Getting Started
The tutorials on this site provide all the source code necessary to follow along in your own Jupyter Notebook.
Notebook Tutorials¶
If you prefer to download the full tutorials as Jupyter Notebooks, they are available here. There is a detailed notebook for each 'step' of using shadie and an example full workflow.
You must have Jupyter Notebooks and shadie installed locally to use these notebooks. You must also install SLiM 4 to access all the functionality in the notebooks.
binder Tutorials¶
Finally, if you do not have Jupyter on your machine, you are able to run the notebooks in your web broswer using binder. This is a great way to use shadie for teaching applications, with students that do not need to learn how to Jupyter or run SLiM themselves. However, keep in mind that any changes made in binder cannot be saved for later use.
Note: the notebooks hosted by binder will be able to perform most of the functionality of shadie, but memory limitations make it difficult to run anything but the simplest SLiM simulations.
.trees files are provided in the trees files folder on GitHub to allow you to use the post-sim module of shadie without having to run simulations in SLiM.