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h3_indicators

Notebooks and documentation about computing H3 biodiversity indicators

https://github.com/noaa-gis4ocean/h3_indicators

Science Score: 54.0%

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (12.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Notebooks and documentation about computing H3 biodiversity indicators

Basic Info
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 1
  • Open Issues: 3
  • Releases: 3
Created over 1 year ago · Last pushed 11 months ago
Metadata Files
Readme Contributing License Citation

README.md

H3_indicators

Notebooks and documentation about computing biodiversity indicators from the Ocean Biodiversity Information System (OBIS) snapshots (periodic full exports of the OBIS database) on H3 grids.

image

💾 Source data

The data sourced for this effort comes from the publicly available OBIS snapshots, which can be found at https://api.obis.org/export.

❓ What's in this repo?

  • GIS4Ocean_h3_indicators.Rmd
    • downloads the most recent snapshot,
    • clips the data to US Waters as identified in the shapefiles.
    • grids the data to a determined H3 grid resolution,
    • computes various indicators using the obisindicators R package,
    • saves the results to .geojson files in the data/ directory.
  • GIS4Ocean_h3_indicators.R
    • Same as above but in an R script file instead of Rmarkdown. In an attempt to simplify the infrastructure needed to run the code (ie. remove requirement to run Rmarkdown files)
  • GIS4Ocean_h3_indicators.ipynb
    • Work In Progress: Draft conversion of the R code above into Python for use in cloud computing infrastructure (eg. Dask).
  • read_and_plot_geojson_heatmap.ipynb
    • Example notebook showing how to read geojson files and plot the data on an interactive map.
  • data/
    • Output .geojson indicator files at various resolutions.
    • Includes shapefile for "US Waters".
  • website/:
    • create_indicator_webpages.py reads .geojson data and creates an html map to serve on the GitHub Pages website.

👁️Where can I see the results?

The resultant data are served as interactive maps at https://noaa-gis4ocean.github.io/H3_indicators/.

The maps are generated via GitHub Action which update everytime a file is changed in data/.

🖐️ Want to help out?

Repository citation

DOI

Owner

  • Name: NOAA-GIS4Ocean
  • Login: NOAA-GIS4Ocean
  • Kind: organization

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: H3_indicators
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Mathew
    family-names: Biddle
    orcid: 'https://orcid.org/0000-0003-4897-1669'
  - given-names: Laura
    family-names: Brenskelle
    orcid: 'https://orcid.org/0000-0002-9284-8871'
  - given-names: Mimi
    orcid: 'https://orcid.org/0000-0002-4026-1390'
    family-names: Diorio
repository-code: 'https://github.com/NOAA-GIS4Ocean/H3_indicators/'
url: 'https://noaa-gis4ocean.github.io/H3_indicators/'
abstract: >-
  Notebooks and documentation about computing H3
  biodiversity indicators.
keywords:
  - H3
  - biodiversity
  - OBIS
  - IOOS
  - NMS
license: CC0-1.0
version: v0.6
date-released: '2025-03-31'

GitHub Events

Total
  • Create event: 4
  • Release event: 2
  • Issues event: 6
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 5
  • Push event: 11
  • Pull request event: 11
Last Year
  • Create event: 4
  • Release event: 2
  • Issues event: 6
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 5
  • Push event: 11
  • Pull request event: 11

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 4
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.25
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.25
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MathewBiddle (8)
Pull Request Authors
  • MathewBiddle (11)
Top Labels
Issue Labels
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Dependencies

.github/workflows/website_create_and_deploy.yml actions
  • JamesIves/github-pages-deploy-action v4 composite
  • actions/checkout v4 composite
  • mamba-org/setup-micromamba v1 composite
DESCRIPTION cran
  • R >= 4.1.1 depends
  • dplyr * imports
  • ggplot2 * imports
  • gsl * imports
  • h3 * imports
  • jsonlite * imports
  • rgdal * imports
  • sf * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
environment.yml conda
  • dask
  • dask-geopandas
  • fastparquet
  • geojson
  • geopandas >=0.13.2
  • h3
  • h3-py 3.7.7.*
  • h3pandas
  • ipykernel
  • pandas
  • pyarrow
  • python 3.12.*