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)
![Demo](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/demo_viewer.png)
- 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) ![NMFE button](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/nonmem.png)
Run PsN tool ![PsN button](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/psn.png)
Run R script ![R button](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/r.png)
Visualization - heatmap, line plotting, histograms, scatter plot matrix ...
Heatmap
Line plotting
Histogram
More functions will be added in demand...
Demo
![Demo](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/demo.gif)
Visualization
Button will appear on certain file types
Heatmap viewer for matrix type data (.cov, .cor, .coi)
![Demo](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/demo_matrix.png)
Data inpesctor for table dataset (File name conatining ~tab, ~table)
![Demo](https://raw.githubusercontent.com/tnzo12/nmbench/main/resources/readme/demo_hist.png)
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 - 0.0.8
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