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Define a infection transition

Source: R/hestia_functions.R
transmit.Rd

Defines a state transition in the infection process model which is the result of a transmission (infection) event

Usage

transmit(from, to, source = NA, split = NA)

Arguments

from

string giving name of origin compartment

to

string giving the name of the destination compartment

source

string (or vector of strings) designating which compartments are infectious. If NA, the destination compartment is presumed to be the infectious compartment.

split

an optional character or numeric vector indicating what proportion of individuals transition into each of the to compartments

Value

Data frame with a row for each unique transition and the following columns:

  • "from", the name of the origin compartment

  • "to", the name of the destination compartment

  • "split_name", name of split parameter if fitting

  • "split_value", numeric value of split if not fitting

  • "source", names of compartment(s) that are the source of new infections i.e. the infectious compartments

Examples

# Specify S > E transition in an SEIR model
transmit(from = "S", to = "E", source = "I")
#>   from to split_name split_value source
#> 1    S  E         NA          NA      I

# Upon infection, individuals either enter Is (symptomatic infections) or
# Ia (asymptomatic infection) where 30% of infections are symptomatic.
transmit(from = "S", to = c("Is", "Ia"), split = 0.3)
#>   from to split_name split_value source
#> 1    S Is         NA         0.3 Is, Ia
#> 2    S Ia         NA         0.7 Is, Ia