• 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 S-Plus or 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.

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