Nothing
context("estimate transdist bootstraps")
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=5,
trans.kern.func=dist.func)
expect_that(est.transdist.bootstrap.ci(epi.data=as.character(a),
gen.t.mean=7,
gen.t.sd=2,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=10),
throws_error())
})
test_that("Outputs list and numerics", {
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.bootstrap.ci(epi.data=a,
gen.t.mean=7,
gen.t.sd=2,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=3,
boot.iter=3)
expect_true(is.list(b))
expect_true(is.numeric(b$mu.est))
})
test_that("Confidence intervals are calculated appropriately", {
set.seed(1)
dist.func <- alist(n=1,
a=100,
b=100,
rnorm(n, a, b))
a <- sim.epidemic(R=3,
gen.t.mean=7,
gen.t.sd=2,
min.cases=5,
tot.generations=5,
trans.kern.func=dist.func)
b <- est.transdist.bootstrap.ci(epi.data=a,
gen.t.mean=1,
gen.t.sd=0.001,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=3,
boot.iter=3)
expect_true(is.numeric(b$mu.ci.low))
expect_true(is.numeric(b$mu.ci.low))
expect_true(b$mu.ci.low <= b$mu.est)
expect_true(b$mu.ci.high >= b$mu.est)
})
test_that("Border condition: zero transmission distance", {
tmax <- 10
x <- rep(0, tmax)
y <- rep(0, tmax)
t <- rep(0, tmax)
for(i in 2:tmax) t[i] <- t[i-1] + 1
a <- cbind(x, y, t)
set.seed(1)
b <- est.transdist.bootstrap.ci(epi.data=a,
gen.t.mean=1,
gen.t.sd=0.001,
t1=0,
max.sep=1e10,
max.dist=1e10,
n.transtree.reps=3,
boot.iter=3)
expect_true(b$mu.est == 0)
expect_true(b$mu.ci.low == 0)
expect_true(b$mu.ci.high == 0)
})
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