t4d-gmbh/endemicpy

Python package to simulate a vast range of transmission processes on various structures

EndemicPy

NOTE: This is a rather old package and was written for python 2.x.

A python 3 version is pending. Let me know if you would like to contribute to the happening of this.

Transmission dynamics in various structures

EndemicPy, or simply endemic is a python package under development aiming to simulate a vast range of transmission dynamics on various host structure models.

How to use endemic

endemic can either be installed or one can simply copy the endemic folder into the same folder as the python script that is using the package. If you decide to simply copy the folder, you can ignore the installation step below.

Versions

endemic has different releases that were (and are) developed for various projects.

You need to use the correct release for the type of simulations you plan to do. Using the wrong version might result in errors or incoherent output.

If you are using EndemicPy for your own work, please make sure that you correctly refer to this package and to the research article related to the specific release you are using.

To learn which release is the right one for you, here is a list of the published projects along with the used release:

• v0.1.0 for Short-term activity cycles impede information transmission in ant colonies

• v0.3.0 for Host population structure impedes reversion to drug sensitivity after discontinuation of treatment

Dependencies

The only non-standard python package endemic uses in numpy, so please make sure that you have a recent numpy version installed.

Installation

To install the package you might want to setup a virtualenv which is not a requirement but a recommendation. To install the package, simply open a console, cd into the EndemicPy folder and type:

python setup.py install

If everything works fine, you can now simply import endemic as a package in your python scripts.

Examples

Check out the examples for more information on how EndemicPy is used in different projects.

endemicpy's Issues

Hello @j-i-l! Thanks for opening this PR. We checked the lines you've touched for [PEP 8](https://www.python.org/dev/peps/pep-0008) issues, and found:

Hello @j-i-l! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file endemic/nw_spread/Spreading.py:

Line 63:80: E501 line too long (82 > 79 characters)

Originally posted by @pep8speaks in #6 (comment)

Get the current master from alt. remote

Migrate uncurrated reversion branch

What is the version used in the publication 'Host population structure impedes reversion to ...'?

I've been reading this article and wanted to have a closer look at the software package used.
I'm not sure which his the tag used in the paper.

Could you point me to the correct version?