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.
EndemicPy, or simply endemic is a python package under development aiming to simulate a vast range of transmission dynamics on various host structure models.
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.
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
The only non-standard python package endemic uses in numpy, so please make sure that you have a recent numpy version installed.
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.
Check out the examples for more information on how EndemicPy is used in different projects.