Singapore Trait Diversity Manuscript (SGTraitDiversity)

Analyses for coral metric trends on Singapore reefs through time.

Please see the following paper for details.

Chan et al. 2024 Decadal decline of functional diversity despite increasing taxonomic and phylogenetic diversity of coral reefs under chronic urbanisation stress. Ecological Indicators 164, 112143. https://doi.org/10.1016/j.ecolind.2024.112143

Data sources

database

Original data files before processing

RSTBtree.tre, Genus.tre

Species-level phylogenetic tree for all coral species, and same tree trimmed to genus level from https://doi.org/10.1098/rstb.2014.0010

fulltraits.csv

Full traits list downloaded from https://coraltraits.org/

genera.t.csv, modgenera.t.csv, species.t.csv

Genera, modern genera and species level transect data

rdbspecieslist.csv

Singapore Red Data Book species list from https://www.nparks.gov.sg/biodiversity/wildlife-in-singapore/species-list/cnidaria-(scleractinia)---stony-corals

database processed

Data files after processing for use with analyses

globalspptraits.csv

Processed trait values for all species

sgspptraits.csv

Processed trait values for all Singapore species

sgspptraits_edit.csv

Infilled sgspptraits.csv with measured trait values

Codes

01_Preprocessing.qmd

Preprocessing of data files, mainly for processing traits from the coraltraits database download

02_Processing.qmd

Diversity calculations and compilation for modelling

03_Modelling.qmd

Models for analyses

04_Outputs.qmd

Figures and posteriors from models

05_SupplementaryModels.qmd

Supplementary models and material for supplementary file