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Jupyter notebooks containing python implementations of the models presented in Ch. 6 of 'The Theory of Ecological Communities'

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Ch. 6 Notebooks

This is a collection of python Jupyter notebook implementations of the models described in Vellend's Theory of Ecological Communities in Chapter 6 "Simulating Dynamics"

Using the notebooks

While you can click on them in here, they don't really work. They will render some stuff and give you nice looking formatted code but you won't be able to do anything with them.

The best thing to do is to download them but you will need python and the required packages installed in order to use them.

Installing python

The easiest way to do this if you dont want to use the command line is using Anaconda which is a really great python distribution that comes with a bunch of useful tools. You can find the downloads for Anaconda here. It looks weird and corporate but its all open source and very chill.

If you are interested in using the command-line I'm sure you can figure it out, seeing as you're some kind of technical computer genius.

Installing dependencies

Once Anaconda is installed you will want to make a new conda environment. This is a way of keeping all of your ducks in a row in terms of installing packages. You can use conda environments for R as well, I think.

If you are on windows or don't want to use the command line I recommend using Anaconda's graphical interface to do this.

If you are using mac or linux its really easy to do using the command line. You can also do it all in one step but if you're interested in that you probably already know how this works.

First, open a terminal and make a new environment:

conda create --name vellend_notebooks

Now you have an environment named vellend_notebooks. Let's use it. We can 'go into' that environment with:

conda activate vellend_notebooks

Your terminal should now say (vellend_notebooks) and then some other stuff. Finally, we can install the dependencies with:

conda install numpy matplotlib tqdm jupyter ipywidgets

This will install all of the packages that we need to run these notebooks and everything that they depend on. It will print lots of stuff and ask you to say yes at least once.

Also yes, the numpy core team are assholes.

Opening the notebooks

At this point I think you can just click on them??

I usually do it through the command line by typing:

jupyter notebooks

when I'm in the appropriate conda environment. This will open a browser window with a file browser which you can use to open the notebooks.

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