Defines a state transition in the infection process model which does not represent an transmission (infection) event
Arguments
- from
string giving name of origin compartment
- to
string or vector of strings giving the name of the destination compartment
- split
an optional character or numeric vector indicating what proportion of individuals transition into each of the
tocompartments- ...
Argument specifying the name and optionally the value of the transition rate parameter. For example if the parameter name is "gamma" and it is being fit this argument should be
gamma = NA. If we want to provide a numeric value, x, for "gamma" this argument should begamma = x.
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
"source", NA (so output columns match with
transmit)"rate_name", name of transition rate parameter if fitting
"rate_value", numeric value of transition rate if not fitting
"split_name", name of split parameter if fitting
"split_value", numeric value of split if not fitting
Examples
# Transition from compartment A to B which occurs at rate gamma where
# gamma is a user-specified value of 0.2
progress(from = "A", to = "B", gamma = 0.2)
#> from to rate_name rate_value split_name split_value
#> 1 A B gamma 0.2 NA NA
# Transition from compartment A to B which occurs at rate gamma where
# gamma is fit
progress(from = "A", to = "B", gamma = NA)
#> from to rate_name rate_value split_name split_value
#> 1 A B gamma NA NA NA
# Transition from compartment A split into two destination compartments, B1
# and B2, were individuals leave A at rate delta (fit) and phi (fit) is the
# proportion of those who leave A who go into B1 (i.e. 1-phi go into B2).
# gamma is fit
progress(from = "A", to = c("B1", "B2"), split = "phi", delta = NA)
#> from to rate_name rate_value split_name split_value
#> 1 A B1 delta NA phi NA
#> 2 A B2 delta NA 1-phi NA