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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 generates:
* 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 graphics;
* 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 Tools;
* 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 PLTsoft.com. The free version contains two limitations:
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 (clusters).
Information about licensing is available at PLTsoft.com.
* 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 Macintosh.
* 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 support.-a-.PLTsoft.com.
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 R-project.org.
Dennis Fisher MD
P < (The "P Less Than" Company)
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