Description Usage Arguments Value Author(s) References See Also Examples
View source: R/transdistfuncs.r
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).
1 | est.wt.matrix(case.times, gen.t.dist, basic.wt.weights = NULL)
|
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 |
a numerical matrix with the number of columns and rows equal to the number of cases in the epidemic
John Giles, Justin Lessler, and Henrik Salje
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.
Other est.wt:
est.transdist()
,
est.wt.matrix.weights()
1 2 3 4 5 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.