NONMEM Users Network Archive

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PLT Tools version 3.0

From: Dennis Fisher <fisher>
Date: Mon, 24 May 2010 06:52:26 -0700

PLTsoft is pleased to announce Version 3.0 of PLT Tools, a graphical =
user interface for analyzing data with NONMEM.* The graphical interface =
permits the pharmacometrician to easily:
• Perform NONMEM estimation and simulation with full compliance of =
21 CFR 11, including archiving of data files, control files, results =
files, and complete documentation of the analysis process;
• Calculate and graph a visual predictive check, including within- =
and between-subject stratification;
• Calculate likelihood profiles for all parameters;
• Estimate parameter standard errors with bootstrap analyses;
• Validate models using jackknife analysis;
• Automatically search a matrix of covariates and thetas for =
covariate effects (supplemented with GLM and covariate graphics).

Each of these methods is supported by extensive, customizable, =
high-resolution graphics created with R† and saved in both PDF and =
JPEG formats. NONMEM text and tables outputs are time-stamped for =
regulatory compliance. Text documents are also saved in PDF format. =
Tables are reformatted to CSV format to facilitate user access; data is =
saved in SAS transport format to facilitate submission to regulatory =
agencies. Source files (control stream, input file, FDATA) are archived =
so that runs can be repeated if necessary.

PLT Tools also automates many of the tasks required to prepare study =
reports and support regulatory submissions. Specifically, PLT Tools =
• Summary tables that compare the change in objective function and =
reports the likelihood ratio test for selected NONMEM runs. A flowchart =
depicts these comparisons graphically.
• A brief summary of each NONMEM run (objective function, =
parameter estimates on one page).
• A character-by-character comparison of control streams to ensure =
that differences between runs are exactly as desired.
• Summaries of population estimates (tables for THETAs, OMEGAs, =
SIGMAs), post hoc parameters (summary tables), covariates (summary =
statistics and graphics for categorical and continuous covariates), and =
data (tables for number of observations and doses, Cmax, Tmax, etc.).
• An RTF document (which can be opened in Word or OpenOffice) that =
includes tables, JPEG graphics, and text documents (control streams, =
NONMEM outputs). This document can be edited for regulatory submission.

Additional features of PLT Tools include:
• A built-in text editor for control streams (or access your =
preferred editor from PLT Tools);
• A graphics editor permitting user customization of the generated =
• The ability to interface with scripts written in R by the user =
(if the user wants customized graphics or data analysis beyond those =
supported by PLT Tools). These R scripts run in the PLT Tools =
environment, so that formatting can match PLT Tools’ graphics should =
the user want a consistent appearance to all graphics;
• Automated tools to rerun a series of NONMEM control files (as =
might be required if the data have changed between an initial analysis =
and the final analysis) or to recreate diagnostic graphics (as might be =
required if a drug name has changed, or if the user wishes to invoke a =
set of diagnostic graphics not anticipated in the original analysis),
• The ability to access NONMEM’s help files directly from PLT =
• Extensive error checking and improved NONMEM diagnostics. =
NONMEM’s built in error checking and diagnostics are notoriously =
difficult to understand. For example, NONMEM reads up to 12 digits on =
input but defaults to 5 digits on output. Seven-digit IDs would be =
truncated to 5 digits (exponential format), potentially causing 2 =
subjects to have identical IDs in output tables. PLT Tools identifies =
this and informs the user. The advanced error checking is based on =
thousands of hours of NONMEM use by the developers of PLT Tools, and =
also on feedback from PLT Tools users over the past three years.

PLT Tools is available at The free version contains two =
1. All PDF documents contain a footer “Unregistered version of =
PLT Tools”. For licensed users this is replaced with “Property of =
COMPANYNAME (Confidential)”.
2. Only one instance of NONMEM runs at a time (runs can be stacked =
to run in sequence). Licensed users can perform simultaneous runs =
(ideal with a multi-core computer). Users with a network license can =
submit large numbers of jobs simultaneously to remote computers =
Information about licensing is available at

Technical issues:
• NONMEM versions: PLT Tools is compatible with versions 5, =
6, and 7 (including appropriate handling of version 7’s new methods =
and output tables),
• Fortran: PLT tools is compatible with G77, G95, =
GFortran, and Intel Fortran compilers. PLT Tools is not compatible with =
Digital Fortran or Microsoft PowerStation Fortran.
• Platforms: PLT Tools runs on Windows XP, Windows Vista, and =
Windows 7. PLT Tools also supports OS X (10.4 or later) on the =
• Additional software: PLT Tools requires R, version 2.9 or =
later† (knowledge of R is not required for the use of PLT Tools).
• Installation issues: Setting Fortran environment variables =
for NONMEM can be complicated. PLT Tools provides instructions; =
typically, this can be addressed with a one-line modification to a batch =
file that we provide. Additional support is available at =

Dennis Fisher and Steven Shafer

        * Requires a licensed NONMEM installation; NONMEM is available =
from ICON / Globomax.
        † R is open-source and is available at no charge at =

Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
Received on Mon May 24 2010 - 09:52:26 EDT

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