This directory contains the code, analyses, case study results and manuscript for the joint model framework presented in the Bimler et. al 2023 Methods in Ecology and Evolution paper Estimating interaction strengths for diverse horizontal systems using performance data (https://doi.org/10.1111/2041-210X.14068).
A previous version of this manuscript which runs on a single Markov chain and with slightly different parameterisation is also available on bioRxiv: https://www.biorxiv.org/content/10.1101/2022.03.28.486154v1
1.code - scripts and functions to run the joint model framework
2.case_study - data, specific functions, scripts and model output from the joint model framework applied to our case study
3.analyses - analyses and figures from the case study
4.mss - associated manuscript
If you would like to apply the joint model framework to your own dataset, everything you need should be in the ~/1.code folder, along with another README. The remaining three folders are specific to the case study and associated manuscript, and are made available in the interest of open access and reproducibility.
I have tried to provide as detailed comments as possible throughout the code, if anything remains unclear please refer first to the manuscript and supps for this project. If those are of no help, you can either contact me here or by email (malyon.bimler@unimelb.edu.au).