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Data and R code accompanying:

Tipping points and interactive effects of chronic human disturbance and acute heat stress on coral diversity

Authors: Dominique G. Maucieri, Samuel Starko and Julia K. Baum

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Scripts Folder

• Alpha_Diversity.Rmd: Script used to:

  • Conduct alpha diversity analyses
  • Figures 4a-c and S2-6
  • Table 1, S1, and S3-5
  • Alpha_Diversity.html: HTML file containing the output of Alpha_Diversity.Rmd

• Beta_Diversity.Rmd: Script used to:

  • Conduct beta diversity analyses
  • Figure 3, 4d and S7
  • Beta_Diversity.html: HTML file containing the output of Beta_Diversity.Rmd

Data Folder

• Alpha_Diversity.RData contains:

  • Alpha_Diversity_df.csv: Raw coral cover data from Kiritimati island from sites used in alpha diversity analyses
    • UniqueID: Unique identification for each quadrat at each site in each year sampled
    • Year: Year that the data was collected
    • Site: Site number
    • Quadrat: Quadrat ID
    • SiteYear: Site year combination ID
    • HD_Cat: Estimate of local human disturbance at each site as a categorical variable
    • HD_Cont: Estimate of local human disturbance at each site as a continuous variable
    • NPP: Max net primary productivity at each site (mg C m^-2 day^-1)
    • MHW: If the sampling season was before, during or after the El Niño event
    • Acropora.spp: Coral cover (%) for Acropora spp
    • Astrea.spp: Coral cover (%) for Astrea spp
    • Astreopora.spp: Coral cover (%) for Astreopora spp
    • Cladiella.spp: Coral cover (%) for Cladiella spp
    • Dipsastraea.spp: Coral cover (%) for Dipsastraea spp
    • Favites.spp: Coral cover (%) for Favites spp
    • Fungiidae: Coral cover (%) for Fungiidae
    • Gardineroseris.planulata: Coral cover (%) for Gardineroseris planulata
    • Goniastrea.edwardsi: Coral cover (%) for Goniastrea edwardsi
    • Goniastrea.stelligera: Coral cover (%) for Goniastrea stelligera
    • Hydnophora.exesa: Coral cover (%) for Hydnophora exesa
    • Hydnophora.microconos: Coral cover (%) for Hydnophora microconos
    • Leptastrea.spp: Coral cover (%) for Leptastrea spp
    • Leptoseris.myceteroides: Coral cover (%) for Leptoseris myceteroides
    • Lobophyllia.spp: Coral cover (%) for Lobophyllia spp
    • Lobophytum.spp: Coral cover (%) for Lobophytum spp
    • Montipora.spp: Coral cover (%) for Montipora spp
    • Pavona.duerdeni: Coral cover (%) for Pavona duerdeni
    • Pavona.varians: Coral cover (%) for Pavona varians
    • Platygyra.spp: Coral cover (%) for Platygyra spp
    • Pocillopora.spp: Coral cover (%) for Pocillopora spp
    • Porites.spp: Coral cover (%) for Porites spp
    • Psammocora.profundacella: Coral cover (%) for Psammocora profundacella
    • Sarcophyton.spp: Coral cover (%) for Sarcophyton spp
    • Sinularia.spp: Coral cover (%) for Sinularia spp
    • Turbinaria.spp: Coral cover (%) for Turbinaria spp
    • Not.Coral: Cover (%) for all non-coral organisms and benthic substrates

• Beta_Diversity.RData contains:

  • Beta_Diversity_df.csv: Raw coral cover data from Kiritimati island from sites used in beta diversity analyses

    • UniqueID: Unique identification for each quadrat at each site in each year sampled
    • Year: Year that the data was collected
    • Site: Site number
    • Quadrat: Quadrat ID
    • SiteYear: Site year combination ID
    • HD_Cat: Estimate of local human disturbance at each site as a categorical variable
    • HD_Cont: Estimate of local human disturbance at each site as a continuous variable
    • NPP: Max net primary productivity at each site (mg C m^-2 day^-1)
    • MHW: If the sampling season was before, during or after the El Niño event
    • Acropora.spp: Coral cover (%) for Acropora spp
    • Astrea.spp: Coral cover (%) for Astrea spp
    • Astreopora.spp: Coral cover (%) for Astreopora spp
    • Cladiella.spp: Coral cover (%) for Cladiella spp
    • Dipsastraea.spp: Coral cover (%) for Dipsastraea spp
    • Favites.spp: Coral cover (%) for Favites spp
    • Fungiidae: Coral cover (%) for Fungiidae
    • Gardineroseris.planulata: Coral cover (%) for Gardineroseris planulata
    • Goniastrea.edwardsi: Coral cover (%) for Goniastrea edwardsi
    • Goniastrea.stelligera: Coral cover (%) for Goniastrea stelligera
    • Hydnophora.exesa: Coral cover (%) for Hydnophora exesa
    • Hydnophora.microconos: Coral cover (%) for Hydnophora microconos
    • Leptastrea.spp: Coral cover (%) for Leptastrea spp
    • Leptoseris.myceteroides: Coral cover (%) for Leptoseris myceteroides
    • Lobophyllia.spp: Coral cover (%) for Lobophyllia spp
    • Lobophytum.spp: Coral cover (%) for Lobophytum spp
    • Montipora.spp: Coral cover (%) for Montipora spp
    • Pavona.duerdeni: Coral cover (%) for Pavona duerdeni
    • Pavona.varians: Coral cover (%) for Pavona varians
    • Platygyra.spp: Coral cover (%) for Platygyra spp
    • Pocillopora.spp: Coral cover (%) for Pocillopora spp
    • Porites.spp: Coral cover (%) for Porites spp
    • Psammocora.profundacella: Coral cover (%) for Psammocora profundacella
    • Sarcophyton.spp: Coral cover (%) for Sarcophyton spp
    • Sinularia.spp: Coral cover (%) for Sinularia spp

  • Least_Cost_Distance.csv: Least cost distances between sites without crossing land

    • start.site: Start site where distance is measured from
    • end.site: End site where the distance is measured to
    • cost: Cost associated with the distance between sites
    • distance_km The distance in km between the sites
    • site_comb The site combination ID

  • quadrats_sampled.csv: Data frame containing all possible quadrats that were randomly sampled to produce the final Beta_Diversity_df.csv

    • UniqueID: Unique identification for each quadrat at each site in each year sampled
    • Year: Year that the data was collected
    • Site: Site number
    • Quadrat: Quadrat ID
    • SiteYear: Site year combination ID
    • MHW: If the sampling season was before, during or after the El Niño event
    • MHW_Site: MHW Site combination ID

  • siteyear_factor: a factor containing the possible site year combination IDs that contain more than 25 quadrats each

Figures and Tables Folder

• Figure 2
• Figure 3
• Figure 4a
• Figure 4b
• Figure 4c
• Figure 4d
• Figure S2
• Figure S3
• Figure S4
• Figure S5
• Figure S6
• Figure S7
• Table S1
• Table S4