nmbench README

nmbench is a package that supports Nonlinear mixed effect modeling with NONMEM, majorly focusing on utilizing PsN (Perl-Speaks-NONMEM) commands. It adds addtional viewer below the genuine explorer that provides filtered shows '.mod' and '.ctl' file in directory, and adds necessary GUI elements in editor windows

Features

nmbench provides following features:

Viewer functions: NMBENCH: BROWSER (Basically in the primary sidebar)

• Both viewer functions can be moved onto secondary sidebar, you can enable/disable by View > Appearance Secondary Side Bar

(Basically, it’s in the primary sidebar, but you can move it to the secondary sidebar by dragging)

By right clicking,

1. Model fit summary - run 'sumo' command in PsN to summarize run result
2. Run PsN tool
3. Show related files - Create a quick pick menu for the files with identical name
4. Run R script
5. Show R scripts

Multiple selection supported (shift/cmd/ctrl + click)

Viewer functions NMBENCH: ESTIMATES (Basically in the primary sidebar)

Editor functions (as a upper right side buttons in the editor pane)

1. Run nmfe (command for NONMEM only)

2. Run PsN tool

3. Run R script

4. Visualization - heatmap, line plotting, histograms, scatter plot matrix ...

   • Heatmap
   • Line plotting
   • Histogram More functions will be added in demand...

Demo

Visualization Button will appear on certain file types Heatmap viewer for matrix type data (.cov, .cor, .coi)

Data inpesctor for table dataset (File name conatining ~tab, ~table)

Requirements

The extension is made in follwing system settings:

• NONMEM® (ICON, v7.5.1 recommended)

• PsN (Perl-Speaks-NONMEM, version 5.3.1)

• R (v4.4.0)

• R packages (xpose, xpose4, reshape2, dplyr, ggpubr...)

Be sure to add needed PATHs in system environment variable to call the R, PsN and NONMEM functions. For example 'C:\Program Files\R\R-4.4.2\bin' for R, 'C:\PsN-5.5.0\strawberry\perl\bin' for PsN. (Check your software installtion path!)

Optional (recommended):

• VS Code extension - NMTRAN (by Viktor Rognås)
• For MacOS, it is recommanded to use homebrew for R
• For Windows, in order to use Run R script function, environment variable should be added in PATH. For example, "C:\Program Files\R\R-4.4.0\bin" must be in system PATH

Extension Settings

To be added later

Known Issues

Currently, 'Run R script' function cannot perform is not working on multiple models For feedbacks, https://github.com/tnzo12/nmbench

Release Notes

0.1.1 - 0.1.3 (Hotfix)

• Corrected estimates viewer algorithm

0.1.0

Explorer renamed

• NMBENCH: BROWSER - mod file viewer + command (original function)
• NMBENCH: ESTIMATES - .lst file estimates/status viewer (new)

0.0.7 - 0.0.9

Minor fixes

0.0.4 - 0.0.6

Fixed Rscript working directory problem Renewed heatmap function to use plotly Minor fix: Command prompt settings in Windows

0.0.3

Minor fix: Command prompt as terminal in Windows

0.0.2

Data visualization, minor updates