Gempyor plugins for Seeding and InitialConditions, fixes issue #101 🧩

[jcblemai]

Let the user put tiny (or big) bit of R and and python code to replace a module within gempyor. Solves #101. Documentation here

There are two ways of doing this:

• monkey patching the methods of the class: smaller syntax but less powerful and possible side effect
• based on inheritance, as described here. issue is that it depends on cpython implementation

Example: random number of infected between 0 and 10%

in config:

initial_conditions:
  method: plugin
  plugin_file_path: model_input/my_initial_conditions.py

in model_input/my_initial_conditions.py

import gempyor.seeding_ic
import numpy as np

class InitialConditions(gempyor.seeding_ic.InitialConditions):

    def get_from_config(self, sim_id: int, setup) -> np.ndarray:
        y0 = np.zeros((setup.compartments.compartments.shape[0], setup.nsubpops))
        S_idx = setup.compartments.get_comp_idx({"infection_stage":"S"})
        I_idx = setup.compartments.get_comp_idx({"infection_stage":"I"})
        prop_inf = np.random.uniform(low=0,high=.1)
        y0[S_idx, :] = setup.subpop_pop * (1-prop_inf)
        y0[I_idx, :] = setup.subpop_pop * prop_inf

        return y0
    
    def get_from_file(self, sim_id: int, setup) -> np.ndarray:
        return self.draw(sim_id=sim_id, setup=setup)

and from R

import gempyor.seeding_ic
import numpy as np

class InitialConditions(gempyor.seeding_ic.InitialConditions):

    def get_from_config(self, sim_id: int, setup) -> np.ndarray:
        import rpy2.robjects as robjects
        robjects.r.source("path_to_your_Rscript.R", encoding="utf-8")
        y0 = robjects.r["initial_condition_fromR"]

        return y0
    
    def get_from_file(self, sim_id: int, setup) -> np.ndarray:
        return self.draw(sim_id=sim_id, setup=setup)