Simulation study with abundance trends

This repository contains all the scripts and data used in the simulation study titled “Simulation study with abundance trends”, presented in the manuscript “Longer time series with missing data improve parameter estimation in State-Space mode in coral reef fish communities”. There are 66 files in total.All model fits were run on the HPC cluster at James Cook University. Depending on the simulated dataset, run times ranged from several hours up to 1-2 days per fit.Simulated datamultisp_sim_dat_dec.R: Simulates communities of 20 species across 41 reefs. We used this script to generate 20 simulated communities, which were saved as sim_dec_s1.RData through sim_dec_s20.RData.Model fitting to simulated datafit_fixed_a.R: Script to implement the Fixed a model fit from the manuscript. For each simulated dataset, it: 1) saves posterior model parameters, 2) computes diagnostics (divergent transitions, tree depth saturation, E-BFMI), and 3) generates effective sample size (ESS) and R-hat plots. Example output: input simulated dataset sim_dec_s1.RData and the output fit_fixed_a_s1.RData. We include all fit output files up to fit_fixed_a_s20.RData. We did not include the diagnostic figures in this repository, but users can get them by running the code.fit_change_a.R: Script to implement the Changing a model fit from the manuscript. It follows the same process as above. Output files range from fit_chang_a_s1.RData up to fit_chang_a_s20.RData.Stan modelmodel_fixed_a.stan: Stan code for the multivariate autoregressive Poisson-Lognormal model with the latent variables. This model is used in the file fit_fixed_a.Rmodel_chang_a.stan: Same as the model above, but it this model assumes that the intrinsic population growth parameter is a linear function of time. This model is used in the file fit_change_a.R.Figure and analysis scriptFigure S14 and S15.R: This script calculates the accuracy and precision estimates for all key parameters across simulations and generates Figures S14 and S15 from the supplementary materials.