SISe3_sp {SimInf} | R Documentation

## Create a SISe3_sp model

### Description

Create a SISe3_sp model to be used by the simulation framework.

### Usage

    SISe3_sp(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, distance = NULL,
      coupling = 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).
`distance` | The distance matrix between neighboring nodes
`coupling` | The coupling between neighboring nodes

### 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

### Value

`SISe3_sp`

### 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)

[Package SimInf version 6.3.0 Index]