Simulation study comparing length of time series

This repository contains all the scripts and data used in the simulation study titled “Simulation study comparing length of time series”, presented in the manuscript “Longer time series with missing data improve parameter estimation in State-Space mode in coral reef fish communities”. There are 108 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.R: Simulates communities of 20 species across 41 reefs. We used this script to generate 20 simulated communities, which were saved as sim_s1.RData through sim_s20.RData.Model fitting to simulated datafit_11y.R: Script to implement the Short 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_s1.RData and the output fit_11y_s1.RData. We include all fit output files up to fit_11y_s20.RData. We did not include the diagnostics figures in this repository, but users can get them by running the code.fit_18y.R: Script to implement the Intermediate fit from the main text. It follows the same process as above. Output files range from fit_18y_s1.RData up to fit_18y_s20.RDatafit_25yNA.R: Script to implement the Missing-data fit from the main text. It follows the same process as above. Output files range from fit_25yNA_s1.RData up to fit_25yNA_s20.RDatafit_25yc.R: Script to implement the Full fit from the main text. It follows the same process as above. Output files range from fit_25yc_s1.RData up to fit_25yc_s20.RDataStan modelMARPLN_LV.stan: Stan code for the multivariate autoregressive Poisson-Lognormal model with the latent variables. This model is used in the files fit_11y.R, fit_18y.R and fit_25yc.RMARPLN_LV_withNA.stan: Same as the model above, but it can also handle missing data. This model is used in the file fit_25yNA.R.Figure and analysis scriptFigure 2.R: This script calculates the accuracy and precision estimates for all key parameters across simulations and generates Figure 2 from the manuscript.