Fisher/Shafer NONMEM Workshop
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Workshop Overview

The Fisher/Shafer NONMEM Workshop covers NONMEM, data handling, model building, and model diagnostics. The workshop includes an extensive set of example problems ranging from simple didactic examples to demonstrate basic concepts to complex examples from the instructors' own experience. Registrants are provided with a comprehensive set of graphical tools programmed in the R and S Plus statistical languages to create high-quality diagnostic and analysis plots, as well as a powerful graphical user interface for NONMEM to facilitate rapid analysis of clinical trial data.

The workshop runs 3 and 1/2 days, from Sunday through Wednesday. Each day starts at 8:30 am except for Wednesday, which starts at 8 am. The workshop ends at 5 PM on Sunday, Monday, and Tuesday. On Wednesday it ends at 11:30 am. The organization of each day is as follows:

  • Sunday Morning: Basic Theory: (Shafer) Population Approaches, Fixed vs. Random Effects, Structural and Variance Models
  • Sunday Afternoon: (Fisher) Model Building and Diagnostics (PLT Tools)
  • Monday Morning: (Shafer) Pharmacokinetic Models, ADVAN vs. PRED, Closed Form vs. Differential Equations, Goodness of Fit Metrics
  • Monday Afternoon: (Fisher) Pharmacokinetic Models: Input Functions, ETAs, Time Varying Covariates, NONMEM Performance Enhancement
  • Tuesday Morning: (Shafer) Pharmacodynamic Models
  • Tuesday Afternoon: (Fisher) Simulation and Validation
  • Wednesday Morning: (Fisher) Reporting a NONMEM Analysis

The distinguishing characteristic of the Fisher / Shafer NONMEM Workshop is that each individual brings his or her laptop computer. A copy of NONMEM, the GNU Fortran Compiler, the Windows and UNIX scripts, PLT Tools, the full set of examples, and R are all provided to the users on a USB drive (flash drive). At the end of the course, the NONMEM installation is removed. Users may keep the unregisteredd version of PLT Tools on their system after the course, as well as the GNU Fortran compiler, and the course instructional material. The registrant follows along with the instructors, testing examples on his or her laptop as the instructor works through the concepts.

The workshop runs from Sunday morning until Wednesday at 11:30. Each day (except Wednesday) includes 6 hours of instruction, ending at approximately 3 pm. From 3 pm until 5 pm, registrants work on either the example problems, or on a data set of the registrant's choosing (frequently a difficult problem from work). Wednesday starts at 8:00 am, and ends at 11:30 am

The course is intended for individuals at the intermediate level. Those without substantial NONMEM experience are encouraged to sign up for the Saturday beginner's workshop described below. This should be adequate preparation to allow the novice to follow the main workshop.

Because NONMEM is such a flexible tool, experienced NONMEM users have found the NONMEM Workshop valuable. In part, this is because the course instructors bring their unique perspectives to the application of NONMEM to data analysis. It is also because of the breadth of examples provided. Experienced users will find the introduction to NONMEM on Saturday afternoon too basic. However, all participants will find the R workshop on Saturday morning and afternoon to be useful.

The Fisher / Shafer NONMEM Workshop runs NONMEM using the PLT Tools software suite.

PLT Tools provides a graphical interface for controlling and organizing NONMEM analyses, comprehensive graphics to analyze model results, powerful features including visual predictive check, log likelihood profiling, bootstrap analysis, and jackknife model validation. It also has tools for comprehensive auditability and automated report generation. The fully functional PLT Tools is freely available for download. PLT Tools is introduced during the NONMEM Workshop. Course attendees are encouraged to download PLT Tools in advance of the course to gain familarity.

We integrated PLT Tools into the workshop curriculum three years ago. In the workshops since registrants who brought their own data were typically able to assemble datasets (often using the R code learned in the R workshop), and analyze their data using the PLT Tools diagnostic graphics (e.g., log likelihood, profiling, automatic covariate searching, booststrap, and VPC).

A special Wednesday afternoon workshop is devoted to PLT Tools for users interested in incorporating it into their NONMEM projects.

PLT Tools runs on 32 and 64 bit Windows (XP, Vista, Windows 7, Windows 8) and Mac OSX.

Saturday Half-Day Courses

Introduction to R: Data Manipulation (Fisher / Shafer)
Saturday, 8 am - noon
The morning R course covers basic data manipulation using the R statistical programming language. The participant will learn how to read files, parse data, manipulate times and dates, perform error checking, and merge multiple files. The goal is to provide an introduction into the R commands that are typically used to create a NONMEM data set. The use of R to create graphics and statistics is NOT covered in the morning course.

Introduction to R: Statistics and Graphics (Fisher)
Saturday, 1 pm - 4 pm
The afternoon R course covers starts where the morning course ends. It is assumed that the participant has basic knowledge about the structure of an R script. This course introduces the elements required to make graphs with R. The focus is on simple X-Y plots, labeling plots and axes, controlling point and line types, and arranging graphs on the page. Basic statistics with R will also be introduced. By the end of the course, the participant will have been introduced to the R commands that are needed to produce straightforward graphs with R and perform basic statistical analyses.

Introduction to NONMEM (Shafer)
Saturday, 1 pm - 5 pm
For those with no prior experience with NONMEM, we will provide a half day session on the Tuesday afternoon before the course to prepare you for the Intermediate course described above. Registrants will be taught the basics of using the NONMEM system to analyze data, including the structure of a control stream and data file, and the basic mechanics of running NONMEM.

Wednesday Afternoon Course

PLT Tools - Advanced Features (Fisher)
Wednesday, 12:30 pm - 3:30 pm
As described above, PLT Tools software suite is an extension of the R tools developed by Dennis Fisher over nearly two decades of working with NONMEM, and refined for the Fisher/Shafer NONMEM Workshop as a general purpose NONMEM graphics program. It is distributed to course participants, and us used throughout the workshop to run NONMEM and produce the extensive NONMEM diagnostics. The unlicensed version distributed during the course is fully functional, except for the ability to place a company name on the output. Replacing "unlicensed version" with the name of your company requires the licensed version of the software, and the ability to run multiple concurrent versions. PLT Tools takes a comprehensive and integrated approach to NONMEM analysis, graphics, and auditability.

During the workshop registrants learn the basics of PLT tools. However, PLT Tools has many advanced features, including automated covariate searching, automated generation of analysis, and automated report generation. These features are not covered in the NONMEM Workshop. The Saturday afternoon course is provided for individuals interested in incorporating PLT Tools into their own work, and is focused on the productivity aspect of PLT Tools: automation of data analysis and report generation.

Course fee
  • New registrants: $2500
  • Saturday workshops: $400 each, however registration for the morning and afternoon R workshops together will be $650 total.
  • Wednesday afternoon workshop: $500 ($250 of which can be applied to the purchase of a licensed version of PLT Tools within three months of the course)
  • The registration fee includes coffee breaks each morning and afternoon. These food items are valued at approximately $250.

  • Registrants from previous Fisher/Shafer NONMEM courses: 50% off the $2500 registration
  • Academic / Government (email address must indicate that affiliation) -- 40% off the $2500 registration
  • Multiple registrants from the same company:
    • 2-3: 10% discount from the $2500 registration
    • 4-6: 20% discount from the $2500 registration
    • More than 6 registrants: 25% discount from the $2500 registration
  • The number of discounted registrations is limited in each course. If you are interested in a registration discount please contact us at within a few weeks of the course announcement to make certain that discounted registrations are still available.
  • Discounts for 1/2-day courses: $100 / course for registrants of three half-day courses


Do not submit payment until your application has been approved. Once you have been accepted into the course, a check or money order (in US dollars), payable to NONMEM Workshop, should be mailed the P Less Than Company. Bank transfers can also be arranged. There is an additional fee of $20 if payment is made via bank transfer. Payment can also be made by credit card. Credit card payments incur a 3% processing fee. If you wish to arrange payment via bank transfer or credit card, please contact us for details..

The Bethesda 2013 course is our 17th and last workshop. We thank the hundreds of students who have made this course one of the highlights of our lives for the past 10 years.