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SimBIID

https://github.com/tjmckinley/simbiid

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: tjmckinley
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 400 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 3
  • Releases: 8
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

SimBIID

Lifecycle:maturing CRAN Status <!-- badges: end -->

R package that implements various simulation-based inference routines for infectious disease models. At the current time it is mainly used for education purposes.

Package provides some code to run simulations of state-space models, and then use these in the ABC-SMC algorithm of Toni et al. (2009) and the bootstrap particle filter based particle MCMC algorithm (Andrieu et al., 2010). Also provides functions to plot and summarise the outputs.

A detailed vignette is provided at: https://tjmckinley.github.io/SimBIID_tutorial/

To install package

The package depends on the Rcpp and RcppArmadillo packages, which require the installation of the correct C++ compilers. The guidance below is taken from Sections 2.1.1, 2.1.2 or 2.1.3 here:

https://teuder.github.io/rcpp4everyoneen/020install.html

Windows

Install Rtools.

(Make sure you tick the option to add Rtools to the PATH whilst installing.)

Mac

Install Xcode command line tools. Execute the command xcode-select --install in a Terminal.

You might also need to install the gfortran libraries from:

https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg

Linux

Install gcc and related packages (you might also need gcc-fortran for some of the dependencies).

In Ubuntu Linux, execute the command sudo apt-get install r-base-dev in a Terminal.

Install package

Once the compilers have been installed, then the CRAN version can be installed in the usual way, e.g.

install.packages("SimBIID")

Alternatively, the development version can be installed from source using the remotes package in R. That is, install the remotes package and then run:

library(remotes) install_github("tjmckinley/SimBIID")

Owner

  • Name: TJ McKinley
  • Login: tjmckinley
  • Kind: user

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Push event: 5
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 1
  • Push event: 5
  • Create event: 1

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 320
  • Total Committers: 3
  • Avg Commits per committer: 106.667
  • Development Distribution Score (DDS): 0.059
Top Committers
Name Email Commits
TJ McKinley t****y@e****k 301
TJ McKinley t****y@u****m 11
Stefan Widgren s****n@g****m 8
Committer Domains (Top 20 + Academic)
exeter.ac.uk: 1

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 4
  • Total pull requests: 5
  • Average time to close issues: about 19 hours
  • Average time to close pull requests: about 23 hours
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • tjmckinley (3)
  • NedaJalali-codes (1)
Pull Request Authors
  • stewid (5)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 319 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
  • Total maintainers: 1
cran.r-project.org: SimBIID

Simulation-Based Inference Methods for Infectious Disease Models

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 319 Last month
Rankings
Forks count: 21.9%
Dependent packages count: 29.8%
Stargazers count: 31.7%
Average: 34.6%
Dependent repos count: 35.5%
Downloads: 54.1%
Maintainers (1)
t.mckinley@exeter.ac.uk
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • RColorBrewer * imports
  • Rcpp * imports
  • RcppXPtrUtils * imports
  • coda * imports
  • dplyr * imports
  • ggplot2 * imports
  • grDevices * imports
  • mvtnorm * imports
  • purrr * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
  • GGally * suggests
  • parallel * suggests
  • testthat * suggests
.github/workflows/rhub.yaml actions
  • r-hub/actions/checkout v1 composite
  • r-hub/actions/platform-info v1 composite
  • r-hub/actions/run-check v1 composite
  • r-hub/actions/setup v1 composite
  • r-hub/actions/setup-deps v1 composite
  • r-hub/actions/setup-r v1 composite