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gradmcmc

Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo

https://github.com/colemonnahan/gradmcmc

Science Score: 46.0%

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
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.0%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo

Basic Info
  • Host: GitHub
  • Owner: colemonnahan
  • License: mit
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 941 MB
Statistics
  • Stars: 15
  • Watchers: 2
  • Forks: 13
  • Open Issues: 0
  • Releases: 1
Created over 10 years ago · Last pushed over 9 years ago
Metadata Files
Readme License Citation

README.md

DOI

This repository contains code for the paper:

Monnahan, C.C., J.T. Thorson, T.A. Branch (In press). Faster estimation of Bayesian models in ecology using Hamiltonian Monte Carlo. Methods in Ecology and Evolution.

This study can be reproduced by installing necessary software and R packages, and then running the script run_simulation.R. See that file for more information.

The models directory contains case studies, with data (as .RDS files), Stan and JAGS implementations (as .stan and .jags files), and an R script to run them (using some functions defined in startup.R). Within each model there is a folder containing plots of results.

The algorithms directory contains an R script containing versions of the static HMC and NUTS algorithms implemented in R. These versions do not contain the full suite of features used in Stan, but may be useful for learning more about their behavior. The script mcmc.R contains the algorithms and helper functions, and examples.R a short script showing how to use them.

Owner

  • Name: Cole Monnahan
  • Login: colemonnahan
  • Kind: user
  • Location: Seattle, WA

Personal account. See @Cole-Monnahan-NOAA for professional account.

GitHub Events

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  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 252
  • Total Committers: 1
  • Avg Commits per committer: 252.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
colemonnahan m****c@u****u 252
Committer Domains (Top 20 + Academic)
uw.edu: 1

Issues and Pull Requests

Last synced: over 1 year ago

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  • Total issues: 0
  • Total pull requests: 4
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  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • 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
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  • Average comments per issue: 0
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  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
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  • colemonnahan (3)
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