Science Score: 59.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
12 of 38 committers (31.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary
Keywords
Repository
The base NIMBLE package for R
Basic Info
- Host: GitHub
- Owner: nimble-dev
- License: bsd-3-clause
- Language: C++
- Default Branch: devel
- Homepage: http://R-nimble.org
- Size: 72.5 MB
Statistics
- Stars: 181
- Watchers: 19
- Forks: 23
- Open Issues: 99
- Releases: 26
Topics
Metadata Files
README.md
NIMBLE
Website | Documentation | Examples | Developing | Workshop materials
NIMBLE is an R package for hierarchical statistical modeling (aka graphical modeling). It enables writing general models along with methods such as Markov chain Monte Carlo (MCMC), particle filtering (aka sequential Monte Carlo), Laplace approximation and other general methods.
For writing statistical models, NIMBLE adopts and extends the BUGS language, making it largely compatible with BUGS and JAGS. NIMBLE makes BUGS extensible, allowing users to add new functions and new distributions.
For writing algorithms (aka analysis methods), NIMBLE provides a model-generic programming system embedded within R. This provides control over models as generic objects and mathematical manipulation of model variables. In this way, NIMBLE's programming paradigm treats probabilistic graphical models as a basic programming construct.
Both models and algorithms are compiled via generating customized C++ and providing seamless interfaces to compiled C++ from R.
NIMBLE's most developed methods are for MCMC. Users can easily customize sampler configurations from R and write new samplers in NIMBLE's algorithm programming system.
Developers of new computational statistical methods can build them in NIMBLE to gain the benefits of its graphical modeling language, compilation, and distribution via CRAN.
Installation
Install prerequisites
NIMBLE needs a C++ compiler and the GNU make utility.
Typically, Mac users can obtain these by installing Xcode, including
command line utilities, while Windows users can obtain them by
installing Rtools.
See the User Manual for more details.
Install NIMBLE
The easiest way to install NIMBLE is via CRAN:
r
install.packages("nimble")
To install from the NIMBLE website:
r
library(devtools)
install.packages("nimble", type = "source", repos = "https://r-nimble.org")
Note that NIMBLE's sequential Monte Carlo (SMC; aka particle filtering) methods are now (as of version 0.10.0) in the nimbleSMC package.
Note that MCMCsuite and compareMCMCs have been migrated to the compareMCMCs package, now available on CRAN.
Citation
In published work that uses or mentions NIMBLE, please cite:
de Valpine, P., D. Turek, C.J. Paciorek, C. Anderson-Bergman, D. Temple Lang, and R. Bodik. 2017. Programming with models: writing statistical algorithms for general model structures with NIMBLE. Journal of Computational and Graphical Statistics 26:403-413. https://doi.org/10.1080/10618600.2016.1172487.
In published work that uses NIMBLE, please also cite the package version:
de Valpine, P., C. Paciorek, D. Turek, N. Michaud, C. Anderson-Bergman, F. Obermeyer, C. Wehrhahn Cortes, A. Rodriguez, D. Temple Lang, W. Zhang, S. Paganin, and P. van Dam-Bates. 2024. NIMBLE: MCMC, Particle Filtering, and Programmable Hierarchical Modeling. doi: 10.5281/zenodo.1211190. R package version 1.2.1, https://cran.r-project.org/package=nimble.
To help us track usage to justify funding support for NIMBLE, please include the DOI in the citation.
Licenses
Nimble is released under a mixture of licenses, and depends on additional third-party libraries with compatible licenses.
- Nimble's non-C++ code (R, bash, Make, etc.) is released under Revised BSD.
- Nimble's C++ code is released under GPL 2.
- Nimble's User Manual is released under the CC BY 4.0 license.
- The Eigen C++ library included with Nimble is licensed under MPL 2.
Acknowledgements
The development of NIMBLE has been funded by:
- an NSF Advances in Biological Informatics grant (DBI-1147230) to P. de Valpine, C. Paciorek, and D. Temple Lang;
- an NSF SI2-SSI grant (ACI-1550488) to P. de Valpine, C. Paciorek, and D. Temple Lang;
- an NSF Collaborative Research grant (DMS-1622444) to P. de Valpine, A. Rodriguez, and C. Paciorek; and
- an NSF Collaborative Research grant (DMS-2152860) to P. de Valpine, C. Paciorek, and D. Turek.
with additional support provided by postdoctoral funding for D. Turek from the Berkeley Institute for Data Science and Google Summer of Code fellowships for N. Michaud (2015) and C. Lewis-Beck (2017).
Owner
- Name: nimble-dev
- Login: nimble-dev
- Kind: organization
- Repositories: 15
- Profile: https://github.com/nimble-dev
GitHub Events
Total
- Create event: 41
- Release event: 1
- Issues event: 61
- Watch event: 22
- Delete event: 36
- Issue comment event: 127
- Push event: 250
- Gollum event: 1
- Pull request review comment event: 1
- Pull request review event: 1
- Pull request event: 89
- Fork event: 5
Last Year
- Create event: 41
- Release event: 1
- Issues event: 61
- Watch event: 22
- Delete event: 36
- Issue comment event: 127
- Push event: 250
- Gollum event: 1
- Pull request review comment event: 1
- Pull request review event: 1
- Pull request event: 89
- Fork event: 5
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Christopher Paciorek | p****k@s****u | 1,698 |
| perrydv | p****e@b****u | 694 |
| danielturek | d****k@g****m | 506 |
| Nicholas Michaud | n****d@g****m | 472 |
| danielturek | d****k@b****u | 341 |
| perrydv | p****y@P****l | 232 |
| Fritz Obermeyer | f****r@g****m | 91 |
| pistacliffcho | c****s@u****u | 71 |
| NLMichaud | m****d@i****u | 71 |
| Duncan Temple Lang | d****n@r****g | 59 |
| perrydv | p****y@a****t | 39 |
| Wei Zhang | w****2@g****k | 32 |
| Christopher Paciorek | p****k@C****l | 19 |
| paciorek@stat.berkeley.edu | p****k@C****l | 19 |
| DRJP | d****l@a****r | 16 |
| perrydv | p****y@P****l | 10 |
| Peter Sujan | p****n@g****m | 4 |
| Duncan Temple Lang | d****g@u****u | 4 |
| perrydv | p****y@P****l | 3 |
| paciorek@stat.berkeley.edu | p****k@C****u | 3 |
| pistacliffcho | p****o@h****m | 3 |
| jpdunc23 | j****3 | 3 |
| Ken Kellner | k****r | 3 |
| David LeBauer | d****r@g****m | 2 |
| Lauren Ponisio | l****o@b****u | 2 |
| danielturek | d****k@a****u | 2 |
| danielturek | m****8@g****m | 2 |
| rpatin | r****n@f****r | 1 |
| Lauren Ponisio | l****p@f****u | 1 |
| David Pleydell | d****l@i****r | 1 |
| and 8 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 177
- Total pull requests: 219
- Average time to close issues: 3 months
- Average time to close pull requests: about 1 month
- Total issue authors: 33
- Total pull request authors: 8
- Average comments per issue: 2.29
- Average comments per pull request: 2.36
- Merged pull requests: 175
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 41
- Pull requests: 80
- Average time to close issues: about 1 month
- Average time to close pull requests: 18 days
- Issue authors: 8
- Pull request authors: 7
- Average comments per issue: 1.0
- Average comments per pull request: 1.35
- Merged pull requests: 52
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- paciorek (91)
- perrydv (28)
- danielturek (13)
- paul-vdb (3)
- BertvanderVeen (2)
- csbrown (2)
- DRJP (2)
- hiroshi-in-uk (2)
- SILIZ4 (2)
- ralmond (2)
- pehkawn (2)
- luchinoprince (2)
- kenkellner (2)
- stephematician (1)
- cwliu007 (1)
Pull Request Authors
- paciorek (133)
- danielturek (70)
- perrydv (61)
- kenkellner (14)
- paul-vdb (4)
- adamlilith (2)
- JimmyJHickey (2)
- adamgorm (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 2,791 last-month
- Total docker downloads: 107,964
- Total dependent packages: 16
- Total dependent repositories: 42
- Total versions: 37
- Total maintainers: 1
cran.r-project.org: nimble
MCMC, Particle Filtering, and Programmable Hierarchical Modeling
- Homepage: https://r-nimble.org
- Documentation: http://cran.r-project.org/web/packages/nimble/nimble.pdf
- License: BSD_3_clause + file LICENSE | GPL-2 | GPL-3 [expanded from: BSD_3_clause + file LICENSE | GPL (≥ 2)]
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Latest release: 1.3.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- R >= 3.1.2 depends
- R6 * imports
- coda * imports
- igraph * imports
- methods * imports
- testthat * suggests