SISe_sp: Create a 'SISe_sp' model

Description Usage Arguments Details Value Beta

View source: R/SISe_sp.R

Description

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

Usage

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SISe_sp(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, coupling = NULL, distance = 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.

coupling

The coupling between neighboring nodes

distance

The distance matrix between neighboring nodes

Details

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

S

The number of sucsceptible

I

The number of infected

Value

SISe_sp

Beta

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

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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)


SimInf documentation built on May 19, 2017, 8:39 p.m.
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