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 (in primary side bar; by right clinking tree view item)
- Model fit summary - run 'sumo' command in PsN to summarize run result
- Run PsN tool
- Show related files - Create a quick pick menu for the files with identical name
- Run R script
- Show R scripts
Editor functions (as a upper right side buttons in the editor pane)
Run nmfe (command for NONMEM only)
Run PsN tool
Run R script
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)
Be sure to add needed PATHs in system environment variable to call the R/PsN/NONMEM functions
Optional:
- 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
0.0.7 - 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