plectranthus_barbatus

This code reproduces the results and Figures from our article

Botella, C., Bonnet, P., Hui, C., Joly, A., & Richardson, D. M. (2022). Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion. Biology, 11(9), 1293. https://doi.org/10.3390/biology11091293

Guidelines to reproduce:

1. Download data files (data_for_model, data_full, validation_kit, toAnalyse_Validation.Rdata and pre-fitted posterior samples if needed) from our Zenodo repository (V2): https://doi.org/10.5281/zenodo.6921965
2. Download R scripts from this repository in the same folder as the data files.
3. Optional: Run script fit_model.R which will load the data files data_for_model.R and data_full to fit the model on the full data. If you run all chains sequentially as proposed by default in the script, it should take at least a week to be completed. You should obtain exactly the Rdata files samples_pt33_seed1, samples_pt33_seed1_logLik, etc. which are also provided in the Zenodo repository for a quicker reproduction.
4. Run script convergence_check.R which will load all posterior sample files, thin them (and save as "toAnalyse.Rdata"), produce trace plots and compute convergence criterions (see Appendix S3).
5. Run script output_Figures.R which will load all data files, create and save all the Figures of our manuscript as .png files.