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inlatools

An R package with useful functions to diagnose INLA models

https://github.com/inbo/inlatools

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (14.3%) to scientific vocabulary

Keywords

bayesian-statistics gplv3 inla mixed-models model-checking model-validation r
Last synced: 6 months ago · JSON representation ·

Repository

An R package with useful functions to diagnose INLA models

Basic Info
Statistics
  • Stars: 4
  • Watchers: 9
  • Forks: 2
  • Open Issues: 1
  • Releases: 1
Topics
bayesian-statistics gplv3 inla mixed-models model-checking model-validation r
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Zenodo

README.md

The inlatools package

Project Status: Active – The project has reached a stable, usable state and is being actively developed. lifecycle Licence minimal R version codecov

Rationale

The inlatools package provides a set of function which can be useful to diagnose INLA 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 of all available functions. Click on the name the function to open the corresponding help file. The vignettes illustrate

Folder structure

  • R: The source scripts of the R functions with documentation in Roxygen format
  • man: The helpfile in Rd format
  • test: unit tests using the testthat framework
  • vignettes: the source code of the vignettes

inlatools ├── man ├── R ├─┬ tests │ └── testthat └── vignettes

Owner

  • Name: Research Institute for Nature and Forest (INBO)
  • Login: inbo
  • Kind: organization
  • Location: Belgium

Open source, data and science initiatives of the Research Institute for Nature and Forest (INBO)

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: "inlatools: Diagnostic Tools for INLA Models"
authors:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
keywords:
- INLA
- dispersion
- distribution
- prior
- anomaly
- residuals
contact:
- given-names: Thierry
  family-names: Onkelinx
  affiliation: Research Institute for Nature and Forest (INBO)
  orcid: 0000-0001-8804-4216
doi: ~
license: GPL-3.0
repository-code: https://github.com/inbo/inlatools/
type: software
abstract: "Several functions which can be useful to choose sensible priors and diagnose
  the fitted model."
identifiers:
- type: url
  value: https://inbo.github.io/inlatools/
version: 0.0.3

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 7
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 8 months
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.43
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: 7 months
  • Average time to close pull requests: 12 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • peterdesmet (1)
  • holliecalley (1)
Pull Request Authors
  • ThierryO (7)
  • florisvdh (2)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 3.4.0 depends
  • INLA >= 19.09.03 imports
  • assertthat * imports
  • dplyr * imports
  • ggplot2 * imports
  • methods * imports
  • purrr * imports
  • rlang * imports
  • scales * imports
  • tibble * imports
  • tidyr * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/check_on_branch.yml actions
  • inbo/actions/check_pkg master composite
.github/workflows/check_on_different_r_os.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
.github/workflows/check_on_main.yml actions
  • inbo/actions/check_pkg master composite
.github/workflows/release.yml actions
  • actions/checkout v2 composite
  • actions/create-release v1 composite
.github/workflows/remove_old_artifacts.yml actions
  • c-hive/gha-remove-artifacts v1 composite