Description Usage Arguments Value Author(s) References See Also Examples
View source: R/transdistfuncs.r
Estimates the change in mean transmission distance over the duration of the epidemic by running est.trandsdist
on all cases
occuring up to each time point.
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epi.data |
a three-column matrix giving the coordinates ( |
gen.t.mean |
mean generation time of the infecting pathogen |
gen.t.sd |
standard deviation of generation time of the infecting pathogen |
t1 |
time step to begin estimation of transmission distance |
max.sep |
maximum number of time steps allowed between two cases (passed to the |
max.dist |
maximum spatial distance between two cases considered in calculation |
n.transtree.reps |
number of time to simulate transmission trees when estimating the weights of theta (passed to the |
mean.equals.sd |
logical term indicating if the mean and standard deviation of the transmission kernel are expected to be equal (default = FALSE) |
theta.weights |
use external matrix of theta weights. If NULL (default) the matrix of theta weights is automatically estimated by calling the |
parallel |
run time steps in parallel (default = FALSE) |
n.cores |
number of cores to use when |
a numeric matrix containing the point estimate for mean transmission distance for each unique time step of the epidemic and the sample size $n$ used to make the estimate NAs are returned for time steps which contain fewer than three cases
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 transdist:
est.transdist.bootstrap.ci()
,
est.transdist.temporal.bootstrap.ci()
,
est.transdist.theta.weights()
,
est.transdist()
,
get.transdist.theta()
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set.seed(123)
# Exponentially distributed transmission kernel with mean and standard deviation = 100
dist.func <- alist(n=1, a=1/100, rexp(n, a))
# Simulate epidemic
a <- sim.epidemic(R=2,
gen.t.mean=7,
gen.t.sd=2,
tot.generations=7,
min.cases=30,
trans.kern.func=dist.func)
a <- a[sample(1:nrow(a), 50),] # subsample a to 50 observations
# Estimate mean transmission kernel over time
b <- est.transdist.temporal(epi.data=a,
gen.t.mean=7,
gen.t.sd=2,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=5,
mean.equals.sd=TRUE,
n.cores=2)
b
plot(b[,2], pch=19, col='grey', ylim=c(min(b[,2], na.rm=TRUE), max(b[,2], na.rm=TRUE)),
xlab='Time step', ylab='Estimated mean of transmission kernel')
abline(h=100, col='red', lty=2)
axis(3, b[,2])
low <- loess(b[,2] ~ as.vector(1:length(b[,2])))
low <- predict(low, newdata=data.frame(as.vector(1:length(b[,2]))))
lines(low, lwd=3, col='blue')
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