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coralreef_stressorinteractions

https://github.com/secanno/coralreef_stressorinteractions

Science Score: 54.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: secanno
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 93.8 KB
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  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme Citation

README.md

Coral Reef Stressor Interactions

Data and R code for a manuscript currently in review that investigates interactions between local human disturbance and past exposure to heat stress in the central Pacific Islands.

Included in this repository are:

  • Raw data (includes the percent cover data by taxa and environmental variables; data.RData):

  1. data_coral contains the relative abundance for all coral taxa

  2. data_cover contains the relative abundance for all benthic taxa and categories

  3. data_env contains all environmental variables

  4. data_ma contains the relative abundance for all macroalgae taxa

  • R scripts for analyses:

  1. 1envirovarscorrelation.R: estimating the correlation of environmental variables.

  2. 2_HCPC.R: Hierarchical Clustering on Principle Components. This analysis uses the first three principal components of a scaled PCA that includes 99% of the benthic taxa in the dataset.

  3. 3_BIOENV.R: Analysis to identify environmental variables that have maximum correlation with community dissimilarities.

  4. 4_PERMANOVA.R: Permutational Analysis of Variance to estimate amount that variables of interest contribute to differences in (1) all benthic cover, (2) live coral percent cover, and (3) macroalgae percent cover.

  5. 5_LinearRegressions.R: Linear regressions of key taxa and functional groups by cvSST, NDVI, and the interaction between cvSST and NDVI. Loops through a list of taxa and outputs regression results and diagnostic plots.

  6. 6_TobitRegressions.R: Left-censored tobit regression models of key taxa and functional group by cvSST, NDVI, and the interaction between cvSST and NDVI. Loops through a list of taxa and outputs regression results.

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: Coral Reef Stressor Interactions
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Sara Cannon
    name-particle: Sara
    family-names: Cannon
    email: s.cannon@oceans.ubc.ca
    affiliation: University of British Columbia
    orcid: 'https://orcid.org/0000-0002-1402-6370'
identifiers:
  - type: doi
    value: 10.5281/zenodo.7114574
repository-code: >-
  https://github.com/secanno/coralreef_stressorinteractions
keywords:
  - coral reefs
  - stressor interactions
  - ecology
  - climate change
version: v1.0.0
date-released: '2022-09-26'

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