Baum Lab

Gitting-started

Readme for Baum lab: how to set up repos, write R-markdown docs, and collaborate with Git

McPherson_etal_2018_MEE_sim-ecol-communities

Code for McPherson et al. 'A simulation tool to scrutinise the behaviour of functional diversity metrics' (in review)

Claar_etal_2020_SciRep

Data and R code accompanying: Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reef

Chalifour_etal_2019_MEPS

R code accompanying Chalifour et al. Habitat use by juvenile salmon, other migratory fish, and resident fish species underscores the importance of estuarine habitat mosaics

Chalifour_etal_2021_CJFAS

Code accompanying Chalifour et al. 2021. Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, B.C., a large urban estuary. CJFAS

Claar_etal_2020_NatCom

Hertz_etal_2014_MEPS

Code accompanying Hertz, Robinson et al. Estimation of predator-prey mass ratios (2014, Marine Ecology Progress Series)

Magel_etal_2020_EcolApp

Data and R code for: Direct and indirect effects of climate change-amplified pulse heat stress events on coral reef fish communities

Robinson_etal_2017_GlobalChangeBiology

Code accompanying Robinson et al. Fishing degrades size structure of coral reef fish communities (2016, Global Change Biology).

Robinson_etal_2018_CoralReefs

R code accompanying Robinson et al. Environmental conditions and herbivore biomass determine coral reef benthic community composition: implications for quantitative baselines.

Baum_etal_2023_ScienceAdvances

Claar_etal_2018_PLoSOne

Code, data, and figures for Claar et al manuscript "Global patterns and impacts of El Niño events on coral reefs: a meta-analysis." (PLOS ONE)

Magel_etal_2019_SciRep

Data and R code for: Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance

RobinsonBaum_2016_CJFAS

Code accompanying Robinson & Baum (2016, Canadian Journal of Fisheries & Aquatic Sciences)

White_etal_2015_ConsBiol

This repository contains code and additional figures for work on Cocos Island

DunicBaum_2017_JAnimEcol

gya-research

GYA fundamental research - survey response

Iacarella_etal_2018_GlobalChangeBiology

R scripts for beta-diversity analysis

open-science-project

Ideas, data, R scripts, figures, and writing for Baum lab #OpenDerby

Osgood_etal_2019_PLOSOne

Data and code for Osgood et al. 2019 PLOS One

Osgood_etal_2020_AfrMarSci

Data and R code accompanying: Chondrichthyans as an umbrella species-complex for conserving South African biodiversity

Osgood_etal_2021_JAE

Data and R code for: Effects of climate-change driven gradual and acute temperature changes on shark and ray species

Sean_Fish_Acoustics17-18

All data related to Sean's acoustics chapter of his Masters thesis

Starko_et_al_Porites_KI

Code and data associated with Starko et al. (2023): Marine heawaves threaten cryptic coral diversity and erode associations amongst coevolving partners.

BarkleySound_CanopyKelp

Data and code associated with Starko et al. 2022. Ecological Applications.

Claar_etal_2020_MolecEcol

Maucieri_Baum_2021_BioCon

Data and R code for: Impacts of heat stress on soft corals, an overlooked and highly vulnerable component of coral reef ecosystems, at a central equatorial Pacific atoll

Maucieri_etal_2023_ProcRoyB

Data and R code for: Tipping points and interactive effects of chronic human disturbance and acute heat stress on coral diversity

McDevittIrwin_etal_2019_CoralReefs

This is the repository for McDevitt-Irwin et al. 2019 in Coral Reefs

WestGridIntro

This repository serves as a learning space for Baum lab members wishing to learn about using WestGrid for data storage, and advanced computation.