epipack - v0.1.7

Added

• it's possible to set explicit time dependence of rates now when starting a simulation

Fixed

• changed references to deprecated classes in examples and docstrings
• better handling of detecting explicit time-dependence in functional rates.

Scientific Software - Peer-reviewed - Python
Published by benmaier about 4 years ago

epipack - v0.1.6

Changed

• renamed a parameter in StochasticEpiModel.simulate to stop_simulation_on_vanishing_total_event_rate, because it describes the mechanism better (adjusted TemporalNetwork) accordingly

Fixed

• Disallowing resizing a visualization app on Linux OSes to avoid a recursion error
• metadata such as epipack.__version__ is now correctly given out

Added

• a SymbolicSEIRModel
• a routine to generate random geometric graphs
• the possiblity to add a callback function in StochasticEpiModel.simulate such that event tracking is possible

Scientific Software - Peer-reviewed - Python
Published by benmaier over 4 years ago

epipack - v0.1.5

Added

• methods to the IntegratorMixin class that allow integration until a stop condition is reached

Fixed

• specified for MatrixEpiModel that the leading eigenvalue of a Jacobian should be measured by largest real part
• specified for MatrixEpiModel that the leading eigenvalue of the next generation matrix should be measured by largest magnitude (because R is the matrix's spectral radius)
• in StochasticEpiModel, convert rate values to float by default

Scientific Software - Peer-reviewed - Python
Published by benmaier over 4 years ago

epipack - v0.1.4

Added

• A new small-world network styling method based on 1d lattice distance (in epipack.networks)
• methods to compute Jacobian and next generation matrices (NGMs) in MatrixEpiModel, as well as R0 from said NGMs (TODO: add docs)
• tests for these methods
• epipack.distributions module, which deals with fitting empirical distributions to sums of exponentially distributed random variables (still in dev mode, also TODO: add docs)
• tests for this module
• methods to EpiModel that save events that have been set. This will be used to generate model flowcharts with graphviz at some point
• the possibility to pass a function to StochasticEpiModel.simulate that checks for a custom stop condition

Scientific Software - Peer-reviewed - Python
Published by benmaier over 4 years ago

epipack - v0.1.3

• fixed dependency issues with pyglet, apparently the "shapes" module did not appear until lately. Defined a range of versions for pyglet
• fixed bug in example code in README.md

Scientific Software - Peer-reviewed - Python
Published by benmaier over 4 years ago

epipack - v0.1.2

1. paper review at JOSS done (https://github.com/openjournals/joss-reviews/issues/3097)
2. fixed bug where the reset_events flag was ignored in EpiModel.set_processes()

Scientific Software - Peer-reviewed - Python
Published by benmaier almost 5 years ago

epipack - v0.1.1

Added

• GeneralInteractiveWidget was added to allow interactive display of general functions
• a very basic SDE integrator was added (no diffusion coefficent matrix, and no system-dependent diffusion coefficients)

Changed

• InteractiveIntegrator can now plot derivatives
• Range and LogRange classes will behave like floats whenever necessary

Fixed

• behavior of the SamplableSet class
• a bug where the reaction rate of nodes in weighted networks is scaled by the node's degree and not by its strength

Scientific Software - Peer-reviewed - Python
Published by benmaier almost 5 years ago

epipack - v0.1.0

First public version. Added temporal networks, an interactive jupyter widget and more symbolic methods.

Scientific Software - Peer-reviewed - Python
Published by benmaier about 5 years ago

epipack - Visualizations

Added a complete visualization framework for stochastic simulations.

Scientific Software - Peer-reviewed - Python
Published by benmaier over 5 years ago

epipack - Catch situations with endless loops

It might happen that the maximum total event rate is non-zero but the true total event is zero. In this case, a mechanism now counts the number of unsuccessful events. If this number is above a threshold, the true event rate is evaluated and checked.

Scientific Software - Peer-reviewed - Python
Published by benmaier over 5 years ago

epipack - First workable version

Workable version.

Scientific Software - Peer-reviewed - Python
Published by benmaier over 5 years ago