https://github.com/inbo/inlatools
An R package with useful functions to diagnose INLA models
https://github.com/inbo/inlatools
bayesian-statistics gplv3 inla mixed-models model-checking model-validation r
Last synced: 9 months ago
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An R package with useful functions to diagnose INLA models
- Host: GitHub
- URL: https://github.com/inbo/inlatools
- Owner: inbo
- License: gpl-3.0
- Created: 2018-10-08T13:08:58.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2024-10-04T11:21:04.000Z (over 1 year ago)
- Last Synced: 2025-04-12T05:02:23.175Z (10 months ago)
- Topics: bayesian-statistics, gplv3, inla, mixed-models, model-checking, model-validation, r
- Language: R
- Homepage: https://inbo.github.io/inlatools/
- Size: 7.65 MB
- Stars: 4
- Watchers: 9
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Zenodo: .zenodo.json
Awesome Lists containing this project
README
# The `inlatools` package
[](https://www.repostatus.org/#active)
[](https://lifecycle.r-lib.org/articles/stages.html)
[](https://www.gnu.org/licenses/gpl-3.0.en.html)
[](https://cran.r-project.org/)
[](https://app.codecov.io/gh/inbo/inlatools)
## Rationale
The `inlatools` package provides a set of function which can be useful to diagnose [INLA](https://www.r-inla.org/) models.
- calculate Pearson residuals
- simulation based checks for over- or underdispersion
- simulation based checks for the distribution
- visualise the effect of the variance or precision on random effects
- random intercept
- first order random walk
- second order random walk
## Installation
```r
ip <- rownames(installed.packages())
if (!"remotes" %in% ip) {
install.packages("remotes")
}
if (!"INLA" %in% ip) {
install.packages(
"INLA",
repos = c(getOption("repos"), "https://inla.r-inla-download.org/R/stable")
)
}
remotes::install_github("inbo/inlatools")
```
## Documentation
All documentation is available at the package website: https://inlatools.netlify.app.
This website contains an [overview](https://inlatools.netlify.app/reference/index.html) of all available functions.
Click on the name the function to open the corresponding help file.
The [vignettes](https://inlatools.netlify.app/articles/index.html) illustrate
- how to [check the dispersion](https://inlatools.netlify.app/articles/dispersion.html)
- how to [check the distribution](https://inlatools.netlify.app/articles/distribution.html) and
- how to visualise [random effects](https://inlatools.netlify.app/articles/prior.html) for a given variance or precision.
## Folder structure
- `R`: The source scripts of the [R](https://cran.r-project.org/) functions with documentation in [Roxygen](https://github.com/r-lib/roxygen2) format
- `man`: The helpfile in [Rd](https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Rd-format) format
- `test`: unit tests using the [`testthat`](https://testthat.r-lib.org/) framework
- `vignettes`: the source code of the vignettes
```
inlatools
├── man
├── R
├─┬ tests
│ └── testthat
└── vignettes
```