SimInf (version 5.0.0)

SISe: Create a SISe model

Description

Create a SISe model to be used by the simulation framework.

Usage

SISe(u0, tspan, events = NULL, phi = NULL, upsilon = NULL, gamma = 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. Default NULL which gives 0 in each node.

upsilon

Indirect transmission rate of the environmental infectious pressure

gamma

The recovery rate from infected to susceptible

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

The non-inclusive day of the year that ends interval 1.

end_t2

The non-inclusive day of the year that ends interval 2.

end_t3

The non-inclusive day of the year that ends interval 3.

end_t4

The non-inclusive day of the year that ends interval 4.

epsilon

The background environmental infectious pressure

Value

SISe

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

The number of sucsceptible in each node

I

The number of infected in each node