inst/tests/test-transdistbootstrapci.r

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

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)
})