pygom
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publichealthengland
ODE modelling in Python
To keep track of cumulative numbers of infections, say, it would be useful to be able to couple up the disease transition (TransitionType.T) with a cumulative counter (TransitionType.B), so that...
Just in case you update scipy note that a function seems to be lost in later version. This causes the error below when importing PyGOM. I found that reverting scipy...
The problem is in the parsing of the Target_State for initial condition fitting. A list of lists is returned instead of a list of integer indices. Fixing this in base_loss.py...
This code implements a cython version of firstReaction. I still want to run some further tests before this code is merged.
For transparencies sake I am posting the following email correspondence with Ediwn Tye the original author of PyGOM: Dear Edwin Thanks for the response. I did think for a while...
We can integrate a stochastic object to get the determininistic solution but there isn't an easy constructor for a stochastic model when you have the deterministic one. This is just...
# Problem The current setup in travis is confusing due to the *almost* duplicated steps in line 31 and 33 https://github.com/PublicHealthEngland/pygom/blob/18bdd6ad8c3ecd66371a0ee8d72457d3d695ef0d/.travis.yml#L31-L33 because `python setup.py install` in fact checks the environment...
Depending on the nature of the stochastic simulation if certain class/es have gone extinct it is not necessary to continue running the simulation. A break clause could be added to...
Can the simulate_param method spit out the parameter values that have been used?