Package epispot
epispot v3
A Python package for the mathematical modeling of infectious diseases via compartmental models. Originally designed for epidemiologists, epispot can be adapted for almost any type of modeling scenario.
Features
The epispot package currently only supports compartmental models, though we plan to expand the package to work for stochastic agent-based and spatial models as well. Currently, epispot offers the following:
- Quick compilation of compartmental models with the following compartments:
- Susceptible
- Infected
- Recovered
- Removed
- Exposed
- Dead
- Critical
- Hospitalized
- Custom-defined compartments for research
- Built-in graphing and visualization engine
- Plots model predictions interactively
- Creates comparisons between models
Due to its diverse range of features, epispot can be used for both research and experimental modeling. If you would like to add more modeling support, please see the contributing section.
Installation
Notice: The epispot nightly package is now officially deprecated.
The epispot package can be installed from PyPI, Anaconda, or be built from the source. Below are the steps for each installation process:
PyPI
This is the easiest way to install epispot. From a terminal, enter:
pip install epispot
Anaconda
The standard version of epispot is published to conda
using the conda-forge
channel. To install, please use:
conda config --add channels conda-forge
conda install -c conda-forge epispot
Building from the source
This is the hardest way to install epispot and it is recommended that you use either PyPI or Anaconda to install it instead. However, if you would like to contribute to the repository, this will be particularly useful.
Clone the repository and install the dependencies with:
git clone https://github.com/epispot/epispot
cd epispot
pip install -r requirements.txt
pip install -r bin/requirements.txt
Then, build the latest version with:
python setup.py install
For older releases, first checkout a version tag before installing; e.g.:
git checkout v2.1.1
python setup.py install
Quick Demo
Using epispot in a Python REPL to create the well-known SIR model (in less than three lines of code):
Documentation
Right now, documentation for some of the latest releases is quite shaky. The official docs are located at https://epispot.github.io/epispot/ but may be incomplete in many areas.
Examples
The GitHub repository has a vast array of samples using epispot. We are currently working on a tutorial, but for now the documentation is the best place to start.
Badges
Feedback
If you have any feedback, please
- Create a discussion on GitHub
- Create an issue if you've found a bug
- Submit a PR if you want to add a new feature
- Contact a CODEOWNER
Contributing
Contributions are always welcome! See CONTRIBUTING.md for instructions on how to get started, including environment setup and instructions to build from the source. Please note also that epispot has many guides dedicated to certain types of contributions. Please see
- DOCUMENTATION.md for documentation additions
- SECURITY.md for epispot's security policy
Citation
If you plan on using epispot in your project, please abide by the GPLv3 license. This requires that any changes you make to epispot are open-sourced under the GPLv3 license as well and that you give credit to the author, which you can do by citing the project in your research, linking back to the original repository, or mentioning the author @quantum9innovation.
For research, you can also use epispot's DOI to reference the project:
The recommended citation for epispot is:
quantum9innovation (2022, August 20). epispot/epispot: (Version 3.0.0-rc-1). Zenodo. http://doi.org/10.5281/zenodo.5136721
Related Work
There are many related projects to epispot, although we believe that epispot has greater extensibility than many of these other projects. Additionally, epispot is quite portable (graphs can be used as web components, displayed as images, etc.). However, below we would like to acknowledge a few projects that may be better suited to certain use cases:
- EpiJS by @Quantalabs contains the same functionality of epispot but in pure JavaScript, making it more suitable for use in a web browser
- covasim by the Institute for Disease Modeling offers agent-based stochastic models as opposed to epispot's compartmental modeling structure
- CovsirPhy by @lisphilar offers greater support for loading and analyzing real COVID-19 data instead of running simulations
Authors
Please see our CODEOWNERS file for authors. Because epispot is an open-source project, different pieces of our code have different authors. However, if citing epispot or using it in another project, you can cite @quantum9innovation as the lead author.
Acknowledgements
Idea & Inspiration
The original idea for epispot came from a 3Blue1Brown video on basic infectious disease dynamics and an interactive article in the Washington Post. This in turn inspired the very basic infectious disease dynamics simulated here. However, what finally set the package into motion was a series of articles by Henry Froese, available on Medium here, along with their corresponding interactive notebooks.
Code Development & Maintenance
The epispot project is built on open source code and is itself open-source. The initial core development was fueled by @quantum9innovation and much of the codebase was maintained by @Quantalabs. Additionally, thank you to all of epispot's open-source contributors!
Expand source code
"""
.. include:: ../README.md
<!--
Documentation available at:
https://epispot.github.io/epispot/en/v3.0.0-rc-1
-->
"""
def dependency_check():
"""Checks dependencies"""
try:
import numpy
except ImportError: # pragma: no cover
raise ImportError('In order to integrate `epispot` models, '
'`numpy` is a required dependency.\n'
'Install with either:\n'
' $ pip install epispot\n'
' $ conda install epispot')
try:
import matplotlib # lgtm [py/import-and-import-from]
except ImportError: # pragma: no cover
raise ImportError('In order to display plots, `matplotlib` is '
'a required dependency.\n'
'Install with either:\n'
' $ pip install matplotlib\n'
' $ conda install matplotlib')
# imports
import random
import warnings
# dependencies
import dill
import numpy as np
from matplotlib import colors
from matplotlib import pyplot as plt
# helper funcs
def _check_versions():
"""Checks for version conflicts"""
pass
def _check_install(): # pragma: no cover
"""Checks for installation errors"""
raise RuntimeError(
'It seems that this installation of epispot '
+ 'may have been corrupted.\n'
+ 'Please check for the latest version of epispot listed here:\n'
+ 'https://pypi.org/project/epispot/\n'
)
def _check_updates():
"""Checks for updates"""
pass
# global funcs
def sanity_check():
"""
Sanity check to check for basic installation errors,
version conflicts, upgrades, etc.
**Run this if you experience any problems with epispot and before
submitting any issues**
"""
# check for installation errors
if not source or not version: # pragma: no cover
_check_install()
# check for version conflicts
import sys
if (sys.version_info[0] < 3) or \
(sys.version_info[0] == 3 and sys.version_info[1] < 7):
raise RuntimeError(
'epispot requires Python 3.7 or later'
) # pragma: no cover
_check_versions()
# check for updates
_check_updates()
def cite(bibtex=False):
"""
Returns the citation string for the package.
Use `bibtex=True` to return the BibTeX-formatted citation.
"""
if bibtex:
return '''@software{q9i_2022_5136721,
author = {quantum9innovation},
title = {epispot/epispot:},
month = aug,
year = 2022,
publisher = {Zenodo},
version = {3.0.0-rc-1},
doi = {10.5281/zenodo.5136721},
url = {https://doi.org/10.5281/zenodo.5136721}
}'''
else:
return 'quantum9innovation (2022, August 20). epispot/epispot: (Version 3.0.0-rc-1). Zenodo. <http://doi.org/10.5281/zenodo.5136721>'
# version info
version = '3.0.0-rc-1'
"""
epispot's version info (updated every release)\n
Check version information with:
```
>>> print(epispot.version)
```
Version information is also available through the `__version__`
property, included for legacy support.
"""
__version__ = version # alias for version
stable = True
"""
Build stability:
- True ⇒ main package (stable)
- False ⇒ nightly (unreleased) package (possibly unstable)
"""
# local
from . import analysis, comps, estimates, models, params, plots, pre
# metadata
source = 'https://www.github.com/epispot/epispot'
"""URL to VCS source"""
raw = f'https://raw.githubusercontent.com/epispot/epispot/v{version}/'
"""URL to raw VCS source (must append file path)"""
docs = f'https://epispot.github.io/epispot/en/v{version}/'
"""Project documentation (version-specific)"""
issues = 'https://www.github.com/epispot/epispot/issues'
"""Bug tracker"""
citation = cite()
"""Static citation string"""
Sub-modules
epispot.analysis
-
The analysis sub-package contains various utilities for forecasting and processing real-time epidemiological data …
epispot.comps
-
The
epispot.comps
module is a collection of compartments used to initialize theModel
object to create a compartmental model. Each of these … epispot.estimates
-
This sub-package contains various estimates from the literature to be used in conjunction with epispot's models …
epispot.models
-
The
epispot.models
classes store different types of epidemiological models in a compact form useful for integration. Models can be differentiated, … epispot.params
-
The
epispot.params
module stores various parameter distributions and estimations. These parameter distributions are divided into two classes: those … epispot.plots
-
This sub-package is responsible for plotting epispot models of the
Model
class. This is done independently of any other modules and … epispot.pre
-
This module (short for 'pre-compiled') contains models that have already been compiled and can be put to use immediately. Each function returns an …
Global variables
var citation
-
Static citation string
var docs
-
Project documentation (version-specific)
var issues
-
Bug tracker
var raw
-
URL to raw VCS source (must append file path)
var source
-
URL to VCS source
var stable
-
Build stability:
- True ⇒ main package (stable)
- False ⇒ nightly (unreleased) package (possibly unstable)
var version
-
epispot's version info (updated every release)
Check version information with:
>>> print(epispot.version)
Version information is also available through the
__version__
property, included for legacy support.
Functions
def cite(bibtex=False)
-
Returns the citation string for the package. Use
bibtex=True
to return the BibTeX-formatted citation.Expand source code
def cite(bibtex=False): """ Returns the citation string for the package. Use `bibtex=True` to return the BibTeX-formatted citation. """ if bibtex: return '''@software{q9i_2022_5136721, author = {quantum9innovation}, title = {epispot/epispot:}, month = aug, year = 2022, publisher = {Zenodo}, version = {3.0.0-rc-1}, doi = {10.5281/zenodo.5136721}, url = {https://doi.org/10.5281/zenodo.5136721} }''' else: return 'quantum9innovation (2022, August 20). epispot/epispot: (Version 3.0.0-rc-1). Zenodo. <http://doi.org/10.5281/zenodo.5136721>'
def dependency_check()
-
Checks dependencies
Expand source code
def dependency_check(): """Checks dependencies""" try: import numpy except ImportError: # pragma: no cover raise ImportError('In order to integrate `epispot` models, ' '`numpy` is a required dependency.\n' 'Install with either:\n' ' $ pip install epispot\n' ' $ conda install epispot') try: import matplotlib # lgtm [py/import-and-import-from] except ImportError: # pragma: no cover raise ImportError('In order to display plots, `matplotlib` is ' 'a required dependency.\n' 'Install with either:\n' ' $ pip install matplotlib\n' ' $ conda install matplotlib')
def sanity_check()
-
Sanity check to check for basic installation errors, version conflicts, upgrades, etc.
Run this if you experience any problems with epispot and before submitting any issues
Expand source code
def sanity_check(): """ Sanity check to check for basic installation errors, version conflicts, upgrades, etc. **Run this if you experience any problems with epispot and before submitting any issues** """ # check for installation errors if not source or not version: # pragma: no cover _check_install() # check for version conflicts import sys if (sys.version_info[0] < 3) or \ (sys.version_info[0] == 3 and sys.version_info[1] < 7): raise RuntimeError( 'epispot requires Python 3.7 or later' ) # pragma: no cover _check_versions() # check for updates _check_updates()