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Set the select matrix for a SimInf_model object

Source: R/SimInf_events.R
select_matrix-set.Rd

Utility function to set events@E in a SimInf_model object, see SimInf_events.

Usage

select_matrix(model) <- value

# S4 method for class 'SimInf_model'
select_matrix(model) <- value

Arguments

model

The SimInf_model object to set the select matrix for.

value

The new value for E in the model. E is a matrix to handle scheduled events, see SimInf_events. Each row in E corresponds to one compartment in the model. The non-zero entries in a column indicate the compartments to include in an event. For the exit, internal transfer and external transfer events, the values in E[, select] are used as weights when sampling individuals without replacement, with probability proportional to the weight. For the enter event, the values in E[, select] are used as weights when determining which compartment to add individuals to. If the column E[, select] contains several non-zero entries, the compartment is sampled with probability proportional to the weight in E[, select]. The select matrix E can either be specified as a matrix, or as a data.frame. When E is specified as a data.frame, it must have one column named compartment that defines which compartment is referred to, and one column select that defines the column in E. In addition, the data.frame can contain an optional column named value with the value in E. When the value column is missing, 1 is used as the default value.

Examples

## Create an SIR model.
model <- SIR(u0 = data.frame(S = 99, I = 1, R = 0),
             tspan = 1:5, beta = 0.16, gamma = 0.077)

## Set the select matrix.
select_matrix(model) <- matrix(c(1, 0, 0, 1, 1, 1, 0, 0, 1), nrow = 3)

## Extract the select matrix from the model.
select_matrix(model)
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>   1 2 3
#> S 1 1 .
#> I . 1 .
#> R . 1 1

## Set the select matrix using a data.frame instead.
select_matrix(model) <- data.frame(
    compartment = c("S", "S", "I", "R", "R"),
    select      = c( 1,   2,   2,   2,   3))

## Extract the select matrix from the model.
select_matrix(model)
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>   1 2 3
#> S 1 1 .
#> I . 1 .
#> R . 1 1