• Project Controller: Select a Working Folder (within a Project Folder), then select a Control Stream and a Graphics Script (described below). Click"Run NONMEM": NONMEM is run with its progress appearing in a console. At completion, NONMEM's control stream, outputfile, tables, and the data used in the analysis are time-stamped and filed in a consistent set of folders. In addition to the non-processed tables, a set of tables is created in which fixed-format spaces are replaced with (user-selected) tabs, commas, or semicolons, thereby facilitating viewing tables with Excel. A suite of standardized diagnostic graphics are created (using R) from the tables. Copies of files for the most recent run also appear in a local subfolder. Samples of the brief summary, a formatted table, and graphics are available. Finally, a graphic is prepared displaying each pair of covariates.

• Compare Runs Tool: At completion of a series of analyses (or partway through), comparisons can be made between multiple pairs of runs. Using pull-down menus, populate a table showing the runs to be compared, then push "Compare Runs" (an example can be downloaded). Comparisons include the change in the objective function, the corresponding P value for the likelihood ratio test (the user must supply the change in degrees of freedom) and the output of a line-by-line comparison of the two control streams showing all differences. In addition, a table is created summarizing the differences between runs. This table includes the timestamp of the runs being compared, the objective function, the P value for the likelihood ratio test, the number of non-fixed thetas, etas, and sigmas in each model, and comments entered by the user. Finally, the brief summaries described above are bundled into a single file, suitable for insertion into a report.

• Create Archive Tool: At completion of a series of analyses (or partway through), with one click, the user can bundle together the outputs of the desired runs into a time-stamped archive.

• Graphics Editor: Using a graphical interface, the user selects options (the "Graphics Script") for the creation of the graphics identified above.

• Run Listing Editor: Using a graphical interface, identify runs for the Compare Runs tool and the Create Archive tool.

• User-Defined Scripts: A user can write his/her own scripts using R and can incorporate code provided by PLTsoft so that these graphics have the same "look and feel" of the graphics created by PLT Tools. These scripts can be executed during each NONMEM run and will be named with the same conventions as other files.

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