• Default Graphics: If the user has not populated, then selected a Graphics Script (using the Graphics Editor), PLT Tools will attempt to create graphics. These graphics will be limited.
• Error Detection: Many levels of error protection added. For example, if a subject ID contains 7 digits, NONMEM will output only 6 digits to a table, potentially leading to ambigious IDs.
• Graphics: Multiple minor changes in appearance and minor bug fixes.
• Naming of Tables: The names 'AllRecords.txt' and 'FirstRecords.txt' are now accepted.
• Elements Required for Tables: If the user omits certain key elements from a table, these are accessed from FDATA.
• Parameter Table: The parameters for a NONMEM run are displayed in spreadsheet form.
• Simulation and Simulation / Estimation: Now fully supported including separate graphics for each subproblem and a single table displaying the parameters from all subproblems. In addition, separate tables are provided for each subproblem.
• Batch Processing: The user can stack NONMEM runs to be performed sequentially.
• Simulataneous Processing: The user can perform more than one simultaneous run on a single computer. If the computer contains multiple processors, this increases throughput. Requires registration.
• Network Processing: If the user can access a network on which computers are configured to run NONMEM, PLT Tools will determine which computer is available, copy files to that computer, run NONMEM, then copies files back to the local machine for post-processing. Requires registration and a supplemental fee.
• NONMEM 5: PLT Tools is now compatible with NONMEM 5. See User's Manual for instructions on implementation. Users can select between NONMEM 5 and 6 for a single control stream, a Working Folder, or a Project.
• NONMEM 6, version 2.0: PLT Tools is fully compatible with NONMEM 6, version 2.0. See FAQ to ensure that PLT Tools will access the correct version of nmfe6.bat.
• Fortran compilers: Additional Fortran compilers, including Intel Fortran 10.1, have been evaluated successfully with PLT Tools.
• Use of R: Previous versions of PLT Tools required that registered users use S-Plus rather than R. The Free Software Foundation (home of the GNU Project) has determined that PLT Tools does not violate Râs GPL (General Public License). As a result, all users of PLT Tools can now select freely between R and S-Plus.
• Bootstrap: PLT Tools now provides fully automated support for bootstrap; reformmating of the dataset is not required. All parameter estimates are accumulated in a spreadsheet.
• Visual Predictive Check: PLT Tools provides fully automated support for visual predictive checks.
• Consultant Mode: Licensed users can tailor the footer of each page of PDF output to indicate "Property of [CLIENT NAME] (Confidential)".
• Print Objective Function: Selecting this option results in the minimum value of the objective function being printed on each page of graphics.
• Print Control Stream: Selecting this option results in the name of the control stream being printed on each page.
• Wider margins: Selecting this option results in graphics having a wider margin (1â on all sides, compared to 1â2â without the option).
• NONMEM Only: Clicking this button causes NONMEM to be executed with no attempt to create graphics.
• Analysis Conducted In: This field displays the folder in which NONMEM is being executed. It is relevant only for registered users who are configured for simultaneous conduct of NONMEM runs or for network access.
• Run Log: A log of all runs is maintained.
• Options: Options were reorganized and several new options have been added.
• Control Stream Editor: Users can edit control streams directly from PLT Tools.
• Control Stream Library: Users can access a library of control streams, then edit these control streams for their own purposes.
• Likelihood Profile: PLT Tools can perform a fully-automated likelihood profile; the results of the profile are presented in a new graphic.

• Project Log: A "Project Log" tracks information relevant to each run (Run #, $PROBLEM statement, objective function, # of significant digits, etc.); the log can be saved as a csv file for archival purposes.
• Parameter Log: A "Parameter Log" (which opens as a csv file) records THETAs, OMEGAs, and SIGMAs for each run.
• Jackknife: PLT Tools now provides fully automated support for jackknife; reformmating of the dataset is not required. All parameter estimates are accumulated in a spreadsheet and new graphic displays the results of each jackknife iteration.
• Graphics: "Time after dose" graphics: If the text "Time after dose" appears in the header text for spaghetti graphic, a new set of graphics is created in which observations are displayed relative to â¨the most recent dose.
• Seed for bootstrap and jackknife analyses: The user can enter a seed to control random- â¨number generation for bootstrap and jackknife analyses.
• Displays: The Project Controller window has been reorganized to improve communication regarding the status of NONMEM runs.
• Automation: The user can prepare a script listing a series of NONMEM runs to perform in an automated manner. Examples are provided.
• By-Subject Graphics: Previously, if the user invoked "reset" events (EVID = 3 or 4), PLT Tools would overlay more than one set of observations in a single panel. Now, PLT Tools assigns sequential periods and displays the data in separate panels.
• Display IDs in Graphics: An option in the Graphics Editor allows the user to display IDs in certain graphics. this is particularly useful for identifying outliers.
• Post-run Cleanup: Previous versions may have left copies of R running. This no longer occurs.
• NMTRAN Error Messages: When NMTRAN identifies an error in the control stream, a popup window displays the relevant text.
• NONMEM 7: NONMEM 7 is supported. The user selects NONMEM 5, 6, or 7 in Workspace / Options.
• Progress Bar: A progress bar in the Project Controller window shows progress of loading of code.
• NMQUAL: PLT Tools now allows the user to select either the Globomax / ICON installer (nmfe) or the Metrum installer (nmqual). Full support is provided for both. XML files created by nmqual are saved in a designated folder.
• Covariate Search: Univariate covariate searches are now supported.
• Single panel graphics: During assembly of routine graphics, in addition to creating a PDF document, PLT Tools creates single panel graphics (JPEG format) for a number of graphics that the user might consider embedding in a report.
• Summary tables: At the completion of each NONMEM run, PLT Tools creates tables summarizing population and post hoc parameters.
• Support for Linux: Due to lack of interest, support for Linux was eliminated.
• S-Plus: Many features of PLT Tools could not be provided via S-Plus. As a result, support for S-Plus was discontinued.

• Reports: The "Report" Tool was improved markedly. Use of landscape / portrait page layouts allows better organization of tables. Dynamic table of contents / table of tables / table of figures now included.
• Run Listing: Improved interface to select runs for a run listing.
• Flow Chart: The "Summarize / Report" Tool prepares a flow chart showing the dependency of NONMEM runs.
• SAS xport tables: FDATA files and input files can now be output in SAS xport format (for regulatory submissions). Column headers are written to a separate text file which acts as a template for a "define.pdf" file requested by FDA.
• Population/post hoc parameter tables: Summary tables prepared for each run include population half-lives, post hoc parameters, and post hoc half-lives.
• NUMSIGDIG: If NONMEM aborts before achieving 3 significant digits (or a different value, if selected as an option) and more than 0 digits, it reports the number of significant digits for each parameter estimated. These values are now incorporated into the Brief Summary document.
• ETA shrinkage: For each ETA term displayed in graphics, ETA shrinkage is calculated. The calculation ignores values of ETA equal 0 (the approach recommended by Karlsson [personal communication]), in contrast to NONMEM’s approach (which is to calculate ETA shrinkage using all values).
• Graphics: histograms and qq plots for parameters and ETAS added to graphics.
• A new “within-group” grouping variable added to Graphics Script.
• Graphics: histograms and qq plots for parameters and ETAS added to graphics.
• CHECKOUT option in Control Stream: A Control Stream is now provided to facilitate use of NONMEM’s CHECKOUT option.
• Graphics: histograms and qq plots for parameters and ETAS added to graphics.
• FROMDATASET: A new option is permitted for the $INPUT record in the Control Stream. If this option is invoked, PLT Tools replaces the text FROMDATASET with a list of data items obtained from the first row of the dataset.