This subdirectory contains a SLiM recipe for simulating the invasion and expansion of Cane Toads into Australia.
In addition to the recipe,
we have included all the necessary code needed to download inputs
(observed distributions, shape files, bioclim, etc.)
and to analyze outputs.
Please be sure to create the conda environment and use for downstream steps.
mamba env create -f pipelines/spatial_sims.yml
mamba activate spatial_sims
The required inputs are already included in this repository,
but for completeness, can be downloaded again using snakemake with
cd pipelines/
snakemake --snakefile get_data.smk -c 1
Downstream analyses are computed in a jupyter notebook, notebooks/gbif_toads.ipynb,
which includes commands used to run the SLiM recipe with and without the environment’s impact on fitness.
The code is generally the same as what was used in the manuscript,
but we have reduced local carrying capacity (K) to speed things up.
The overall final distributions are similar to the scaled-up versions.
The format of code has been slightly modified to match the conventions used in the rest of this repository.
SLiM recipe for range expansion case study can be found in
recipes/CaneToads_RangeExpansion_Environment_Australia.slim