All data analysis is done using R 4.0.0. The environment can be replicated using a Docker container.
- Build the Docker container from the Dockerfile
- Open up a shell terminal and run
bash docker_build.sh
- Open up a shell terminal and run
- Run the Docker container
- Run
bash docker_rstudio.sh
- Open up a web browser and go to http://localhost:8787 (Linux) or http://{your IP address}:8787 (Mac or Windows)
- Run
- Run R scripts from the
R-Scripts
directory in the order of their name (i.e., 01_data..., 02_analyze..., 03_...)
DISCLAIMER: Geographic breeding range sympatry calculations, Bayesian multilevel regression models, k-fold information criterion model iterations and kfold IC model comparisons can only be done if they are run on a server with sufficient CPU and RAM specs (original run on server with 8 cores and 64Gb of RAM). Results from these computations are saved and can be accessed in the Turdus_Data
and Results
directories.
├── Bash-Scripts
├── Data
│ └── Data_Copy_CSV
├── Figures
│ ├── Figure_Data
│ └── Posterior_Predictive_Fits
├── Phylogenies
├── Results
│ ├── model_kfold_IC
│ └── Model_Posterior_Draws
├── R-Scripts
└── Turdus_Data
├── turdus_birdlife_ranges
├── turdus_birdlife_ranges_gdb
└── turdus_letsR_data