pygom

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Switching to state*parameter when defined in transistion object as parameter*state

1

If when constructing a model with transitions the standard parameter*state is used in the equation argument that defines a transition, when using the methods on the model class model.get_ode_eqn(), model.print_ode()...

m-d-grunnill

Cannot install via ```python setup.py install``` if using setuptools-scm for getting version.

2

I have tried to install making sure all the required package are in place. I get the following error when ```python setup.py install``` in conda: ``` Traceback (most recent call...

m-d-grunnill

DFE (and hence R0) fails for conservative systems

1

For example, a simple SIR model should have disease free equilibrium equation given by S=N0, R=0 (or S=S0, R=N0-S0). However, DFE(model,['I']) returns S=0, R=0. This also gives R0((model,['I']) = 0...

timothywhiteley

Cannot function pygom.R0() thoughs erroe if model is defined by ODE type transitions.

1

When running the function: ``` pygom.R0(model, disease_state) ``` if the ```model ``` used is defined using ode type transition objects then the error below occurs: ``` OutputError: ode was defined...

m-d-grunnill

The list is not the same between the yml file and the readme file. A note about requiring Microsofts C++ compiler from https://visualstudio.microsoft.com/visual-cpp-build-tools/ may also be required in the readme.

m-d-grunnill

This solves a problem with the ordering of parameters for ABC. Previously, it was necessary to specify the model parameters before any initial conditions, and the initial conditions needed to...

jontycarruthersphe

Using something like PyFlow could we do graphical model creation ? https://github.com/wonderworks-software/PyFlow

twomagpi

Can we develop Center popular calculation tools, focus calculation tools, balance point and its stability type calculation tools

mathwyz

Code tidied up with pylint.

MGrunnill

Add a simple serialisation scheme for PyGOM models

2

With SBML removed (#3) we need a simple scheme to read/write models

twomagpi