probability_extinct {superspreading} | R Documentation |
Calculate the probability a branching process will go extinct based on
R, k and initial cases
Description
Calculates the probability a branching process will not causes
an epidemic and will go extinct. This is the complement of the probability
of a disease causing an epidemic (probability_epidemic()
).
Usage
probability_extinct(
R,
k,
num_init_infect,
ind_control = 0,
pop_control = 0,
...,
offspring_dist
)
Arguments
R |
A number specifying the R parameter (i.e. average secondary cases
per infectious individual).
|
k |
A number specifying the k parameter (i.e. overdispersion in
offspring distribution from fitted negative binomial).
|
num_init_infect |
An integer (or at least
"integerish" if
stored as double) specifying the number of initial infections.
|
ind_control |
A numeric specifying the strength of individual-level
control measures. These control measures assume that infected individuals
do not produce any secondary infections with probability ind_control ,
thus increasing the proportion of cases that do not create any subsequent
infections. The control measure is between 0 (default) and 1 (maximum).
|
pop_control |
A numeric specifying the strength of population-level
control measures that reduce the transmissibility of all cases by a
constant factor. Between 0 (default) and 1 (maximum).
|
... |
<dynamic-dots > Named elements to replace
default optimisation settings. Currently only "fit_method" is accepted
and can be either "optim" (default) or "grid" for numerical
optimisation routine or grid search, respectively.
|
offspring_dist |
An <epiparameter> object. An S3 class for working
with epidemiological parameters/distributions, see
epiparameter::epiparameter() .
|
Value
A value with the probability of going extinct.
References
Lloyd-Smith, J. O., Schreiber, S. J., Kopp, P. E., & Getz, W. M. (2005).
Superspreading and the effect of individual variation on disease emergence.
Nature, 438(7066), 355-359. doi:10.1038/nature04153
See Also
probability_epidemic()
Examples
probability_extinct(R = 1.5, k = 0.1, num_init_infect = 10)
[Package
superspreading version 0.3.0
Index]