Simulation Study

This repository contains the all the scripts to simulate the data, the model fitting to the simulated data and the Stan code to implement the simulation study in the manuscript “High response diversity and conspecific density-dependence, not species interactions, drive dynamics of coral reef fish communities”. There are 20 files in total. We ran the model fits on the HPC at James Cook University.Simulated dataSim_data_cov.R: Simulates the data from the Correlated responses to environmental fluctuations scenario in appendix 6. It stores the simulated data in this scenario as simDat_cov.RData.Sim_data_full.R: Simulates the data from the Both scenario in appendix 6. It stores the simulated data in this scenario as simDat_full.RData.Sim_data_inter.R: Simulates the data from the Between species interactions scenario in appendix 6. It stores the simulated data in this scenario as simDat_inter.RData.Sim_data_simple.R: Simulates the data from the Baseline scenario in appendix 6. It stores the simulated data in this scenario as simDat_simple.RData.Model fitting to simulated datafit_covD2.R, fit_covD4.R, fit_covD6.R, fit_covD8.R, fit_covD10.R and fit_covD12.R fit the model with 2, 4,6, 8, 10 and 12 latent variables, respectively, to the simulated data in the Correlated responses to environmental fluctuations scenario.fit_full.R fit the model to the simulated data in the Both scenario.fit_inter_p0_10.R, fit_inter_p0_50.R and fit_inter_p0_100.R fit the model with p0 (prior guess in the number of non-zero interspecific interactions) equals to 10, 50 and 100, respectively, to the simulated data in the Between species interactions scenario.fit_simple.R fit the model to the simulated data in the Baseline scenario.Stan modelMARPLN_RHS_LV.stan: Stan script for the multivariate autoregressive Poissson-Lognormal model with the regularised horseshoe prior and latent variables. This model does not include the Pomacentrid parameterization as the simulated species abundances do not differ in sampling area as in the LTMP data in the main text.