individual
individual: An R package for individual-based epidemiological models - Published in JOSS (2021)
Science Score: 98.0%
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org -
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2 of 6 committers (33.3%) from academic institutions -
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Organization mrc-ide has institutional domain (www.imperial.ac.uk) -
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
R Package for individual based epidemiological models
Basic Info
- Host: GitHub
- Owner: mrc-ide
- License: other
- Language: R
- Default Branch: master
- Homepage: https://mrc-ide.github.io/individual
- Size: 13.6 MB
Statistics
- Stars: 30
- Watchers: 5
- Forks: 17
- Open Issues: 9
- Releases: 25
Topics
Metadata Files
README.md
Individual 
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An R package for specifying and simulating individual-based models.
This package is designed to:
- encourage clear and testable components for defining your individual-based models, and
- provide memory efficient, fast code for executing your model
Installation
The package can be installed from github using the "remotes" library
R
library('remotes')
install_github('mrc-ide/individual')
Alternatively you can install individual directly from CRAN, but be aware that the CRAN version may not be the most recent version of the package:
R
install.packages("individual")
For development it is most convenient to run the code from source. You can install the dependencies in RStudio by opening the project and selecting "Build" > "Install and Restart"
Command line users can execute:
R
library('remotes')
install_deps('.', dependencies = TRUE)
Docker users can build a minimal image with
bash
docker build . -f docker/Dockerfile -t [your image name]
Or if you would like devtools and documentation tools you can run
bash
docker build . -f docker/Dockerfile.dev -t [your image name]
Usage
We recommend first reading vignette("Tutorial") which describes
how to simulate a simple SIR model in "individual", and later vignette("API")
which describes in detail how to use the data structures in "individual" to
build more complicated models. If you are running into performance issues,
learn more about how to speed up your model in vignette("Performance").
Statement of need
Individual-based models are important tools for infectious disease epidemiology, but practical use requires an implementation that is both comprehensible so that code may be maintained and adapted, and fast. "individual" is an R package which provides users a set of primitive classes using the R6 class system that define elements common to many tasks in infectious disease modeling. Using R6 classes helps ensure that methods invoked on objects are appropriate for that object type, aiding in testing and maintenance of models programmed using "individual". Computation is carried out in C++ using Rcpp to link to R, helping achieve good performance for even complex models.
"individual" provides a unique method to specify individual-based models compared to other agent/individual-based modeling libraries, where users specify a type for agents, which are subsequently stored in an array or other data structure. In "individual", users instead instantiate a object for each variable which describes some aspect of state, using the appropriate R6 class. Finding subsets of individuals with particular combinations of state variables for further computation can be efficiently accomplished with set operations, using a custom bitset class implemented in C++. Additionally, the software makes no assumptions on the types of models that may be simulated (e.g. mass action, network), and updates are performed on a discrete time step.
We hope our software is useful to infectious disease modellers, ecologists, and others who are interested in individual-based modeling in R.
Contributing
Thank you! Please refer to the vignette on vignette("Contributing") for info on how to
contribute :)
Alternatives
Non R Software
Non R Software for Epi
- EpiFire
- SimpactCyan
- Numerus Model Builder
- NOVA
- EMOD
- Pathogen.jl, a package for individual-based simulation of common compartmental models.
General R Packages
- nlrx, RNetLogo, NetLogoR are NetLogo interfaces
- RRepast is a repast interface
- simecol, provides classes and methods to enhance reproducibility of ecological models.
R based DES
R based IBMs
R based Epi
- EpiModel
- SimInf
- hybridModels
- epinet
- EpiDynamics
- nosoi, generate synthetic data for phylogenetic analysis
- EpiILMCT
- EpiILM
- SPARSEMODr
Owner
- Name: MRC Centre for Global Infectious Disease Analysis
- Login: mrc-ide
- Kind: organization
- Location: London, UK
- Website: https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis
- Repositories: 413
- Profile: https://github.com/mrc-ide
MRC Centre hosted within the Department of Infectious Disease Epidemiology at Imperial College London
JOSS Publication
individual: An R package for individual-based epidemiological models
Authors
MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
Editor
Mikkel Meyer Andersen
Tags
epidemiology individual based agent based infectious disease simulation stochasticGitHub Events
Total
- Issue comment event: 4
- Push event: 6
- Pull request review event: 7
- Pull request review comment event: 2
- Pull request event: 4
- Create event: 1
Last Year
- Issue comment event: 4
- Push event: 6
- Pull request review event: 7
- Pull request review comment event: 2
- Pull request event: 4
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| slwu89 | 1****9 | 224 |
| Giovanni Charles | g****s@g****m | 212 |
| Paul Lietar | p****3@i****k | 30 |
| Pietro Monticone | 3****e | 12 |
| Peter Winskill | p****l@i****k | 7 |
| Darío Hereñú | m****a@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 30
- Total pull requests: 71
- Average time to close issues: 4 months
- Average time to close pull requests: 4 days
- Total issue authors: 6
- Total pull request authors: 5
- Average comments per issue: 1.73
- Average comments per pull request: 0.9
- Merged pull requests: 67
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 3.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- giovannic (20)
- slwu89 (5)
- cwhittaker1000 (2)
- OJWatson (2)
- pwinskill (2)
- marialma (1)
- richfitz (1)
Pull Request Authors
- giovannic (42)
- slwu89 (26)
- plietar (25)
- pwinskill (4)
- cwhittaker1000 (2)
- kant (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 7
- Total versions: 5
cran.r-project.org: individual
Framework for Specifying and Simulating Individual Based Models
- Homepage: https://github.com/mrc-ide/individual
- Documentation: http://cran.r-project.org/web/packages/individual/individual.pdf
- License: MIT + file LICENSE
- Status: removed
-
Latest release: 0.1.9
published over 3 years ago
Rankings
Dependencies
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- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
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- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- actions/cache v2 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- R6 * imports
- Rcpp * imports
- bench * suggests
- ggplot2 * suggests
- knitr * suggests
- mockery * suggests
- pkgdown * suggests
- rmarkdown * suggests
- testthat >= 2.1.0 suggests
- xml2 * suggests
- rocker/r-ver 4.0.2 build