This project models the functional consequences of range-shifting tropical fish and performs analyses for the accompanying paper: Temperate functional niche availability not resident-invader competition shapes tropicalisation in reef fishes, authored by Mark Miller, James Reimer, Katie Cook, John M. Pandolfi, Brigitte Sommer, Masami Obuchi and Maria Beger.
fish_trait_master.R handles formatting and updates from the global tropical fish trait database (M Beger)
fish_sites_master.R handles survey data from Japan and Australia: summarising and correcting biomass (then clustering sites based on species biomass); running species accumulation curves and estimating species richness
optimal_clusters.R explores optimal clustering solution of trait data calling clVal.R function
clVal.R performs cluster validation based on n iteration bootstrapping (set at 95% subsample) of trait dendrogram, selection of optimal clusters based on average silhouette width, Jaccard stability index and Rand matching index
code.R performs step by step analyses to recreate results and figues in the accompanying paper