SimInf (version 6.2.0)

SISe3: Create a ‘SISe3’ model

Description

Create a ‘SISe3’ model to be used by the simulation framework.

Usage

SISe3(u0, tspan, events = NULL, phi = NULL, upsilon_1 = NULL,
  upsilon_2 = NULL, upsilon_3 = NULL, gamma_1 = NULL,
  gamma_2 = NULL, gamma_3 = NULL, alpha = NULL, beta_t1 = NULL,
  beta_t2 = NULL, beta_t3 = NULL, beta_t4 = NULL, end_t1 = NULL,
  end_t2 = NULL, end_t3 = NULL, end_t4 = NULL, epsilon = NULL)

Arguments

u0

A data.frame with the initial state in each node (see ‘Details’).

tspan

A vector (length >= 2) of increasing time points where the state of each node is to be returned. Can be either an integer or a Date vector. A Date vector is coerced to a numeric vector as days, where tspan[1] becomes the day of the year of the first year of tspan. The dates are added as names to the numeric vector.

events

a data.frame with the scheduled events, see SimInf_model.

phi

A numeric vector with the initial environmental infectious pressure in each node. Will be repeated to the length of nrow(u0). Default is NULL which gives 0 in each node.

upsilon_1

Indirect transmission rate of the environmental infectious pressure in age category 1

upsilon_2

Indirect transmission rate of the environmental infectious pressure in age category 2

upsilon_3

Indirect transmission rate of the environmental infectious pressure in age category 3

gamma_1

The recovery rate from infected to susceptible for age category 1

gamma_2

The recovery rate from infected to susceptible for age category 2

gamma_3

The recovery rate from infected to susceptible for age category 3

alpha

Shed rate from infected individuals

beta_t1

The decay of the environmental infectious pressure in interval 1.

beta_t2

The decay of the environmental infectious pressure in interval 2.

beta_t3

The decay of the environmental infectious pressure in interval 3.

beta_t4

The decay of the environmental infectious pressure in interval 4.

end_t1

vector with the non-inclusive day of the year that ends interval 1 in each node. Will be repeated to the length of nrow(u0).

end_t2

vector with the non-inclusive day of the year that ends interval 2 in each node. Will be repeated to the length of nrow(u0).

end_t3

vector with the non-inclusive day of the year that ends interval 3 in each node. Will be repeated to the length of nrow(u0).

end_t4

vector with the non-inclusive day of the year that ends interval 4 in each node. Will be repeated to the length of nrow(u0).

epsilon

The background environmental infectious pressure

Value

SISe3

Beta

The time dependent beta is divided into four intervals of the year

where 0 <= day < 365
Case 1: END_1 < END_2 < END_3 < END_4
INTERVAL_1 INTERVAL_2     INTERVAL_3     INTERVAL_4     INTERVAL_1
[0, END_1) [END_1, END_2) [END_2, END_3) [END_3, END_4) [END_4, 365)
Case 2: END_3 < END_4 < END_1 < END_2
INTERVAL_3 INTERVAL_4     INTERVAL_1     INTERVAL_2     INTERVAL_3
[0, END_3) [END_3, END_4) [END_4, END_1) [END_1, END_2) [END_2, 365)
Case 3: END_4 < END_1 < END_2 < END_3
INTERVAL_4 INTERVAL_1     INTERVAL_2     INTERVAL_3     INTERVAL_4
[0, END_4) [END_4, END_1) [END_1, END_2) [END_2, END_3) [END_3, 365)

Details

The argument u0 must be a data.frame with one row for each node with the following columns:

S_1

The number of sucsceptible in age category 1

I_1

The number of infected in age category 1

S_2

The number of sucsceptible in age category 2

I_2

The number of infected in age category 2

S_3

The number of sucsceptible in age category 3

I_3

The number of infected in age category 3