Nothing
context("Test function outbreaker_data")
## test data ##
test_that("test: data are processed fine", {
## get data
data(toy_outbreak_short)
x <- toy_outbreak_short
dt_cases <- x$cases
dt_cases <- dt_cases[order(dt_cases$Date), ]
dt_regions <- x$dt_regions
all_dist <- geosphere::distGeo(matrix(c(rep(dt_regions$long, nrow(dt_regions)),
rep(dt_regions$lat, nrow(dt_regions))),
ncol = 2),
matrix(c(rep(dt_regions$long, each = nrow(dt_regions)),
rep(dt_regions$lat, each = nrow(dt_regions))),
ncol = 2))
dist_mat <- matrix(all_dist/1000, nrow = nrow(dt_regions))
pop_vect <- dt_regions$population
names(pop_vect) <- rownames(dist_mat) <- colnames(dist_mat) <- dt_regions$region
w <- dnorm(x = 1:100, mean = 11.7, sd = 2.0)
w <- w[which(w > 1e-15)]
out <- outbreaker_data(dates = dt_cases$Date, age_group = dt_cases$age_group,
region = dt_cases$Cens_tract, population = pop_vect,
distance = dist_mat, a_dens = x$age_contact,
f_dens = dgamma(x = 1:100, scale = 0.43, shape = 27),
w_dens = w)
max_range <- as.numeric(max(dt_cases$Date) - min(dt_cases$Date))
## check output
expect_is(out, "list")
expect_equal(out$max_range, max_range)
expect_equal(out$N, nrow(dt_cases))
expect_equal(out$import, rep(FALSE, nrow(dt_cases)))
expect_equal(out$is_cluster, rep(1, nrow(dt_cases)))
expect_is(out$log_w_dens, "matrix")
expect_is(out$log_a_dens, "list")
expect_is(out$log_f_dens, "numeric")
expect_error(outbreaker_data(dates = 1, w_dens = c(0,-1)),
"w_dens has negative entries")
expect_error(outbreaker_data(dates = 1, w_dens = c(0,1), f_dens = c(0,-1)),
"f_dens has negative entries")
expect_error(outbreaker_data(dates = 1, region = 1, population = pop_vect[1:5],
distance = dist_mat[11:15, 11:15]),
"The vector population should have the same names as the distance matrix")
expect_error(outbreaker_data(dates = 1, region = names(pop_vect[6]),
population = pop_vect[1:5],
distance = dist_mat[1:5, 1:5]),
"Some regions are not in the population vector")
expect_error(outbreaker_data(dates = 1, region = names(pop_vect[6]),
population = pop_vect[1:5],
distance = dist_mat[2:5, 2:5]),
"The vector population should have the same names as the distance matrix")
expect_error(outbreaker_data(dates = 1, region = 6,
population = pop_vect[1:5],
distance = dist_mat[1:5, 1:5]),
"The length of the population vector is lower than the maximum value of the region vector")
})
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