spatPomp
spatPomp: An R package for spatiotemporal partially observed Markov process models - Published in JOSS (2024)
Science Score: 95.0%
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Published in Journal of Open Source Software
Repository
R package for statistical inference of spatiotemporal partially observed Markov processes
Basic Info
- Host: GitHub
- Owner: kidusasfaw
- License: gpl-3.0
- Language: R
- Default Branch: master
- Size: 9.88 MB
Statistics
- Stars: 11
- Watchers: 4
- Forks: 9
- Open Issues: 0
- Releases: 3
Metadata Files
README.md
spatPomp has moved to spatPomp-org/spatPomp
What is this package?
The spatPomp package provides facilities for inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models.
To do so, it relies on and extends a number of facilities that the pomp package provides for inference on time series data using partially-observed Markov process (POMP) models.
Why use spatPomp?
The spatPomp package concerns models consisting of a collection of interacting units.
The methods in spatPomp may be applicable whether or not these units correspond to spatial locations.
Installing spatPomp
To install the package from this GitHub source, type the following command into your console (assumes you have the devtools package installed):
devtools::install_github('kidusasfaw/spatPomp').
The CRAN version of spatPomp can be installed by install.packages("spatPomp").
Documentation
Details on the motivation and use of this package can be found in Asfaw et al. (2021) (https://arxiv.org/abs/2101.01157).
Further information can be found on the spatPomp website.
Owner
- Name: Kidus Asfaw
- Login: kidusasfaw
- Kind: user
- Location: Ann Arbor, MI
- Repositories: 2
- Profile: https://github.com/kidusasfaw
Data science. My PhD research in statistics focused on inference for complex, high-dimensional processes.
JOSS Publication
spatPomp: An R package for spatiotemporal partially observed Markov process models
Authors
University of Michigan, Department of Statistics.
University of Kansas, Department of Mathematics.
University of Michigan, Departments of Ecology & Evolutionary Biology and Complex Systems., Santa Fe Institute, Santa Fe, New Mexico.
University of Michigan, Department of Statistics.
Editor
George K. Thiruvathukal
Tags
statistics POMP models sequential Monte Carlo particle filterGitHub Events
Total
- Release event: 1
- Push event: 9
- Create event: 1
Last Year
- Release event: 1
- Push event: 9
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Kidus Asfaw | k****0@g****m | 287 |
| Ed Ionides | i****s@u****u | 141 |
| Aaron A. King | k****a@u****u | 27 |
| allistho | a****o@u****u | 12 |
| joonhap | j****k@k****u | 8 |
| joonhap | j****p@b****u | 3 |
| Haogao | k****o@g****m | 2 |
| Jesse Wheeler PC | j****l@u****u | 2 |
| Ning Ning | p****g@t****u | 1 |
| Jifan Li | 1****i | 1 |
| Kidus | k****s@K****l | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 4
- Total pull requests: 25
- Average time to close issues: about 2 months
- Average time to close pull requests: 14 days
- Total issue authors: 3
- Total pull request authors: 9
- Average comments per issue: 2.25
- Average comments per pull request: 0.96
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 2
- Average time to close issues: 6 days
- Average time to close pull requests: 1 day
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- johnlees (2)
- Koohoko (1)
- kingaa (1)
Pull Request Authors
- kingaa (15)
- kidusasfaw (5)
- allistho (2)
- Koohoko (2)
- ionides (2)
- jifanli (1)
- jeswheel (1)
- patning (1)
- nanyyyyyy (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 4.0.0 depends
- methods * depends
- pomp >= 4.1 depends
- abind * imports
- dplyr * imports
- foreach * imports
- ggplot2 * imports
- magrittr * imports
- rlang * imports
- stringr * imports
- tidyr * imports
- doParallel >= 1.0.11 suggests
- parallel * suggests
- testthat * suggests
- actions/checkout v3.1.0 composite
- actions/upload-artifact v3.1.1 composite
- r-lib/actions/setup-r v2.3.1 composite
- r-lib/actions/setup-r-dependencies v2.3.1 composite
- actions/checkout v3.1.0 composite
- actions/upload-artifact v3.1.1 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-r v2.3.1 composite
- r-lib/actions/setup-r-dependencies v2.3.1 composite
- actions/checkout v3.1.0 composite
- r-lib/actions/setup-r v2.3.1 composite
- r-lib/actions/setup-r-dependencies v2.3.1 composite