https://github.com/insightrx/luna
Lightweight Universal NLME Administrator
https://github.com/insightrx/luna
Last synced: 12 months ago
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Lightweight Universal NLME Administrator
- Host: GitHub
- URL: https://github.com/insightrx/luna
- Owner: InsightRX
- License: other
- Created: 2025-04-14T18:39:35.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-07-08T14:02:57.000Z (12 months ago)
- Last Synced: 2025-07-08T14:49:23.721Z (12 months ago)
- Language: R
- Homepage: https://insightrx.github.io/luna/
- Size: 1.4 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
**THIS R PACKAGE IS UNDER DEVELOPMENT, NOT READY FOR PRODUCTION USE!!**
# Luna
Luna is a tool to organize your NONMEM and nlmixr2 modeling workflows in
a structured and traceable manner. Luna is an acronym for
**Light-weight Universal NLME Admininstrator**
The organization of projects is implemented through YAML files, which
forces the modeler to define each step during the modeling process prior
to execution of the step. This ensures that all steps are properly
logged and at any time during the model development a clear log of
modeling steps is available.
## Goals and rationale
The goal of Luna is to implement a structured model development: if model development
and results are structured, it’s easier for anyone to interpret (human and AI agents).
## Justification
__But don't we already have workflow managers, like Pirana, Finch Studio, ShinyMixR, etc?__
Yes, and those tools are great and work for a lot of folks. However, we believe
that, especially for advanced modelers or modelers who come in from a
(software-) engineering background, often prefer an interface that is accessible
either programmatically (from R) or from the command line (CLI). This is the
primary target audience of Luna. However, we do think that many novice modelers will
also like the flexibility of Luna.
__But why not just keep a modeling workflow in RMarkdown or Quarto notebooks__
That is certainly an option, and may work for some projects. However,
we feel that for most model development projects, having an R notebook as the
primary source of your model workflow quickly becomes unwieldy: after a few
model runs the notebook file quickly becomes too long to navigate easily. Luna
will have features to export to R notebooks in the future, so the ability to
use R notebooks for creating automated reports and slides will still be
available.
# Implementation
## Structure
All high-level luna functions that the user needs start with `luna_`. For example,
to run a model, use `luna_run(...)`, and to get a list of models in the current
project, use `luna_list()`.
The luna package also exposes various other functions to perform certain tasks, but those
do not make use of the `luna` workflow and in principle should not be used within
a luna workflow.
## Dependencies and extensions
Luna depends on Pharmpy and pharmr (the R wrapper around Pharmpy). The dependency
is primarily to use parsing of models and result files. It can of course also
leverage Pharmpy's model execution tools, bootstrap tool, and the automated model
development tools. Luna is, however, flexible in what tools are used to perform
modeling analyses. It provides an interface to PsN for running models, bootstraps,
and any other PsN tools.
# Example usage
```
library(luna)
## Create a new project (only if starting from scratch, or if creating a new Luna project from existing model folder)
project <- luna_new_project(
"uvm",
description = "UVM vancomycin in obese patients",
folder = proj_path,
# force = TRUE,
return_object = TRUE
)
## Load an existing project
project <- luna_load_project(
folder = proj_path
)
## To list runs, just print the luna project object
project
## To run models:
luna_run("run4")
## If the model was already run, use `force` to rerun:
luna_run("run4", force=TRUE)
## Show model run info:
luna_info("run1")
## Show model run info side-by-side for multiple runs:
luna_compare("run1", "run2", "run3")
## Load the dataset from a model into R
dat <- luna_dataset("run2")
```
## Available functions
```
## Projects
luna_new_project()
luna_load_project()
luna_list()
## Model run workflow
luna_run()
luna_info()
luna_compare()
luna_help()
luna_note()
luna_tag()
luna_edit()
## External tools
luna_tool()
## Diagnostic plots
luna_gof()
luna_ind()
luna_xpose()
## Misc
luna_dataset()
luna_tables()
```