covid.models.SEIR

class covid.models.SEIR(parameters=None)

Bases: CompartmentalModel

Susceptible, Exposed, Infected, Recovered Model

Methods

define_parameters()	Define compartmental model parameters
define_transfer_matrix()	Define transfer matrix used in simulating model
fit_parameters(data, lower_bounds, ...)	Determine model parameters from data fit
get_parameters_from_data(data)	Get model parameters from data
initialize([initial_values])	Initialize each model compartment
last_compartment_value(compartment)	Get last entry in timeseries
model_eqns(last_compartments, step_number)	Model equation definition used in rk step
model_fit_function(t, *args)	Model function providing fit interface
rk_step(last_compartments, step_number)	Runge-Kutta step for model simulation
run_model([n_days])	Run model simulation for n_days
set_initial_values(initial_values)	Set initial values for model compartments
transfer_value(to_compartment, from_compartment)	Get transfer matrix entry
update_parameters(params)	Update model parameters from dict
update_transfer_matrix(last_compartments)	Update transfer matrix values to calculate next time step
update_transfer_value(value, to_compartment, ...)	Update transfer matrix entry

define_parameters()

Define compartmental model parameters

define_transfer_matrix()

Define transfer matrix used in simulating model

fit_parameters(data, lower_bounds, upper_bounds, initial_parameters)

Determine model parameters from data fit

get_parameters_from_data(data)

Get model parameters from data

initialize(initial_values=None)

Initialize each model compartment

last_compartment_value(compartment)

Get last entry in timeseries

model_eqns(last_compartments, step_number)

Model equation definition used in rk step

model_fit_function(t, *args)

Model function providing fit interface

rk_step(last_compartments, step_number)

Runge-Kutta step for model simulation

run_model(n_days=100)

Run model simulation for n_days

set_initial_values(initial_values)

Set initial values for model compartments

transfer_value(to_compartment, from_compartment)

Get transfer matrix entry

update_parameters(params)

Update model parameters from dict

update_transfer_matrix(last_compartments)

Update transfer matrix values to calculate next time step

update_transfer_value(value, to_compartment, from_compartment)

Update transfer matrix entry