor of Pharmacometrics Dept. of Pharmacy Uppsala University Box 580, 751 23, Uppsala, Sweden Phone: +46 18 471 4355 https://katalog.uu.se/profile/?id=N4-631 N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: 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
[NMusers] Two online NONMEM courses May 11-13 and 14-15
Dear all, Uppsala Pharmacometrics will give two online courses on advanced topics in pharmacometrics using Zoom a solution for online meetings ranked #1 in customer reviews. The online courses will offer: - Live video lectures and hands-on - Engaging Q&A and polling - Enriching discussions in small breakout rooms - Possibility for remote assistance - Hands-on material developed for NONMEM 7.4 Perl-speaks-NONMEM (PsN) and Xpose - A vast amount of hands-on examples, code, code snippets, and lecture material - Virtual coffee breaks to connect with other participants "I thought it was a great course!", "I am really liking this course.", "You got all this information with a single command?" (Some participant feedback from the previous iteration of the course) For more information see below. For even more information and registration please visit http://www.uppsala-pharmacometrics.com. Course 1: Advanced methods for population model building, evaluation, and usage in NONMEM ========= May 11-13, 2020 Andrew Hooker & Mats Karlsson Pharmacometric modeling has become a pillar in model informed drug development (MIDD). With this comes expectations with respect to quality, efficiency, transparency, and innovation in the implementation of the modeling and decision-making process. In this course we will present methods that will help make model building of standard problems more efficient and improve the final product. Further, it will give modelers a larger toolset of diagnostics and model components when it comes to development of models for challenging situations. Automated procedures recently developed for PsN & R facilitates a comprehensive assessment of a model and tailored functionality allow command-line transformations of models. If you want to learn how to use tools and methods for fast, efficient and comprehensive model building, evaluation and usage, come join us in May! Course 2: Pharmacometric modeling of composite score outcomes === May 14-15, 2020 Sebastian Ueckert & Mats Karlsson The EDSS in multiple sclerosis, the ACR scale for rheumatoid arthritis, or the MDS-UPDRS in Parkinson’s disease; these composite scales are as diverse as the diseases they are designed to measure. Composite scores also arise through patient-reported outcomes (PROs) that aim at measuring symptom status, physical function, mental health, and other measures important to patients. The wide range of novel pharmacometric models and approaches developed during the past years is a testament to the growing importance of this data type. This course will cover recent innovations and provide participants with a rich set of tools for analyzing composite scores in a wide variety of therapeutic areas. The course will illustrate how one can leverage finely grained item-level information but also how summary score data are most efficiently utilized. Throughout the course, questions of both model building and model-use will be discussed and presented in an interactive format including hands-on exercises. Best regards, Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 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
[NMusers] 2 courses in NJ, March 9-13, 2020
Dear all, We are pleased to offer 2 courses “Advanced methods for population model building, evaluation and usage in NONMEM” and “Pharmacometric modeling of composite score outcomes” in Lambertville, New Jersey March 9-11 and March 12-13, 2020. For more information see below and at http://www.uppsala-pharmacometrics.com. Advanced methods for population model building, evaluation and usage in NONMEM Pharmacometric modeling has become a pillar in model informed drug development (MIDD). With this comes expectations with respect to quality, efficiency, transparency and innovation in the implementation of the modeling and decision-making process. In this course we will present methods that will help make model building of standard problems more efficient and improve the final product. Further, it will give modelers a larger toolset of diagnostics and model components when it comes to development of models for challenging situations. Automated procedures recently developed for PsN & R facilitates a comprehensive assessment of a model and tailored functionality allow command-line transformations of models. On March 9-11 in Lambertville, NJ, Mats Karlsson and Andrew Hooker will give a 2.5-day course on “Advanced methods for population model building, evaluation and usage in NONMEM”. The course presents strategies for model building and improvement, the latest methods for model evaluation, as well as strategies to consider when utilizing models for model-informed drug development. The course consists of both lectures and hands-on computer exercises applying the methods discussed. This hands-on material is based on the most recent developments from NONMEM 7.4, PsN and Xpose. Participants get a vast amount of hands-on examples, code, code snippets and lecture material that can be useful on a daily basis. If you want to learn how to use tools and methods for fast, efficient and comprehensive model building, evaluation and usage, come join us in March! Topics covered: * Model building and model components * Overall modeling strategies * Random effects models (standard and extended) * Residual error models (standard and extended) * Mixture modeling * Handling censored data (e.g. BQL and dropout) * Covariate models and model building * Estimation methods and settings * Model evaluation * Prediction- and Residual-based * Empirical Bayes Estimate (EBE) and sampling-based diagnostics * Simulation and Simulation-Evaluation/Estimation-Based * Outlier and influential individual diagnostics * Automated evaluations * Covariate model focused diagnostics * Parameter uncertainty (bootstrap, SIR, COV) * To consider when applying models for informed drug development * Bias assessment * Power and Type I error * Model averaging For more information and registration, see http://www.uppsala-pharmacometrics.com/build_diagnose_use_NJ_2020.html Pharmacometric modeling of composite score outcomes The EDSS in multiple sclerosis, the ACR scale for rheumatoid arthritis, or the MDS-UPDRS in Parkinson’s disease; these composite scales are as diverse as the diseases they are designed to measure. Composite scores also arise through patient-reported outcomes (PROs) that aim at measuring symptom status, physical function, mental health, and other measures important to patients. The wide range of novel pharmacometric models and approaches developed during the past years are a testament to the growing importance of this data type. This course will cover recent innovations and provide participants with a rich set of tools for analyzing composite scores in a wide variety of therapeutic areas. The course will illustrate how one can leverage finely grained item-level information but also how summary score data are most efficiently utilized. Throughout the course, questions of both model building and model-use will be discussed and presented in an interactive format including hands-on exercises. On March 12-13 in Lambertville, NJ, Mats Karlsson and Sebastian Ueckert will give a 2-day course on “Pharmacometric modeling of composite score outcomes”. The course covers data aspects, model building, evaluation and use for composite score outcomes. Topics covered: * Modeling data with item-level resolution using item response theory * Modeling total score data either as continuous or discrete data under a variety of models * Models for responder analysis to handle, e.g., ACR20/50/70 and PASI70/90 * Pharmacometric modeling of Patient Reported Outcomes (PROs). * Model-based optimization of clinical trials with composite score outcomes Intended course participants: The course is designed for those who have a good working knowledge of pharmacometric analysis with experience in performing NONMEM analyses and/or have attended a NONMEM basic workshop. For
[NMusers] Last chance: Course in model building and evaluation, Boston, MA, USA
Dear all, Mats Karlsson and I (Andrew Hooker) will give a 2.5-day course on “Advanced methods for population model building and evaluation in NONMEM", 28-30 November, 2018 in Boston, MA, USA. The course presents the latest methods for model evaluation, strategies for model improvement as well as strategies to consider when utilizing models for informed drug development. The course provides tools for fast, efficient and comprehensive model building, evaluation and usage. The course will consist of lectures that describe and evaluate the various strategies used to develop robust and useful population models as well as hands-on computer exercises where students will actually use those strategies in the classroom. The hands-on material will be based on the most recent developments from NONMEM 7.4, PsN and Xpose. Topics covered: • Model evaluation – Numerical – Prediction-Based – Residual-Based – Empirical Bayes Estimate (EBE)-Based – Simulation-Evaluation/Estimation-Based – Covariate model focused diagnostics – Parameter uncertainty • Model improvement strategies – Parameter variability – Covariate models – Residual error – Handling censored data (BQL) • To consider when applying models for informed drug development – Type I and II errors – Estimation methods – Model averaging Intended course participants: The course is designed for those who have a good working knowledge of pharmacometric analysis with experience in performing NONMEM analyses and/or have attended a NONMEM basic workshop. Support from Alnylam for facilities is greatly acknowledged. For more information and registration, see <http://www.uppsala-pharmacometrics.com/build_diagnose_boston_2018.html> http://www.uppsala-pharmacometrics.com/build_diagnose_boston_2018.html Best regards, Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 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/om-uu/dataskydd-personuppgifter/
[NMusers] Course in model building and evaluation, Boston, MA, USA
Dear all, Uppsala Pharmacometrics will give a 2.5-day course on “Advanced methods for population model building and evaluation in NONMEM", 28-30 November, 2018 in Boston, MA, USA. The course presents the latest methods for model evaluation, strategies for model improvement as well as strategies to consider when utilizing models for informed drug development. The course will provide tools for fast, efficient and comprehensive model building, evaluation and usage. The course will consist of lectures that describe and evaluate the various strategies used to develop robust and useful population models as well as hands-on computer exercises where students will actually use those strategies in the classroom. The hands-on material will be based on the most recent developments from NONMEM 7.4, PsN and Xpose. Topics covered: • Model evaluation – Numerical – Prediction-Based – Residual-Based – Empirical Bayes Estimate (EBE)-Based – Simulation-Evaluation/Estimation-Based – Covariate model focused diagnostics – Parameter uncertainty • Model improvement strategies – Parameter variability – Covariate models – Residual error – Handling censored data (BQL) • To consider when applying models for informed drug development – Type I and II errors – Estimation methods – Model averaging Intended course participants: The course is designed for those who have a good working knowledge of pharmacometric analysis with experience in performing NONMEM analyses and/or have attended a NONMEM basic workshop. Support from Alnylam for facilities is greatly acknowledged. For more information and registration, see http://www.uppsala-pharmacometrics.com/build_diagnose_boston_2018.html Best regards, Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 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/om-uu/dataskydd-personuppgifter/
[NMusers] Course: Advanced methods for population model building and evaluation
Dear all, This is just a reminder that Uppsala Pharmacometrics will give a 2.5-day course on “Advanced methods for population model building and evaluation in NONMEM", 23-25 January, 2017 in Lambertville, NJ, USA. The course presents model building and evaluation strategies, techniques and implementations in population models and will consist of both lectures and hands-on computer exercises using NONMEM 7, PsN and Xpose. For more information and registration, see: http://www.uppsala-pharmacometrics.com/build_diagnose_NJ_2017.html. Best regards, Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
[NMusers] Course on Advanced methods for population model building and evaluation in NONMEM, 23-25 January, 2017 in Lambertville, NJ, USA.
Dear all, Uppsala Pharmacometrics will give a 2.5-day course on “Advanced methods for population model building and evaluation in NONMEM", 23-25 January, 2017 in Lambertville, NJ, USA. The course presents model building and evaluation strategies, techniques and implementations in population models and will consist of both lectures and hands-on computer exercises using NONMEM 7, PsN and Xpose 4. For more information and registration, see http://www.uppsala-pharmacometrics.com/build_diagnose_NJ_2017.html. Best regards, Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
[NMusers] PODE 2016 and 3 day course on "Optimal Design for Pharmacometrics"
Dear All, This is a reminder of the 11th Workshop on Population Optimum Design of Experiments, PODE 2016, that will take place on Monday, 20 June 2016, in Uppsala, Sweden. To register for this free conference, and for more information, please follow this link: http://pode-2016.eventbrite.com To get you up to speed for the PODE conference, Steve Duffull, France Mentre and myself are offering a 3 day course on "Optimal Design for Pharmacometrics”, June 17-19 in Uppsala. To register and for more information, please follow this link: https://www.eventbrite.com/e/optimal-design-for-pharmacometrics-registration-24567591327 If you have any questions please do not hesitate to ask me. Best wishes, Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
[NMusers] PODE 2016
Dear All, I am very happy to announce that the 11th Workshop on Population Optimum Design of Experiments, PODE 2016, will take place on Monday, 20 June 2016, in Uppsala, Sweden. The registration is simple - just send me an e-mail by March 31 with your name, company/Institution name and address. As it has always been at PODE, there is no registration fee. If you would like to give a talk, please send me an email by the end of February with a title and a short abstract. Please see http://www.maths.qmul.ac.uk/~bb/PODE/PODE.html for more information about the PODE meeting. If you have any questions please do not hesitate to ask me. Best wishes, Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
[NMusers] Workshop on PKPD-modeling in NONMEM
Dear all, Uppsala Pharmacometrics will give a 2.5-day course on Pharmacokinetic-Pharmacodynamic modeling of continuous and categorical data in NONMEM for intermediate and advanced users from May 31 - June 2 in Hersonissos, Crete, Greece as a satellite workshop before PAGE 2015. The course presents modeling strategies, techniques and implementations (using NONMEM) for the handling of PKPD information in population models. PD models for continuous data as well as binary, ordered categorical, count and time to event data will be discussed. Model diagnostics for PKPD models will be covered. The course will consist of both lectures and hands-on computer exercises using NONMEM 7, PsN and Xpose 4. The participants will be provided with a large library of NONMEM code as well as self-instructive material for further studies and exploration of examples for a wide range of PKPD models applied in different disease areas. A prerequisite for the course is basic experience with performing NONMEM analyses. For more information and registration, see www.uppsala-pharmacometrics.com<http://www.uppsala-pharmacometrics.com>. Best regards, Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
[NMusers] Xpose 4.5.3 available from CRAN
Hi All, I am pleased to announce that Xpose 4.5.3 is available from CRAN. Get the latest version by running at your R command prompt: install.packages(“xpose4") This release is a mostly a maintenance release: * Updated xpose.gam to work with the latest version of the gam package * Update to ind.plots() to allow subsets on a per-y-variable basis. Useful to show IPRED and PRED in a finer grid than DV. See option “y.vals.subset”. * Update to how axes limits are computed with xpose.plot.default. * Fix for using expression() in the ylb argument of xpose.VPC. * Updates to read.bootscm.par.est() * Update to kaplan.plot for ylim specification when using the “cov” argument (KMMC plots) * Updated compute.cwres and associted functions to work with NONMEM 7. * various small bug fixes Please see https://github.com/andrewhooker/xpose4/releases for a complete list of changes. More information about xpose can be found at http://xpose.sourceforge.net. Best regards Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
[NMusers] PopED 0.1.2 available from CRAN
Hi All,
I am very pleased to announce that PopED 0.1.2 is available from CRAN. PopED
is a tool that computes optimal experimental designs for both population and
individual studies based on nonlinear mixed-effect models. Often this is based
on a computation of the Fisher Information Matrix (FIM).
Get the latest version by running at your R command prompt:
install.packages("PopED")
New for this release:
* An updated model_prediction() function to allow for creation of NONMEM
datasets with user defined or optimized designs. This is useful for testing
optimized designs via PsN's (http://psn.sf.net) SSE tool, for example.
* Added new examples to the system.file("examples",package="PopED")
directory of the PopED installation including
* evaluation and optimization of a one-target quasi-steady-state target
mediated drug disposition model (TMDD)
* How to write compiled model code for 10-100 times speed-up of
calculation time.
* Improvements in the computation of the global design criteria “ED" via
the Laplace approximation.
* Various small bug fixes.
Please see the release
notes<https://github.com/andrewhooker/PopED/releases/tag/v0.1.2> for a complete
list of changes.
More information about PopED can be found at http://poped.sourceforge.net.
Best regards
Andrew
Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
Re: [NMusers] Adding a greek letter in Y-axis label using xpose.VPC
Hi Yulan,
You have found a feature (ok….maybe a bug)!
To get around this problem before the next release of xpose on CRAN you can use
the following code:
# create your VPC and save the results as a variable
vpc_plots <- xpose.VPC()
# update the y-axis label of any plot in the list of plots created using the
xpose.VPC command
# Here I update the label for the first plot
vpc_plots@plotList[[1]] <-
update(vpc_plots@plotList[[1]],ylab=expression(hat(beta)))
Hope this helps.
Best regards,
Andy
Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
On 18 Sep 2014, at 22:52 , Yulan Qi mailto:y...@bmrn.com>> wrote:
Here is what I tested:
xpose.VPC (PI="lines", PI.real="lines",PI.ci=NULL,xlb=expression("Concentration
(" * mu * "g/L)"),ylb="",main="",by="STRT") -working
xpose.VPC (PI="lines",
PI.real="lines",PI.ci=NULL,main=expression("Concentration (" * mu *
"g/L)"),xlb="",ylb="",by="STRT",) -working
xpose.VPC (PI="lines",
PI.real="lines",PI.ci=NULL,main="",ylb=expression("Concentration (" * mu *
"g/L)"),xlb="",by="STRT") - not working and giving error message “Error in ylb
!= "Default" : comparison is not allowed for expressions”
Thanks,
Yulan
From: NIYI [mailto:niyiadedo...@hotmail.com]
Sent: Thursday, September 18, 2014 11:26 AM
To: Yulan Qi
Subject: RE: [NMusers] Adding a greek letter in Y-axis label using xpose.VPC
Hi, Sharing the code you tried may help troubleshoot the issue.
From: y...@bmrn.com<mailto:y...@bmrn.com>
To: nmusers@globomaxnm.com<mailto:nmusers@globomaxnm.com>
Subject: [NMusers] Adding a greek letter in Y-axis label using xpose.VPC
Date: Thu, 18 Sep 2014 16:54:29 +
Dear All,
I want to add a greek letter in Y-axis label of a VPC plot using xpose.VPC
plotting function. I am able to do it with expression() in X-axis and main
title. However, when I use it in Y-axis, it didn’t work and gave me an error
message “Error in ylb != "Default" : comparison is not allowed for
expressions”. Does anyone know how to add a greek letter in Y-axis label when
using xpose.VPC function for a VPC plot?
Thanks,
Yulan
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Re: [NMusers] XPOSE for R-3.1.1?
Hi Masaki, I find Xpose using both windows and mac versions of R-3.1.1. Perhaps you need to change the mirror that your R installation is pointing to? Best regards Andrew Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/> On 03 Aug 2014, at 1:16 , Masaki Hiraoka mailto:gca02...@nifty.ne.jp>> wrote: Dear NMusers, Does anyone know if there's any version of XPOSE works with R-3.1.1? I failed to find XPOSE package on CRAN using R-3.1.1. Thanks in advance. Masaki
[NMusers] PopED available as an R package on CRAN
Dear all,
I am happy to announce that our optimal experimental design software PopED has
been translated from MATLAB to R and is now available as a package on the
Comprehensive R Archive Network (CRAN). This means that installation is as
simple as typing at your R command prompt:
install.packages("PopED")
PopED is a tool to test and optimize experimental designs for both population
and individual studies based on nonlinear mixed-effect models. Often this is
based on a computation of the Fisher Information Matrix (FIM). Key
functionality includes:
* Flexible model description — structural, between subject variability and
residual unexplained variability models can be easily and flexibly described by
the user.
* Incorporation of uncertainty in design optimization — one can take into
account parameter and/or model uncertainty in computing optimal designs.
* Wide range of optimization criteria — numerous defined design criteria
including D-family, E-family and S-family designs, plus the ability to define
your own design criteria to optimize (e.g., cost or the power to detect a drug
effect).
* Optimization of virtually any design variable such as time, dose, number
of patients per study arm, number of samples per study arm, start and stop time
of treatment, treatment length, etc.
* Full range of model and FIM approximation methods.
For more information about the R release of PopED please see
https://github.com/andrewhooker/PopED.git, for general information about PopED
please see http://poped.sourceforge.net/.
Best regards
Andrew Hooker
Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
Re: PopDesign: [NMusers] PopED and SSE comparison
Hi Pavan I, too, am confused by how you compute the relative standard errors (RSE) of your parameters and don't understand your logic in computing the RSE of the back-transformed value. Can you explain how you get to these approximations? My initial suggestion would be to use the same model in estimation and with your FIM calculation (PopED), meaning you should log-transform the parameters in the PopED model as well. Then you just use the same calculation in both the SSE and from the FIM, RSE = sd/param*100%. As for your other questions: 2. estimation method can play a role but France Mentre and colleagues have shown for a number of examples that the reduced FIM does well in predicting SAEM results. 3. I would consider SSE the gold standard in predicting RSEs (but it is clearly much slower at evaluating many designs). The fact that you can take Bias into account is a bonus enabling you to better evaluate your design. 4. If you FIX a parameter in PopED you are assuming that you will FIX a parameter in estimation as well, so if you want to compare RSE between an SSE and FIM calculation then you should have the parameter fixed in both settings. However, fixing a parameter in an optimal design calculation can also be used to force a design to focus on other parameters in your model, but for predictions of RSE values one should always match how the estimation model will do things. Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 768 000 725 www.farmbio.uu.se/research/researchgroups/pharmacometrics/ On Oct 8, 2013, at 18:54 , pavan kumar wrote: > Hi Leonid, > > The model parameters were log transformed and I was calculating the SE of > back-transformed parameter. That should be ~ SE (log transformed > parameter)*100, since > SE (log-tranformed parameter) ~ SE (back-transformed > parameter)/Popmean(back-transformed parameter). > In case of SSE, that is equivalent to sd*100/sqrt(N). > > Thanks, > Pavan. > > > From: Leonid Gibiansky > To: pavan kumar > Cc: "popdes...@lists.otago.ac.nz" ; nmusers > > Sent: Tuesday, 8 October 2013 11:48 AM > Subject: Re: [NMusers] PopED and SSE comparison > > Was this a typo: > "When I ran an SSE, the %RSE (calculated as the sd *100/sqrt(200)" ? > > I think this should be divided by the mean of the parameter values to > get %RSE. > > Same for > "the precision of the parameters from the expected FIM (calculated as > sqrt(expected parameter variances) * 100)", > should it be divided by the parameter value? > > Leonid > > > -- > Leonid Gibiansky, Ph.D. > President, QuantPharm LLC > web:www.quantpharm.com > e-mail: LGibiansky at quantpharm.com > tel:(301) 767 5566 > > > > On 10/8/2013 10:50 AM, pavan kumar wrote: > > Hi, > > I have been working on a fairly complex differential equation based > > model with an objective to optimize study design particularly for number > > of subjects in an experiment. The PK model is a lme model between dose > > and AUC and the PKPD model consists of a placebo component and a drug > > effect component with fixed PK model parameters from the PK model (both > > developed in NONMEM). Design optimization is run using PopED. > > My interest lies particularly in the drug effect parameters of the model > > (Emax and EAUC50). I have log transformed parameters as part of the MU > > model (I am using SAEM, in NM7.2) and I calculated NONMEM %RSEs for > > the untransformed parameters as SE(log_transformed)*100, which were > > around 11 and 25 %RSE. > > When the same design was set up in PopED and evaluated using FO and > > reduced FIM option, the precision of the parameters from the expected > > FIM (calculated as sqrt(expected parameter variances) * 100) were over > > predicted for the drug effect parameters particularly EAUC50 (~18% and > > 75%). > > When I ran an SSE (N=200, given the complexity of the model and the long > > run times associated with it, inspite of using parallelization) with the > > original design, the %RSE (calculated as the sd *100/sqrt(200) from the > > sse_results.csv), showed much smaller imprecision smaller than what > > NONMEM provided (< 2%RSE). I evaluated the precision for other designs > > using PopED and for a few of those designs ran the SSE as well. I have a > > similar observation that the PopED precisions were much larger than the > > SSE runs. > > I have the following questions: > > 1. Am I missing something in the calculation of %RSE involving log
RE: [NMusers] Error files when using multicore runs and psn ==> Fatal Error: Record SIZES is not valid
Hi Pascal This is not an error in PsN, this is a feature! NONMEM, by default, recompiles the sizes component of a run before each execution. This can take time, so there is an option to turn it off and use the default sizes (as in NONMEM versions 7.1.x and 6.x) with the "-prdefault" command, i.e. "nmfe72 run1.mod run1.lst -prdefault". PsN allows you to specify these extra NONMEM command line options in the configuration file "psn.conf". If you look in your psn.conf file I suspect you will find something like: [default_options] nmfe_options=prdefault,xmloff In the case you mention below you actually need to recompile the sizes before your NONMEM run, so this "prdefault" option should be removed. In PsN you can do this on the command line using the "-nmfe_options" argument. For example: execute run1.mod -nmfe_options=xmloff Here, I turn off the "prdefault" NONMEM option but keep the "xmloff" option. You can find this information in the following documentation: http://psn.sourceforge.net/pdfdocs/common_options_defaults_versions_psn.pdf http://psn.sourceforge.net/pdfdocs/psn_configuration.pdf Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 www.farmbio.uu.se/research/researchgroups/pharmacometrics/ From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of pascal.gir...@merckgroup.com Sent: den 12 juli 2012 17:43 To: Kassir Nastya Cc: nmusers@globomaxnm.com; Bauer, Robert; Ekaterina Gibiansky Subject: RE: [NMusers] Error files when using multicore runs and psn ==> Fatal Error: Record SIZES is not valid Hi Nastya, You were right : it is my psn installation that refuses to see something else than $PROB as first line as I just checked by running it directly from nmfe72 You cannot stop the progress! Thanks again and Kind regards Pascal From:"Kassir Nastya" To:, "Bauer, Robert" , Date:12/07/2012 17:25 Subject:RE: [NMusers] Error files when using multicore runs and psn ==> Fatal Error: Record SIZES is not valid _ Hi Pascal, I have already used it with NONMEM 72 and it works, but not in psn. $SIZES LIM6=1000 $PROBLEM XX Best regards, Nastya
RE: [NMusers] Memory problems with Xpose
Hi Toufigh,
R has updated its memory handling in recent updates, so if you are using an
older version of R then updating to the latest version may help. Otherwise
you might try subsetting the plot to reduce the number of plots created.
For example:
# Change the covariate scope
change.xvardef(xpdb,var="covariates") <- c("SEX","AGE","WT")
# then run the plot again:
parm.vs.cov(xpdb)
The scope can also be changed in the classic menu system.
Best regards
Andy
Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>
www.farmbio.uu.se/research/researchgroups/pharmacometrics/
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Toufigh Gordi
Sent: den 13 januari 2012 09:29
To: nmusers@globomaxnm.com
Subject: [NMusers] Memory problems with Xpose
Hi,
I am trying to plot model parameters vs. covariates suing Xpose. The data
file is rather large and I get the following message:
In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
Error in print(parm.vs.cov(.cur.db)) :
error in evaluating the argument 'x' in selecting a method for function
'print': Error: cannot allocate vector of size 171 Kb
Can anybody offer a remedy?
Thanks!
Toufigh
Re: [NMusers] Epsilon shrinkage and IWRES
Hi rik If you have multiple eps() in your model then the default nonmem calculation will be wrong (understandably). In those instances I define iwres myself and calculate using the psn option "-shrinkage". Best regards Andy On 22 sep 2011, at 17:14, "Rik Schoemaker" wrote: > Dear Leonid, > > Thank you! > > I do believe this means that the simple representation in the manual is not > covering this ingenious construct, and although theoretically they might be > the same (who am I to judge? :-) ) it might explain why I get different > numbers when I calculate it myself... > > Kind regards, > > Rik > > -Original Message- > From: Leonid Gibiansky [mailto:lgibian...@quantpharm.com] > Sent: 22 September 2011 4:36 PM > To: Rik Schoemaker > Cc: 'nmusers'; Bauer, Robert > Subject: Re: [NMusers] Epsilon shrinkage and IWRES > > I spare Bob Bauer from the need to re-type the answer since we discussed it > at some point, and he provided the following info (see below). The following > error model was discussed: > > Y=IPRED(1+EPS1)+EPS2 >that is equivalent to > Y=IPRED + W*EPS(1) > where > > W=SQRT(sigma1^2+sigma2^2*IPRED^2) > > where sigma 1 and sigma 2 are some parameters and variance of EPS1 is 1 > > ;; > For each data point i, > > Wi=SQRT(sigma1^2+sigma2^2*IPREDi^2) > > Each Wi from each data point is used in assessing sigma1 and sigma2. As > long as IPREDi is non-zero for every data point, then every Wi is used in > assessing both sigma1 and sigma2 in the optimization process. > However, when IPREDi=0, then that particular Wi is > > Wi=SQRT(sigma1^2) > > Which contributes to evaluation of sigma1, but does not contribute to > sigma2. How does the EPSshrink algorithm figure this out? By in fact using > the H gradient that NONMEM provides, which NONMEM uses to estimate > sigma1 and sigma2. The actual residual variance is in matrix form evaluated > as > > H'SigmaH > > Here H is the partial derivative of yi with respect to sigmaj. The Wi is > itself not decomposed, but the decision to add the Wi to the accumulator for > sigmaj is determined by whether partial hi with respect to sigmaj is > non-zero. > > And wherever H' is not 0, the EPS shrink accumulator adds the contribution > of that Wi for a sigma, and where-ever H is zero, it does not attribute that > Wi for that sigma. This is how it is known which Wi pertain to PK data, and > which Wi pertain to PD data as well, by assessment of the H gradient that > NONMEM assesses. > > The epsilon shrinkage formula honors the H'SigmaH structure, as it should, > since NONMEM's FO and FOCE methods themselves utilize that structure to > estimate Sigma1 and Sigma2. > > To reiterate, normally with proportional and additive sigma, all Wi are > involved in both sigmas, and hence both sigmas have identical shrinkage, > since they are always having non-zero H together. But when some IPREDi are > zero, the additive error has contributions from all Wi, whereas the > proportion sigma collects Wi information only from non-zero IPREDi. > > > -- > Leonid Gibiansky, Ph.D. > President, QuantPharm LLC > web:www.quantpharm.com > e-mail: LGibiansky at quantpharm.com > tel:(301) 767 5566 > > > > On 9/22/2011 9:26 AM, Rik Schoemaker wrote: >> Dear all, >> >> Can someone enlighten me on a NONMEM implementation? >> Since NONMEM 7, epsilon shrinkage is reported in the output, and the >> manual states that it is calculated as: >> 100%*[1-SD(IWRES)] >> in accordance with "Karlsson MO and Savic RM. Diagnosing Model > Diagnostics. >> Clinical Pharmacology and Therapeutics, 2007; 82(1): 17-20" as one >> would expect. >> However, as far as I know, the user needs to manually code the IWRES >> bit using the "Uppsala implementation": >> >> IPRED = F >> IRES = DV - IPRED >> W = THETA(3) >> IWRES = IRES/W >> Y = IPRED+W*EPS(1) >> >> SIGMA 1 FIXED >> >> So how does NONMEM arrive at epsilon shrinkage? And is there by any >> chance an (undocumented?) IWRES item that can be exported in a table file > as well? >> >> Kind regards, >> >> Rik >> >> >> >> Rik Schoemaker, PhD >> Exprimo NV >> Tel: +31 (0)20 4416410 >> E-mail: rik.schoema...@exprimo.com >> Web: www.exprimo.com >> >> This e-mail is confidential. It is also privileged or otherwise >> protected by work product immunity or other legal rules. The >> information is intended to be for use of the individual or entity >> named above. If you are not the intended recipient, please be aware >> that any disclosure, copying, distribution or use of the contents of >> this information is prohibited. You should therefore delete this >> message from your computer system. If you have received the message in >> error, please notify us by reply e-mail. The integrity and security of > this message cannot be guaranteed on the Internet. >> >> Thank you for your co-operation. >> >> >> >> >> This e-mail message has been
RE: [NMusers] Time-to-event analysis with $DES
Hi All I would just like to point out that in the Weibull hazard that Nick proposes: HAZNOW=LAMD*ALPH*(TIME+DEL2)**(ALPH-1) The units of LAMD would have to be TIME**(-ALPH). That is, as soon as ALPH changes then the units of LAMD change. This seems strange and unnecessary to include this type of correlation in the parameters. If we instead reparameterize the model to: HAZNOW=LAMD*ALPH*(LAMD*(TIME+DEL2))**(ALPH-1) Then LAMD has units of 1/TIME no matter the value of ALPH. I have tested the two parameterizations in one simple simulation example and found that the relative standard errors were significantly lower with this second parameterization. Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 <http://www.farmbio.uu.se/research/Research+groups/Pharmacometrics/> www.farmbio.uu.se/research/Research+groups/Pharmacometrics/ From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Nick Holford Sent: den 24 mars 2011 07:54 To: nmusers Subject: Re: [NMusers] Time-to-event analysis with $DES Hyewon, Sorry -- I just realized that EFF is not the drug effect but 1-drug effect so that it has a value of 1 when AUC is zero. Please ignore my remarks about EFF being zero when AUC is zero in my comments below and consider this code to describe the effect of AUC on hazard: HAZNOW=LAMD*ALPH*(TIME+DEL2)**(ALPH-1)*(1-BETAE*AUC/(EC+AUC)) I think it is a very strong assumption that the drug will reduce the hazard to zero at infinite AUC which you can test by estimating a parameter (such as BETAE). If BETAE is significantly less than 1 then this means the assumption is not supported. Nick On 24/03/2011 8:17 a.m., Nick Holford wrote: Hyewon, The most obvious problem with your code is in $DES. You must use the variable T not the variable TIME when referring to a time varying hazard. TIME is the time on each data record. It does not change in $DES. T is the time from the last data record upto the current data record and changes within $DES. You are predicting the likelihood of an event at the exact time of the event observation record with multiple events per subject. As you seem to realize you need to compute the cumulative hazard (CUMHAZ) either from TIME=0 or from the TIME of the last non-censored event for each subject. In my opinion the following code is clearer and less dependent on your data structure than the method you are using which works only if your data has just event records after the TIME=0 record. IF (MDV.EQ.0.AND.CS.EQ.0) THEN OLDCHZ=A(1) ; cum haz upto time of this event ELSE OLDCHZ=OLDCHZ ; need to do this if OLDCHZ is a random variable ENDIF Your hazard model looks rather complicated. It seems to be based on the product of a Weibull baseline hazard LAMD*ALPH*(TIME+DEL2)**(ALPH-1) then something odd involving the Weibull parameters *EXP(-LAMD*(TIME+DEL2)**ALPH) and then forces the hazard to be zero if AUC is zero. *EFF Is this really what you want? Do you know the hazard of event is zero if AUC is zero? Or is the last right parenthesis in the wrong place? I would suggest something like this where LAMD and ALPH are the two parameters of the Weibull baseline hazard (when AUC is zero) and BETAE is a parameter describing the effect of the drug on the overall hazard. HAZNOW=LAMD*ALPH*(TIME+DEL2)**(ALPH-1)*EXP(BETAE*EFF) You may also find it easier to develop the model if you do not try to estimate a random effect on LAMD until you have got reasonable estimates for the other parameters. You may find it helpful to look at this presentation showing how to code time to event models in NM-TRAN: http://pkpdrx.com/holford/docs/time-to-event-analysis.pdf Best wishes, Nick On 24/03/2011 3:25 a.m., Hyewon Kim wrote: Dear NMuser I am trying to analyze time to repeated event data using NONMEM. The response were obtained till 24 hours after drug administration. Inhibitory Emax model was implemented. I am getting unreasonable parameter estimates which is far beyond what data say. If some body can point out what i am doing wrong, it would be very helpful. Thank you in advance. Hyewon Data set (# of observations =62, # of patients=50 ) CIDTIME CS MDVAUC . 101 0.11.111 . 101 0.05 00 1.111 . 101 2 001.111 . 102 0.1 0 . 102 24 100 . 103 0.10.999 . 103 0.75 . 00.999 Model File $PROB RUN# 101 $INPUT C ID TIME CS MDV AUC ;CS:0=having e
RE: [NMusers] Calculating shrinkage when some etas are zero
Resent with fewer trailing messages. Sorry for the spam if both reached NMusers Hi Marco, I suspect what is happening in PsN is that IWRES has not been defined in your model. If you ask for shrinkage then PsN will compute ETA shrinkage (removing the ETA=0 values) as well as “EPS” shrinkage, which is computed using IWRES. The IWRES is computed as: IWRES = (DV – IPRED)/Residual_variance Where the Residual_variance is the total expected residual variance of each data point. For an additive+ proportional error model on the normal scale the IWRES would be defined as: IPRED = F W = SQRT((IPRED*THETA(prop))**2+THETA(add)**2) ; log transformed data ; IPRD = F ;DEL = 0.0001 ;IF(IPRD.LE.DEL) IPRD=DEL ;IPRED= LOG(IPRD) ;W= SQRT(THETA(prop)**2+THETA(add)**2/IPRD**2) IRES = DV - IPRED IF(W.EQ.0) W = 1 IWRES= IRES/W Y = IPRED + W*EPS(1) $SIGMA 1 FIX Of course, if you are just interested in calculating the shrinkage of an ETA without the zero values then you can print ETA values out in a table file and compute via: Shrinkage_eta = 1 – sd(ETA)/Omega Removing the ETA=0 before computation of the sd(ETA). Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 www.farmbio.uu.se/research.php?avd=5 From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of marco.campi...@merckserono.net Sent: December 07, 2010 11:16 To: Gastonguay, Marc Cc: Eleveld, DJ; Ribbing, Jakob; nmusers@globomaxnm.com; owner-nmus...@globomaxnm.com; Pyry Välitalo Subject: Re: [NMusers] Calculating shrinkage when some etas are zero Hi to all, Do you know if there is a quick method to exclude subjects with ETA=0 from the calculation of ETA shrinkage using NONMEM 7? I also tried to use the option –shrinkage of PsN, but I get the following error: AN ERROR WAS FOUND IN THE CONTROL STATEMENTS. 187 $TABLE RECORD REQUESTS AN UNKNOWN ITEM. at /usr/lib/perl5/site_perl/5.8.8/PsN_3_2_4/nonmem.pm line 40 Kind Regards Marco -- Marco Campioni, PhD Modelling & Simulation Senior Scientist Exploratory Medicine Merck Serono S.A. - Geneva
[NMusers] New Xpose version released
Hi All A new version of Xpose is now available at http://xpose.sf.net . In this version we have updated Xpose so that it works with NONMEM 7. We have also added support for odd-type data, including odd-type VPCs. Please report any bugs to the Xpose mailing list xpose-gene...@lists.sourceforge.net. Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 <http://www.farmbio.uu.se/research.php?avd=5> www.farmbio.uu.se/research.php?avd=5
[NMusers] Uppsala pharmacometrics workshop before PAGE in June
Dear all, This is a reminder that the Uppsala Pharmacometrics group will be having a NONMEM Workshop for intermediate and advanced users immediately before the PAGE meeting in St. Petersburg in June entitled: Pharmacokinetic-Pharmacodynamic modeling of Continuous and Categorical data in NONMEM – June 21-23 Don’t miss out! For more information see below or visit <http://www.uppsala-pharmacometrics.com> www.uppsala-pharmacometrics.com. Best regards Andy --- Brief information: The course presents modeling strategies, techniques and implementations (using NONMEM) for the handling of PKPD information in population models. PD models for continuous data as well as binary, ordered categorical, count and time to event data will be discussed. The course will include new models and methods for evaluation of models. The course will consist of both lectures and hands-on computer exercises using NONMEM VI, PsN and Xpose 4. The participants will be provided with a library of NONMEM code for the entire field as well as self-instructive material for further studies and exploration of examples for a wide range of PKPD models applied in different disease areas. The course will be given by Prof. Mats Karlsson, Dr Lena Friberg, Dr Andrew Hooker and Dr Ulrika Simonsson. A prerequisite for the course is experience with performing NONMEM analyses and basic knowledge of PK/PD models. --- Course Fees: Regular fee: € 2,300 Student/Post-doc fee: € 1,250 Registration fee includes: hardcopy folder, extensive electronic material including lectures, exercises, programs (PsN and Xpose), additional self-study material including hands-on and solutions. Morning and afternoon refreshments, lunch and a welcome reception are included. Attendance is strictly limited to 50 with a limited “reduced fee” places available for students and post-docs. Registration and student/post-doc fees will be offered on the basis of first come, first served. Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 701 679 048 <http://www.farmbio.uu.se/research.php?avd=5> www.farmbio.uu.se/research.php?avd=5
RE: [NMusers] 20 variable limit in $INPUT
Hi All, PsN does this automatically when using the '-wrap_data' option of the 'execute' command. See http://psn.sourceforge.net/PDF_docs/common_options_defaults_versions_psn.pdf for more details. Best regards, Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 701 679 048 www.farmbio.uu.se/research.php?avd=5 -Original Message- From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Nick Holford Sent: Monday, March 16, 2009 15:48 To: nmusers Subject: Re: [NMusers] 20 variable limit in $INPUT Look in your NONMEM html\cont.htm. The CONT data item lets you specify additional input records which can be continued to allow more than 20 data items. Here is a description in more detail. http://www.cognigencorp.com/nonmem/nm/99aug272005.html I found this by searching with Google for "NONMEM cont data item". Much better than trying to use the NONMEM archive search which responded with: No matches were found for 'cont and data and (item or items)' andreas.kra...@actelion.com wrote: > > I am looking for a solution to get around the limit of 20 input > variables in nonmem. > The message you get with more than 20 variables in $INPUT is this: > > 16 $INPUT: NO. OF DATA ITEMS EXCEEDS 20. > STOP 4 statement executed > > I did not find anything in the archives or on the Web. I recall having > successfully done that in nonmem V, and I think it was about changing > the value of 20 to another value in a few files. > My original naive idea was that this was just a single change to the > SIZES file in nm VI but that seems to not be the case. > > To keep the discussion focused, I am not looking for workarounds like > solutions with concatenated values and an indicator variable. > For a change I am trying to get the software to adapt to the user's > needs instead of the usual opposite situation. > > Thanks for any pointers. > > Andreas > > - > > Andreas Krause, PhD > Lead Scientist Modeling and Simulation > > Actelion Pharmaceuticals Ltd > Gewerbestrasse 16 > CH-4123 Allschwil > Switzerland > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by letter. > Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com > -- Nick Holford, Dept Pharmacology & Clinical Pharmacology University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand n.holf...@auckland.ac.nz tel:+64(9)923-6730 fax:+64(9)373-7090 http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
[NMusers] NONMEM Workshops for intermediate and advanced users
Dear all, This is a reminder that the Uppsala Pharmacometrics group will be having two NONMEM Workshops for intermediate and advanced users immediately before and after the ASCPT meeting in Washington D.C. in March: 1.Pharmacokinetic-Pharmacodynamic modeling of Continuous and Categorical data in NONMEM - March 16-18 2.New features and advanced methods for model building and evaluation in NONMEM VI - March 21-23 Don't miss out! Workshops can be taken together or separately. For more information see below or visit www.uppsala-pharmacometrics.com. Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 701 679 048 <http://www.farmbio.uu.se/research.php?avd=5> www.farmbio.uu.se/research.php?avd=5 --- Brief information for workshop 1: The course presents modeling strategies, techniques and implementations (using NONMEM) for the handling of PKPD information in population models. PD models for continuous data as well as binary, ordered categorical, count and time to event data will be discussed. The course will include new models and methods for evaluation of models. The course will consist of both lectures and hands-on computer exercises using NONMEM VI, PsN and Xpose 4. The participants will be provided with a library of NONMEM code for the entire field as well as self-instructive material for further studies and exploration of examples for a wide range of PKPD models applied in different disease areas. The course will be given by Prof. Mats Karlsson, Dr Lena Friberg, Dr Andrew Hooker and Dr Ulrika Simonsson. A prerequisite for the course is experience with performing NONMEM analyses and basic knowledge of PK/PD models. --- Brief information for workshop 2: During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the freeware programs Perl-speaks-NONMEM (PsN) and Xpose 4. In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. The course will be given by Prof. Mats Karlsson, Dr Andrew Hooker and Dr Radojka Savic. A prerequisite for the course is experience with performing NONMEM analyses or having attended a NONMEM basic workshop. --- Course Fees (per workshop): Regular fee: 2800 USD Academic/Government fee: 1800 USD Registration fee includes: hardcopy folder, extensive electronic material including lectures, exercises, programs (PsN and Xpose), additional self-study material including hands-ons and solutions. Continental breakfast, morning and afternoon refreshments, lunch and a welcome reception are included. Attendance is strictly limited to 50 with a limited "reduced fee" places available for academic/government participants. Registration and academic fees will be offered on the basis of first come, first served.
[NMusers] NONMEM Intermediate Workshops - 2nd announcement
Dear all, This is a reminder that the Uppsala Pharmacometrics group will be having two NONMEM Intermediate Workshops immediately before and after the ASCPT meeting in Washington D.C. in March. The deadline for early-bird registration is fast approaching (Dec. 10), so don't miss out! For more information see below or visit www.uppsala-pharmacometrics.com/. Best regards Andy Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 701 679 048 <http://www.farmbio.uu.se/research.php?avd=5> www.farmbio.uu.se/research.php?avd=5 Workshop 1: Pharmacokinetic-Pharmacodynamic (PK/PD) modeling of Continuous and Categorical data Location: Washington DC, USA, Dates:16th-18th of March 2009. Workshop 2: New features and advanced methods for model building and evaluation in NONMEM VI Location: Washington DC, USA, Dates:21st-23rd of March 2009. Workshops can be taken together or separately. They are organized to run immediately before and after the Annual ASCPT meeting. For more information and registration please visit www.uppsala-pharmacometrics.com or send an e-mail to [EMAIL PROTECTED] . --- Brief information for workshop 1: The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years and has extensive experience in modeling continuous and categorical data in a wide range of disease areas. In this course the Uppsala group will present modeling strategies, techniques and implementations (using NONMEM) for the handling of PK and PD information in population models. PD models for continuous data as well as binary, ordered categorical, count, and time to event data will be discussed. The course will include methods for graphical evaluation of continuous and categorical PK/PD models. The course will consist of both lectures and hands-on computer exercises using NONMEM VI, PsN and Xpose 4. The course will be given by Prof. Mats Karlsson, Dr Lena Friberg, Dr Andrew Hooker and Dr Ulrika Simonsson. A prerequisite for the course is experience with performing NONMEM analyses and basic knowledge of PK/PD models. --- Brief information for workshop 2: During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the freeware programs Perl-speaks-NONMEM (PsN) and Xpose 4. In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. The course will be given by Prof. Mats Karlsson, Dr Andrew Hooker and Dr Radojka Savic. A prerequisite for the course is experience with performing NONMEM analyses or having attended a NONMEM basic workshop. --- Course Fees (per workshop): Regular fee: 2500 USD Early Bird (received by 12/10/08), 2800 USD Late Bird Academic/Government fee: 1800 USD Registration fee includes: syllabus, continental breakfast, morning and afternoon refreshments, lunch and a welcome reception. Attendance is strictly limited to 50 with a limited "reduced fee" places available for academic/government participants. Registration and academic fees will be offered on the basis of first come, first served.
[NMusers] NONMEM intermediate workshops from Uppsala Pharmacometrics
The Uppsala Pharmacometrics group is happy to announce two NONMEM Intermediate Workshops Workshop 1: Pharmacokinetic-Pharmacodynamic (PK/PD) modeling of Continuous and Categorical data Location: Washington DC, USA, Dates:16th-18th of March 2009. Workshop 2: New features and advanced methods for model building and evaluation in NONMEM VI Location: Washington DC, USA, Dates:21st-23rd of March 2009. Workshops can be taken together or separately. They are organized to run immediately before and after the Annual ASCPT meeting. For more information and registration please visit <http://www.uppsala-pharmacometrics.com/> www.uppsala-pharmacometrics.com or send an e-mail to <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] . --- Brief information for workshop 1: The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years and has extensive experience in modeling continuous and categorical data in a wide range of disease areas. In this course the Uppsala group will present modeling strategies, techniques and implementations (using NONMEM) for the handling of PK and PD information in population models. PD models for continuous data as well as binary, ordered categorical, count, and time to event data will be discussed. The course will include methods for graphical evaluation of continuous and categorical PK/PD models. The course will consist of both lectures and hands-on computer exercises using NONMEM VI, PsN and Xpose 4. The course will be given by Prof. Mats Karlsson, Dr Lena Friberg, Dr Andrew Hooker and Dr Ulrika Simonsson. A prerequisite for the course is experience with performing NONMEM analyses and basic knowledge of PK/PD models. --- Brief information for workshop 2: During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the freeware programs Perl-speaks-NONMEM (PsN) and Xpose 4. In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. The course will be given by Prof. Mats Karlsson, Dr Andrew Hooker and Dr Radojka Savic. A prerequisite for the course is experience with performing NONMEM analyses or having attended a NONMEM basic workshop. --- Course Fees (per workshop): Regular fee: 2500 USD Early Bird (received by 12/18/08), 2800 USD Late Bird Academic/Government fee: 1800 USD Registration fee includes: syllabus, continental breakfast, morning and afternoon refreshments, lunch and a welcome reception. Attendance is strictly limited to 50 with a limited "reduced fee" places available for academic/government participants. Registration and academic fees will be offered on the basis of first come, first served. Andrew Hooker, Ph.D. Associate Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Phone: +46 18 471 4355 Mobile: +46 701 679 048 www.farmbio.uu.se/research.php?avd=5
RE: [NMusers] Too many PRED-generated items in $TABLE
Hi Sebastien, One solution is to just print out the first 20 items in the initial estimation, then run a second NONMEM run with the initial parameter estimates of that run set to the final parameter estimates of the first run. This second run should be run with MAXEVAL=0 in the $ESTIMATION section and can then contain the other table values you need. Cheers, Andy Andrew Hooker, Ph.D. Assistant Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591, 751 24, Uppsala, Sweden Tel: +46 18 471 4355 www.farmbio.uu.se/research.php?avd=5 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sébastien Bihorel Sent: Friday, March 21, 2008 21:05 To: nmusers@globomaxnm.com Subject: [NMusers] Too many PRED-generated items in $TABLE Dear All, I am working on a PK model, that can be implemented using $PRED but requires the definition of many parameters. I need most of these parameters to be reported in the output table. Unfortunately, this is the recurrent error message that I get when I start the estimation: "AN ERROR WAS FOUND IN THE CONTROL STATEMENTS. 314 MORE THAN 20 PRED-GENERATED ITEMS SPECIFIED FOR $TABLE, $SCAT." I have tried to split my list of parameters in one or two $TABLE statements (see below) but it does not change anything... $TABLE ID DOSE TIME DVID Y FAST CL V ALPH TK01 KA1 LAG1 KA2 KA3 ADLA ONEHEADER NOPRINT FILE=param.fit $TABLE ID DOSE TIME DVID Y FAST ECL EV EALP ELA1 ETK1 ETB1 ETK2 ELA2 ETB2 ETB3 ETB4 EADL ELA3 ETK3 ETB5 ONEHEADER NOPRINT FILE=eta.fit (ID, DOSE, TIME, DVID, and FAST are defined in the data file) I am using NONMEM 6 with the Wings for NONMEM interface (v 6.1.3). Any suggestion to report that many parameters would be welcome. Sebastien Bihorel SUNY at Buffalo
[NMusers] NONMEM Intermediate Workshop - 2nd announcement
2nd announcement . NONMEM Intermediate Workshop: New features and advanced methods for model building and evaluation in NONMEM VI San Francisco, CA March 17-19, 2008 Overview: The Center for Drug Development Science (CDDS) is happy to announce the NONMEM Intermediate Workshop co-sponsored with the pharmacometrics group at Uppsala University. The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years. During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the programs Perl-speaks-NONMEM (PsN) and Xpose 4 (described below). In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. Agenda (3 full days): The course will last for 3 days and consists of both lectures and hands-on computer exercises. Participants will use NONMEM VI, PsN and Xpose 4. PsN and Xpose 4 are freeware and may be installed on participants' computers for use after the course. In addition to the agenda below consultation sessions will be offered during each day of the course. Day 1: Model building and diagnostics using NONMEM VI with PsN and XPOSE 4 - Introduction to new features of NONMEM VI - Improved model building and diagnostics using PsN and XPOSE 4 - Automation of NONMEM VI runs - Introduction to diagnostics for NONMEM VI runs - Shrinkage and Empirical Bayes estimates based diagnostics - Simulation based reference diagnostics - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 2: Model building and diagnostics using NONMEM VI with PsN and XPOSE 4 - Conditional weighted residuals - Bootstrapping - Case deletion diagnostics - Visual and numerical predictive checks - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 3: Advanced methods in NONMEM VI - The use of prior information on parameter values in NONMEM evaluations - Using nonparametric parameter estimation in model building using NONMEM VI - Simultaneous modeling of continuous and categorical data - Handling data below the limit of quantification (BLQ) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Prerequisite: Having used NONMEM with an understanding of population PK-PD modeling and/or having attended a NONMEM basic workshop Instructors: Prof. Mats Karlsson Mats Karlsson is professor of Pharmacometrics at Uppsala University, Sweden where he leads a research group of about twenty modelers. He received his PhD in pharmacokinetics from this university in 1989 and has been a research fellow at University of Glasgow and University of California, San Francisco, and a visiting professor at Georgetown University, Washington DC. He has received the Giorgio Segre Prize from EUFEPS and is editor for the Journal of Pharmacokinetics and Pharmacodynamics. His research interests focus on methodological aspects of non-linear mixed effects model building and applied PKPD modeling. He has published over one hundred original research articles in the area of PK and PKPD. Dr. Andrew Hooker Andrew Hooker is an assistant professor of pharmacometrics at Uppsala University, Sweden. Andrew received his PhD in Bioengineering from the University of Washington, Seattle, USA in 2003, and then moved to Sweden as a Pfizer post-doctoral fellow at Uppsala University. His research focuses on methodological problems associated with building and evaluating pharmacometric models as well as optimal experimental design. Andrew is a primary developer of both Xpose 4 and the optimal design program PopED. Rada Savic Rada Savic joined the Pharmacometric research group at Uppsala University, Sweden in 2003 after receiving her pharmacist degree from University of Belgrade, Serbia. Since then, she has been actively working on evaluating new features of NONMEM VI. Her research interests focus on nonparametric methods for population analysis, improved diagnostics for NONMEM VI and development of new absorption models. Details: The course will emphasize hands on training, with the participants working on their own computers. All programs will run from an USB memory-stick and participants will not be required to install any programs on their computer. NOTE: All participants must bring their own laptops. Xpose 4 is a model building aid for population analysis using NONMEM. Xpose produces various plots and analyses to facilitate data set checkout, goodness-of-fit analysis, model exploration and visualization, model diagnostics, candidate cova
[NMusers] NONMEM Intermediate Workshop
NONMEM Intermediate Workshop: New features and advanced methods for model building and evaluation in NONMEM VI San Francisco, CA March 17-19, 2008 Overview: The Center for Drug Development Science (CDDS) is happy to announce the NONMEM Intermediate Workshop co-sponsored with the pharmacometrics group at Uppsala University. The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years. During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the programs Perl-speaks-NONMEM (PsN) and Xpose 4 (described below). In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. Agenda (3 full days): The course will last for 3 days and consists of both lectures and hands-on computer exercises. Participants will use NONMEM VI, PsN and Xpose 4. PsN and Xpose 4 are freeware and may be installed on participants' computers for use after the course. In addition to the agenda below consultation sessions will be offered during each day of the course. Day 1: Model building and diagnostics using NONMEM VI with PsN and XPOSE 4 - Introduction to new features of NONMEM VI - Improved model building and diagnostics using PsN and XPOSE 4 - Automation of NONMEM VI runs - Introduction to diagnostics for NONMEM VI runs - Shrinkage and Empirical Bayes estimates based diagnostics - Simulation based reference diagnostics - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 2: Model building and diagnostics using NONMEM VI with PsN and XPOSE 4 - Conditional weighted residuals - Bootstrapping - Case deletion diagnostics - Visual and numerical predictive checks - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 3: Advanced methods in NONMEM VI - The use of prior information on parameter values in NONMEM evaluations - Using nonparametric parameter estimation in model building using NONMEM VI - Simultaneous modeling of continuous and categorical data - Handling data below the limit of quantification (BLQ) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Prerequisite: Having used NONMEM with an understanding of population PK-PD modeling and/or having attended a NONMEM basic workshop Instructors: Prof. Mats Karlsson Mats Karlsson is professor of Pharmacometrics at Uppsala University, Sweden where he leads a research group of about twenty modelers. He received his PhD in pharmacokinetics from this university in 1989 and has been a research fellow at University of Glasgow and University of California, San Francisco, and a visiting professor at Georgetown University, Washington DC. He has received the Giorgio Segre Prize from EUFEPS and is editor for the Journal of Pharmacokinetics and Pharmacodynamics. His research interests focus on methodological aspects of non-linear mixed effects model building and applied PKPD modeling. He has published over one hundred original research articles in the area of PK and PKPD. Dr. Andrew Hooker Andrew Hooker is an assistant professor of pharmacometrics at Uppsala University, Sweden. Andrew received his PhD in Bioengineering from the University of Washington, Seattle, USA in 2003, and then moved to Sweden as a Pfizer post-doctoral fellow at Uppsala University. His research focuses on methodological problems associated with building and evaluating pharmacometric models as well as optimal experimental design. Andrew is a primary developer of both Xpose 4 and the optimal design program PopED. Rada Savic Rada Savic joined the Pharmacometric research group at Uppsala University, Sweden in 2003 after receiving her pharmacist degree from University of Belgrade, Serbia. Since then, she has been actively working on evaluating new features of NONMEM VI. Her research interests focus on nonparametric methods for population analysis, improved diagnostics for NONMEM VI and development of new absorption models. Details: The course will emphasize hands on training, with the participants working on their own computers. All programs will run from an USB memory-stick and participants will not be required to install any programs on their computer. NOTE: All participants must bring their own laptops. Xpose 4 is a model building aid for population analysis using NONMEM. Xpose produces various plots and analyses to facilitate data set checkout, goodness-of-fit analysis, model exploration and visualization, model diagnostics, candidate covariate identification and
RE: [NMusers] different COMRES statements
Hi Alison, Yes I was referring to the prior functionality of NWPRI an TNPRI not the $PRIOR. The COMRES problem is a separate issue I think. Best Regards, Andy Andrew Hooker, Ph.D. Assistant Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591 751 24 Uppsala Sweden Tel: +46 18 471 4355 www.farmbio.uu.se/research.php?avd=5 -Original Message- From: Alison Boeckmann [mailto:[EMAIL PROTECTED] Sent: Tuesday, October 16, 2007 4:22 PM To: Andrew Hooker; 'Frederik Gorter de Vries'; nmusers@globomaxnm.com Subject: RE: [NMusers] different COMRES statements Frederick: I don't understand the references to $PRIOR. This is not a feature of NONMEM VI 1.0 or 1.2, although it will be of 2.0. Perhaps you are referring to the new feature introduced with NONMEM VI: user-supplied PRIOR subroutine and utility programs NWPRI and TNPRI. How does the use of COMRES interact with the use of these subroutines? COMRES and the COM(i) variables are used to provide values for NONMEM to display in tables, and can also be used to preserve values of the same variable between different passes through the data (e.g., between passes when etas are 0 vs. conditional.) Are you perhaps attempting to put values of CNT (the contribution to the objective function computed by NWPRI or TNPRI) in a table? Or are you using some other feature of NONMEM that involves use of COM(i), and $PRIOR was a typing error? Andrew, I agree with everything you wrote, except that I can't understand what it has to do with "$PRIOR functionality in NONMEM." Perhaps you mean "PRIOR functionality", and the difficulty is that, when all of OMEGA is written, some of the OMEGA values were fixed values supplied in the control stream for computation of the priors, and are of no interest in the output table. I can see the difficulty, but cannot understand its relationship to the COMRES/COM(i) feature. On Mon, 15 Oct 2007 15:50:17 +0200, "Andrew Hooker" <[EMAIL PROTECTED]> said: > Hi Frederik, > > > > It is possible to compute the CWRES using the $PRIOR functionality in > NONMEM. However, it's a little tricky. The problem is this code: > > > > $INFN > > IF (ICALL.EQ.3) THEN > > OPEN(50,FILE=CWTAB1.EST) > > WRITE(50,*) 'ETAS' > > DO WHILE(DATA) > > >IF (NEWIND.LE.1) WRITE (50,*) ETA > > > ENDDO > > > WRITE(50,*) 'THETAS' > > WRITE(50,*) THETA > > WRITE(50,*) 'OMEGAS' > > WRITE(50,*) OMEGA(BLOCK) > > WRITE(50,*) 'SIGMAS' > > WRITE(50,*) SIGMA(BLOCK) > > ENDIF > > > > Which writes out all the thetas and omegas and sigmas including the > prior stuff (which we don't need for the CWRES calculation). What I > do is just remove, by hand, the extra values in the "cwtab1.est" file > to have only the values for the etas, thetas, omegas and sigmas for > the data and not the prior (only the "first" thetas, omegas and > sigmas). After that, calculating the CWRES using XPOSE 4 should not > be a problem. > > > > For the COMRES values: If you need x COMRES values for the CWRES > calculation and y COMRES values for some other portion of your NONMEM > model then you just need to use the statement > > > > $ABB COMRES= z > > > > Where z = x+y. > > > > Hope this helps! > > > > -Andy > > > > > > Andrew Hooker, Ph.D. > > Assistant Professor of Pharmacometrics > > Div. of Pharmacokinetics and Drug Therapy > > Dept. of Pharmaceutical Biosciences > > Uppsala University > > Box 591 > > 751 24 Uppsala > > Sweden > > Tel: +46 18 471 4355 > > www.farmbio.uu.se/research.php?avd=5 > > > > _ > > From: [EMAIL PROTECTED] [mailto:owner- > [EMAIL PROTECTED] On Behalf Of Frederik Gorter de Vries Sent: > Monday, October 15, 2007 1:40 PM To: nmusers@globomaxnm.com Subject: > [NMusers] different COMRES statements > > > > Dear NMuser, > > > > I have a problem with implementing the CWRES in a model that's using > $PRIOR. Both need a $ABB COMRES= x statement, but with different > numbers of x. Which number should I take here? NONMEM seems to have no > problem when using the one from CWRES, but the CWRES cannot be > calculated anymore in R using Xpose. The following message appears: > > > > > cwres <- compute.cwres(1, printToOutFile = FALSE,onlyNonZero = > > FALSE) > > Error in `[.data.frame`(x, r, vars, drop = drop) : > > undefined columns selected >
RE: [NMusers] different COMRES statements
Hi Frederik, It is possible to compute the CWRES using the $PRIOR functionality in NONMEM. However, it's a little tricky. The problem is this code: $INFN IF (ICALL.EQ.3) THEN OPEN(50,FILE=CWTAB1.EST) WRITE(50,*) 'ETAS' DO WHILE(DATA) IF (NEWIND.LE.1) WRITE (50,*) ETA ENDDO WRITE(50,*) 'THETAS' WRITE(50,*) THETA WRITE(50,*) 'OMEGAS' WRITE(50,*) OMEGA(BLOCK) WRITE(50,*) 'SIGMAS' WRITE(50,*) SIGMA(BLOCK) ENDIF Which writes out all the thetas and omegas and sigmas including the prior stuff (which we don't need for the CWRES calculation). What I do is just remove, by hand, the extra values in the "cwtab1.est" file to have only the values for the etas, thetas, omegas and sigmas for the data and not the prior (only the "first" thetas, omegas and sigmas). After that, calculating the CWRES using XPOSE 4 should not be a problem. For the COMRES values: If you need x COMRES values for the CWRES calculation and y COMRES values for some other portion of your NONMEM model then you just need to use the statement $ABB COMRES= z Where z = x+y. Hope this helps! -Andy Andrew Hooker, Ph.D. Assistant Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591 751 24 Uppsala Sweden Tel: +46 18 471 4355 www.farmbio.uu.se/research.php?avd=5 _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Frederik Gorter de Vries Sent: Monday, October 15, 2007 1:40 PM To: nmusers@globomaxnm.com Subject: [NMusers] different COMRES statements Dear NMuser, I have a problem with implementing the CWRES in a model that's using $PRIOR. Both need a $ABB COMRES= x statement, but with different numbers of x. Which number should I take here? NONMEM seems to have no problem when using the one from CWRES, but the CWRES cannot be calculated anymore in R using Xpose. The following message appears: > cwres <- compute.cwres(1, printToOutFile = FALSE,onlyNonZero = FALSE) Error in `[.data.frame`(x, r, vars, drop = drop) : undefined columns selected When I use the COMRES number from the $PRIOR NMTRAN gives an error regarding the table with the wrong number of COM ARRAY . I hope someone have seen this problem before and can tell me more about the COMRES statement. Thank you in advance and best regards, Frederik Gorter de Vries ___ Frederik Gorter de Vries LACDR / Pharmacology Gorleaus Laboratories Einsteinweg 55 2333 CC Leiden The Netherlands Tel : ++31 71 527 6142 Email: [EMAIL PROTECTED]
RE: [NMusers] Xpose31 fails to be redirected to the working directory
Hi James, Xpose 4 does not yet have the bootstrap of the gam implemented (coming soon!). Occasionally s-plus '.SData' items get corrupted, so the first thing I always do if there is a problem is close s-plus, delete the '.SData' item in the directory I was working in, and then re-start s-plus. The other possible problem is the capital letters in your table file names...I don't work much with Xpose 3.1, but I always used to use lowercase letters when I did use it. Let me know if this helps! -Andy Andrew Hooker, Ph.D. Assistant Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591 751 24 Uppsala Sweden Tel: +46 18 471 4355 www.farmbio.uu.se/research.php?avd=5 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Lane, Jim Sent: Friday, May 25, 2007 1:31 AM To: nmusers@globomaxnm.com Subject: [NMusers] Xpose31 fails to be redirected to the working directory I have been using Xpose 4 release 5.1 in R with excellent results. However, at least with my downloaded version, the bootstrap of the gam has an ' * ' infront of it indicating that this function is not yet available. Because of this I have been attempting to use the bootstrap of the gam funciton in Xpose3.1 running in Splus 6.0 (Windows Xp Professional spk 2). Xpose31 has failed to recognize the presence of the standard Xpose31 table names; SDTAB001, SDTAB01, SDTAB1, COTAB001, COTAB01, COTAB1 etc. I have created a new chapter in the subdirectory where the needed tables are located and attached that chapter accordingly. Running a search() in the Splus6 command window confirms that the working directory has been attached and is in the first location. Any ideas as to why Xpose31 is not able to recognize these tables? James R. Lane, Pharm.D. Pharmacist Specialist-Pharmacokinetics Department of Pharmacy UCSD Medical Center-Hillcrest Associate Clinical Professor-Pharmacy UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences San Diego, California 92103-8765 619 543 2455
RE: [NMusers] XPOSE4 cur.db error
Hi Paul, Thanks for the comments. I was wondering if, when you ask Xpose to read the files, you ask it to read run number '3' or '003'. I think the later should work if your files are named 'sdtab003' for example. -Andy Andrew Hooker, Ph.D. Assistant Professor of Pharmacometrics Div. of Pharmacokinetics and Drug Therapy Dept. of Pharmaceutical Biosciences Uppsala University Box 591 751 24 Uppsala Sweden Tel: +46 18 471 4355 www.farmbio.uu.se/research.php?avd=5 _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Hutson Sent: Thursday, May 24, 2007 5:22 PM Cc: NMUSERS@GLOBOMAXNM.COM Subject: Re: [NMusers] XPOSE4 cur.db error XPOSE team: My apologies and thanks to Niclas as well. The shift to R is welcome. Bill: I tried caps vs lower case, since R (and SPlus) can be sensitive to that unless the source code permits either. I couldn't get it to work with the 003 in either case in either XPOSE31 or 4 (build 5.1). I was using NOPRINT ONEHEADER as well. Curious that yours is working. Maybe it has something to do with the humidity. Paul Bachman, William (MYD) wrote: First of all, let me second Paul's opinion of Xpose4. They have done a great job with it and we have been able to integrate xpose4 into PDx-Pop not only on Windows but Linux and Mac OS X as well. Second, I don't think the issue is the zeros. I just tried it successfully with 003. It may be a case sensitivity thing and be looking for capitals? My tables looked like this: $TABLE ID SID TIME TAD IPRED CL WT APGR NOPRINT ONEHEADER FILE=003.TAB $TABLE ID CL V NOPRINT ONEHEADER FILE=PATAB003 $TABLE ID WT APGR NOPRINT ONEHEADER FILE=COTAB003 $TABLE ID APGR NOPRINT ONEHEADER FILE=CATAB003 $TABLE ID TIME IPRED IWRES NOPRINT ONEHEADER FILE=SDTAB003 Bill _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Hutson Sent: Thursday, May 24, 2007 9:33 AM To: NMUSERS@GLOBOMAXNM.COM Subject: [NMusers] XPOSE4 cur.db error I have been getting consistent fatal error messages when I have tried to bring up NONMEM files set up for evaluation with XPOSE. The text of the error line varies with what I have asked of XPOSE, but the consistent component is "cur.db not found". XPOSE 3.1 also had trouble, but more clearly told me that the file with the requested number was not found. It turns out that XPOSE at present apparently does not like leading zeros in the file name. Thus, it was rejecting patab003 but accepting patab3. Everybody else probably knows this by now. Mats, Andrew, and Justin - great program. Thanks. Paul -- Paul R. Hutson, Pharm.D. Associate Professor UW School of Pharmacy 777 Highland Avenue Madison WI 53705- Tel 608.263.2496 Fax 608.265.5421 Pager 608.265.7000, p7856 ___ This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that ICON can arrange for proper delivery, and then please delete the message. Thank You. -- Paul R. Hutson, Pharm.D. Associate Professor UW School of Pharmacy 777 Highland Avenue Madison WI 53705- Tel 608.263.2496 Fax 608.265.5421 Pager 608.265.7000, p7856
[NMusers] FW: NONMEM VI Intermediate level workshop - US location in Washington, DC
Second announcement: NONMEM Intermediate Workshop - New features and advanced methods for model building and evaluation in NONMEM VI When/Where: Washington, D.C., June 18-20th, 2007 The Center for Drug Development Science (CDDS) The Beacon Hotel & Corporate Quarters 1615 Rhode Island Ave. NW Washington, DC 20036 Overview: The Center for Drug Development Science (CDDS) is happy to announce the NONMEM Intermediate Workshop co-sponsored with the pharmacometrics group at Uppsala University. The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years. During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the programs Perl-speaks-NONMEM (PsN) and Xpose 4 (described below). In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. Agenda (3 full days): The course will last for 3 days and consists of both lectures and hands-on computer exercises. Participants will use NONMEM VI, PsN and Xpose 4. PsN and Xpose 4 are freeware and may be installed on participants' computers for use after the course. In addition to the agenda below consultation sessions will be offered during each day of the course. Day 1: Model building and diagnostics using NONMEM VI - Introduction to new features of NONMEM VI - Introduction to diagnostics for NONMEM runs - Improved model building and diagnostics using PsN and XPOSE 4 - Automation of NONMEM runs - Shrinkage and Empirical Bayes estimates based diagnostics - Residual based diagnostics (conditional weighted residuals) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 2: Computer intensive model building and diagnostics using NONMEM VI - Simulation based reference diagnostics - Visual and numerical predictive checks - Bootstrapping - Case deletion diagnostics - Additional new features of NONMEM VI - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 3 - Advanced methods in NONMEM VI - Nonparametric estimation in NONMEM VI - Semi-parametric estimation in NONMEM VI - Prior functionality in NONMEM VI - Simultaneous Modeling of Continuous and Categorical Data - Handling Data below the Quantification Limit (BQL) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Prerequisite Having used NONMEM with an understanding of population PK-PD modeling and/or having attended a NONMEM basic workshop Instructors: Prof. Mats Karlsson Mats Karlsson is professor of Pharmacometrics at Uppsala University, Sweden where he leads a research group of about twenty modelers. He received his PhD in pharmacokinetics from this university in 1989 and has been a research fellow at University of Glasgow and University of California, San Francisco, and a visiting professor at Georgetown University, Washington DC. He has received the Giorgio Segre Prize from EUFEPS and is editor for the Journal of Pharmacokinetics and Pharmacodynamics. His research interests focus on methodological aspects of non-linear mixed effects model building and applied PKPD modeling. He has published over one hundred original research articles in the area of PK and PKPD. Dr Andrew Hooker Andrew Hooker is an assistant professor of pharmacometrics at Uppsala University, Sweden. Andrew received his PhD in Bioengineering from the University of Washington, Seattle, USA in 2003, and then moved to Sweden as a Pfizer post-doctoral fellow at Uppsala University. His research focuses on methodological problems associated with building and evaluating pharmacometric models as well as optimal experimental design. Andrew is a primary developer of both Xpose 4 and the optimal design program PopED. Dr Lars Lindbom Lars Lindbom is a researcher in Pharmacometrics at Uppsala University, Sweden. He received his PhD in pharmacokinetics and drug therapy from Uppsala University in 2006. He is leading the development of Perl-speaks-NONMEM. Rada Savic Rada Savic joined the Pharmacometric research group at Uppsala University, Sweden in 2003 after receiving her pharmacist degree from University of Belgrade, Serbia. Since then, she has been actively working on evaluating new features of NONMEM VI. Her research interests focus on nonparametric methods for population analysis, improved diagnostics for NONMEM VI and development of new absorption models. Details: The course will emphasize hands on training, with the participants working on their own computers. All programs will run from an USB memory-stick and participants will not be required t
[NMusers] NONMEM VI Intermediate level workshop - US location in Washington, DC
Second announcement: NONMEM Intermediate Workshop - New features and advanced methods for model building and evaluation in NONMEM VI When/Where: Washington, D.C., June 18-20th, 2007 The Center for Drug Development Science (CDDS) The Beacon Hotel & Corporate Quarters 1615 Rhode Island Ave. NW Washington, DC 20036 Overview: The Center for Drug Development Science (CDDS) is happy to announce the NONMEM Intermediate Workshop co-sponsored with the pharmacometrics group at Uppsala University. The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years. During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the programs Perl-speaks-NONMEM (PsN) and Xpose 4 (described below). In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. Agenda (3 full days): The course will last for 3 days and consists of both lectures and hands-on computer exercises. Participants will use NONMEM VI, PsN and Xpose 4. PsN and Xpose 4 are freeware and may be installed on participants' computers for use after the course. In addition to the agenda below consultation sessions will be offered during each day of the course. Day 1: Model building and diagnostics using NONMEM VI - Introduction to new features of NONMEM VI - Introduction to diagnostics for NONMEM runs - Improved model building and diagnostics using PsN and XPOSE 4 - Automation of NONMEM runs - Shrinkage and Empirical Bayes estimates based diagnostics - Residual based diagnostics (conditional weighted residuals) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 2: Computer intensive model building and diagnostics using NONMEM VI - Simulation based reference diagnostics - Visual and numerical predictive checks - Bootstrapping - Case deletion diagnostics - Additional new features of NONMEM VI - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 3 - Advanced methods in NONMEM VI - Nonparametric estimation in NONMEM VI - Semi-parametric estimation in NONMEM VI - Prior functionality in NONMEM VI - Simultaneous Modeling of Continuous and Categorical Data - Handling Data below the Quantification Limit (BQL) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Prerequisite Having used NONMEM with an understanding of population PK-PD modeling and/or having attended a NONMEM basic workshop Instructors: Prof. Mats Karlsson Mats Karlsson is professor of Pharmacometrics at Uppsala University, Sweden where he leads a research group of about twenty modelers. He received his PhD in pharmacokinetics from this university in 1989 and has been a research fellow at University of Glasgow and University of California, San Francisco, and a visiting professor at Georgetown University, Washington DC. He has received the Giorgio Segre Prize from EUFEPS and is editor for the Journal of Pharmacokinetics and Pharmacodynamics. His research interests focus on methodological aspects of non-linear mixed effects model building and applied PKPD modeling. He has published over one hundred original research articles in the area of PK and PKPD. Dr Andrew Hooker Andrew Hooker is an assistant professor of pharmacometrics at Uppsala University, Sweden. Andrew received his PhD in Bioengineering from the University of Washington, Seattle, USA in 2003, and then moved to Sweden as a Pfizer post-doctoral fellow at Uppsala University. His research focuses on methodological problems associated with building and evaluating pharmacometric models as well as optimal experimental design. Andrew is a primary developer of both Xpose 4 and the optimal design program PopED. Dr Lars Lindbom Lars Lindbom is a researcher in Pharmacometrics at Uppsala University, Sweden. He received his PhD in pharmacokinetics and drug therapy from Uppsala University in 2006. He is leading the development of Perl-speaks-NONMEM. Rada Savic Rada Savic joined the Pharmacometric research group at Uppsala University, Sweden in 2003 after receiving her pharmacist degree from University of Belgrade, Serbia. Since then, she has been actively working on evaluating new features of NONMEM VI. Her research interests focus on nonparametric methods for population analysis, improved diagnostics for NONMEM VI and development of new absorption models. Details: The course will emphasize hands on training, with the participants working on their own computers. All programs will run from an USB memory-stick and participants will not be required t
[NMusers] NONMEM Intermediate Workshop VI
(3rd try to send this mail...sorry for the spam if you get multiple copies!) What: NONMEM Intermediate Workshop: New features and advanced methods for model building and evaluation in NONMEM VI When/Where: Washington, D.C., June 18-20th, 2007 The Center for Drug Development Science (CDDS) The Beacon Hotel & Corporate Quarters 1615 Rhode Island Ave. NW Washington, DC 20036 Overview: The Center for Drug Development Science (CDDS) is happy to announce the NONMEM Intermediate Workshop co-sponsored with the pharmacometrics group at Uppsala University. The Uppsala group has been involved in developing NONMEM models and methodology for over fifteen years. During the last decade they have been involved in the testing and evaluation of NONMEM VI as it has been developed and several research projects have focused on new functionality in NONMEM VI. In parallel, diagnostics for model building have been developed, evaluated and integrated into NONMEM VI-adapted versions of the programs Perl-speaks-NONMEM (PsN) and Xpose 4 (described below). In this course the Uppsala group will present some of the most exciting new features of NONMEM VI and how these tools can be used in the development and evaluation of non-linear mixed effects models. Agenda (3 full days): The course will last for 3 days and consists of both lectures and hands-on computer exercises. Participants will use NONMEM VI, PsN and Xpose 4. PsN and Xpose 4 are freeware and may be installed on participants' computers for use after the course. In addition to the agenda below consultation sessions will be offered during each day of the course. Day 1 - Model building and diagnostics using NONMEM VI with PsN and XPOSE 4 - Introduction to new features of NONMEM VI - Improved model building and diagnostics using PsN and XPOSE 4 - Automation of NONMEM VI runs - Introduction to diagnostics for NONMEM VI runs - Shrinkage and Empirical Bayes estimates based diagnostics - Simulation based reference diagnostics - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 2 - Model building and diagnostics using NONMEM VI with PsN and XPOSE 4 - Conditional weighted residuals - Bootstrapping - Case deletion diagnostics - Visual and numerical predictive checks - Hands-on computer exercises with NONMEM VI, PsN and Xpose Day 3 - Advanced methods in NONMEM VI - The use of prior information on parameter values in NONMEM evaluations - Using nonparametric parameter estimation in model building using NONMEM VI - Simultaneous modeling of continuous and categorical data - Handling data below the limit of quantification (BLQ) - Hands-on computer exercises with NONMEM VI, PsN and Xpose Prerequisite Having used NONMEM with an understanding of population PK-PD modeling and/or having attended a NONMEM basic workshop Instructors: Prof. Mats Karlsson Mats Karlsson is professor of Pharmacometrics at Uppsala University, Sweden where he leads a research group of about twenty modelers. He received his PhD in pharmacokinetics from this university in 1989 and has been a research fellow at University of Glasgow and University of California, San Francisco, and a visiting professor at Georgetown University, Washington DC. He has received the Giorgio Segre Prize from EUFEPS and is editor for the Journal of Pharmacokinetics and Pharmacodynamics. His research interests focus on methodological aspects of non-linear mixed effects model building and applied PKPD modeling. He has published over one hundred original research articles in the area of PK and PKPD. Dr Andrew Hooker Andrew Hooker is an assistant professor of pharmacometrics at Uppsala University, Sweden. Andrew received his PhD in Bioengineering from the University of Washington, Seattle, USA in 2003, and then moved to Sweden as a Pfizer post-doctoral fellow at Uppsala University. His research focuses on methodological problems associated with building and evaluating pharmacometric models as well as optimal experimental design. Andrew is a primary developer of both Xpose 4 and the optimal design program PopED. Dr Lars Lindbom Lars Lindbom is a researcher in Pharmacometrics at Uppsala University, Sweden. He received his PhD in pharmacokinetics and drug therapy from Uppsala University in 2006. He is leading the development of Perl-speaks-NONMEM. Rada Savic Rada Savic joined the Pharmacometric research group at Uppsala University, Sweden in 2003 after receiving her pharmacist degree from University of Belgrade, Serbia. Since then, she has been actively working on evaluating new features of NONMEM VI. Her research interests focus on nonparametric methods for population analysis, improved diagnostics for NONMEM VI and development of new absorption models. Details: The course will emphasize hands on training, with the participants working on their own computers. All programs will run from an USB mem
