README.md

In dsidavis/SpilloverDA: Munging and Exploring the Viral Spillover Data Set

Spillover Data Analysis Package

This is a collection of scripts for munging the spillover data set, cleaning the columns that we are interested in for the data analysis, and then creating plots from these data.

This also contains code for extracting information from PDF documents, currently using a modified/forked version of EcoHealth Alliance's epitator Python module.

Getting the EpiTator

Our forked version of Epitator is at github.com:dsidavis/EpiTator and can be cloned via

git clone [e-mail]:dsidavis/EpiTator.git

Installing EpiTator (and epitator)

First, you need python3 installed centrally on your machine. Check by running the shell command

python3

If this does not work, check if the command python gives you a python3 version. a) Just run python and look at the first line of the output

python
Python 2.7.5 (default, Aug  4 2017, 00:39:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 

OR, b)

python --version
Python 2.7.5

If this is python 2, install python3. Ask a system administrator or install yourself centrally. Alternatively, you can install this in your own working local directory, separately from everybody. It may be simplest to instal from source rather than a package manager. YMMV.

With python3 installed, install the required python modules that epitator needs. The best thing to do is to create a virtual environment so that these will be installed locally into your own directory and you can easily remove and/or update. Just a good thing.

virtualenv --python=python3 MyPyEnv

This creates MyPyEnv in the current directory. You can do this anywhere.

Activate or turn-on this virtual environment with

source MyPyEnv/bin/activate

This assumes you are running the bash shell. If not, run it - just issue the command bash.

Now we install the epitator required modules. To do this, change directory to the EpiTator directory and issue the command

cd EpiTator
pip3 install -r requirements.txt

We will not verify that the modules are in this virtual environment

python3

and run the python commands

import inspect
import lazy
print(inspect.getsourcefile(lazy))

Now, we can also install the epitator code into this virtual environment,

python3 setup.py install

Again, we can check the epitator modules were installed there.

python3

import inspect
import epitator.version
print(inspect.getsourcefile(epitator.version))

If you are likely to be changing any of the epitator code, it probably makes more sense to not install it explicitly but to leave here in the EpiTator directory. Then we tell python3 to find that code by setting the environment variable PYTHONPATH

The set the environment variable PYTHONPATH to the top-level director EpiTator in which are currently located, i.e.

export PYTHONPATH=`pwd`

Left over - same idea from earlier.

Alternatively, install the module using

python3 setup.py install

Using PYTHONPATH allows us to a) not install in a centralized directory for which we do not have write permissions, and b) also have different local versions of EpiTator that we can switch between very easily.

To use the epitator code, we use Python3. Using pip3, install all the required python modules

pip3 install -r requirements.txt 

or with

sudo -H pip3 install -r requirements.txt 

dsidavis/SpilloverDA documentation built on June 1, 2019, 2:55 p.m.