Update: Epipy is coming right along! I've added multiple plot types, and a few functions for epip analyses. You can learn more at cmrivers.github.io/epipy, or browse the code at github.com/cmrivers/epipy.
I'm excited to share a new side project I've been working on - epipy, a python package for epidemiology.
The package right now primarily consists of a new(ish)* way to visualize clusters of disease and other contagions. I think the case tree plot, as I'm calling it, is particularly useful for zoonoses like MERS CoV. The nodes at generation zero represent cases with no known contact with other cases, which suggests that the infection may have been contracted from an animal. Nodes at generations 1+ have a link with the index node, suggesting human to human transmission. In the above plot the node color represents membership to a cluster. However, node color can be changed to represent health status, patient sex, or any other case attributes.
I think the case tree plot is useful for a few reasons. In the case of a zoonosis you can get a sense for how many times the disease may have spilled over from animals to humans. You can also get a feel of how human to human transmissible the contagion is. Finally, it's possible to see patterns in case severity (or whatever you choose to represent with node color) either over time, or for secondary cases vs index cases, etc.
Why am I sharing this obviously unpolished package now? Because I want you to contribute! What I've developed so far could benefit immensely from more skilled coders, and I think there's a lot more that could be added. I haven't found any good epidemiology packages for python like exist for R, and I think there's a big gap in the open source market there - so feel free to contribute brand new functions as you see fit. Even if you aren't an ace pythonista, I'd still greatly welcome your participation. I'm a novice coder in many ways myself, so the more the merrier. The code is available at github, and I am available on twitter @cmyeaton.
*I have found one other example of a similar plot in the literature. If you know of any more, please do let me know!
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