probability_emergence {superspreading} | R Documentation |
Calculate the probability a disease will emerge and cause a sustained
outbreak (R > 1
) based on R and initial cases
Description
The method for the evolution of pathogen emergence described in
Antia et al. (2003) (doi:10.1038/nature02104). The model is a multi-type
branching process model with an initial (wild-type) reproduction number,
usually below 1, and a evolved reproduction number that is
greater than 1, and thus can cause a sustained human-to-human epidemic.
The reproduction number for a pathogen changes at the mutation_rate
.
Usage
probability_emergence(
R_wild,
R_mutant,
mutation_rate,
num_init_infect,
tol = 1e-10,
max_iter = 1000
)
Arguments
R_wild |
A |
R_mutant |
A |
mutation_rate |
A |
num_init_infect |
An |
tol |
A |
max_iter |
A |
Details
Following Antia et al. (2003), we assume that the mutation rate for all variants is the same.
Value
A value with the probability of a disease emerging and causing an outbreak.
References
Antia, R., Regoes, R., Koella, J. & Bergstrom, C. T. (2003) The role of evolution in the emergence of infectious diseases. Nature 426, 658–661. doi:10.1038/nature02104
See Also
probability_epidemic()
, probability_extinct()
Examples
probability_emergence(
R_wild = 0.5,
R_mutant = 1.5,
mutation_rate = 0.5,
num_init_infect = 1
)