Nothing
context("estimate transdist temporal")
test_that("Data checks performed", {
set.seed(1)
dist.func <- alist(n=1,
a=100,
b=100,
rnorm(n, a, b))
a <- sim.epidemic(R=3,
gen.t.mean=7,
gen.t.sd=2,
min.cases=5,
tot.generations=3,
trans.kern.func=dist.func)
a$t <- as.character(a$t)
expect_that(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),
throws_error())
expect_that(est.transdist.temporal.bootstrap.ci(epi.data=a,
gen.t.mean=7,
gen.t.sd=2,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=5,
boot.iter=5,
ci.low=0.025,
ci.high=0.975),
throws_error())
})
test_that("Outputs numeric vector of appropriate length", {
set.seed(1)
dist.func <- alist(n=1,
a=100,
b=100,
rnorm(n, a, b))
a <- sim.epidemic(R=3,
gen.t.mean=7,
gen.t.sd=2,
min.cases=5,
tot.generations=5,
trans.kern.func=dist.func)
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=3)
expect_true(is.data.frame(b))
expect_true(is.numeric(b$pt.est))
expect_true(length(unique(a[,3])) == nrow(b))
})
test_that("Border condition: zero transmission distance", {
tmax <- 10
x <- rep(0, tmax)
y <- rep(0, tmax)
t <- rep(0, tmax)
for(i in 2:tmax) t[i] <- t[i-1] + 1
a <- cbind(x, y, t)
set.seed(1)
b <- est.transdist.temporal(epi.data=a,
gen.t.mean=1,
gen.t.sd=0.001,
t1=0,
max.sep=5,
max.dist=1e10,
n.transtree.reps=2)
expect_true(length(unique(a[,3])) == nrow(b))
expect_true(sum(b$pt.est, na.rm=T) == 0)
b <- est.transdist.temporal.bootstrap.ci(epi.data=a,
gen.t.mean=1,
gen.t.sd=0.001,
t1=0,
max.sep=5,
max.dist=1e10,
n.transtree.reps=2,
boot.iter=2)
expect_true(length(unique(a[,3])) == nrow(b))
expect_true(sum(b$ci.low, na.rm=T) == 0)
expect_true(sum(b$ci.high, na.rm=T) == 0)
})
test_that("Estimates confidence intervals", {
set.seed(1)
dist.func <- alist(n=1, a=1/100, rexp(n, a))
a <- sim.epidemic(R=3,
gen.t.mean=7,
gen.t.sd=2,
min.cases=5,
tot.generations=5,
trans.kern.func=dist.func)
b <- est.transdist.temporal.bootstrap.ci(epi.data=a,
gen.t.mean=7,
gen.t.sd=2,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=5,
boot.iter=10,
ci.low=0.025,
ci.high=0.975)
expect_true(is.data.frame(b))
expect_true(is.numeric(b$pt.est))
expect_true(is.numeric(b$ci.low))
expect_true(is.numeric(b$ci.high))
expect_true(length(unique(a[,3])) == nrow(b))
})
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