pygom
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publichealthengland
ODE modelling in Python
In addition to deprecation warnings, after running `conda install -c conda-forge gcc` to solve `gcc not found` I get the error: `error: command '/home/.../miniconda3/envs/pygom-test/bin/gcc' failed with exit code 1` Other...
Following an upgrade to use Python 3.11 and numpy 2.0.0, we've been getting some odd results from the influenza like illness model. Other associated packages were upgraded too and a...
When running the ABC Parameter Estimation with PyGOM, it seems to only work with a numpy dataframe, and doesn't accept a pandas dataframe as input. Converting pandas dataframe using .to_numpy()...
Since most epi data comes in the form of incidence, would be very useful to have this as a model output. Maybe as a derived parameter.
As the new documentation outlines, we only need to use the SimulateOde class to access all the features of PyGOM. SimulateOde inherits from DeterministicOde which itself inherits from BaseOdemodel. It...
Please could you add units for the variables in the notebook of the Legrand Ebola model. It appears based on ``` ('omega_I',10.0/7.0) ``` that the units for this variable and...
If there are many states, it can be annoying to remember to add death processes to every one. Could be worth adding an option to incorporate death processes globally.
I think the unrolling of equations into transitions could be reframed in terms of a linear algebra problem, hopefully giving more reliable outputs.
Would be useful to have the time series of derived parameters alongside the solutions for the compartments post simulation. Derived parameters might be useful to know, but it's also good...
I've noticed that stochastic simulations run without end if all state populations hit zero. I think this is because the adaptive tau leap algorithm is allocating very small or possibly...