est.wt.matrix {IDSpatialStats} | R Documentation |
Calculate the Infector-Infectee Wallinga-Teunis matrix
Description
A function which takes the time of each case occurrence, the generation time distribution of the infecting pathogen, and the matrix of basic Wallinga-Teunis weights and estimates the probability that an infectee occurring time step j (columns) was infected by a case occurring at time i (rows).
Usage
est.wt.matrix(case.times, gen.t.dist, basic.wt.weights = NULL)
Arguments
case.times |
a vector giving the occurrence time for each case |
gen.t.dist |
a vector giving the generation time distribution for the infecting pathogen |
basic.wt.weights |
a matrix giving the basic normalized Wallinga-Teunis weights for each time step (output from the |
Value
a numerical matrix with the number of columns and rows equal to the number of cases in the epidemic
Author(s)
John Giles, Justin Lessler, and Henrik Salje
References
Salje H, Cummings DAT and Lessler J (2016). “Estimating infectious disease transmission distances using the overall distribution of cases.” Epidemics, 17, pp. 10–18. ISSN 1755-4365, doi: 10.1016/j.epidem.2016.10.001.
See Also
Other est.wt:
est.transdist()
,
est.wt.matrix.weights()
Examples
case.times <- c(1,2,2,3,3)
gen <- c(0, 2/3, 1/3, 0, 0)
t.density <- gen/sum(gen)
a <- est.wt.matrix(case.times=case.times, gen.t.dist=t.density)