time dependant functions not working for stratified parameters

[woldmuyn]

Technical questions

• Python version: 3.10.6
• Operating System: windows10 64 bit

Description

Time dependant functions is not working for stratified parameters, because of bug in parameter check.

What I Did

The specified time-dependent parameter 'alpha' is not an existing model parameter

in _validate_time_dependent_parameters(self)

all_param_names = model.parameter_names.copy()

for lst in model.parameters_stratified_names:
    all_param_names.extend(lst)

if model.stratification:
    all_param_names.extend(model.stratification)

print(all_param_names)

output: ['Ki', 'Kp', 'covid_H', 'covid_dH', 'covid_min', 'a', 'l', 'p', 'h', 'a', 'b', 'e', 't', 'a', 'g', 'a', 'm', 'm', 'a', 'MDC_keys']

Solution

Change extend to append

[twallema]

Note that in the following model, there is one stratified parameter alpha, which is stratified according to the only stratification Nc in this model. If the parameter alpha is defined as a list inside a list in the parameters_stratified_names.

class ODE_influenza_model(BaseModel):
    """
    Simple SEIR model for influenza with undetected carriers
    """

    state_names = ['S','E','Ia','Im','R','Im_inc']
    parameter_names = ['beta','sigma','f_a','gamma']
    parameters_stratified_names = [['alpha'],]
    stratification = ['Nc']

    @staticmethod
    def integrate(t, S, E, Ia, Im, R, Im_inc, beta, sigma, f_a, gamma, alpha, Nc):

        # Calculate total population
        T = S+E+Ia+Im+R
        # Calculate differentials
        dS = -beta*Nc@((Ia+Im)*S/T)
        dE = beta*Nc@((Ia+Im)*S/T) - 1/sigma*E
        dIa = f_a*E/sigma - 1/gamma*Ia
        dIm = (1-f_a)/sigma*E - 1/gamma*Im
        dR = 1/gamma*(Ia+Im)
        # Calculate incidence mild disease
        dIm_inc_new = (1-f_a)/sigma*E - Im_inc

        return dS, dE, dIa, dIm, dR, dIm_inc_new

as opposed to,

parameters_stratified_names = ['alpha',]

Then the TDPFs do work..