Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/cole-monnahan-noaa/stpollock

A spatio-temporal CPUE analysis combining bottom and acoustic trawl survey data for pollock

https://github.com/cole-monnahan-noaa/stpollock

Science Score: 36.0%

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 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A spatio-temporal CPUE analysis combining bottom and acoustic trawl survey data for pollock

Basic Info
  • Host: GitHub
  • Owner: Cole-Monnahan-NOAA
  • Language: R
  • Default Branch: master
  • Size: 68.4 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created almost 8 years ago · Last pushed about 5 years ago
Metadata Files
Readme

README.md

stpollock

A spatio-temporal CPUE analysis combining bottom and acoustic trawl survey data for eastern Bering sea pollock

This repo contains code to reproduce the following paper:

Cole C Monnahan, James T Thorson, Stan Kotwicki, Nathan Lauffenburger, James N Ianelli, Andre E Punt, Incorporating vertical distribution in index standardization accounts for spatiotemporal availability to acoustic and bottom trawl gear for semi-pelagic species, ICES Journal of Marine Science, 2021;, fsab085, https://doi.org/10.1093/icesjms/fsab085

A demo of the method is posted at: https://github.com/James-Thorson-NOAA/VAST/wiki/Combine-acoustic-and-bottom-trawl-data

Note that this example uses maximum likelihood, while the paper above uses Bayesian inference via tmbstan. See paper for a discussion of why.

To reproduce the analysis, clone the repo, open the script "run_analysis.R" and step through calculations. The whole thing may take a month or so to run.

The result files are far too large to save so are excluded. Otherwise all files necessary to run the analysis are included.

Owner

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

Quantitative ecologist at NOAA's AFSC

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 439
  • Total Committers: 4
  • Avg Commits per committer: 109.75
  • Development Distribution Score (DDS): 0.052
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 416
Cole-Monnahan-NOAA c****n@n****v 16
Cole.Monnahan C****n@n****l 6
Cole.Monnahan c****n 1
Committer Domains (Top 20 + Academic)
noaa.gov: 1 uw.edu: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 8 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • jimianelli (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels