An S4 object representing the SEIRDVAge. — SEIRDVAge-class • comomodels

Defines an age-structured SEIRDV model and solves the set of ordinary differential equations of the model with a chosen method of numerical integration. Vaccinated individuals are considered in their own compartment.

Usage

# S4 method for SEIRDVAge
initial_conditions(object)

# S4 method for SEIRDVAge
initial_conditions(object) <- value

# S4 method for SEIRDVAge
transmission_parameters(object)

# S4 method for SEIRDVAge
transmission_parameters(object) <- value

# S4 method for SEIRDVAge
interventions(object)

# S4 method for SEIRDVAge
interventions(object) <- value

# S4 method for SEIRDVAge
run(object, times, solve_method = "lsoda")

Arguments

object: An object of the class SEIRDVAge.
value: (list) list of interventions. Each intervention has the following parameters: starts, stops and coverages.
times: (vector) time sequence over which to solve the model. Must be of the form seq(t_start,t_end,by=t_step). Default time series is seq(0, 100, by = 1).
solve_method: A string indicating the chosen numerical integration method for solving the ode system. Default is lsoda which is also the default for the ode function in the deSolve package used in this function.

Value

Initial conditions of SEIRDVAge model. Updated version of the age-structured SEIRDV model. Transmission parameters of SEIRDVAge model. Updated version of the age-structured SEIRDV model. object of class SEIRDVAge with intervention parameters assigned. data frame containing the time vector and time series of S, E, I, R, V, VR and D population fractions for each age group outputs with incidence numbers for each age group.

Methods (by generic)

initial_conditions: Retrieves initial_conditions for an age-structured SEIRDV model.
initial_conditions<-: Sets initial_conditions of an age-structured SEIRDV model.

If the initial conditions provided to do not sum to 1 or of different sizes compared to the number of age groups, an error is thrown.
transmission_parameters: Retrieves transmission_parameters for an age-structured SEIRDV model.
transmission_parameters<-: Sets transmission_parameters of an age-structured SEIRDV model.

If the transmission parameters provided to are not 1-dimensional an error is thrown.
interventions: Retrieves interventions of age-structured SEIRDV model.
interventions<-: Setter method for intervention of the age-structured SEIRV model.

Intervention parameters have same size. A tanh function is used to smooth interventions during simulation. This class is designed for interventions which last several days at least and have several days between them; interventions involving rapid fluctuations may be distorted.
run: Method to simulate output using from model.

Solves a system of ODEs which form an age-structured SEIRDV model. The system of equations for the time evolution of population fractions in Susceptible (S), Exposed (E), Infected (I), Recovered (R), Vaccinated (V) and Dead (D) groups in a given age group indexed by i is given by

$$\frac{dS_i(t)}{dt} = - \beta S_i(t) \Sigma_{j}C_{ij} I_j(t) - \nu Inter(t) S_i(t) + \delta_V V_i(t) + \delta_R R_i(t) + \delta_VR VR_i(t)$$ $$\frac{dE_i(t)}{dt} = \beta S_i(t) \Sigma_{j}C_{ij} I_j(t) - \kappa E_i(t)$$ $$\frac{dI_i(t)}{dt} = \kappa E_i(t) - \gamma I_i(t) - \mu I_i(t)$$ $$\frac{dR_i(t)}{dt} = \gamma I_i(t) - \delta_R R_i(t) - \nu Inter(t) R_i(t)$$ $$\frac{dV(t)}{dt} = \nu Inter(t) S_i(t) - \delta_V V_i(t)$$ $$\frac{dVR(t)}{dt} = \nu Inter(t) R_i(t) - \delta_VR VR_i(t)$$ $$\frac{dC(t)}{dt} = \beta S_i(t) \Sigma_{j}C_{ij} I_j(t)$$ $$\frac{dD_i(t)}{dt} = \mu I_i(t)$$

where C is a contact matrix whose elements represents the contact between different age groups (rows) with age groups of people they come in contact with (columns). This function relies on the package deSolve to numerically integrate the set of equations above.

Slots

output_names: list of compartments name which are used by the model and incidence.
initial_condition_names: list of names of initial conditions (characters). Default is list("S0", "E0", "I0", "V0", "R0", "VR0", "D0").
transmission_parameter_names: list of names of transmission parameters (characters). Default is list("beta", "kappa", "gamma", "mu", "nu", "delta_V", "delta_R", "delta_VR").
intervention_parameter_names: list of names of parameters for each intervention (characters). Default is list ("starts", "stops", "coverages").
initial_conditions: list of values for initial conditions (double).
transmission_parameters: list of values for transmission parameters (double).
interventions: list interventions. Each intervention has the parameters in the same format (list of double).
contact_matrix: A square matrix with dimension equal to n_age_categories x n_age_categories. This matrix represents the contact between different age groups (rows) with age groups of people they come in contact with (columns).
n_age_categories: number of age categories.
age_ranges: list of string characters representing the range of ages of people in each age category. This object must have length n_age_categories (otherwise an error is returned) and each element must be formatted as 'age1-age2'.