est.wt.matrix.weights: Estimate matrix of basic Wallinga-Teunis weights

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

Estimate matrix of basic Wallinga-Teunis weights

Description

A function called by est.wt.matrix, which calculates the basic weights in the Wallinga-Teunis matrix given the time of each case occurrence and the generation time distribution of the pathogen. Code adapted from the R0 package.

Usage

est.wt.matrix.weights(case.times, gen.t.dist)

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

Value

a numerical matrix with the number of columns and rows equal to the number of time steps in the epidemic

Author(s)

John Giles, Justin Lessler, and Henrik Salje

References

Boelle P and Obadia T (2015). R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics. R package version 1.2-6, https://CRAN.R-project.org/package=R0.

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()

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.weights(case.times=case.times, gen.t.dist=t.density)

IDSpatialStats documentation built on Sept. 11, 2024, 5:14 p.m.